title: 3M_TSCmKO_RAPA_rep5

description:
average insert size: 216
standard deviation: 36.2
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

value: post natal month 3

value: TSCmKO


title: 3M_TSCmKO_RAPA_rep4

status: Public on Jun 19 2020

type: SRA

city: Basel

first: Anastasiya

last: Boersch

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

description:
average insert size: 239
standard deviation: 38.1
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

library_source: transcriptomic

data_processing:
RNA-seq reads were subjected to 3’ adapter and poly(A) tail trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011. The following 3’ adapter sequence was utilized for generating RNA-Seq libraries and subsequently trimmed: mate1 5’-TGGAATTCTCGGGTGCCAAG-3’.
Reads shorter than 20 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--single”, “-l”, “-s”, “--fr-stranded” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
Genome_build: As the reference mouse transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCm38 (release 92) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002).
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values at the gene level for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Extensor digitorum longus muscle

growth_protocol: Mice were maintained on standard laboratory chow.

extract_protocol:
RNA was extracted from whole EDL muscle lysates using the Dynabeads mRNA DIRECT Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were injected I.P. with either vehicle or rapamycin (4 mg.kg-1) for 3 days prior to extraction.

tag: strain

tag: tissue

value: Extensor digitorum longus muscle

tag: age

tag: genotype

tag: treatment

value: rapamycin


title: 9M_CTRL_RAPA_rep1

description:
average insert size: 263
standard deviation: 27.84
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

value: post natal month 9


title: T1

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

department: Animal Science

country: USA

institute: Michigan State University

library_source: genomic

data_processing:
Only uniquely mapped reads were used for subsequent analyses. MACS2 (version 2.1.1) (cite) was then applied to identify signal peaks of H3K27me3 signals, in broad peak calling mode since H3K27me3 distribution along the genome is more diffusive and demonstrate broader peaks.
PCR duplicates were removed in peak calling. Peaks with q-value <= 0.05 were used as the significant signal peaks. Peaks in control samples and treatment samples are center-aligned separately with +/-10kb flanking regions.
Gene promoters overlapping with control-specific H3K27me3 peaks were center-aligned with +/- 1kb flanking regions, and the average peak densities per 50bp bins were plotted.
Hi-C and Capture-C, were used to identify candidate distal enhancers that can interact with promoters of differentially expressed genes. Hi-C datasets include: GSE81503, GSE82144, GSE119171, GSE121753, and GSE63525. Capture-C dataset includes GSE81503.
For the long-range chromatin interactions profiled in these dataset, they were first compared with promoters of differentially expressed genes and a subset of chromatin interactions was then identified, if one of the interacting anchors overlaped with promoters. Only enhancer-gene pairs with correlations < -0.4 were considered as true regulatory pairs and the corresponding enhancers were used for subsequent analysis. For each group of enhancers, the top five enriched sequence motifs were identified using MEME. TomTom (version 5.0.4) was then applied on the top-enriched motifs
Genome_build: mouse genome (mm9) using Bowtie2 (version 2.3.4)
Supplementary_files_format_and_content: Upregulated_gene_body_overlap_peaks.txt  The list of up-regulated genes with their gene body (TSS to TES) overlapping the H3K27me3 peaks (control peaks or treatment peaks)  Downregulated_gene_body_overlap_peaks.txt  The list of down-regulated genes with their gene body (TSS to TES) overlapping the H3K27me3 peaks (control peaks or treatment peaks) Gene_body_overlapping_control_peaks_gene_list.txt  The list of genes with their gene body (TSS to TES) overlapping the 16345 control H3K27me3 peaks  Gene_body_overlapping_treatment_peaks_gene_list.txt  The list of genes with their gene body (TSS to TES) overlapping the 3975 treatment H3K27me3 peaks  Promoter_overlapping_control_peaks.txt  The list of genes with their promoter regions (TSS +/- 1KB) overlapping the 16345 control H3K27me3 peaks  UpRegulated_genes_regulated_by_H3K27me3_enhancers.txt  The list of up-regulated genes that regulated by enhancers. The H3K27me3 signals on these enhancers are negatively-correlated with the gene expression.   DownRegulated_genes_regulated_by_H3K27me3_enhancers.txt  The list of down-regulated genes that regulated by enhancers. The H3K27me3 signals on these enhancers are negatively-correlated with the gene expression.

molecule: genomic DNA

source_name: Ovary

extract_protocol:
Granulosa cells were collected from 30 mice and plated in six petri dishes (each with at least 1×107 cells). Chromatin was isolated using the ChromaFlash Chromatin Extraction Kit (EpiGentek, Cat. #P-2001) and sheared using the EpiSonic 2000 Sonication System (EpiGentek, Cat. #EQC-2000). DNA fragment size distribution was determined to be 100 to 300 bp by Agilent Bioanalyzer analysis. The concentration of DNA following ChIP was between 3.5-16.3 ng.
Library Preparation was done by DNA end polishing and adaptor ligation, library amplification using indexed primers and library purification. Library was verified on a Bioanalyzer and KAPA qPCR Library Quantification.RNA sequencing libraries were prepared using 500 ng RNA, and the NEB Next Ultra RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: Granulosa cells were treated with  DHT (dihydrotestosterone, 25nM) for 24h

value: Granulosa cells

value: 8-9 weeks

tag: agent

value: dihydrotestosterone, 25nM

tag: antibody

value: wild type


title: Cord blood ID_157

type: genomic

city: Diepenbeek

first: Michelle

last: Plusquin

address: Campus Diepenbeek Agoralaan Gebouw D

country: Belgium

institute: Hasselt University

hyb_protocol: Bisulphite converted DNA (using the Zymo EZ DNA methylationTM kit - Zymo, Irvine, CA, USA) was hybridized to Illumina HumanMethylation 450K BeadChip arrays

scan_protocol: Arrays were scanned using an Illumina iScan

data_processing:
An in-house software written for the R statistical computing environment was used to preprocess the data as follows: removal of probes based on signal intensities and control probes, background subtraction and dye bias correction (for probes using the Infinium II design). Additionally, data were trimmed removing the outliers as defined by observations exceeding three interquartile ranges below the first quartile or above the fourth quartile. Sample failing quality control and with potential sex mismatch were removed.
normalized Average Beta in supplementary file

label: Cy3, Cy5

organism: Homo sapiens

source_name: cord blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from buffy coats according to standard protocol

value: cord blood

tag: birthweight


title: C3


title: Cord blood ID_156


title: 30m_GAS_RM_rep4

description:
direction_1st_mate: antisense, direction_2nd_mate: sense
aging_rm_counts.txt.gz
aging_rm_tpms.txt.gz

data_processing:
RNA-seq reads were subjected to 3’ adapter and poly(A)/poly(T) tail trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011. The following 3’ adapter sequences were utilized for generating RNA-Seq libraries and subsequently trimmed: mate1 5’-AGATCGGAAGAGCACACGTC-3’, mate2 5’-AGATCGGAAGAGCGTCGTGT-3’.
Reads shorter than 30 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--rf-stranded” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
Genome_build: As the reference mouse transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCm38 (release 92) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002).
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values at the gene level for each sample.

source_name: Gastrocnemius muscle

growth_protocol: Mice were singly caged throughout the treatment period.

extract_protocol:
Snap frozen muscles were pulverized and lysed in RLT buffer (Qiagen). RNA was extracted using an AccuPure Tissue RNA Mini Kit (R20096) with an iColumn 24 (AccuBioMed). TruSeq Stranded mRNA HT Sample Prep Kit was used for the library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were fed encapsulated rapamycin incorporated into a standardised AIN93M diet at 42 ppm (i.e. mg per kg of food), equating to a dose of ~4mg/kg/day starting at 15 months of age.

