title: mycelia - H3K27me3_set7_rep2_input

description: input

value: input


title: A_1001 Yec_chow

status: Public on Feb 13 2021

type: SRA

city: New York

first: Mohammad

last: Kabbani

state: NY

address: 1230 York Ave, Box 64

country: USA

institute: The Rockefeller University

library_source: transcriptomic

data_processing:
STAR(v2.5) for reference genome alingment
HTseq-count for gene level count tables
lima/voom for for differential gene expression
g:profiler for GO, KEGG, REAC and TF
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Ca. 25 mg of freshly harvested liver tissue was placed into 1ml 4ºC TRIzol homogenized, weighed and stored at -80ºC. Chloroform extraction was performed together with DNAse treatment to purify RNA.
Library construction and sequencing were performed using Illumina S4 flowcell on Novaseq 6000 platform with a paired-end read length of 150 bp.

tag: diet

value: chow

tag: rs738409 pnpla3 genotype

tag: human hepatocyte donor


title: P11A04557A

city: Lund

first: Yvonne

last: Ceder

address: Scheelevägen 2

country: Sweden

institute: Lund University

description:
FC5_S7
Single-end small RNA sequencing
Urinary_miRNA_counts.txt

data_processing:
Demultiplexed, adapters trimmed and 4N random nucleotides removed.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Urinary_miRNA_counts.txt: Tab-delimited text file includes counts.

organism: Homo sapiens

source_name: Urinary extracellular vesicles

extract_protocol:
RNA isolation were performed using the Norgen single cell isolation kit.
Libraries were constructed using the Perkin Elmer's NEXTFlex library preparation with overnight 3'-ligation, and libraries were size selected by Blue Pippin 3% agarose gel to ~ 145 - 165 nt in length.

treatment_protocol: Urinary Evs were isolated by acoustic trapping followed by RNase A treatment at 37oC.

tag: cell type

value: Urinary extracellular vesicles

value: low

tag: gleason_category (low

value: gleason grade <=3 and bx-negative, high:gleason grade >=4):low


title: WT mycelia 2 days rep3

city: Hangzhou

first: Chuyu

last: Lin

state: Zhejiang

address: 866#, Yuhangtang Road

department: College of Agriculture and Biotechnology

country: China

institute: Zhejiang University

data_processing:
RNAs were sequenced separately at Novogene, using Illumina Hiseq X-Ten with Hiseq-PE150 strategy.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to the reference genome of M. oryzae (MSU release 7) using TopHat software with default settings (Daehwan Kim, 2013). For analysis of differential expression, the assembled transcripts from three independent biological replicates in the WT and deletion mutants were included and compared using Cuffdiff with default settings (Trapnell et al., 2010).
To calculate the significance of the overlap of two sets of genes, P value with Fisher’s exact test for overlapping was performed with online test (the total number of genes in the M. oryzae genome used was 14317). (http://nemates.org/MA/progs/overlap_stats.html).
Genome_build: MG8
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Pyricularia oryzae

source_name: mycelia

growth_protocol: The Magnaporthe oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 4-5 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
Total RNA was extracted from mycelia cultured in the liquid CM for 2 days from three biological repeats using the TRIzol (Invitrogen, USA) reagent according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: wild type

tag: developmental stage

value: mycelia

tag: time

value: 2 days


title: P11A06094A

description:
FC1_S24
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: P17A04427A

description:
FC1_S23
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: WT mycelia 2 days rep1


title: mycelia - H3K27me3_set7_rep1_IP

library_source: genomic

data_processing:
High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China) for Illumina (Langmead et al., 2009).
The clean read pairs were mapped to the reference genome with Bowtie2 (Version 2.2.8) (Langmead and Salzberg, 2012)
Enriched peaks were called by MACS2 (Version 2.1.1) with default parameters (Zhang et al., 2008).
Genome_build: MG8
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

growth_protocol: TheMagnaporthe oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 10-12 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
The ChIP experiments with mycelia cultured in liquid CM for 2 days were conducted as previous reports with minor modification (He et al., 2018; Tao et al., 2017). Briefly, 1.0 g mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature. Samples were ground with liquid nitrogen and resuspended in nuclei isolating buffer. Subsequently the precipitated nuclei were used to total chromatin extraction with 1mL lysis buffer. The lysis chromatin was sonicated into DNA fragments between 200-500 bp using Diagenode Bioruptor. 20μL chromatin was used to input DNA extraction and the remainder was pre-cleared with 10μL protein A Dynabeads (Thermofisher, 10001D) for 1 hour. Subsequently the chromatin was incubated with anti-H3K27me3 (Abcam, ab6002) or anti- H3K4ac (Active Motif, 39381) overnight at 4°C. Another 20μL protein A Dynabeads was used capture protein-DNA mixture and followed by three washing. Protein-DNA mixture was reverse-crosslinked, and DNA was recovered with phenol-chloroform extraction. The recovery DNA was used as template for followed ChIP-qPCR and ChIP-seq. Two biological repeats were conducted.
The purified DNA was used as libraries construction with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L).

treatment_protocol: The mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature

value: mutant

tag: antibody


title: P11A06084A

description:
FC4_S4
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: A_9547 F_20w

value: 20wk WD


title: P11A06355A

description:
FC4_S26
Single-end small RNA sequencing
Urinary_miRNA_counts.txt

value: high


title: A_9544 F_20w


title: WT mycelia 2 days rep 1


title: P16A04424A

description:
FC3_S14
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: A_9542 F_20w


title: P12A04576A

description:
FC5_S17
Single-end small RNA sequencing
Urinary_miRNA_counts.txt

value: unk


title: mycelia - H3K27me3_set7_rep1_input

description: input


title: P11A04558A

description:
FC4_S15
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: A_9540 F_20w


title: mycelia - H3K27me3_WT_rep2_IP


title: P12A04458A

description:
FC2_S8
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: P17A04428A

description:
FC2_S6
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: A_9546 F_12w

value: 12wk WD


title: P11A04581A

description:
FC1_S22
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: P11A06990A

description:
FC5_S14
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: mycelia - H3K27me3_WT_rep1_IP


title: P17A04192A

description:
FC5_S16
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: mycelia - H3K27me3_WT_rep2_input

description: input


title: P11A06089A

description:
FC2_S4
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: mycelia - H3K4AC_WT_rep2_input

growth_protocol: The Magnaporthe oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 10-12 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.


title: mycelia - H3K27me3_WT_rep1_input

description: input


title: P12A04486A

description:
FC2_S3
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: P11A04524A

description:
FC3_S8
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: A_9539 F_12w


title: P11A04585A

description:
FC1_S29
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: mycelia - H3K4AC_WT_rep1_input


title: A_9654 F_8w

value: 8wk WD


title: P12A04489A

description:
FC1_S28
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: P06A02997A

description:
FC2_S1
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: mycelia - H3K4AC_SIN3_rep2_input


title: A_9649 F_8w


title: P12A04571A

description:
FC5_S2
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: A_9645 F_8w


title: mycelia - H3K4AC_WT_rep2_IP


title: mycelia - H3K4AC_WT_rep1_IP


title: A_9650 F_4w

value: 4wk WD


title: mycelia - H3K4AC_SIN3_rep1_input


title: A_9648 F_4w


title: A_9541 F_12w


title: P12A04446A

description:
FC3_S10
Single-end small RNA sequencing
Urinary_miRNA_counts.txt


title: K562_PROseq_untrt

city: Boulder

first: John

last: Rinn

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

description: nascent RNA

data_processing:
Library strategy: PRO-seq
Fastp was used to identify and trim adaptor sequences from raw FASTQ files. Default settings were used.
Bowtie2 v2.3.5 was used to align trimmed rreads to the hg38 genome. Bowtie2 parameters: --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 8 -X 700 -p 10
Reads over promoter regions +/-3kb from Gencode v32 TSS were quantified with Rsubread featureCounts v.2.0.1. Default settings were used.
Raw counts were normalized to TPM and averaged over the two samples.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts for each promoter region are given along with the coordinates in hg38. Additional columns specify the TPM normalized counts in each sample and the source of the TSS annotation (Gencode v32).

source_name: chronic myelogenous leukemia cells

growth_protocol: K562 cells were cultured in RPMI supplemented with 10% FBS and 1x pen/strep and subcultured every 2-3 days in T75 flasks.

extract_protocol:
Cells were permeabilized and run-on reaction was performed at 30°C for 5min with biotinylated-NTPs. Run-on reaction was halted with TRIzol reagent buffer and total RNA was extracted using chloroform/ethanol precipitation. Dynabeads M-280 streptavidin beads (cat#: 11206D) were used to isolate biotinylated RNA.
RNA libraries were generated from isolated biotinylated RNA for sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit (cat#: E7760L) protocol for Illumina sequencing.

treatment_protocol: K562 cells were treated with 0.1% DMSO for 1 hour or untreated.

value: chronic myelogenous leukemia cells

tag: treatment

value: Untreated

tag: cell line


title: CITCO_replicate 3

city: Jupiter

first: Mark

last: Sundrud

state: FL

address: 120 Scripps Way

department: Immunology and Microbiology

institute: The Scripps Research Institute

data_processing:
Alignment: Salmon
Differential gene expression: DESEQ2
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene abundance in raw counts and TPMs

growth_protocol: Sorted a4b7+CCR9+ CD4+ Teff cells from human PBMC were stimulated with human anti-CD3 and anti-CD28 Dynabeads and cultured in complete media supplemented with 10U/mL rhIL-2

extract_protocol:
Total RNA (RIN > 9 by Bioanalyzer; Agilent Technologies) was isolated using RNeasy columns with on-column DNase treatment (QIAGEN) and processed with the NEBNext Ultra II ribosomal (r)RNA-depletion module Human/Mouse/Rat (New England BioLabs Inc.).
Using 400 ng total RNA as input rRNA-depleted RNA was processed using the NEBNext Ultra II directional RNA kit for Illumina (New England BioLabs Inc.) to generate strand-specific libraries. Final libraries were amplified by PCR (10-cycles), size selected using beads to enrich for fragments > 400 bp and purified using Ampure XP beads (Beckman Coulter). Final libraries were validated on the Agilent 2100 Bioanalyzer DNA chips and quantified on the Qubit (Thermo Fisher Scientific). Libraries were pooled at equimolar ratios and loaded onto the Illumina NextSeq500 flow cell and sequenced using 40 bp paired-end chemistry.

treatment_protocol: Sorted a4b7+CCR9+ CD4+ Teff cells from human PBMC were treated with either 10uM of CITCO or DMSO vehicle control for 24 hours

tag: tissue

value: PBMC

value: CD4+ effector T cells

value: 50uM TC, 24 hours


title: K562_PROseq_DMSO

description: nascent RNA

value: DMSO 0.1percent


title: mycelia - H3K4AC_SIN3_rep2_IP


title: DMSO_replicate 3

source_name: Sorted a4b7+CCR9+ CD4+ Teff cells from human PBMC

value: DMSO, 24 hours


title: A_9647 F_4w


title: DMSO_replicate 2


title: mycelia - H3K4AC_SIN3_rep1_IP


title: CITCO_replicate 2


title: A_1290 F_chow

value: chow


title: P11A06259A

description:
FC3_S29
Single-end small RNA sequencing
Urinary_miRNA_counts.txt

value: Urinary extracellular vesicles

value: gleason grade <=3 and bx-negative, high:gleason grade >=4):low


title: CITCO_replicate 1


title: A_1287 F_chow


title: P12A04444A

description:
FC5_S29
Single-end small RNA sequencing
Urinary_miRNA_counts.txt

value: low


title: siH19 rep3 (AoSMC)

city: New Haven

first: Ying

last: Jiang

address: 310 Cedar Street

institute: Department of Obstetrics, Gynecology & Reproductive Sciences

description:
AoSMC_counts_data.txt
AoSMC_siCon_vs_siH19_sig_diff_pooled.txt

data_processing:
RTA 2.4.11 software was used for basecalling
Alignments were made using Tophat v2.1.1,  read counts for each gene were estimated using featureCounts v1.5.0
Differential expression of genes between siCon and siH19 samples was determined using DESeq2 v1.14.1 (within R v3.3.3)
Genes that have significant differentiatial expression between siCon and siH19 triplicates (q Value <0.1) were presented in the processed data file
Genome_build: hg38
Supplementary_files_format_and_content: [AoSMC_counts_data.txt] Tab-delimited text file includes counts.
[AoSMC_siCon_vs_siH19_sig_diff_pooled.txt] Tab-delimited text file includes log2 fold change of relative gene expression levels between siCon and siH19 conditions.

source_name: AoSMC (Lonza, Cat: CC-2571)

growth_protocol: AoSMC cells purchased from Lonza were maintained in smooth muscle cell basal medium supplemented with growth supplements including hEGF, Insulin, hFGF-B, FBS and GA-1000. The smooth muscle cell basal medium and the growth supplements were included in the Clonetics™ SmGM™-2 BulletKit™ (CC-3182) from Lonza.

extract_protocol:
Total RNA was harvested using PureLink RNA Mini Kit.
RNA-seq libraries were prepared using illumina TruSeq Stranded Total RNA LT kit with Ribo-Zero Human/Mouse/Rat, setA (Cat# rs-122-2201) according to the sample preparation protocol. Briefly, 1 ug total RNA was subjected to Ribo-Zero depletion to remove rRNAs. The remaining RNA was purified, fragmented, and primed with random hexamers for cDNA synthesis. After first and second cDNA synthesis, cDNA fragments were adenylated and then ligated to indexing   adapters. The cDNA fragments were enriched by PCR, purified, and then sequenced on an illumina NextSeq500 using paired-end chemistry and 76-bp cycles.

treatment_protocol: Cells were transfected with either control siRNA or H19 siRNA. 48h later, cells were harvested for RNA extraction.

value: Aortic Smooth Muscle Cell (AoSMC)

tag: sirna

value: H19 knockdown


title: siH19 rep1 (AoSMC)


title: siH19 rep2 (AoSMC)


title: siCon rep3 (AoSMC)

value: siControl

value: control


title: homo-2 (STHdhQ111/Q111)

first: Srinivasa

last: Subramaniam

address: 130 Scripps Way

data_processing:
We used an Illumina NextSeq 500 system and a HIGH output 75 Kit with 2x40 bp read length. Base-calling was performed online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.2.0.
RNAseq reads were trimmed using Cutadapt with the following parameters : -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=15 –pair-filter=any.
Reads were mapped to the mouse genome using Bowtie v1.1.2. Any reads mapping to rRNA and tRNA were filtered out.
Reads were aligned to the mouse transcriptome with RSEM v1.3.0 using the GRCm38.p5 genome annotation.
Differential gene expression analysis was performed using Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: The raw data files are in the fastq format and need to be need to be trimmed to remove the Illumina TruSeq adapters. -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Supplementary_files_format_and_content: comma-separated file includes the gene count data for all samples

source_name: Striatal cells

extract_protocol:
Total RNA from these samples were isolated using miRNeasy Mini Kit (Qiagen)
NEBNext Ultra II directional library prep with poly(A) mRNA Magnetic isolation module
mRNA-seq

value: Expressing knock-in mutant Htt exon 1 with 111 Glu repeats


title: homo-1 (STHdhQ111/Q111)


title: scATAC for Thymus cells, CD8-31132

city: Hefei

first: Kun

last: Qu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

description:
scATAC for Thymus cells
scATAC_Accesson.txt

data_processing:
Sequences were aligned using Cell Ranger version 1.3.1 from 10x Genomics with default parameters.
The GRCm38.p5 assembly was used as the reference genome, and ribosomal RNA, mitochondrial RNA (Mt-RNA) and pseudogenes were removed.
Cells with fewer than 500 detected genes and more than 4500 detected genes for which total mitochondrial gene expression exceeded 40% were removed. Genes that were expressed in fewer than three cells were also removed.
Quantile normalization was performed using qnorm in R.
Genome_build: hg38
Supplementary_files_format_and_content: 10x_log2_q_norm.txt - tab-delimited text file includes quantile normalized gene expression values for each cell
Supplementary_files_format_and_content: scATAC_Accesson.txt - tab delimited text file includes normalized accesson count values predicted by APEC for each cell

source_name: CD8+ T cells

extract_protocol:
Thymus tissues were harvested from mice aged 6 - 8 weeks and gently ground in 1 mL of RPMI-1640.
Single cells were captured in droplet emulsions using a GemCode Single-Cell Instrument (10x Genomics), and scRNA-seq libraries were constructed with the 10x Genomics protocol using a GemCode Single-Cell 3′ Gel Bead and Library V2 Kit. The libraries were sequenced using a HiSeq X-10 Sequencing System (Illumina). scATAC-seq experiments were performed as previously described by Li B et al, Genome Biology, 2020.

tag: age

value: 7 weeks

tag: Sex

value: male

value: Thymus


title: siCon rep2 (AoSMC)


title: siCon rep1 (AoSMC)


title: Sheep 7 S07 Left Caudal lung segment (LC)

type: RNA

city: Melbourne

first: Udari

middle: Eshani

last: Perera

state: Victoria

address: Corner Flemington Road and Parkdrive, Parkville

country: Australia

institute: University of Melbourne

description: S07 7 LC-cy3 Signal

hyb_protocol: multiple control probes are included on each chip.  The control probes are used for quality controls of chip production, sample labeling and assay conditions.  Among the control probes, PUC2PM-20B and PUC2MM-20B are the perfect match and single-based match detection probes, respectively, of a 20-mer RNA positive control sequence that is spiked into the RNA samples before labeling.  One may assess assay stringency from the intensity ratio of PUC2PM-20B and PUC2MM-20B, which is normally larger than 30.

scan_protocol: Axon GenePix 4000B Microarray Scanner. Pixel Size 10 µm and sample Gain - 420. Chip images these Cy3 (or Af3) images one may directly read miRNA profiles.  The images are displayed in pseudo colors so as to expand visual dynamic range.  As signal intensity increases from 1 to 65,535 the corresponding color changes from blue to green, to yellow, and to red.

data_processing: The signal mean values are derived by values of repeating spots after background subtraction.  All transcripts that are considered detected are written in black font color.  During data processing, “bad spots” that have signal values deviated more than 50% of average values of repeating spots and/or spot CV larger than 0.5 are discarded.  Signal p-values are provided to indicate how significantly the signal is differentiated from background.  When a signal has a detection p-value larger than 0.01 or is bellow the detection limit, its mean value is written in grey color.

organism: Ovis aries

source_name: Normal_caudal lung

label_protocol: The content of each chip is listed in the layout file named “MRA-1002B1_miRMouse_22” in the main folder.  Multiple redundant regions are included.  Each region consists of miRNA probes, which detect miRNA transcripts listed in Sanger miRBase Release 22 (http://www.mirbase.org/).

extract_protocol: Total RNA extraction was done using the miRNeasy Mini Kit according to manufactures instruction (QIAGEN Pty Ltd, Doncaster, Australia. RNA quality was determined by an Agilent Bioanalyzer 2100

value: Female

value: 9 months

tag: histology

value: Normal

tag: status after 4 weeks

value: Euthenized

value: Caudal Lung


title: Sheep 10 S10 Left Caudal lung segment (LC)

description: S09 10 LC-cy3 Signal


title: Sheep 10 S10 Right Caudal lung segment (RC)

description: S010 10 RC-cy3 Signal

source_name: Fibrosis_caudal lung

value: Fibrosis


title: Sheep 7 S07 Right Caudal lung segment (RC)

description: S08 7 RC-cy3 Signal


title: DMSO_replicate 1

value: PBMC

value: CD4+ effector T cells

value: DMSO, 24 hours


title: Sheep 6 S06 Left Caudal lung segment (LC)

description: S05 6 LC-cy3 Signal


title: MECP2-S423A_rep4

city: Kuopio

first: Mikko

last: Hiltunen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
RNA concentration: 74,8 ng/µl, MECP2 expression normalized to control samples: 171,7 %
R16

data_processing:
Illumina sequencing adapter sequences were removed, and reads were quality trimmed using the cutadapt version 2.8.
The trimmed reads were mapped against the ribosomal reference sequences using the Bowtie 2 version 2.2.3. Successfully mapped reads were abandoned.
The trimmed and filtered reads were subjected to pseudo alignment to mouse reference transcriptome and transcript abundance quantification using kallisto version 0.46.1.
Transcript abundance estimates were collapsed to gene-level counts using R package tximport version 1.14.
Raw gene-level counts were imported into R package DESeq2 version 1.26.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file with raw gene-level counts for every gene and every sample.

source_name: primary cortical neurons and BV2 secondary cells

growth_protocol: Mouse primary cortical neurons were harvested from JAXC57BL/6J mice on embryonic day 18. Cortices were dissected and single-cell suspension was prepared by trypsin digestion and trituration. Cells were plated in Neurobasal Medium (12348017, Gibco, Waltham, MA, USA) supplemented with 1x B27 (17504044, Gibco, Waltham, MA, USA), 2 mM L-glutamine and 1% (v/v) penicillin-streptomycin (feeding medium). Plating was done on poly-D-Lysine (P6407, Sigma-Aldrich, St. Louis, MO, USA) -coated 24-well plates (142475, Nunc A/S, Roskilde, Denmark) at a density of 4 x 105 cells/well. After transduction of the neurons (described under treatment protocol), co-cultures were prepared by adding immortalized murine microglial BV2 cells. On day 6 in vitro (DIV6), BV2 cells suspended in Neurobasal medium were added to the neurons at 1:5 ratio (BV2:neurons) and let to settle down for two hours before starting further treatments. Prior to co-culturing, BV2 cells were cultured in RPMI-1640 medium (R0883, Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% (v/v) fetal bovine serum (FBS, 10270-106, Gibco, Waltham, MA, USA), 2 mM L-glutamine (17-605E, Lonza, Basel, Switzerland) and 1 U/ml penicillin-streptomycin (DE17-602E, Lonza, Basel, Switzerland). All cells were maintained at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted with High Pure RNA Isolation Kit (11828665001, Roche, Basel, Switzerland). Briefly, cells were scraped in PBS, lysed, and nucleic acids were immobilized by glass fiber fleece filters. Samples were treated with DNase I and RNA was washed twice before elution. RNA integrity was measured with an Agilent 2100 Bioanalyzer system.
Library preparation and RNA sequencing was conducted by Novogene (Cambridge, UK). In brief, mRNA enrichment was performed with oligo(dT) bead pulldown, from where pulldown material was subjected to fragmentation, followed by reverse transcription, second strand synthesis, A-tailing, and sequencing adaptor ligation. The final amplified and size selected library comprised of 250-300 bp insert cDNA and paired-end 150bp.