value: Gastrocnemius muscle

value: post natal month 30


title: 3M_TSCmKO_RAPA_rep3

description:
average insert size: 179
standard deviation: 25.8
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 9M_CTRL_rep2

description:
average insert size: 266
standard deviation: 47.75
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

value: vehicle


title: 3M_TSCmKO_RAPA_rep2

description:
average insert size: 186
standard deviation: 32.1
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: TKO_2i_1

city: Edinburgh

first: Heidi

middle: Katharina

last: Mjoseng

address: Crewe Road South

country: United Kingdom

institute: HGU, IGMM, The university of Edinburgh

data_processing:
A sailfsh (version 0.9.2) index was built using kmer length 25 against the Ensembl  mm10 transcript database
RNA transcript abundance was calculated using  Sailfish version 0.9.2, libType": "ISR","numBootstraps": "30".
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Ensembl Transcript ID, Length, EffectiveLength, TPM, NumReads

molecule: total RNA

source_name: Mouse ES cells

growth_protocol: Serum culture conditions: Dulbecco's Modified Eagle's medium (DMEM) high-glucose supplemented with 15% FCS, 1x Non-essential amino acids, 1mM Sodium Pyruvate, 50mg/ml Penicillin/Streptomycin, 0.1% beta-mercaptoethanol and 500U/ml ESGRO LIF (Millipore).

extract_protocol:
Snap frozen pellets of mESCs were stored in -80 ̊C prior to extraction of RNA. Qiashredder columns (Qiagen) were used to homogenise the samples according to manufacturers protocol. Total RNA was extracted using an RNeasy kit (Qiagen), following the manufacturer’s protocol. RNA was then treated with Turbo Dnase (Ambion, ThermoFisher) according to manufacturers protocol. Total RNA samples were quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) and the Qubit RNA HS assay kit (#Q33855). RNA integrity (RIN) was assessed using an Agilent 2100 Bioanlyser System (Agilent Technologies Inc, # GS2938B) and Agilent RNA 6000 Nano kit (#5067-1511), samples used had a RIN score of ≥9.9.
Libraries were prepared from 500ng of each total-RNA sample using the TruSeq Stranded  mRNA Library Kit (Illumina Inc, #20020594) according to the provided protocol. PolyA selection method was used. Libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for  quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626).
Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (#FC-404-2002). This was done on the NextSeq 550 platform (Illumina Inc, #SY-415-1002). 24 libraries were  combined in two equimolar pools of 12 based on the library quantification results and each  pool was run across a single High-Output Flow Cell.

treatment_protocol: 2i culture conditions: N2B27 medium (DMEM F-12:  GIBCO,  Neurobasal: GIBCO, N2: GIBCO, B27: GIBCO,  50ug/ml Penicillin/streptomycin, 3.3% BSA (GIBCO), 0.15 mM monothioglycerol and MEK inhibitor PD0325901 [1uM] and Gsk3 beta inhibitor CHIR99021 (3uM) with 1000U/ml ESGRO LIF (Millipore).

tag: culture condition

tag: biologial replicate

tag: cell line

value: TKO


title: C2


title: 3M_TSCmKO_RAPA_rep1

description:
average insert size: 199
standard deviation: 35
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 30m_GAS_RM_rep3


title: C1


title: Cord blood ID_155


title: 30m_GAS_RM_rep2


title: 3M_TSCmKO_rep5

description:
average insert size: 179
standard deviation: 30.9
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_154


title: Cord blood ID_153


title: 30m_GAS_rep6


title: NG2DsRed+ [35]

city: Blacksburg

first: Robert

last: Settlage

state: VA

address: 1 Washington St

department: Advanced Research Computing

institute: Virginia Tech

description:
P15-46
35
FACS isolated cells

data_processing:
ea-utils clipping of sequencing adaptor from sequencing reads
btrim quality trimming of reads
map data to genome using hisat2
count reads mapping to genes using htseq
Genome_build: NCBI Mus musculus GRCm38, annotation build 93
Supplementary_files_format_and_content: matrix of read counts mapped and counted by htseq, csv format

source_name: Diaphragm, pectoralis, forelimb and hindlimb muscles

extract_protocol:
The PicoPure RNA Isolation Kit (ThermoFisher) was used to isolate RNA from cells collected with FACS.
Takara SMART-Seq v4 Ultra Low Input RNA Kit for ultra-low RNA-Seq library preparation

tag: cell type


title: NG2DsRed+/S100GFP+ [36]

description:
P15-46
36
FACS isolated cells


title: Cord blood ID_152


title: 3M_TSCmKO_rep4

description:
average insert size: 211
standard deviation: 37.6
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_151


title: 3M_TSCmKO_rep3

description:
average insert size: 179
standard deviation: 20.6
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: S100GFP+  [33]

description:
P15-46
33
FACS isolated cells


title: 30m_GAS_rep5


title: 30m_GAS_rep4


title: 3M_TSCmKO_rep2

description:
average insert size: 175
standard deviation: 15.7
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_150


title: 30m_GAS_rep3


title: S100GFP+  [32]

description:
P15-46
32
FACS isolated cells


title: 3M_TSCmKO_rep1

description:
average insert size: 226
standard deviation: 41.5
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 30m_GAS_rep2


title: Cord blood ID_15


title: 3M_CTRL_RAPA_rep5

description:
average insert size: 221
standard deviation: 38.8
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_148


title: 30m_GAS_RM_rep1


title: NG2DsRed+/S100GFP+ [31]

description:
P15-46
31
FACS isolated cells


title: 3M_CTRL_RAPA_rep4

description:
average insert size: 225
standard deviation: 35.8
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: NG2DsRed+ [30]

description:
P15-46
30
FACS isolated cells


title: NG2DsRed+/S100GFP+ [29]

description:
P15-46
29
FACS isolated cells


title: 3M_CTRL_RAPA_rep3

description:
average insert size: 207
standard deviation: 42
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_146


title: NG2DsRed+/S100GFP+ [34]

description:
P15-46
34
FACS isolated cells


title: 3M_CTRL_RAPA_rep2

description:
average insert size: 204
standard deviation: 31.3
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 30m_GAS_rep1


title: 10m_GAS_rep6

value: post natal month 10


title: 3M_CTRL_RAPA_rep1

description:
average insert size: 201
standard deviation: 28.3
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: S100GFP+  [27]

description:
P15-46
27
FACS isolated cells


title: Cord blood ID_144


title: Cord blood ID_145


title: 10m_GAS_rep4


title: NG2DsRed+ [28]

description:
P15-46
28
FACS isolated cells


title: 10m_GAS_rep3


title: NG2DsRed+ [26]

description:
P15-46
26
FACS isolated cells


title: 3M_CTRL_rep5

description:
average insert size: 236
standard deviation: 41.7
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 10m_GAS_rep2


title: 3M_CTRL_rep4

description:
average insert size: 204
standard deviation: 33.4
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: Cord blood ID_147


title: Cord blood ID_142


title: S100GFP+  [25]

description:
P15-45
25
FACS isolated cells


title: Cord blood ID_141


title: 3M_CTRL_rep3

description:
average insert size: 180
standard deviation: 22.3
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 10m_GAS_rep1

description:
direction_1st_mate: antisense, direction_2nd_mate: sense
aging_rm_counts.txt.gz
aging_rm_tpms.txt.gz


title: NG2DsRed+ [24]

description:
P15-44
24
FACS isolated cells


title: 30m_TRI_RM_rep6

source_name: Triceps brachii muscle

value: Triceps brachii muscle


title: 10m_GAS_rep5


title: NG2DsRed+/S100GFP+ [23]