treatment_protocol: Prior to transduction of primary cortical mouse neurons on DIV4, half of the culture medium was collected and replaced with fresh feeding medium. The cells were transduced with lentiviral particles at MOI 10. After 24 h, the medium containing lentiviral particles was replaced with the previously collected medium mixed 1:2 with fresh feeding medium. Neuroinflammation was induced 2 h after addition of BV2 cells on DIV6 with 200 ng/ml LPS and 20 ng/ml IFNγ in PBS or PBS only (vehicle). Samples were collected 48 h later.

value: E18 primary cortical neurons

tag: lentivirus transduction

value: pLVX‑EF1alpha-MECP2-S423A-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subjected to site-directed mutagenesis (S423A) and subcloned into 631982, Takara)

tag: added cell line

value: 48 h with 200 ng/ml LPS and 20 ng/ml IFNgamma


title: MECP2-S80A_rep4

description:
RNA concentration: 83,4 ng/µl, MECP2 expression normalized to control samples: 246,2 %
R15

tag: cell type

value: pLVX‑EF1alpha-MECP2-S80A-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subjected to site-directed mutagenesis (S80A) and subcloned into 631982, Takara)

value: immortalized murine microglial BV2 cells


title: GR_KO_HFSC_Replicate_2

city: Cambridge

first: Sekyu

last: Choi

state: Massachusetts

address: 7 Divinity Ave, Sherman-fairchild 312

institute: Harvard University

data_processing:
Adaptor triming: Trim Galore! (0.4.1)
Alignment: STAR (2.5.3)
Differential Expression Analysis: DESeq2 (1.22.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

extract_protocol:
RNA was harvested using an RNeasy Micro Kit (Qiagen), using QIAcube according to manufacturer instruction. RNA concentration and RNA integrity were determined by Bioanalyzer (Agilent) using the RNA 6000 Pico chip. High quality RNA samples with RNA Integrity Number ≥ 8 were used as input for RNA-sequencing.
SMART-Seq v4 was used for cDNA synthesis. Sequencing libraries were then made using Illumina's Nextera XT Library Prep kit.

tag: strain background

tag: genotype/variation

value: Pdgfra-CreER; GR fl/fl

value: Injection of tamoxifen intraperitoneally for 6 days

value: FACS purified mouse hair follicle stem cells


title: GR_KO_HFSC_Replicate_1

value: Female


title: Control_HFSC_Replicate_2

value: wild type


title: Sheep 6 S06 Right Caudal lung segment (RC)

description: S06 6 RC-cy3 Signal

value: 9 months


title: Control_HFSC_Replicate_1


title: CD45+ cells from tumor-bearing cerebellum treated with radiation, QB66

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

data_processing:
Data was processed using the Cellranger pipeline (10x genomics, v.3.0.2) for demultiplexing and  alignment of sequencing reads to the mm10 transcriptome and creation of feature-barcode matrices. Individual  single cell RNAseq libraries were aggregated using the cellranger aggr pipeline. Libraries were normalized for  sequencing depth across all libraries during aggregation. Secondary analysis on the aggregated feature barcode matrix  was performed using the Seurat package (v.3.0) within the R computing environment.
Supplementary_files_format_and_content: Processed data files for each sample consist of a barcode ID file, feature ID file, and count matrix file as produced from the Cellranger Pipeline (10x Genomics).

extract_protocol:
Mononuclear cells were extracted from mouse cerebellum, brain, tumor tissue using Percoll discontinuous gradient separation and subpopulations were isolatd using either CD11+ or CD45+ microbeads
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v2  per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled,  and sequenced on an Illumina Hiseq sequencer in a paired-end, single indexing run. Sequencing for each library  targeted 20,000 mean reads per cell.
scRNA-seq

tag: genotype

value: 8 weeks

value: tumor-bearing cerebellum

value: CD45+ cells

value: 3x 10Gy radiation + 5 days


title: CD45+ cells from tumor-bearing cerebellum treated with radiation, CB67


title: Sheep 3 S03 Left Caudal lung segment (LC)

description: S03 3 LC-cy3 Signal

value: Fibrosis

value: Euthenized

value: Caudal Lung


title: Sheep 3 S03 Right Caudal lung segment (RC)

description: S04 3 RC-cy3 Signal

value: Normal


title: MECP2-WT_rep4

description:
RNA concentration: 78,9 ng/µl, MECP2 expression normalized to control samples: 197,2 %
R14

value: E18 primary cortical neurons

tag: strain

value: pLVX‑EF1alpha-MECP2-WT-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subcloned into 631982, Takara)

value: 48 h with 200 ng/ml LPS and 20 ng/ml IFNgamma


title: Control_rep4

description:
RNA concentration: 75,3 ng/µl, MECP2 expression normalized to control samples: 103,9 %
R13

value: immortalized murine microglial BV2 cells


title: MECP2-S423A_rep3

description:
RNA concentration: 61,8 ng/µl, MECP2 expression normalized to control samples: 169,9 %
R12

value: pLVX‑EF1alpha-MECP2-S423A-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subjected to site-directed mutagenesis (S423A) and subcloned into 631982, Takara)


title: control-1 (STHdhQ7/Q7)

value: Expressing knock-in wild-type Htt exon 1 with 7 Glu repeats


title: ADX_HFSC_Replicate_2

value: Female

value: Adrenalectomy

value: FACS purified mouse hair follicle stem cells


title: ADX+CORT_HFSC_Replicate_1

value: wild type

value: Adrenalectomy with corticosterone feeding


title: control-2 (STHdhQ7/Q7)


title: MECP2-S80A_rep3

description:
RNA concentration: 65,8 ng/µl, MECP2 expression normalized to control samples: 228,1 %
R11

value: pLVX‑EF1alpha-MECP2-S80A-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subjected to site-directed mutagenesis (S80A) and subcloned into 631982, Takara)


title: Sheep 2 S02 Left Caudal lung segment (LC)

description: S01 2 LC-cy3 Signal

value: 9 months


title: ADX_HFSC_Replicate_1


title: ADX+CORT_HFSC_Replicate_2


title: Sham_HFSC_Replicate_1

value: Sham-operation


title: invitro_MIX_PE_2_r2

city: Lausanne

first: Silvia

last: Brochet

state: Vaud

address: UNIL campus, Biophore building

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

data_processing:
Trimming for adapters and quality using trimmomatic
For the in vivo: separation of rRNA and non-rRNA reads using sortmerna
Mapping to reference with bowtie2
Generation of count files with HtSeq
Differential gene expression analysis with EdgeR
Genome_build: Lapi = https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP029476.1
Genome_build: Lhel = https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP029544.1
Genome_build: Lmel = https://www.ncbi.nlm.nih.gov/nuccore/NZ_QGLG00000000.1
Genome_build: Lkul = https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP029477.1
Supplementary_files_format_and_content: .count files containing counts per gene obtained with HtSeq

organism:
Lactobacillus apis
Lactobacillus kullabergensis
Lactobacillus helsingborgensis
Lactobacillus melliventris

source_name: In vitro culture

growth_protocol: For the in vitro samples: bacteria were grown in basal medium supplemented with either glucose (G) or pollen extract (PE) for 16 hours at 34˚C in anarobic conditions

extract_protocol:
For the in vivo samples: bacteria were harvested from rectums of bees that were fed with sugar water + pollen grains (SWPG) or with sugar water (SW) only 5 days post-colonization
For the in vitro samples libraries were prepared following the protocol published in Nature Protocols by Avraham et al. (2016). For the in vivo samples libraries were prepared using the Zymo-Seq RiboFree Total RNA Library kit (Zymo Research).

tag: phylotype

value: Lactobacillus Firm5

value: Pollen extract

value: Community (mixture of all species)

tag: Stage

value: 16 hours post-inoculation


title: invitro_MIX_PE_3_r2

tag: treatment


title: Control_rep3

description:
RNA concentration: 74,3 ng/µl, MECP2 expression normalized to control samples: 102,5 %
R9

value: E18 primary cortical neurons


title: MECP2-WT_rep3

description:
RNA concentration: 79,0 ng/µl, MECP2 expression normalized to control samples: 188,5 %
R10

value: pLVX‑EF1alpha-MECP2-WT-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subcloned into 631982, Takara)

value: 48 h with 200 ng/ml LPS and 20 ng/ml IFNgamma


title: siLP_CD45.1+_replicate 3

data_processing:
Alignment: Salmon
Differential gene expression: DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: Gene abundance in raw counts and TPMs

source_name: Sorted week 3 CD4+ Teff cells post T cell Transfer into Rag deficient mice

extract_protocol:
Clontech SMART-Seq v4 ultra low input RNA kit
Enriched cDNA was converted to Illumina-compatible libraries using NEBNext Ultra II DNA kit with 1ng input

value: small intestine lamina propria

tag: strain/genotype

value: CD4+ effector T cells


title: siLP_CARko_replicate 3

tag: tissue


title: cLP_CARko_replicate 3

value: colon lamina propria


title: cLP_CD45.1+_replicate 3


title: Sheep 2 S02 Right Caudal lung segment (RC)

description: S02 2 RC-cy3 Signal

value: Female

value: Normal

value: Euthenized

value: Caudal Lung


title: MECP2-S423A_rep2

description:
RNA concentration: 70,5 ng/µl, MECP2 expression normalized to control samples: 176,5 %
R8

value: pLVX‑EF1alpha-MECP2-S423A-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subjected to site-directed mutagenesis (S423A) and subcloned into 631982, Takara)

value: immortalized murine microglial BV2 cells


title: spleen_CARko_replicate 3

value: spleen


title: spleen_CD45.1+_replicate 3


title: invitro_MIX_PE_1_r2

value: Lactobacillus Firm5


title: invitro_MIX_G_3_r2

value: Glucose


title: MECP2-S80A_rep2

description:
RNA concentration: 68,8 ng/µl, MECP2 expression normalized to control samples: 232,1 %
R7

value: pLVX‑EF1alpha-MECP2-S80A-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subjected to site-directed mutagenesis (S80A) and subcloned into 631982, Takara)


title: siLP_CARko_replicate 2


title: MECP2-WT_rep2

description:
RNA concentration: 66,7 ng/µl, MECP2 expression normalized to control samples: 174,7 %
R6


title: siLP_CD45.1+_replicate 2


title: invitro_MIX_G_2_r2

value: Community (mixture of all species)

value: 16 hours post-inoculation


title: Sham_HFSC_Replicate_2

value: wild type

value: Sham-operation

value: FACS purified mouse hair follicle stem cells


title: cLP_CARko_replicate 2

value: CD4+ effector T cells


title: spleen_CARko_replicate 2


title: Control_rep2

description:
RNA concentration: 72,8 ng/µl, MECP2 expression normalized to control samples: 93,0 %
R5

value: E18 primary cortical neurons

value: 48 h with 200 ng/ml LPS and 20 ng/ml IFNgamma


title: spleen_CD45.1+_replicate 2


title: cLP_CD45.1+_replicate 2

value: colon lamina propria


title: invitro_MIX_PE_3

value: Pollen extract


title: siLP_CARko_replicate 1

value: small intestine lamina propria


title: invitro_MIX_G_1_r2


title: siLP_CD45.1+_replicate 1


title: invitro_MIX_PE_2


title: cLP_CARko_replicate 1


title: invitro_MIX_PE_1


title: GR_KO_DP_Replicate_1

data_processing:
Alignment: Salmon
Differential Expression Analysis: DESeq2 (1.22.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts per transcripts for each Sample

tag: genotypes

value: Pdgfra-CreER; GR fl/fl

value: Female

value: Injection of tamoxifen intraperitoneally for 6 days

value: FACS purified mouse dermal papilla (DP) cells


title: invitro_MIX_G_2

value: Lactobacillus Firm5

value: Glucose


title: GR_KO_DP_Replicate_2


title: MECP2-WT_rep1

description:
RNA concentration: 70,7 ng/µl, MECP2 expression normalized to control samples: 225,8 %
R2