description:
P15-43
23
FACS isolated cells


title: Cord blood ID_140


title: 3M_CTRL_rep2

description:
average insert size: 225
standard deviation: 38.1
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz


title: 3M_CTRL_rep1

description:
average insert size: 193
standard deviation: 26.9
direction: sense
tscmko_counts.txt.gz
tscmko_tpms.txt.gz

data_processing:
RNA-seq reads were subjected to 3’ adapter and poly(A) tail trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011. The following 3’ adapter sequences was utilized for generating RNA-Seq libraries and subsequently trimmed: mate1 5’-TGGAATTCTCGGGTGCCAAG-3’
Reads shorter than 20 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--single”, “-l”, “-s”, “--fr-stranded” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
Genome_build: As the reference mouse transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCm38 (release 92) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002)
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values at the gene level for each sample


title: Cord blood ID_14


title: S100GFP+  [22]

description:
P15-42
22
FACS isolated cells


title: 30m_TRI_RM_rep4


title: Cord blood ID_143


title: NG2DsRed+ [21]

description:
P15-41
21
FACS isolated cells


title: Cord blood ID_139


title: NG2DsRed+/S100GFP+ [20]

description:
P15-40
20
FACS isolated cells


title: WT TH1_FoxO4

city: Beijing

first: Chen

last: Dong

state: Beijing

address: 30 Shuangqing Rd

country: China

institute: Tsinghua University

data_processing:
FastQC is used to check the read quality
Bowtie was used to map the reads to mouse genome (mm10) with parameters "-m 1 -v 2"
MACS was used to call peaks from BAM files. The peaks were annoated by mouse RefSeq genes in the order of promoter (TSS upstream 2kb to downstream 200bp), CDS (coding exons), 5' UTR, 3' UTR, upstream (upstream 3kb of promoter) and downstream (gene downstream 3kb).
MEME Suite was used to find motifs or search against existing JASPR motifs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated text files for MACS called peaks.

source_name: Differentiated TH1 cells

growth_protocol: Freshly isolated naïve CD4+ T cells were cultured in TH1 polarizing condition (20 ng/ml IL-12, 5 μg/ml anti-IL-4, and 40 U/ml IL-2) for 60 hours.

extract_protocol:
ChIPed DNAs were prepared with Active Motif’s ChIP assay kit (53035), using anti-FoxO4 antibody (Santa Cruz, sc-5221) or rabbit IgG (Abcam, ab37415).
Libraries for ChIP-Seq were prepared using NEXTflexTM ChIP-Seq DNA Sequencing Kit (Bioo Scientific, 5143)

treatment_protocol: Naive CD4+CD25−CD62LhiCD44lo T cells from spleens and lymph nodes were isolated from 8-week-old C57BL/6 mice using a BD FACSAria sorter

value: Spleen and lymph nodes

value: WT

value: Differentiated TH1 cells

tag: passage


title: WT TH1_Input


title: 30m_TRI_RM_rep2


title: Cord blood ID_138


title: 30m_TRI_RM_rep3


title: S100GFP+  [19]

description:
P15-39
19
FACS isolated cells


title: MZB_GFPposi_rep4

city: Bellinzona

first: Mathilde

last: Foglierini

address: Via Vincenzo Vela 6

institute: Institute for Research in Biomedicine

data_processing:
Illumina software used for basecalling
Sequenced reads were trimmed for adaptor sequence (cutadapt-1.8.1) then  mapped to mm10 whole genome using TopHat v2.0.14 with the option '--no-novel-junctions' and finally differentially expressed genes and transcripts were identified using cuffdiff v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files generated by cuffdiff
[gene_exp.diff]  differentially expressed genes
[genes.count_tracking]  raw counts
[genes.fpkm_tracking]  normalized counts
q1 = ACKR3+ samples, q2 = ACKR3- samples.

source_name: Marginal Zone B cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Marginal Zone B cells (MZBs)


title: 30m_TRI_RM_rep1

value: rapamycin


title: Cord blood ID_136


title: Cord blood ID_137


title: Cord blood ID_135


title: 30m_TRI_rep6


title: MZB_GFPposi_rep3


title: NG2DsRed+/S100GFP+ [18]

description:
P15-38
18
FACS isolated cells


title: S100GFP+  [17]

description:
P15-37
17
FACS isolated cells


title: 30m_TRI_RM_rep5


title: Cord blood ID_133


title: NG2DsRed+/S100GFP+ [16]

description:
P15-36
16
FACS isolated cells


title: MZB_GFPposi_rep2


title: 30m_TRI_rep4


title: MZB_GFPposi_rep1


title: 30m_TRI_rep5


title: Cord blood ID_132


title: 30m_TRI_rep3


title: MZB_GFP-_rep3


title: 30m_TRI_rep2


title: NG2DsRed+ [15]

description:
P15-35
15
FACS isolated cells


title: Cord blood ID_131


title: 30m_TRI_rep1


title: NG2DsRed+ [13]

description:
P15-33
13
FACS isolated cells


title: MZB_GFP-_rep2


title: Cord blood ID_13


title: MZB_GFP-_rep1


title: NG2DsRed+/S100GFP+ [12]

description:
P15-32
12
FACS isolated cells


title: Cord blood ID_129


title: 10m_TRI_rep6


title: S100GFP+  [11]

description:
P15-31
11
FACS isolated cells


title: Tip60 KO HSPC input

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
The paired-end ChIP-seq reads are mapped by bowtie2 to the mouse reference genome GRCm38 (mm10)
PCR duplicates are filtered out from the resulting BAM files using samtools rmdup.
Alignments with mapping quality below 20 are also filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are converted by bedGraphToBigWig from bedGraph generated by bedtools. The ChIP-seq signal will be shrunk to fit the size of its control if the control is smaller in size.
The paired-end RNA-seq reads are mapped by STAR to the mouse reference genome GRCm38 (mm10).
Alignments with mapping quality below 20 are filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are converted by bedGraphToBigWig from bedGraph generated by bedtools. Normalization between the samples was based on the proportionality of the numbers of the mapped reads.

source_name: Tip60f/f Rosa26ERCreT2 embryo

growth_protocol: LSK or c-Kit+ cells were sorted from fetal liver of Rosa26 Cre-ERT2; Tip60f/f and Tip60f/f embryos (E13.5-15.5) by FACS Aria (BD Biosciences), cultured in Stemline II (Sigma-Aldrich) supplemented with 5% FBS, murine recombinant SCF 100ng/uL, IL-3 6 ng/uL, IL-6 10ng/uL, IL-11 20 ng/uL (Peprotech). HPC-7 cells were grown in SCF.

extract_protocol:
RNA was isolated using RNeasy mini columns (Qiagen). As for ChIP, briefly, cells were fixed with 1% formaldehyde and then neutralized with glycine at a final concentration of 0.125M. Fixed chromatin were fragmented using a Bioruptor sonicator (Diagenode) to an average size around 300-500 base pairs. Sonicated chromatin was incubated with antibody overnight at 4°C. The antibodies used are Tip60 50, H2A.Z (abcam, ab4174), acH2A.Z (abcam, ab18262), H3K27ac (abcam, ab4729), and H3K27me3 (CST, 9733BC). Protein A and Protein G Dynabeads (Life Technologies) were added to the mixture and incubated for 2 hours at 4°C. Antibody:chromatin complexes were collected with a magnet and washed two times with a solution of 50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoyxcholate. After a TE wash, samples are eluted, RNase and proteinase K treated and purified using a QIAGEN PCR purification kit. A mimunim of 10 ng of DNA was used for library construction using ThruPLEX kits (Rubicon Genomics).
RNA-seq libraries were prepared using Illumina ScriptSeq™ v2 RNA-Seq  Library Preparation Kit, according to the manufacturer’s instructions (Illumina, San Diego, California, USA). Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted and applied to an Illumina flow cell using the Illumina Cluster Station. ChIP-seq libraries were prepared using ThruPLEX® DNA-seq Kit (Rubicon), and multiplexed.

treatment_protocol: The cells were treated with 4-Hydroxytamoxifen (4-OHT) (Sigma-Aldrich) 400 nM for 72 hours.

value: murine hematopoietic stem and prgenitor cell


title: Tip60 KO HSPC Tip60

extract_protocol:
RNA was isolated using RNeasy mini columns (Qiagen). As for ChIP, briefly, cells were fixed with 1% formaldehyde and then neutralized with glycine at a final concentration of 0.125M. Fixed chromatin were fragmented using a Bioruptor sonicator (Diagenode) to an average size around 300-500 base pairs. Sonicated chromatin was incubated with antibody overnight at 4°C. The antibodies used are Tip60 50, H2A.Z (abcam, ab4174), acH2A.Z (abcam, ab18262), H3K27ac (abcam, ab4729), and H3K27me3 (CST, 9733BC). Protein A and Protein G Dynabeads (Life Technologies) were added to the mixture and incubated for 2 hours at 4°C. Antibody:chromatin complexes were collected with a magnet and washed two times with a solution of 50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoyxcholate. After a TE wash, samples are eluted, RNase and proteinase K treated and purified using a QIAGEN PCR purification kit. A mimunim of 2 ng of DNA was used for library construction using ThruPLEX kits (Rubicon Genomics).
RNA-seq libraries were prepared using Illumina ScriptSeq™ v2 RNA-Seq  Library Preparation Kit, according to the manufacturer’s instructions (Illumina, San Diego, California, USA). Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted and applied to an Illumina flow cell using the Illumina Cluster Station. ChIP-seq libraries were prepared using ThruPLEX® DNA-seq Kit (Rubicon), and multiplexed.


title: S100GFP+  [10]

description:
P15-30
10
FACS isolated cells


title: 10m_TRI_rep5


title: Cord blood ID_128


title: 10m_TRI_rep4


title: Cord blood ID_127


title: MZB_GFP-_rep4


title: Tip60 KO HSPC H3K27me3


title: Tip60 KO HSPC H3K27ac


title: NG2DsRed+ [9]

description:
P15-29
9
FACS isolated cells


title: NG2DsRed+/S100GFP+ [8]

description:
P15-28
8
FACS isolated cells


title: 10m_TRI_rep3


title: S100GFP+  [14]

description:
P15-34
14
FACS isolated cells


title: 10m_TRI_rep2


title: Cord blood ID_130


title: Cord blood ID_126


title: NG2DsRed+ [7]

description:
P15-27
7
FACS isolated cells


title: Tip60 WT HSPC input


title: Tip60 WT HSPC H3K27me3


title: 10m_TRI_rep1


title: 30m_TA_RM_rep6

source_name: Tibialis anterior muscle

value: Tibialis anterior muscle


title: Tip60 WT HSPC H3K27ac


title: Cord blood ID_123


title: Cord blood ID_122


title: NG2DsRed+/S100GFP+ [4]

description:
P15-24
4
FACS isolated cells


title: 30m_TA_RM_rep5


title: 30m_TA_RM_rep4


title: S100GFP+  [3]

description:
P15-23
3
FACS isolated cells


title: Cord blood ID_120


title: Cord blood ID_12


title: 30m_TA_RM_rep3


title: NG2DsRed+ [2]

description:
P15-22
2
FACS isolated cells


title: S100GFP+  [1]

description:
P15-21
1
FACS isolated cells


title: 30m_TA_RM_rep2


title: 30m_TA_RM_rep1


title: Cord blood ID_119


title: 30m_TA_rep6


title: Cord blood ID_125


title: NG2DsRed+/S100GFP+ [6]

description:
P15-26
6
FACS isolated cells


title: PLEC CD102+F4/80+ Female 4

first: Stephen

middle: John

last: Jenkins

state: Midlothian

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
Sequence reads were trimmed using Cutadapt (vesion cutadapt-1.9.dev2)
Reads were aligned to the reference genome using STAR
Generation of counts: featureCounts (version1.5.1)
Differential gene expression analysis, DESeq2
Genome_build: Mus musculus genome from Ensemble assebbly GRCm38, annotation version 84
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: Pleural exudate cells

extract_protocol:
For each population, 25,000 cells were sorted into 500μl RLT buffer (Qiagen) and snap frozen on dry ice. RNA was isolated using the RNeasy Plus Micro kit (Qiagen), at which point triplicates of 25,000 cells for each population were pooled. 10 ng of total RNA were amplified and converted to cDNA using Ovation RNASeq System V2 (Nugen).
Ovation RNASeq System V2 was used to amplify DNA
Preparation of Truseq DNA Nano gel free library and sequencing using the Illumina HiSeq 4000 system (75PE) was performed by Edinburgh Genomics.

treatment_protocol: Peritoneal and pleural cavities were lavaged with RPMI containing 2mM EDTA and 10mM HEPES according to PMID29761387. Cells were stained with antibodies according to PMID29761387 and live single CD45+ SiglecF- CD19- CD3- Ly6G- CD102+ cells were FACS-sorted to >98% purity.

tag: gating strategy


title: Cord blood ID_124


title: PLEC CD102+F4/80+ Female 3

value: single CD45+ SiglecF- CD19- CD3- Ly6G- CD102+


title: NG2DsRed+ [5]

description:
P15-25
5
FACS isolated cells


title: Cord blood ID_117


title: BB3RC94_ALDH_POS

type: RNA

city: Liverpool

first: Eva

last: Caamano-Gutierrez

address: Crown Street

department: Technology Directorate

institute: University of Liverpool

description: Metastatic breast cancer cancer fluid sample.

hyb_protocol: Encore Biotin Module (NuGen) following manufacturer's guidelines. Staining was done using Fluidics Station protocol FS450_0007 and the Affymetrix GeneChip Command Console Software (Affymetrix) following manufacturer’s guidelines.

scan_protocol: The GeneChip array was scanned using the Affymetrix GeneChip Scanner 3000 system with autoloader (Affymetrix).

data_processing:
Results from gene expression studies were initially analysed using two different approaches. Firstly, the Affymetrix Expression Console (EC) software package was used. CEL files containing intensity values of individual probes holding an x,y coordinate position (raw data) were normalised and quality control of the files was performed through the EC software. Subsequently, the AffymetrixTranscriptome Analysis Console (TAC) was used. Secondly, the same CEL files were normalized using Robust Multi-Array Average (RMA) using Bioconductor R as an alternative method.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

label: biotin

source_name: Metastatic breast cancer

label_protocol: Biotin labeled

growth_protocol: Metastatic fluid samples were collected at the Christie NHS Foundation Trusts. All patients provided written informed consent before samples were taken, in agreement with local research ethics committee guidelines.