value: pLVX‑EF1alpha-MECP2-WT-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subcloned into 631982, Takara)

value: immortalized murine microglial BV2 cells


title: invitro_MIX_G_3

value: Community (mixture of all species)

value: 16 hours post-inoculation


title: Control_DP_Replicate_1

value: wild type


title: Control_DP_Replicate_2


title: cLP_CD45.1+_replicate 1

value: CD4+ effector T cells


title: spleen_CD45.1+_replicate 1

value: spleen


title: invitro_MIX_G_1


title: spleen_CARko_replicate 1


title: ADX_DP_Replicate_2

value: Adrenalectomy


title: ADX_DP_Replicate_1


title: Sham_DP_Replicate_2

value: Sham-operation


title: MECP2-S423A_rep1

description:
RNA concentration: 62,1 ng/µl, MECP2 expression normalized to control samples: 191,8 %
R4

value: E18 primary cortical neurons

value: pLVX‑EF1alpha-MECP2-S423A-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subjected to site-directed mutagenesis (S423A) and subcloned into 631982, Takara)

value: 48 h with 200 ng/ml LPS and 20 ng/ml IFNgamma


title: MECP2-S80A_rep1

description:
RNA concentration: 55,2 ng/µl, MECP2 expression normalized to control samples: 283,8 %
R3

value: pLVX‑EF1alpha-MECP2-S80A-IRES-ZsGreen1 (PS100064, OriGene insert (human MECP2, NM_004992) subjected to site-directed mutagenesis (S80A) and subcloned into 631982, Takara)


title: CD45+ cells from tumor-bearing cerebellum treated with radiation, C233

tag: age

value: 8 weeks

value: tumor-bearing cerebellum

value: CD45+ cells

value: 3x 10Gy radiation + 5 days


title: CD11+ myeloid cells from tumor-bearing cerebellum treated with radiation, CU49

value: CD11+ myeloid cells


title: CD11+ myeloid cells from tumor-bearing cerebellum treated with radiation, PN80


title: Control_rep1

description:
RNA concentration: 66,4 ng/µl, MECP2 expression normalized to control samples: 100,7 %
R1

value: immortalized murine microglial BV2 cells


title: CD11+ myeloid cells from tumor-bearing cerebellum treated with GDC-0449, PM44

value: 4 days of 2x/daily GDC-0449 treatment


title: MV5_Cellgroups_R

city: Kiel

first: Joana

middle: Pimenta

last: Bernardes

address: Am Botanischen Garten 11

department: Systems Immunology

country: Germany

institute: Institute of Clinical Molecular Biology

data_processing:
We selected the high-quality reads identified based on FastQC.
We aligned the reads to Chlamydomonas genome version 5.0 reference genome32 using hisat2
We created the feature counts matrix using HTSeq
Genome_build: chlamy_v5-5.fc.gff
Supplementary_files_format_and_content: RawCounts_Average.csv- raw counts for individual samples and their average expression based on selection regiment or treatment
Supplementary_files_format_and_content: NormCounts_Average.csv- norm counts based on DEseq2 (dds) for individual samples and their average expression based on selection regiment or treatment
Supplementary_files_format_and_content: DifExpression_analysis.csv- Differential expression analysis with Logfold change information and p-adjusted value calculated using DESeq2 for comparisons of interest.

organism: Chlamydomonas reinhardtii

source_name: harvested algae

growth_protocol: We picked one pair of cell group and single cell isolate and inoculated them to nine chemostat in COOL80 medium.

extract_protocol:
the harvested algae were prepared for total RNA extraction with RNeasy Plant Mini Kit from Qiagen® for RNASeq analysis
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 10 days we either added rotifers (rotifer treatment), switched the resource supply to lower nitrogen concentration (low nitrogen treatment; 40μM nitrogen)or kept the algae as they were (control treatment). After five additional days we harvested the algae from the chemostats.

tag: selection

value: Cell group

value: harvested algae


title: MV6_Cellgroups_N


title: CD11+ myeloid cells from tumor-bearing cerebellum treated with GDC-0449, PN28


title: Sham_DP_Replicate_1

value: wild type

tag: Sex

value: Female

value: FACS purified mouse dermal papilla (DP) cells


title: CD11+ myeloid cells from tumor-bearing cerebellum, PN04

value: no treatment


title: MV3_Singlecell_N

value: Single cell


title: MV4_Cellgroups_C

value: Control


title: CD11+ myeloid cells from tumor-bearing cerebellum treated with radiation, PO18


title: Pooled Cd11+ myeloid cells from peripheral blood of 3 mice, Mono

value: 2 weeks

value: peripheral blood

value: Cd11+ myeloid cells


title: BMDM_3_Hepcidin_3h

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip mouse Gene 2.0 from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V21 was used for annotation.

label: Biotin

source_name: Primary mouse bone marrow-derived macrophages

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: Bone marrow-derived macrophages (BMDMs) were obtained from bone marrow (BM) precursor cells. In brief, total BM was obtained from 8-10 week old WT by flushing femur and tibiae BM with Dulbecco’s modified Eagle’s medium (DMEM). Cells were cultured in plastic tissue culture dishes (150 mm) in 25 ml of DMEM containing 20% FBS (Fetal Bovine Serum) and 30% L cell-conditioned medium as a source of M-CSF. They were then incubated at 37°C in a humidified 5% CO2 atmosphere. After 7 days of culture, a homogeneous population of adherent BMDMs was obtained. BMDMs were scrapped and seeded at 150 000 cells per well into 24-well plate in 0,5 ml of DMEM containing 15% L cell-conditioned medium and 10% FBS. The following day, we change media to DMEM alone for 1 hour and hepcidin (Peptide International) was added to the wells at 1 µg/ml. The BMDMs were incubated for 1 and 3 hours and lysed with Trizol.

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

treatment_protocol: Hepcidin (Peptide International) was added to the wells at 10µg/ml. The BMDMs were incubated for one hour and lysed with Trizol.

value: BMDM

tag: agent

value: Hepcidin

tag: time


title: BMDM_2_Hepcidin_3h


title: BMDM_2_PBS_3h

value: PBS


title: BMDM_1_PBS_3h


title: MV2_Singlecell_R


title: BMDM_1_Hepcidin_3h


title: CD11+ myeloid cells from tumor-bearing cerebellum, PO19

value: 8 weeks

value: tumor-bearing cerebellum

value: CD11+ myeloid cells


title: BMDM_3_PBS_3h


title: 591228Ca and 591228N

city: Xiamen

first: Yong

state: Fujian

address: 201-205 Hubin South Road

department: School of Medicine

institute: Zhongshan Hospital, Xiamen University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7) and Agilent GeneSpring was used to normalization and data process.

source_name: HCC tissue (liver)

label_protocol: Total RNA was reversed transcripted to cDNA and added 4 uL of random primer; after that a PCR reaction with 5X klenow buffer, cy5/3 dCTP, and Klenow Fragment was conducted to label the cDNA.

growth_protocol: Not applicable

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

treatment_protocol: Not applicable

value: HCC

source_name: Non-cancer tissue (liver)

value: Non-cancer liver


title: 587327Ca and 587327N


title: 392193Ca and 392193N


title: MV1_Singlecell_C

value: harvested algae


title: BMDM_3_Hepcidin_1h


title: Pooled Cd11+ myeloid cells from 3 mouse cerebella, MG

value: cerebella


title: 584018Ca and 584018N


title: BMDM_2_Hepcidin_1h


title: 577628Ca and 577628N


title: 558944Ca and 558944N


title: BMDM_1_Hepcidin_1h


title: BMDM_3_PBS_1h


title: BMDM_2_PBS_1h


title: MV4-11 RNA-Seq IRF8KO repl4

status: Public on Feb 12 2021

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to mouse genome hg19 or hg38 using Bowtie, allowing one mismatch.
SAM files were converted to bigwig files using SamTools and deepTools/bamCoverage. Data were normalized to RPKM.
RNA-Seq data were aligned to human transcriptome GENCODE v32  using RNA Star. Counts per gene were determined using FeatureCounts . Differentially expressed genes and normalized reads were determined using DeSeq2.
Genome_build: hg19, hg38
Supplementary_files_format_and_content: bw

growth_protocol: MV4-11 cells were cultured in RPMI medium supplemented with 15% FCS and 1% P/S.

extract_protocol:
ChIP experiments were performed in accordance to the One Day ChIP kit protocol (Diagenode). Total RNA was extracted by using the RNeasy Mini system (Qiagen) including an on-column DNaseI digestion.
For ChIP-Seq library five nanograms of precipitated DNA were used for indexed sequencing library preparation using the Microplex library preparation kit v2 (Diagenode). RNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina).

tag: cell line

value: myeloid leukaemia (AML)

value: IRF8 KO


title: MV4-11 RNA-Seq IRF8KO repl2

tag: cell type


title: MV4-11 RNA-Seq IRF8KO repl1


title: Population SD - 7 ppt - replicate 2 [SD-7-2]

city: Chapel Hill

first: Jeeyun

last: Lee

state: NC

address: Coker Hall, room 418

department: Biology

description:
processed data file: read_counts_SD.xlsx
SD-7-2_TAGCTT_L002

data_processing:
Quality control via FastQC (v.0.11.3)
Discarded reads with Quality Scores lower than 30 were done using CLC Genomics Workbench (v.8.0.3)
SD reads were aligned to the SD genome and AB reads were aligned to the AB genome, and annotated using the SD annotation in CLC Genomics Workbench (v.8.0.3). Exported BAM files from CLC Genomics Workbench.
BAM files imported into R and analyzed with package DESeq2 (v.1.10.1)
GO enrichment analysis done in Blast2GO Basic and Pro (v.5.2.5)
Genome_build: Reference for SD: TCALIF_genome_v3.fasta; reference for AB: AB_genome4_opt_15_merged.fa
Supplementary_files_format_and_content: Excel table of raw read counts per gene, population, treatment, and replicate.