extract_protocol: The Aldefluor reagent system (StemCell Technologies) was used to isolate the cancer stem-like population on the basis of their aldehyde dehydrogenase (ALDH) activity. The protocol was carried out following the manufacturer’s guidelines. Briefly, 5x10e5 cells were resuspended in 0.5 ml of Aldefluor buffer per eppendorf. 10 µl of the internal control Diethylaminobenzaldehyde (DEAB) was added to one of the eppendorfs for each treatment which was used to correct for background staining and to define the ALDH-positive region in the flow cytometer. 2.5 µl of the fluorescent activated aldefluor reagent Bodipy-aminoacetaldehyde (BAAA) was added to all eppendorfs and samples were incubated in the dark at 37ºC for 45 min shaking. Samples were washed with Aldefluor buffer and centrifuged at 400g for 3 min. Samples were resuspended in 300 µl of aldefluor buffer and 3 µl of the cell viability stain 7-aminoactinomycin (7-AAD) was added to each eppendorf for cell death exclusion. ALDH-bright cells were detected in the green fluorescence channel (520-540 nm) by the FACS aria II sorter (BD Bioscience).Unstained cells were always used to ensure accurate gating. Cell debris and doublets were also gated out based on cell size and complexity. Data was analysed using the FlowJo software package. Once the Aldefluor assay was performed, 10,000 cells were sorted with Hank’s Buffered Saline Solution (HBSS) as sheath fluid. ALDH positive and ALDH negative populations were sorted into 100 µl of RLT lysis buffer (Qiagen) for direct lysis. Total RNA extraction from PDS was carried out using the RNase Plus Micro Kit (Qiagen) according to manufacturer’s instructions. The 2100 Bioanalyzer (Agilent 2100 Bioanalyzer system, Agilent Technologies) was used for quantitation and quality control of the RNA from sorted cells.

treatment_protocol: Ascites or pleural effusions were spun for 10min at 1000g and pellets were resuspended in PBS. Red and white blood cells were excluded from the epithelial tumour cells using the density gradient Lymphoprep (Stemcell Technologies) following manufacturer’s protocol.

tag: diagnosis

value: Breast cancer

tag: er status

value: ER+

tag: Stage

value: Metastasis

value: Metastatic fluid

tag: aldh population

value: Positive

tag: patient


title: BB3RC94_ALDH_NEG

tag: tissue

value: Negative


title: BB3RC91A_ALDH_POS


title: BB3RC91_ALDH_POS


title: PLEC CD102+F4/80+ Male 3

tag: strain

tag: age


title: PLEC CD102+F4/80+ Male 4


title: 30m_TA_rep4

value: post natal month 30

tag: genotype

value: wild type

tag: treatment

value: vehicle


title: Cord blood ID_116

value: cord blood

tag: birthweight


title: BB3RC91A_ALDH_NEG


title: 30m_TA_rep5


title: 30m_TA_rep3


title: Cord blood ID_115


title: Cord blood ID_118


title: 30m_TA_rep2


title: Cord blood ID_114


title: PLEC CD102+F4/80+ Male 1


title: Cord blood ID_113


title: Cord blood ID_111


title: BB3RC91_ALDH_NEG


title: PEC CD102+F4/80+ Female 4

source_name: Peritoneal exudate cells


title: 10m_TA_rep6

value: post natal month 10


title: 30m_TA_rep1


title: PEC CD102+F4/80+ Female 3


title: Cord blood ID_110


title: 10m_TA_rep5


title: PEC CD102+F4/80+ Female 1


title: PLEC CD102+F4/80+ Male 2


title: 10m_TA_rep4


title: Cord blood ID_109


title: BB3RC90_ALDH_NEG


title: BB3RC90_ALDH_POS


title: Cord blood ID_107


title: BB3RC89_ALDH_POS


title: BB3RC89_ALDH_NEG


title: 10m_TA_rep2


title: 10m_TA_rep3


title: BB3RC90A_ALDH_POS


title: BB3RC90A_ALDH_NEG


title: 10m_TA_rep1


title: BB3RC69_ALDH_POS


title: 30m_Sol_RM_rep6

source_name: Soleus muscle

value: Soleus muscle


title: Cord blood ID_105


title: Cord blood ID_106


title: MMBN33_RPF depleted state

city: Marseille Cedex 9

first: Marc

last: Bajenoff

address: Parc Scientifique et Technologique de Luminy 163 avenue de Luminy Case 906

country: France

institute: CIML – Centre d’Immunologie Marseille-Luminy

description:
This sample includes data from two mice.
MMBN33

data_processing:
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10. Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 93 and "union" mode. Only non-ambiguously assigned reads have been retained for further analyses.
Read counts have been normalized across samples with the median-of-ratios method proposed by Anders and Huber, to make these counts comparable between samples.
Genome_build: mm10
Supplementary_files_format_and_content: raw, normalized values with statistics

source_name: spleen

extract_protocol:
Lymph Nodes (sample 1, n=6 untreated mice) and/or Spleens (sample 2, n=6 untreated mice ; sample 3 n=6 diphteria-toxin-treated mice) from 12 Wt1CreERT2 RosatdTomato CD64DTR  mice were digested for 40 min at room temperature with dispase/collagenase/DNase . All subsequent procedures were at 0–4°C. CD45- cells were enriched using MACS anti-CD45 microbeads and passing them through a MACS LS column. CD45- cells were incubated on ice for 30 min with 2.4G2 antibody to block Fc receptors and stained for the  surface markers CD45, gp38, CD31, and VCAM1. tdTomato- FRC and tdTomato+ RPF were sorted using a  FACSAria III and processed according to the RNeasy Plus Microkit instruction from QIAGEN.
RNA library was prepared by the IGBMC GenomEast plateform ('France Génomique' consortium)

tag: mouse strain

value: Wt1CreERT2 RosatdTomato CD64DTR (n=2)

value: spleen

tag: mouse age

value: 4 months

tag: diphteria toxin treatment

value: yes


title: Cord blood ID_104


title: Cord blood ID_11


title: BB3RC68_ALDH_POS


title: MMBN34_RPF depleted state

description:
This sample includes data from two mice.
MMBN34


title: BB3RC69_ALDH_NEG


title: Cord blood ID_103


title: ARID1A KO_diff T10_scRNA-seq

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W. Walnut St.

department: Department of Pediatrics

institute: Indiana University School of Medicine

data_processing:
CellRanger 2.1.0 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfificationa.
The CCA function from Seurat was used for integrative analysis of the WT and KO samples.
Genome_build: hg38
Supplementary_files_format_and_content: genes.tsv, matrix.mtx and barcodes.tsv in each tar.gz file

source_name: hESCs H9 cells-derived cells

growth_protocol: For the undifferentiated samples, H9 hESCs were routinely cultured in mTesR medium in a matrigel-coated 6-well plate). For the differentiated samples, H9 hESCs were routinely cultured in mTesR medium (a matrigel-coated 6-well plate). When cells density were 100%, medium were changed to chemically defined medium for cardiac differentiation induction.