organism: Tigriopus californicus

source_name: Population SD - 7 ppt_whole body

extract_protocol:
Total RNA was extracted using Sigma-Aldrich's TRI Reagent Protocol
mRNA library preparations and Illumina HiSeq 2500 50x paired-end sequencing were done at University of North Carolina at Chapel Hill's High-Throughput Sequencing Facility

tag: population

value: San Diego (SD)

value: hypo-osmotic stress

value: Whole body


title: Population SD - recovery 35 ppt - replicate 1 [SD-35-1]

institute: University of North Carolina at Chapel Hill

description:
processed data file: read_counts_SD.xlsx
SD-35-1_CTTGTA_L002

source_name: Population SD - recovery 35 ppt_whole body

value: recovery


title: Population SD - 7 ppt - replicate 1 [SD-7-1]

description:
processed data file: read_counts_SD.xlsx
SD-7-1_GATCAG_L002


title: Population SD - initial 35 ppt (control) - replicate 2 [SD-35C-2]

description:
processed data file: read_counts_SD.xlsx
SD-35C-2_ACTTGA_L002

source_name: Population SD - initial 35 ppt (control)_whole body

value: control


title: Population AB - 7 ppt - replicate 1 [AB-7-1]

description:
processed data file: read_counts_AB.xlsx
AB-7-1_TTAGGC_L002

source_name: Population AB - 7 ppt_whole body

value: Abalone Cove (AB)


title: Population AB - 7 ppt - replicate 2 [AB-7-2]

description:
processed data file: read_counts_AB.xlsx
AB-7-2_TGACCA_L002


title: Population AB - recovery 35 ppt - replicate 1 [AB-35-1]

description:
processed data file: read_counts_AB.xlsx
AB-35-1_ACAGTG_L002

source_name: Population AB - recovery 35 ppt_whole body


title: Population SD - recovery 35 ppt - replicate 2 [SD-35-2]

description:
processed data file: read_counts_SD.xlsx
SD-35-2_AGTTCC_L002


title: Population AB - initial 35 ppt (control) - replicate 1 [AB-35C-1]

description:
processed data file: read_counts_AB.xlsx
AB-35C-1_ATCACG_L002

source_name: Population AB - initial 35 ppt (control)_whole body


title: Population AB - initial 35 ppt (control) - replicate 2 [AB-35C-2]

description:
processed data file: read_counts_AB.xlsx
AB-35C-2_CGATGT_L002


title: MV4-11 RNA-Seq IRF8KO repl3


title: Population AB - recovery 35 ppt - replicate 2 [AB-35-2]

description:
processed data file: read_counts_AB.xlsx
AB-35-2_GCCAAT_L002


title: Population SD - initial 35 ppt (control) - replicate 1 [SD-35C-1]

description:
processed data file: read_counts_SD.xlsx
SD-35C-1_CAGATC_L002


title: MV4-11 RNA-Seq Control repl2

value: Control


title: MV4-11 RNA-Seq Control repl4


title: 558819Ca and 558819N


title: MV4-11 RNA-Seq Control repl1


title: BMDM_1_PBS_1h

value: BMDM

value: PBS


title: MV4-11 IRF8 KO

description: IRF8 ChIP-Seq

tag: chip antibody


title: 582573Ca and 582573N


title: 558900Ca and 558900N


title: 581711Ca and 581711N


title: MV4-11 IRF8 Control

description: IRF8 ChIP-Seq

tag: genotype


title: MV4-11 RNA-Seq Control repl3


title: RNA-seq-delCsn1s2b-E-2_p18

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTseq (Anders et al., bioRxiv 2014) was was applied to calculate raw read counts.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts from RNA-seq samples

source_name: Mammary gland

growth_protocol: Mouse mammary tissues were harvested at pregnancy day 6 and 18 (p6 and p18).

extract_protocol:
Total RNA was extracted from frozen mammary tissue from wild type mice at day one and ten of lactation and purified with RNeasy Plus Mini Kit (Qiagen, 74134). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 2500 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

tag: strain/background

tag: genotype/variation

value: delCsn1s2b-E - a deletion of the enhancer of Csn1s2b

value: Pregnancy day 18

value: Mammary gland


title: RNA-seq-delCsn1s2b-E-3_p18

tag: Stage


title: fthko_spleen_iron_mouse7

city: Innsbruck

first: Piotr

last: Tymoszuk

state: Tirol

address: Anichstrasse 35

department: University Clinic of Internal Medicine VI

country: Austria

institute: Medical University of Innsbruck

hyb_protocol: Labeled cDNA samples (6 γg/sample) were hybridized at 45°C for 16 h on separate Affymetrix Mouse Gene 2.0 ST Arrays. GeneChips were washed and stained in the GeneChip® 3000 Fluidics Station

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® 3000 Scanner

data_processing: Gene expression data were pre-processed with the RMA algortithm (R, package oligo). Genes significantly regulated by iron:genotype interaction were identified by two-way ANOVA

label: biotin

source_name: Salmonella-infected iron-treated FthKO mouse

label_protocol: 200 ng total RNA per sample was labeled with biotin using the Affymetrix GeneChip WT PLUS Reagent Kit

extract_protocol: total RNA was extracted with the TriFAST Reagent (PaqLabs) according to manufacturer’s instructions

treatment_protocol: Snap-frozen spleen samples obtained from PBS- or intravenous iron (2 mg elementary Fe, iron isomaltoside) treated  WT (LysM-Cre-/- Fthfl/fl) and myeloid FthKO (LysM-Cre+/+ Fthfl/fl) mice infected with 500 CFU Salmonella Typhimurium for 12 hours

tag: strain background

value: myeloid FthKO (LysM-Cre+/+ Fthfl/fl)

value: male

value: 8 weeks

tag: treatment

value: intravenous iron

value: whole spleen


title: 1723 RU486-treated, biological replicate 1

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

country: Japan

institute: Mie University

description:
DKO+Dnmt3a2_1
Gene expression data from RU486-treated cells

hyb_protocol: Following fragmentation, 12.5 microg of cRNA were hybridized for 16 hr on Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Data processing, quality control, and output file generation was performed with Affymetrix Gene Expression Console. Raw data (CEL files) were used to perform normalization through Robust Multiaray Analysis (RMA) algorithm.

source_name: Dnmt3a and 3b DKO mESCs_induced Dnmt3a2 protein

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 nanog total RNA

growth_protocol: Cells were maintained on feeder MEF cells in knockout Dulbecco’s modified eagle medium (Thermo Fisher Scientific, Cat#10829) supplemented with 7.5% ES-qualified FBS (GE Healthcare, Cat#SH30070.03E), 7.5% Knockout serum replacement (Thermo Fisher Scientific, Cat#10828-028), 2 mM L-glutamine (Thermo Fisher Scientific, Cat#25030–081), 10 mM Hepes (Thermo Fisher Scientific, Cat#15630–080), 100U/ml penicillin/streptomycin (Thermo Fisher Scientific, Cat#15070–063), 0.1 mM non-essential amino acids (Thermo Fisher Scientific, Cat#11140–050), 0.1 mM beta-mercaptoethanol (Thermo Fisher Scientific, Cat#21985–023), in the presence of leukemia inhibitory factor (LIF) at 37°C with 5% CO2.

extract_protocol: Total cellular RNA was isolated from cells with RNeasy kit (Qiagen), according to the manufacture’s instructions.

treatment_protocol: Cells were cultured in ES medium containing 1 µM RU486 for 14 days on feeder MEFs. As a control, cells were treated with ethanol.

value: Dnmt3a and 3b double knockout (DKO) mESC cell line stably expressing RU486-inducible Dnmt3a2 fused with the ligand binding domain of the human progesterone receptor

value: embryonic stem cell (ESCs)

value: RU486 treatment for 14 days


title: Old 2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: Microarray data processing and analysis was carried out at EMBL. All analyses were carried out in R (v.2.13.0). Microarray data were normalized using Robust Multichip Average (RMA) and differentially expressed genes were identified using Linear Models for MicroArrays (LIMMA). A cut-off of a Benjamini-Hochberg false discovery rate (BH) <0.05 was used to identify significant genes.

source_name: late passage  (p24) IMR90

label_protocol: Biotinylated cRNA were prepared from 500 ng total RNA according to theThe Ambion iii ® WT Expression Kit Protocol For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays protocol in conjunction with the Affymetrix® GeneChip® WT Terminal Labeling Kit.

growth_protocol: Inducible CMV-Vector and CMV-TRF2dBdM were grown in DMEM aupplemented with 10%  tetracycline free FBS. Media was changed at day 4

extract_protocol: RNA was extracted using Qiagen RNeasy Mini kit, using Qiashredder for lysate homogenization.

treatment_protocol: To induce TRF2dMdB, both cell lines were treated with 1uG/ml of doxycyline

tag: passage


title: Young 1

source_name: young passge (p10) IMR90


title: wt_spleen_ctrl_mouse12

source_name: Salmonella-infected control-treated WT mouse

value: WT (LysM-Cre-/- Fthfl/fl)

tag: tissue


title: wt_spleen_ctrl_mouse2

tag: age


title: ICMV-TRF2 - 3

tag: days after doxycycline treatment


title: Old 3


title: fthko_spleen_ctrl_mouse9

source_name: Salmonella-infected control-treated FthKO mouse

tag: Sex


title: fthko_spleen_iron_mouse6


title: fthko_spleen_ctrl_mouse8


title: Young 3


title: iCMV-Vector - 3

source_name: iCMV-Vector

value: iCMV-Vector


title: ICMV-TRF2 - 2


title: Young 2


title: wt_spleen_iron_mouse5

source_name: Salmonella-infected iron-treated WT mouse


title: wt_spleen_ctrl_mouse1


title: Old 1


title: ICMV-TRF2 - 1


title: iCMV-Vector - 2


title: 1723 RU486-treated, biological replicate 2

description:
DKO+Dnmt3a2_2
Gene expression data from RU486-treated cells


title: wt_spleen_iron_mouse4


title: 1723 control, biological replicate 2

description:
DKO_2
Gene expression data from mock (ethanol)-treated cells

source_name: Dnmt3a and 3b DKO mESCs_control

value: Mock (ethanol) treatment for 14 days


title: RNA-seq-delCsn3-PE-1_p18

value: delCsn3-PE - deletion of the proximal enhancer of Csn3


title: iCMV-Vector - 1


title: RNA-seq-delCsn1s2b-E-1_p18


title: fthko_spleen_iron_mouse10


title: fthko_spleen_ctrl_mouse11


title: RNA-seq-delCsn3-PE-2_p18


title: 1723 control, biological replicate 1

description:
DKO_1
Gene expression data from mock (ethanol)-treated cells


title: RNA-seq-Csn_S1-4-3_p18

description: Total RNA-seq

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). Rsubread (Liao et al., Nucleic Acids Research, 2013) was applied to calculate raw read counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw read counts from RNA-seq samples.

extract_protocol:
Total RNA was extracted from frozen mammary tissue from wild type and mutant mice at pregnancy day 6 and 18 and purified with RNeasy Plus Mini Kit (Qiagen, 74134). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 2500 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.


title: RNA-seq-Csn_S1-4-4_p18

description: Total RNA-seq


title: wt_spleen_iron_mouse3


title: RNA-seq-Csn_S1-4-1_p6

description: Total RNA-seq

value: Pregnancy day 6


title: RNA-seq-Csn_S1-4-2_p18

description: Total RNA-seq


title: RNA-seq-Csn_S1-4-4_p6

description: Total RNA-seq


title: RNA-seq-WT2_p18

description: Total RNA-seq

value: wild-type


title: RNA-seq-WT1_p18

description: Total RNA-seq


title: RNA-seq-WT3_p6

description: Total RNA-seq


title: RNA-seq-WT3_p18

description: Total RNA-seq


title: RNA-seq-WT2_p6

description: Total RNA-seq


title: f5-i/i-3

city: Nanning

first: Jianwei

last: Shan

address: Daxue road

department: college of life science and technology

institute: Guangxi University

description: f5-i/i-3 plants spikelet

data_processing:
empty reads, low quality tags, single-copy tags, and tags that were either too long or too short were filtered out.
Burrows-Wheeler Alignment tool (BWA) and use Bowtie were used to map the clean reads to the reference genome and reference genes (http://rice.plantbiology.msu.edu/)
Genes expression level were quantified by Expectation Maximization (RSEM)
Noiseq method, was used to screen DEGs among two groups which contain biological replicates.
Genome_build: http://rice.plantbiology.msu.edu/
Supplementary_files_format_and_content: text files are genereated with differentially expressed genes

molecule: polyA RNA

organism: Oryza sativa

source_name: spikelet

growth_protocol: Each material was planted with 20.0 cm between plants in a row with 10 seedlings, and the rows were 26.7 cm apart. The crop was managed following normal agricultural practices.