extract_protocol:
H9 hESCs and differentiated hESCs were dissociated by Corning™ 0.25% Trypsin (Corning™ 25053CI) to single cells. Single cell 3’ RNA-seq experiments were conducted using the Chromium single cell system (10x Genomics, Inc) and Illumina sequencers at the Center of Molecular Genetics (CMG) of Indiana University School of Medicine. Cell suspension was first inspected on the Countess II FL (Thermo Fisher Scientific) and under microscope for cell number, cell viability, and cell size. Depending on the quality of the initial cell suspension, the single cell preparation included centrifugation, re-suspension, and filtration to remove cell debris, dead cells and cell aggregates. Single cell capture and library preparation were carried out according to the Chromium Single cell 3’ Reagent kits V2 User Guide (10X Genomics PN-120267, PN-1000009, PN-120262). Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics) with a targeted cell recovery of 10,000. Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2 single cell reagent kit (10X Genomics). Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing libraries were then prepared with the amplified cDNA. The resulting libraries were assessed with an Agilent TapeStation or Bioanalyzer 2100. The final libraries of the undifferentiated samples were sequenced using a custom program on Illumina NextSeq 500/550; and the libraries of the differentiated samples were sequenced on Illumina NovaSeq 6000. 26 bp of cell barcode and UMI sequences, and 91 or 98 bp RNA reads were generated with Illumina NextSeq500/550 or NovaSeq 6000.
Single cell 3’ RNA-seq experiments were conducted using the Chromium single cell system (10x Genomics, Inc) and Illumina sequencers at the Center of Molecular Genetics (CMG) of Indiana University School of Medicine. Cell suspension was first inspected on the Countess II FL (Thermo Fisher Scientific) and under microscope for cell number, cell viability, and cell size. Depending on the quality of the initial cell suspension, the single cell preparation included centrifugation, re-suspension, and filtration to remove cell debris, dead cells and cell aggregates. Single cell capture and library preparation were carried out according to the Chromium Single cell 3’ Reagent kits V2 User Guide (10X Genomics PN-120267, PN-1000009, PN-120262). Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics) with a targeted cell recovery of 10,000. Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2 single cell reagent kit (10X Genomics). Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing libraries were then prepared with the amplified cDNA. The resulting libraries were assessed with an Agilent TapeStation or Bioanalyzer 2100.

treatment_protocol: Cells were dissociated by Corning™ 0.25% Trypsin (Corning™ 25053CI) to single cells.

tag: cell type source

value: hESCs H9 cells

tag: status

value: cardiac differentiation for 10 days

tag: genotype/variation

value: ARID1A KO


title: PEC CD102+F4/80+ Male 3

tag: gating strategy

value: single CD45+ SiglecF- CD19- CD3- Ly6G- CD102+


title: MMBN32_RPF depleted state

description:
This sample includes data from two mice.
MMBN32


title: WT_diff T10_scRNA-seq

tag: passage


title: BB3RC68_ALDH_NEG

tag: diagnosis

value: Breast cancer

tag: er status

value: ER+

tag: Stage

value: Metastasis

value: Metastatic fluid


title: MMBN31_RPF steady state

description:
This sample includes data from two mice.
MMBN31

tag: tissue

value: no


title: Cord blood ID_102


title: 30m_Sol_RM_rep5

tag: strain

value: post natal month 30

value: wild type

value: rapamycin


title: MMBN30_RPF steady state

description:
This sample includes data from two mice.
MMBN30


title: 30m_Sol_RM_rep4

value: Soleus muscle

tag: age


title: BB3RC71_ALDH_POS

tag: aldh population

value: Positive

tag: patient


title: 30m_Sol_RM_rep3

tag: genotype

tag: treatment


title: ARID1A KO_diff T4_ATAC-seq

description: ARID1A was completely knocked out

data_processing:
Illumina adapter sequences and low-quality base calls were trimmed off the paired-end reads with Trim Galore v0.4.3.
The resulting high-quality reads were aligned to the human reference genome hg38 using bowtie2.
Duplicate reads were discarded with Picard.
Reads mapped to mitochondrial DNA together with low mapping quality reads were excluded from further analysis.
Peaks were called using MACS2 2.1.2, pyDNase was used to retrieve cleavage event falling in the merged peak. Differential accessibility analysis on the counts was performed using edgeR (v3.26.8)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: hESCs H9 cells

growth_protocol: H9 hESCs were routinely cultured in mTesR medium on matrigel-coated 6-well plate. When cell density was 100%, medium was changed to chemically defined medium for cardiac differentiation for 4 days.

extract_protocol: Briefly, collected cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and the nuclei were pelleted and resuspended in Tn5 enzyme and transposase buffer (Illumina Nextera® DNA library preparation kit, cat# FC-121-1030). The Nextera libraries were amplified using the Nextera® PCR master mix and KAPA biosystems HiFi hotstart readymix (cat # NC0295239) successively. AMPure XP beads (Beckman Coulter cat# A63881) were used to purify the transposed DNA and the amplified PCR products. All libraries were sequenced on a 100 cycle paired-end run on an Illumina NOVAseq instrument. The resulting ATAC-seq libraries were sequenced on Illumina NovaSeq 6000 at CMG of Indiana University School of Medicine and paired-end 50 bp reads were generated. Illumina adapter sequences and low-quality base calls were trimmed off the paired-end reads with Trim Galore v0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim _galore/). The resulting high-quality reads were aligned to the human reference genome hg38 using bowtie2 (version 2.3.2) 63 with parameters “-X 2000 --no-mixed --no-discordant”.  Duplicate reads were discarded with Picard (https://broadinstitute.github.io/picard/). Reads mapped to mitochondrial DNA together with low mapping quality reads (MAPQ<10) were excluded from further analysis. All of ATAC-seq experiments were done in Department of Medical and Molecular Genetics at the Indiana University School of Medicine. And data analysis was finished in The Center for Medical Genomics at Indiana University School of Medicine.

treatment_protocol: WT and ARID1A-/- hESCs were differentiated for 4 days, then cells were dissociated by Trypsin-EDTA (0.25%). Cells were washed by 1X PBS and re-suspended in cold PBS according to ATAC-seq protocol.

tag: cell type

value: hESCs H9 cells-derived cells (cardiac differentiation for 4 days)


title: MMBN29_RPF steady state

description:
This sample includes data from two mice.
MMBN29

tag: mouse strain

value: Wt1CreERT2 RosatdTomato CD64DTR (n=2)

value: spleen

tag: mouse age

value: 4 months

tag: diphteria toxin treatment


title: Cord blood ID_101

value: cord blood

tag: birthweight


title: BB3RC71_ALDH_NEG

value: Negative


title: WT_diff T4_ATAC-seq

description: ARID1A is expressed

value: WT


title: Cord blood ID_100


title: 30m_Sol_RM_rep2


title: PD6_17input_PD_hMeDIP_Seq

city: Grand Rapids

first: Lee

last: Marshall

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

description: Brain bank Sample code:PD471

data_processing:
library strategy: hMeDIP-seq
Adapter sequences were removed from fastq files using TrimGalore (v0.4.4).
Sequenced reads from hMeDIP immunoprecipitated and input control human brain nuclei were mapped to the human reference genome (GRCh37/hg19) with Bowtie2 (v2.3.1).
A combination of Picard and Samtools (v1.9) was used to mark and remove PCR duplicates respectively.
Deeptools (v2.3.1) was used to apply a Signal Extraction Scaling (SES) factor normalized to the input (1 kb wide tiling windows) prior to peak calling.
Broad peaks were called using MACS2 for each normalized sample and a consensus peak list was then defined as contiguous regions covered by at least 22 sample peaks. Consensus peaks in the shortest 5% and and longest 5% range were removed from further analysis.
To determine hydroxymethylation contribution to epigenetic changes at enhancers in PD neurons, hydroxymethylation counts for the differentially methylated cytosines in PD were extracted using bedtools coverage
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Each bed file contains a bed 12 format for the macs2 broad peaks. Each txt file contains the following information in order: cytosine site location, read counts.