extract_protocol:
Total RNA was extracted from each sample using TRIzon Reagent (CWBIO, Beijing, China) following manufacturers’ instruction.
The total RNA samples are first treated with DNase I to eliminate any possible genome DNA contamination. The mRNA was isolated from 6 ug of total RNA using oligo(dT) magnetic beads. To reduce the amount of RNA secondary structure, and 5’ bias of priming reverse transcription with poly(dT) primer, the mRNA is fragmented into short fragment before random-primed cDNA synthesis (Wilhelm, Marguerat et al. 2010). After double strand cDNAs were generated, the cDNA end repair and 3’-end single nucleotide A addition were performed. Then special Illumina sequencing adapters were ligated onto the cDNA pools. After the fragments were enriched by PCR amplification, qualification and quantification of the sample library were carried out with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System. Finally, the library products were ready for deep sequencing via Illumina HiSeqTM2000.

value: homozygous at f5_i/i

value: spikelet


title: f5-i/i-2

description: f5-i/i-2 plants spikelet


title: RNA-seq-WT1_p6

description: Total RNA-seq

value: Mammary gland


title: f5-i/i-1

description: f5-i/i-1 plants spikelet


title: f5-j/j-3

description: f5-j/j-3 plants spikelet

value: homozygous at f5_j/j


title: f5-j/j-2

description: f5-j/j-2 plants spikelet


title: f5-j/j-1

description: f5-j/j-1 plants spikelet


title: f5-i/j-1

description: f5-i/j-1 plants spikelet

value: heterozygous at f5_i/j


title: f5-i/j-3

description: f5-i/j-3 plants spikelet


title: f5-i/j-2

description: f5-i/j-2 plants spikelet


title: RNA-seq-Csn_S1-4-1_p18

description: Total RNA-seq

value: Pregnancy day 18


title: maltose_3

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: moltose treated without heat shock replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for all samples

source_name: maltose treated without heat shock replicate 3

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from UBR4 mKO tibialis anterior muscle at 6 and 24 months of age.
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina HiSeq 2000 platform.

value: cortical brain organoids


title: HS_maltose_3

description: moltose treated with heat shock replicate 3

source_name: maltose treated with heat shock replicate 3


title: maltose_2

description: moltose treated without heat shock replicate 2

source_name: maltose treated without heat shock replicate 2


title: RNA-seq-Csn_S1-4-3_p6

description: Total RNA-seq


title: HS_maltose_1

description: moltose treated with heat shock replicate 1

source_name: maltose treated with heat shock replicate 1


title: maltose_1

description: moltose treated without heat shock replicate 1

source_name: maltose treated without heat shock replicate 1


title: HS_control_3

description: control with heat shock replicate 3

source_name: control with heat shock replicate 3


title: RNA-seq-Csn_S1-4-2_p6

description: Total RNA-seq

source_name: Mammary gland


title: HS_control_2

description: control with heat shock replicate 2

source_name: control with heat shock replicate 2


title: control_3

description: control without heat shock replicate 3

source_name: control without heat shock replicate 3


title: HS_control_1

description: control with heat shock replicate 1

source_name: control with heat shock replicate 1


title: control_1

description: control without heat shock replicate 1

source_name: control without heat shock replicate 1


title: control_2

description: control without heat shock replicate 2

source_name: control without heat shock replicate 2


title: 6V_snRNA

city: Copenhagen

first: Tune

middle: Hannes

last: Pers

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

description:
snRNA_unnormdata.csv.gz
snRNA_normdata.csv.gz
snRNA_metadata.csv.gz

data_processing:
Read alignment of the snRNA-seq data: Raw sequencing reads were processed using the 10x Genomics Cell Ranger version 3.0 pipeline and aligned with default parameters. For each sample, a UMI count matrix was generated using both exonic and intronic reads.
Read alignment of the snATAC-seq data: Raw sequencing reads were processed using the Cell Ranger ATAC version 1.1.0 pipeline and aligned with default parameters.
Quality control of the snRNA-seq data: Cells with a mitochondrial RNA content >5% were discarded and doublets were removed using DoubletFinder version 2.0.0. Furthermore, cells that could not confidently be assigned to a cluster were removed using a multi-step procedure. See article for details.
Quality control of the snATAC-seq data: Fragments that were uniquely mapped (mapping quality score>30) and with proper length (50 bp<length<1000 bp) were kept. Based on visual inspection, high-quality cells were detected based on the number of unique fragments and fragments in promoter ratio (selecting cells with 1,000<unique fragments<100,000; 0.15<fragments in promoter ratio<0.6). Furthermore, cells that could not confidently be assigned to a cluster were removed using a multi-step procedure. See article for details.
Peak calling: Cells belonging to the same cluster were aggregated, and accessible peaks were called clusterwise using MACS2 version 2.2.6.
Normalization of the snRNA-seq data: Counts for each cell were normalized by the total gene expression of that cell, multiplied by 10,000 and log-transformed.
Normalization of the snATAC-seq data: Counts were normalized using term-frequency inverse-document-frequency normalization.
Genome_build: mm10
Supplementary_files_format_and_content: snRNA_unnormdata.csv.gz: comma-separated, gzip archived. Content: gene*cell matrix containing the filtered gene expression counts.
Supplementary_files_format_and_content: snRNA_normdata.csv.gz: comma-separated, gzip archived. Content: gene*cell matrix containing the filtered and normalized gene expression counts.
Supplementary_files_format_and_content: snRNA_metadata.csv.gz: comma-separated, gzip archived. Content: snRNA-seq metadata. Columns: nCount_RNA, nFeature_RNA, sample, percent.mito, percent.ribo, cell.type, neuronal.subtype.
Supplementary_files_format_and_content: snATAC_unnormdata.csv.gz: comma-separated, gzip archived. Content: peak*cell matrix containing the filtered peak counts.
Supplementary_files_format_and_content: snATAC_normdata.csv.gz: comma-separated, gzip archived. Content: peak*cell matrix containing the filtered and normalized peak counts.
Supplementary_files_format_and_content: snATAC_metadata.csv.gz: comma-separated, gzip archived. Content: snATAC-seq metadata. Columns: nCount_peaks, nFeature_peaks, nCount_activity, nFeature_activity, sample, cell.type, neuronal.subtype.

source_name: Single-nucleus RNA-sequencing of the DVC

growth_protocol: Animals were single-housed with ad libitum access to 60% HFD (#12492 Research Diets) and tap water in controlled environment (temperature 22 ± 2°C; relative humidity 50 ± 10%; 12-hour light/dark cycle).

extract_protocol:
Libraries were prepared using the 10x Genomics Chromium single-cell 3' reagent kits (version 2). Libraries were sequenced on an Illumina NextSeq 500 platform.
Nuclei were purified with reagents from the Nuclei Pure Prep Nuclei Isolation Kit (Sigma-Aldrich, NUC-201). See article for details.

treatment_protocol: Amimals were dosed with saline once daily, subcutaneous, for seven days. Animals were terminated by decapitation under CO2/O2 anaesthesia the day after the last dose.

tag: strain

value: male

value: 26 weeks

tag: number of mice

value: DVC

tag: rna population

value: nuclear RNA


title: 21V_snRNA


title: 19S_snRNA

treatment_protocol: Amimals were dosed with semaglutide once daily, subcutaneous, for seven days. Dosing of the animals was gradually up-titrated (0.02, 0.04, 0.1 mg/kg). Animals were terminated by decapitation under CO2/O2 anaesthesia the day after the last dose.


title: 22S_snRNA

extract_protocol:
Libraries were prepared using the 10x Genomics Chromium single-cell 3' reagent kits (version 2). Libraries were sequenced on an Illumina  NextSeq 500 platform.
Nuclei were purified with reagents from the Nuclei Pure Prep Nuclei Isolation Kit (Sigma-Aldrich, NUC-201). See article for details.


title: Bulk RNA-sequencing of the LS_1736

data_processing:
Read alignment: Base calling and demultiplexing was performed with Illumina bcl2fastq version 2.17.1.14. The sequencing data was aligned using STAR version 2.5.2a with default parameters.
Normalization: Counts were subject to variance stabilizing transformation normalization using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: bulkRNA_normdata.csv.gz: comma-separated, gzip archived. Content: gene*sample matrix containing the normalized gene expression counts.
Supplementary_files_format_and_content: bulkRNA_metadata.csv.gz: comma-separated, gzip archived. Content: bulkRNA-seq metadata. Columns: tissue, treatment, animal, file.

source_name: LS

extract_protocol:
RNA extraction was performed using the PicoPure RNA Isolation Kit (Applied Biosystems, Foster City, USA) as recommended by manufacturer, including an Ambion DNase treatment (Invitrogen, Carlsbad, USA).
Stranded mRNA libraries were produced using the TruSeq Stranded mRNA Kit (Illumina, San Diego, USA), followed by sequencing of single-end, 75 base pair reads on an Illumina NextSeq 500 platform.

treatment_protocol: Amimals were dosed with saline once daily, subcutaneous, for seven days and weight-matched to the semaglutide-administered group. Animals were terminated by decapitation under CO2/O2 anaesthesia the day after the last dose.

value: 31 weeks

value: LS


title: Bulk RNA-sequencing of the LS_1722


title: Bulk RNA-sequencing of the LS_1718


title: Bulk RNA-sequencing of the LS_1726


title: Bulk RNA-sequencing of the LS_1730


title: Bulk RNA-sequencing of the LS_1714


title: HS_maltose_2

description: moltose treated with heat shock replicate 2

source_name: maltose treated with heat shock replicate 2


title: Bulk RNA-sequencing of the LS_1710


title: Bulk RNA-sequencing of the LS_1704


title: 12W_snRNA

extract_protocol:
Libraries were prepared using the 10x Genomics Chromium single-cell 3' reagent kits (version 2). Libraries were sequenced on an Illumina NovaSeq 6000 platform.
Nuclei were purified with reagents from the Nuclei Pure Prep Nuclei Isolation Kit (Sigma-Aldrich, NUC-201). See article for details.

treatment_protocol: Amimals were weight-matched to the semaglutide-administered group. Animals were terminated by decapitation under CO2/O2 anaesthesia.


title: Bulk RNA-sequencing of the LS_1692


title: Bulk RNA-sequencing of the LS_1696


title: Bulk RNA-sequencing of the LS_1732

treatment_protocol: Amimals were dosed with liraglutide once daily, subcutaneous, for seven days. Dosing of the animals was gradually up-titrated (0.2, 0.4, 1.0 mg/kg). Animals were terminated by decapitation under CO2/O2 anaesthesia the day after the last dose.


title: Bulk RNA-sequencing of the LS_1735


title: Bulk RNA-sequencing of the LS_1684


title: Bulk RNA-sequencing of the LS_1679


title: Bulk RNA-sequencing of the LS_1728


title: Bulk RNA-sequencing of the LS_1724


title: Bulk RNA-sequencing of the LS_1720


title: Bulk RNA-sequencing of the LS_1716


title: Bulk RNA-sequencing of the LS_1712


title: Bulk RNA-sequencing of the LS_1734


title: Bulk RNA-sequencing of the LS_1708


title: Bulk RNA-sequencing of the LS_1694


title: Bulk RNA-sequencing of the LS_1690


title: Bulk RNA-sequencing of the LS_1698


title: Bulk RNA-sequencing of the LS_1681


title: Bulk RNA-sequencing of the LS_1700


title: Bulk RNA-sequencing of the LS_1737


title: Bulk RNA-sequencing of the LS_1733


title: Bulk RNA-sequencing of the LS_1721


title: Bulk RNA-sequencing of the LS_1688


title: Bulk RNA-sequencing of the LS_1713


title: Bulk RNA-sequencing of the LS_1709


title: Bulk RNA-sequencing of the LS_1725


title: Bulk RNA-sequencing of the LS_1699


title: Bulk RNA-sequencing of the LS_1687


title: Bulk RNA-sequencing of the LS_1702


title: Bulk RNA-sequencing of the LS_1703


title: Bulk RNA-sequencing of the LS_1678


title: Bulk RNA-sequencing of the LS_1727


title: Bulk RNA-sequencing of the LS_1715


title: Bulk RNA-sequencing of the LS_1723


title: Bulk RNA-sequencing of the LS_1711


title: Bulk RNA-sequencing of the LS_1705


title: Bulk RNA-sequencing of the LS_1691


title: Bulk RNA-sequencing of the LS_1701


title: Bulk RNA-sequencing of the LS_1676


title: Bulk RNA-sequencing of the LS_1697


title: Bulk RNA-sequencing of the LS_1729


title: Bulk RNA-sequencing of the LS_1693


title: Bulk RNA-sequencing of the LS_1675


title: Bulk RNA-sequencing of the LS_1685


title: Bulk RNA-sequencing of the LS_1680


title: Bulk RNA-sequencing of the LS_1686


title: Bulk RNA-sequencing of the PVH_1667

source_name: PVH

value: PVH


title: Bulk RNA-sequencing of the LS_1717


title: Bulk RNA-sequencing of the PVH_1671


title: Bulk RNA-sequencing of the LS_1695


title: Bulk RNA-sequencing of the PVH_1660


title: Bulk RNA-sequencing of the PVH_1656


title: Bulk RNA-sequencing of the PVH_1652


title: Bulk RNA-sequencing of the PVH_1640


title: Bulk RNA-sequencing of the LS_1706


title: Bulk RNA-sequencing of the PVH_1634


title: Bulk RNA-sequencing of the LS_1707


title: Bulk RNA-sequencing of the PVH_1626


title: Bulk RNA-sequencing of the PVH_1630


title: Bulk RNA-sequencing of the PVH_1618


title: Bulk RNA-sequencing of the PVH_1677


title: Bulk RNA-sequencing of the PVH_1673


title: Bulk RNA-sequencing of the PVH_1610


title: Bulk RNA-sequencing of the PVH_1662


title: Bulk RNA-sequencing of the PVH_1669


title: Bulk RNA-sequencing of the PVH_1658


title: Bulk RNA-sequencing of the PVH_1666


title: Bulk RNA-sequencing of the PVH_1654


title: Bulk RNA-sequencing of the PVH_1642


title: Bulk RNA-sequencing of the PVH_1624


title: Bulk RNA-sequencing of the PVH_1620


title: Bulk RNA-sequencing of the PVH_1612


title: Bulk RNA-sequencing of the PVH_1682


title: Bulk RNA-sequencing of the PVH_1608


title: Bulk RNA-sequencing of the PVH_1674


title: Bulk RNA-sequencing of the PVH_1663


title: Bulk RNA-sequencing of the PVH_1670


title: Bulk RNA-sequencing of the PVH_1659


title: Bulk RNA-sequencing of the PVH_1622


title: Bulk RNA-sequencing of the PVH_1614


title: Bulk RNA-sequencing of the PVH_1629


title: Bulk RNA-sequencing of the PVH_1639


title: Bulk RNA-sequencing of the LS_1719


title: Bulk RNA-sequencing of the PVH_1633


title: Bulk RNA-sequencing of the PVH_1625


title: Bulk RNA-sequencing of the PVH_1617


title: Bulk RNA-sequencing of the PVH_1621


title: Bulk RNA-sequencing of the PVH_1613


title: Bulk RNA-sequencing of the PVH_1672


title: Bulk RNA-sequencing of the PVH_1609


title: Bulk RNA-sequencing of the PVH_1668


title: Bulk RNA-sequencing of the PVH_1616


title: Bulk RNA-sequencing of the PVH_1657


title: Bulk RNA-sequencing of the PVH_1641


title: Bulk RNA-sequencing of the PVH_1637


title: Bulk RNA-sequencing of the PVH_1635


title: Bulk RNA-sequencing of the PVH_1653


title: Bulk RNA-sequencing of the PVH_1661


title: Bulk RNA-sequencing of the PVH_1615


title: Bulk RNA-sequencing of the PVH_1627


title: Bulk RNA-sequencing of the PVH_1623


title: Bulk RNA-sequencing of the PVH_1607


title: Bulk RNA-sequencing of the DMH_1787

source_name: DMH

value: DMH


title: Bulk RNA-sequencing of the PVH_1611


title: Bulk RNA-sequencing of the DMH_1797


title: Bulk RNA-sequencing of the DMH_1795


title: Bulk RNA-sequencing of the DMH_1775


title: Bulk RNA-sequencing of the PVH_1619


title: Bulk RNA-sequencing of the DMH_1771


title: Bulk RNA-sequencing of the PVH_1636


title: Bulk RNA-sequencing of the DMH_1749


title: Bulk RNA-sequencing of the PVH_1631


title: Bulk RNA-sequencing of the DMH_1745


title: Bulk RNA-sequencing of the DMH_1753


title: Bulk RNA-sequencing of the DMH_1761


title: Bulk RNA-sequencing of the DMH_1765


title: Bulk RNA-sequencing of the DMH_1757


title: Bulk RNA-sequencing of the DMH_1791


title: Bulk RNA-sequencing of the DMH_1741


title: Bulk RNA-sequencing of the DMH_1884


title: Bulk RNA-sequencing of the DMH_1796


title: Bulk RNA-sequencing of the DMH_1789


title: Bulk RNA-sequencing of the DMH_1785


title: Bulk RNA-sequencing of the DMH_1777


title: Bulk RNA-sequencing of the DMH_1779


title: Bulk RNA-sequencing of the DMH_1773


title: Bulk RNA-sequencing of the DMH_1763


title: Bulk RNA-sequencing of the DMH_1769


title: Bulk RNA-sequencing of the DMH_1759


title: Bulk RNA-sequencing of the DMH_1751


title: Bulk RNA-sequencing of the DMH_1755


title: Bulk RNA-sequencing of the DMH_1781


title: Bulk RNA-sequencing of the DMH_1885


title: Bulk RNA-sequencing of the DMH_1747


title: Bulk RNA-sequencing of the DMH_1858


title: Bulk RNA-sequencing of the DMH_1794


title: Bulk RNA-sequencing of the DMH_1790


title: Bulk RNA-sequencing of the DMH_1770


title: Bulk RNA-sequencing of the DMH_1782


title: Bulk RNA-sequencing of the DMH_1786


title: Bulk RNA-sequencing of the DMH_1774


title: Bulk RNA-sequencing of the DMH_1760


title: Bulk RNA-sequencing of the DMH_1756


title: Bulk RNA-sequencing of the DMH_1748


title: Bulk RNA-sequencing of the DMH_1752


title: Bulk RNA-sequencing of the DMH_1764


title: Bulk RNA-sequencing of the DMH_1793


title: Bulk RNA-sequencing of the DMH_1883


title: Bulk RNA-sequencing of the DMH_1792


title: Bulk RNA-sequencing of the DMH_1788


title: Bulk RNA-sequencing of the DMH_1780


title: Bulk RNA-sequencing of the DMH_1784


title: Bulk RNA-sequencing of the ARH_1847

source_name: ARH

value: ARH


title: Bulk RNA-sequencing of the ARH_1801


title: Bulk RNA-sequencing of the ARH_1805


title: Bulk RNA-sequencing of the ARH_1821


title: Bulk RNA-sequencing of the ARH_1825


title: Bulk RNA-sequencing of the ARH_1839


title: Bulk RNA-sequencing of the ARH_1835


title: Bulk RNA-sequencing of the DMH_1778


title: Bulk RNA-sequencing of the ARH_1813


title: Bulk RNA-sequencing of the ARH_1831


title: Bulk RNA-sequencing of the ARH_1856


title: Bulk RNA-sequencing of the ARH_1853


title: Bulk RNA-sequencing of the DMH_1766


title: Bulk RNA-sequencing of the DMH_1754


title: Bulk RNA-sequencing of the DMH_1776


title: Bulk RNA-sequencing of the DMH_1762


title: Bulk RNA-sequencing of the DMH_1750


title: Bulk RNA-sequencing of the ARH_1851


title: Bulk RNA-sequencing of the DMH_1746


title: Bulk RNA-sequencing of the ARH_1857


title: Bulk RNA-sequencing of the ARH_1855


title: Bulk RNA-sequencing of the DMH_1742


title: Bulk RNA-sequencing of the ARH_1809


title: Bulk RNA-sequencing of the ARH_1845


title: Bulk RNA-sequencing of the ARH_1837


title: Bulk RNA-sequencing of the ARH_1841


title: Bulk RNA-sequencing of the ARH_1833


title: Bulk RNA-sequencing of the ARH_1829


title: Bulk RNA-sequencing of the ARH_1815


title: Bulk RNA-sequencing of the ARH_1886


title: Bulk RNA-sequencing of the ARH_1823


title: Bulk RNA-sequencing of the ARH_1854


title: Bulk RNA-sequencing of the ARH_1819


title: Bulk RNA-sequencing of the ARH_1799


title: Bulk RNA-sequencing of the ARH_1803


title: Bulk RNA-sequencing of the ARH_1849


title: Bulk RNA-sequencing of the ARH_1850


title: Bulk RNA-sequencing of the ARH_1842


title: Bulk RNA-sequencing of the ARH_1838


title: Bulk RNA-sequencing of the ARH_1834


title: Bulk RNA-sequencing of the ARH_1830


title: Bulk RNA-sequencing of the ARH_1820


title: Bulk RNA-sequencing of the ARH_1804


title: Bulk RNA-sequencing of the ARH_1824


title: Bulk RNA-sequencing of the ARH_1812


title: Bulk RNA-sequencing of the ARH_1808


title: Bulk RNA-sequencing of the ARH_1852


title: Bulk RNA-sequencing of the ARH_1848


title: Bulk RNA-sequencing of the ARH_1836


title: Bulk RNA-sequencing of the ARH_1840


title: Bulk RNA-sequencing of the ARH_1844


title: Bulk RNA-sequencing of the ARH_1832


title: Bulk RNA-sequencing of the ARH_1811


title: Bulk RNA-sequencing of the ARH_1828


title: Bulk RNA-sequencing of the ARH_1846


title: Bulk RNA-sequencing of the PVH_1664


title: Bulk RNA-sequencing of the ARH_1814


title: Bulk RNA-sequencing of the ARH_1826


title: Bulk RNA-sequencing of the ARH_1822


title: Bulk RNA-sequencing of the ARH_1810


title: Bulk RNA-sequencing of the ARH_1806


title: Bulk RNA-sequencing of the ARH_1818


title: Bulk RNA-sequencing of the LS_1689


title: Bulk RNA-sequencing of the ARH_1816


title: Bulk RNA-sequencing of the ARH_1802


title: Bulk RNA-sequencing of the ARH_1798


title: Bulk RNA-sequencing of the NTS_2038

source_name: NTS

value: NTS


title: Bulk RNA-sequencing of the NTS_2036


title: plus01792_FPKM

city: Wuhan

first: Jialing

last: Hu

address: 1 street of Shizi Shan

department: College of Life Science and Technology

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mycobacterium_smegmatis_MC2_155_uid57701 whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mycobacterium smegmatis str. MC2 155
Supplementary_files_format_and_content: gene_expression file includes FPKM values for each Sample

organism: Mycolicibacterium smegmatis

growth_protocol: Cells were prepared by growing into an exponentially growing culture of M. smegmatis