extract_protocol:
Neuronal nuclei from prefrontal cortex were isolated using an antibody (NeuN) and flow cytometry approach. Human prefrontal cortex brain tissue was homogenized and then filtered through Miracloth before being passed through a 1.4 M sucrose cushion by centrifugation at 4000 × g for 30 min 4°C. Nuclei pellets were resuspended and blocking mix (100 μl of 1X PBS with 0.5% BSA and 10% normal goat serum) was added to each sample. Anti-NeuN antibody with Alex Fluor 488 (1:500; Abcam; ab190195) was added and samples were incubated 45 min at 4°C with gentle mixing, followed by staining with 7-AAD. Nuclei positive for 7-AAD and either NeuN+ (neuronal) or NeuN‒ (non-neuronal) were sorted by flow cytometry. Genomic DNA from NeuN+ nuclei was extracted by standard phenol-chloroform extraction.
Genomic DNA from human prefrontal cortex neuronal nuclei was sheared using a Covaris LE220 sonicator (size range of 200–600 bp) and hMeDIP was performed using the EpiQuik kit (Epigentek). 5-hmC antibody or non-immune IgG was coated on the bottom of a 96-well plate, wells were washed and either 1 µg sheared DNA, 1 µg control DNA, or buffer only was added to appropriate wells. The plate was then covered and incubated for 90 min with orbital rotation at 100 rpm. Wells were then washed 5 times with washing buffer. Captured DNA was then eluted by incubation of each well with a proteinase K mixture at 60°C for 15 min followed by incubation at 95°C for 3 min. The solution containing eluted DNA was transferred to another 96-well plate. DNA in each well was then purified using AMPure XP beads (Beckman Coulter). Libraries were prepared from 10 ng of input material or all available immunoprecipitated material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). End repaired and A-tailed DNA fragments were ligated to IDT for Illumina TruSeq UD Indexed Adapters (Illumina), followed by PCR amplification. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies), and QuantiFluor® dsDNA System (Promega Corp.). Sequencing (single-end 100 bp) was performed on an Illumina NovaSeq6000 sequencer.

tag: Sex

value: M

tag: pmi

tag: braak stage

value: Brain prefrontal cortex

tag: molecule subtype

value: hMeDIP Input DNA

tag: brain bank

value: Parkinson’s UK Brain Bank

tag: replicate

value: Biological Sample


title: Cord blood ID_1

tag: tissue


title: MMBN37_FRC steady state

description:
This sample includes data from two mice.
MMBN37

source_name: lymph node

value: lymph nodes

value: no


title: MMBN35_FRC steady state

description:
This sample includes data from two mice.
MMBN35


title: 30m_Sol_rep5

tag: strain

tag: age

value: post natal month 30

value: wild type

value: vehicle


title: PD4_146input_PD_hMeDIP_Seq

description: Brain bank Sample code:PD368

value: F


title: PD6_9_PD_hMeDIP_Seq

description: Brain bank Sample code:PD201

value: hMeDIP DNA


title: 30m_Sol_rep4

value: Soleus muscle


title: MMBN36_FRC steady state

description:
This sample includes data from two mice.
MMBN36

value: Wt1CreERT2 RosatdTomato CD64DTR (n=2)

value: 4 months


title: IAA_6h_Pol2_Mitotic exit_Hi-C_rep2

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

description: Pol2_IAA_6h_Mitotic_downsampled_75mi_allValidPairs.hic

data_processing:
Linker detection: The bridge linker sequences were trimmed using trimlinker from ChIA-PET2 software, paired-end reads containing at least one instance of the bridge-linker in either end are adapted for further processing.
Reads alignment: The resulting reads were aligned against the mm10 genome and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (special paramters: --very-sensitive-local --local)
Filtering: Discard read-pairs marked as multihits, PCR duplicates, low mapping quality (MAPQ < 20), self-ligated fragments and dangling-end; only the valid read pairs involving two different restriction fragments were used to build the contact matrices.
Matrix generation: For unbiased comparison, we randomly sampled equal numbers of long range (>20 kb) intra-chromosomal read pairs (n=75 million) from each sample, Hi-C contact matrices  with binned interactions (range from 5 kb to 100 kb) were generated.
Normalization: the raw Hi-C contact matrices were normalized using the iterative correction method with iced script to correct for systematic biases and the distance between restriction fragments as recently described.
Processed reads and downsampled allValidPairs were then inputted into the Juicebox pipeline (hicpro2juicebox.sh) to allow for visualization of the interaction matrix.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (.hic) were generated useing juicebox pre

source_name: mouse embryonic stem cells

growth_protocol: The V6.5 mouse ES (mES) cell line was cultured with irradiated mouse embryonic fibroblasts in DMEM-KO containing 15% FBS, leukaemia inhibiting factor (LIF), L-glutamine, β-mercaptoethanol, non-essential amino acids and penicillin/ streptomycin at 37 ℃ with 5% CO2, and passage twice for experiments.

extract_protocol:
Hi-C was conducted as BAT Hi-C (Huang et al., 2019). After AluI digestion, proximal ligation was mediated with biotin labeled linker, then remove unligated linker with ExoI and ligated DNA was extracted with streptavidin beads.
Llibrary was constructed with Illumina Nextera DNA Sample Preparation Kit (FC-121-1030), sequencing adaptor was added with Tn5 transposase.

treatment_protocol: All degron mES cells were pre-treated with 1 μg/ml Doxycycline for 12 hours. Pol II degron mES was treated with or without 500 μM indole-3-acetic acid (IAA) for 6 hours, whereas Pol I and Pol III degron mES were treated for 24 hours with same concentration. For the time course of Pol II degron, IAA was added 1 hour and 6 hours respectively. For synchronization Pol II degron mES cells were treated with 1.25 mM Thymidine for 14 hours, followed by treatment with 50 ng/ml Nocodazole for 7 hours; mitotic cells were collected at this time, mitotic exit cells were collected 1 hour after release. At the same time, all Pol II degron mES cells were pre-treated with 1ug/ml Doxycycline for 12 hours following being treated with or without 500 μM indole-3-acetic acid (IAA) for 6 hours.

value: Pol II degron 6h Mitotic mES

tag: restriction enzyme

value: AluI


title: Untreated_Pol2_Mitotic exit_Hi-C_rep2

description: Pol2_untreated_Mitotic_downsampled_75mi_allValidPairs.hic

value: Untreated Mitotic_mES


title: Untreated_Pol2_Mitotic exit_Hi-C_rep1


title: PD6_169_PD_hMeDIP_Seq

description: Brain bank Sample code:PD336

value: M

value: Brain prefrontal cortex


title: 30m_Sol_rep1

tag: genotype


title: 30m_Sol_rep2

tag: treatment


title: 30m_Sol_RM_rep1

value: rapamycin


title: B lymphocytes, G2_P1

city: Berlin

last: Altwasser

address: Robert-Rössle-Str. 10

department: AG Di Virgilio

country: Germany

institute: Max-Delbrück-centrum

description:
Pdap1 KO B lymphocytes switched to IgG2b
raw_counts.tsv
normalized_counts.tsv

data_processing:
TrimGalore 0.6.1
Aligned using STAR 2.6
Expression counts using htSeq 0.9.1
Differential expression performance using DESeq2
Genome_build: Mus musculus: GRCm38
Supplementary_files_format_and_content: raw_counts.tsv: tsv file with the raw read counts per gene
normalized_counts.tsv: file with the read counts normalized by library size via DESeq2

source_name: B lymphocytes

extract_protocol:
RNA-Seq analysis was performed on three mice per genotype. Splenocytes were cultured in LPS and IL-4 (IgG1) or LPS, BAFF and TGF (IgG2b) for 48 h. Cells were collected by centrifugation and RNA was extracted with TRIzol (Invitrogen) according to manufacturer's instructions. Ribosomal RNA was depleted using Ribo-Zero Gold rRNA Removal Kit (Illumina).
TruSeq Stranded mRNA