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


title: plus01793_FPKM


title: wt2612_FPKM


title: plus01801_FPKM


title: wt2613_FPKM


title: plus01791_FPKM


title: Bulk RNA-sequencing of the NTS_2032


title: plus01803_FPKM


title: Bulk RNA-sequencing of the NTS_2028


title: Bulk RNA-sequencing of the NTS_2024


title: Bulk RNA-sequencing of the NTS_2020


title: wt2611_FPKM


title: Bulk RNA-sequencing of the NTS_2016


title: Bulk RNA-sequencing of the NTS_2012


title: Bulk RNA-sequencing of the NTS_1998


title: Bulk RNA-sequencing of the NTS_2002


title: Bulk RNA-sequencing of the NTS_2006


title: plus01802_FPKM


title: Bulk RNA-sequencing of the NTS_1994


title: Bulk RNA-sequencing of the NTS_1990


title: Bulk RNA-sequencing of the NTS_1982


title: METTL_PolyADMSO_Shape-map

city: Santiago

first: Daniela

last: Toro Ascuy

state: Region Metropolitana

address: Av. Independencia 1027

department: Virology

country: Chile

institute: University of Chile

data_processing:
Library strategy: SHAPE_map
Sequencing results 1-GFP_1M7, 1-GFP_DMSO, 9_GFP_Denat on the one hand, and 3-METTL_1M7, 4_METTL_DMSO, and 13_METTL_Denat were fed into Shapemapper2 public release 2.1.5 using the provided sequence HIV-1 5'UTR in PNL43_347.fa
Reactivity and standard error for the two conditions were recovered from the .map files and copied into the “Delta_shape_analysis_GFP-METTL_1_347.xls” files. Undetermined values (-999) and values inferior to -2 were removed.
For each nucleotide (for i= 1 to 347) the difference reactivity GFP – reactivity METTL (delta shape value) was calculated, then the Z score and the standard score was calculated as described in Smola et al. (2015) Biochemistry, 54, 6867-6874. Deltashape value for nucleotide i was considered as significant if Zi > 0 and Standard score i > 1. All calculations are accessible in the xls file provided.
Genome_build: 5'UTR HIV-1 fasta sequence AF324493.2 vector pNL4-3
Supplementary_files_format_and_content: tab-delimited text files

organism:
Homo sapiens
HIV-1 vector pNL4-3

source_name: embryonic kidney cells

growth_protocol: HEK293T and HeLa cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Hyclone) and antibiotics (Hyclone) at 37ºC and 5% CO2 atmosphere.

extract_protocol:
RNA were recovered from infected cells and splitted in 3 samples: one was trated with 1M7, the second with DMSO and the third with 1M7 in denaturing conditions according to the SHAPEMap protocol as described by smola et al (2015) Nature protocol 10, 1643. After treatment RNA were reverse transcribed with the primers described in Watts et al. (2009) Nature, 460, 711 under the conditions described by Smola et al. (2015); The NGS librairy were then obtained using the appropriate kits from New england Biolabs following the manufacturer instructions
RNA Library Prep kit for Illumina (New England Biolabs)

treatment_protocol: No treatments were performed

tag: sample type

value: HEK293T embryonic kidney cells

tag: antibody


title: Bulk RNA-sequencing of the NTS_2030


title: GFP_denat_Shape-map


title: GFP_DMSO_Shape-map


title: GFP_1M7_Shape-map


title: Bulk RNA-sequencing of the NTS_2034


title: Bulk RNA-sequencing of the NTS_2037


title: METTL_denat_Shape-map


title: METTL_1M7_Shape-map


title: Bulk RNA-sequencing of the NTS_2026


title: Bulk RNA-sequencing of the NTS_2022


title: Bulk RNA-sequencing of the NTS_2010


title: Bulk RNA-sequencing of the NTS_2004


title: Bulk RNA-sequencing of the NTS_2018


title: Bulk RNA-sequencing of the NTS_1992


title: Bulk RNA-sequencing of the NTS_1984


title: Bulk RNA-sequencing of the NTS_2035


title: Bulk RNA-sequencing of the NTS_1988


title: Bulk RNA-sequencing of the NTS_1980


title: Bulk RNA-sequencing of the NTS_2027


title: Bulk RNA-sequencing of the NTS_2000


title: Bulk RNA-sequencing of the NTS_2023


title: Bulk RNA-sequencing of the NTS_2031


title: Bulk RNA-sequencing of the NTS_2019


title: Bulk RNA-sequencing of the NTS_2011


title: Bulk RNA-sequencing of the NTS_2015


title: adjacent non-cancerous liver tissue_T2_G2_1

city: Beijing

first: chen

middle: wen

last: jia

address: Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences

institute: institute

description: Gene expression data from adjacent non-cancerous liver tissues to HCC tissues in primary tumor stage (T2) and tumor grade (G2).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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

growth_protocol: Three paired human primary HCC tissues and adjacent non-cancerous liver tissues were collected according to proper tumor stage (T2) and tumor grade (G2).

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

treatment_protocol: All tissue samples upon collection were placed in a microfuge tube, flash frozen in liquid nitrogen and stored at −80˚C.

value: adjacent non-cancerous liver tissue

tag: gender

tag: grade/stage


title: adjacent non-cancerous liver tissue_T2_G2_3


title: human HCC tissue_T2_G2_2

description: Gene expression data from human HCC tissues in primary tumor stage (T2) and tumor grade (G2).

source_name: HCC tissue_T2_G2

value: HCC tissue


title: Bulk RNA-sequencing of the NTS_2008


title: adjacent non-cancerous liver tissue_T2_G2_2


title: human HCC tissue_T2_G2_1


title: Bulk RNA-sequencing of the NTS_2001


title: human HCC tissue_T2_G2_3


title: Bulk RNA-sequencing of the NTS_2005


title: Bulk RNA-sequencing of the NTS_1993


title: Bulk RNA-sequencing of the NTS_1989


title: Myoblast_T2D_63a

type: genomic

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

institute: Lund University

hyb_protocol: According to the manufacturer’s recommendations. Myoblasts and myotubes from one subject were always analyzed on the same chip and the samples from controls and individuals with type 2 diabetes were evenly distributed on the chips to reduce batch effects.

data_processing: The raw methylation score for each probe represented as methylation β-values was calculated using GenomeStudio Methylation module software. All included samples showed a high quality bisulfite conversion efficiency (signal intensity > 4000) and also passed all GenomeStudio quality control steps based on built in control probes for staining, hybridization, extension and specificity. Before further analysis, the DNA methylation data was exported from GenomeStudio and subsequently analyzed using Bioconductor and the lumi package. β-values were converted to M-values. Next, data were background corrected by subtracting the median M-value of the 600 built in negative controls and was further normalized using quantile normalization. Data were further processed using BMIQ to correct for probe type and COMBAT for batch correction. As a result, 5,365 probes with a mean detection p-value >0.01, 65 rs-probes, 86 Y-chromosome probes, 2,835 ch-probes targeting non-CpG sites, 13,731 probes based on at least 49 cross reactivity 5 and 5,020 probes with a MAF >0.1 were excluded.

label: Cy5, Cy3

source_name: Myoblast, T2D

growth_protocol: Muscle stem cells were isolated from human vastus lateralis muscle biopsies (n=14 individuals with type 2 diabetes [T2D], and n=14 control individuals with normal glucose tolerance [NGT]). Isolated myoblasts were cultured in growth medium (HAM’s/F10 supplemented with 20% fetal bovine serum (FBS), 1% penicillin/streptomycin and 1% Amphotericin B) until 70% confluent. To induce differentiation, cells were incubated in differentiation medium 1 (DMEM with 1.0 g/l L glucose supplemented with 10% FBS and 1% penicillin/streptomycin) for 2 days, followed by differentiation medium 2 (DMEM with 4.5 g/l L glucose supplemented with 2% horse serum and 1% penicillin/streptomycin) until cells were fully differentiated, as determined by visual confirmation of myotube formation (>3 nuclei per myotube in approximately 70% of cells) on day 7. Cells were harvested both as proliferating myoblasts (<50% confluent) and as differentiated myotubes.

extract_protocol: DNA was extracted by using DNeasy Blood and Tissue kit (Qiagen #69504, Hilden, Germany). Quantity and purity of DNA were determined using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

tag: diabetes status

value: Type 2 diabetes (T2D)


title: Bulk RNA-sequencing of the NTS_1985


title: Myotube_T2D_7a

scan_protocol: According to the manufacturer’s recommendations.

source_name: Myotube, T2D


title: Myoblast_T2D_8a

label_protocol: According to the manufacturer’s recommendations.


title: Bulk RNA-sequencing of the NTS_1981


title: Myoblast_T2D_46a


title: Bulk RNA-sequencing of the NTS_2295


title: Myotube_T2D_46a


title: Myoblast_T2D_29H


title: Bulk RNA-sequencing of the NTS_2025


title: Myotube_T2D_29H


title: Bulk RNA-sequencing of the NTS_2021


title: Myotube_T2D_45


title: Myotube_T2D_20a


title: Myotube_T2D_17


title: Myoblast_T2D_129a


title: Myoblast_T2D_128a


title: Myotube_T2D_127a


title: Myotube_T2D_129a


title: Bulk RNA-sequencing of the NTS_2013


title: Myotube_T2D_119a


title: Bulk RNA-sequencing of the NTS_2007


title: Myotube_T2D_117a


title: Myoblast_T2D_117a


title: Bulk RNA-sequencing of the NTS_2003


title: Myotube_T2D_63a


title: Bulk RNA-sequencing of the NTS_2017


title: Bulk RNA-sequencing of the NTS_1999


title: Myoblast_T2D_127a


title: Myotube_T2D_128a


title: Myotube_T2D_8a


title: Myotube_T2D_109a


title: Bulk RNA-sequencing of the NTS_2029


title: Bulk RNA-sequencing of the NTS_1987


title: Myoblast_T2D_7a


title: Bulk RNA-sequencing of the NTS_1997


title: Myoblast_NGT_92a

source_name: Myoblast, NGT

value: Normal glucose tolerance (NGT)


title: Bulk RNA-sequencing of the NTS_1983


title: Myoblast_T2D_17


title: Bulk RNA-sequencing of the NTS_1979


title: Bulk RNA-sequencing of the AP_1978

source_name: AP

value: AP


title: Myoblast_T2D_109a


title: Bulk RNA-sequencing of the AP_1976


title: Bulk RNA-sequencing of the AP_1968


title: Myoblast_NGT_55a


title: Bulk RNA-sequencing of the AP_1964


title: Bulk RNA-sequencing of the AP_1960


title: Myoblast_T2D_20a


title: Bulk RNA-sequencing of the AP_1956


title: Bulk RNA-sequencing of the AP_1952


title: Myoblast_T2D_45


title: Bulk RNA-sequencing of the AP_1946


title: Bulk RNA-sequencing of the AP_1942


title: Myotube_NGT_40a

source_name: Myotube, NGT


title: Bulk RNA-sequencing of the AP_1938


title: Bulk RNA-sequencing of the AP_1930


title: Bulk RNA-sequencing of the AP_1922


title: Myoblast_NGT_32a


title: Myoblast_NGT_40a


title: Myotube_NGT_92a


title: Bulk RNA-sequencing of the AP_1977


title: Myoblast_NGT_35a


title: Myotube_NGT_32a


title: Myotube_NGT_55a


title: Myotube_NGT_35a