tag: class switch

value: PDAP1 KO

tag: cell line

tag: cell type

value: B lymphocytes


title: B lymphocytes, G2_P3


title: B lymphocytes, G2_P2


title: 10m_Sol_rep6

value: post natal month 10


title: PD6_112_PD_hMeDIP_Seq

description: Brain bank Sample code:PD357

value: Parkinson’s UK Brain Bank

value: Biological Sample


title: B lymphocytes, G2_C3

description:
B lymphocytes control
raw_counts.tsv
normalized_counts.tsv


title: PEC CD102+F4/80+ Male 4

tag: gating strategy

value: single CD45+ SiglecF- CD19- CD3- Ly6G- CD102+


title: 10m_Sol_rep5

description:
direction_1st_mate: antisense, direction_2nd_mate: sense
aging_rm_counts.txt.gz
aging_rm_tpms.txt.gz

value: wild type

value: vehicle


title: Brain_M5w_3

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

description: small RNA-deq

data_processing:
Sequence information was extracted in FastQ format using Illumina's bcl2fastq software v1.8.3.
The processing and annotation of small RNA-Seq raw data was performed using the R programming language (version 3.0.2) and the ShortRead Bioconductor package (Morgan et al., 2009). First, raw data were pre-processed with the following parameters: Quality filtering, eliminating all reads containing an “N”; Adapter trimming, by use of the function trimLRPatterns(), allowing up to 2 mismatches and using as adapter sequence "TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC".
Size filtering removed all the reads with length shorter 18 and longer 33 nucleotides.
Reads were aligned, resulting in a direct annotation and quantification. The alignment was divided in two steps, to allow the recognition and the annotation of the reads exceeding reference length. In fact, the algorithm of Bowtie 1.1.2 does not allow aligning longer reads to shorter references. Specifically, first we performed alignment against the reference (mature miRNAs, N. furzeri reference catalouge, Baumgart et al. 2017, PMID: 28874118) with up to 2 mismatches. In this step the reference used was the mature sequence of microRNAs. Each read was aligned using these criteria with Bowtie (settings: “-q", "--threads 8 --best", "—norc”). The remaining reads, which could not align in the previous step, were used as reference for a second alignment step with Bowtie 1.1.2 (settings: -f", "-a", "--threads 8 --norc"). In this case, the annotated mature microRNAs were aligned against the reads.
The information obtained in the two alignment phases was conveyed in one single table, containing a list of all the retrieved sequences and their relative counts.
Genome_build: nfurzeri_genebuild_v1
Supplementary_files_format_and_content: Counts.csv

organism: Nothobranchius furzeri

source_name: N. furzeri brain

growth_protocol: Animal maintenance was performed as described (Baumgart et al., Aging Cell 2014). To avoid effects of circadian rhythms and feeding, animals were always sacrificed at 10 a.m. in fasted state. For tissue preparation, fish were euthanized with MS-222 and cooled on crushed ice. The protocols of animal maintenance and experimentation were approved by the local authority in the State of Thuringia, Germany.

extract_protocol:
RNA was extracted with standard Trizol protocol (Chomczynski 1995), using Qiazol lysis reagent (Qiagen).In brief 0.2mL of Chloroform were added per each mL of Trizol reagent, samples were mixed and centrifuged at 20000g for 20 minutes at 4°C in a tabletop centrifuge. After the centrifugation, the upper aqueous phase was withdrawn and mixed with 0.5 volumes of isopropyl alcohol, 0.16 volumes of Sodium acetate and 1µL of GlycoBlue to precipitate RNA. Samples were then centrifuged at 20000g for 30 minutes at 4°C, washed twice with 80% ethanol and centrifuged at 7500g for 5 minutes at 4°C. The resulting pellet was dried for no more than 5 minutes and dissolved in nuclease-free water
Small RNA library preparation was done using Illumina’s TruSeq small RNA library preparation kit following the manufacturer’s instructions.

value: brain

tag: age group

value: 5 wph


title: PD6_64_PD_hMeDIP_Seq

description: Brain bank Sample code:PD341

tag: Sex

value: hMeDIP DNA


title: Brain_M5w_2

description: small RNA-deq


title: 10m_Sol_rep3

value: Soleus muscle


title: IAA_6h_Pol2_Mitotic exit_Hi-C_rep1

value: Pol II degron 6h Mitotic mES

value: AluI


title: B lymphocytes, G2_C1


title: Brain_M5w_1

description: small RNA-deq


title: PD6_120_PD_hMeDIP_Seq

description: Brain bank Sample code:PD180

value: F

tag: pmi


title: 30m_Sol_rep3

value: post natal month 30


title: PD6_61_PD_hMeDIP_Seq

description: Brain bank Sample code:PD460

value: M

tag: braak stage

value: Brain prefrontal cortex


title: PD6_23_PD_hMeDIP_Seq

description: Brain bank Sample code:PD427

tag: molecule subtype


title: B lymphocytes, G1_P3

description:
Pdap1 KO B lymphocytes switched to IgG1
raw_counts.tsv
normalized_counts.tsv

value: PDAP1 KO

value: B lymphocytes


title: B lymphocytes, G1_P2


title: 10m_Sol_rep2

value: post natal month 10


title: Brain_M5w_4

description: small RNA-deq


title: PD6_121_PD_hMeDIP_Seq

description: Brain bank Sample code:PD188

tag: brain bank

value: Parkinson’s UK Brain Bank

value: Biological Sample


title: Brain_M39w_4

description: small RNA-deq

value: 39 wph


title: Brain_M39w_3

description: small RNA-deq


title: 10m_Sol_rep1

value: wild type

value: vehicle


title: PD5_70_PD_hMeDIP_Seq

description: Brain bank Sample code:AN17984

value: Harvard

tag: replicate


title: BMDMs control untreated rep 3

city: Debrecen

first: Nikolaos

last: Giannakis

address: Egyetem ter 1

department: Department of Biochemistry and Molecular  Biology

country: Hungary

institute: University of Debrecen

description: BMDMs_untreated_vs_treated_RvD1_6h_RNA_seq.txt

data_processing:
Alignment was performed  with TopHat v2.0.7 using default parameters.
mm10
Genome_build: normalised counts based on abundance measurements

source_name: Bone marrow

extract_protocol:
Total RNA was isolated with TRIZOL reagent according to the manufacturer’s recommendation. 20ug glycogen (Ambion) was added as carrier for RNA ethanol precipitation
cDNA library for RNA-Seq was generated from 100ng-400ng total RNA using TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. Briefly poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, and then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.

treatment_protocol: For the bone marrow derived macrophages: Bone marrow was flushed from the tibiae and femurs of 8-10 week old male C57BL/6J mice using a 25 gauge needle and DMEM media (ATCC) containing 10% FBS, 20 mM HEPES and 1% penicillin/streptomycin. Once isolated, the bone marrow was plated in this medium supplemented with 10 ng/ml M-CSF (macrophage colony-stimulating factor; Sigma). On day four of differentiation, the media was replenished with fresh media (containing M-CSF). After seven days, the cells were liberated using a cell scraper centrifuged and re-plated in media lacking M-CSF. After 24 hours, cells were exposed to 10 nM RvD1 (Cayman Chemical) for six hours then collected in Buffer RLT (Qiagen) with 10 µl/ml 2-mercaptoethanol.

tag: tissue

value: Bone marrow

value: bone marrow derived macrophages untreated control

value: male

value: 2-4 months old


title: B lymphocytes, G1_C3

tag: strain


title: Brain_M39w_1

description: small RNA-deq

value: brain


title: B lymphocytes, G2_C2


title: PD5_178_PD_hMeDIP_Seq

description: Brain bank Sample code:AN08067

value: F

tag: age

value: hMeDIP DNA


title: BMDMs control untreated rep 2


title: 10m_Sol_rep4

last: Boersch

address: Klingelbergstrasse 50 / 70

institute: University of Basel

data_processing:
RNA-seq reads were subjected to 3’ adapter and poly(A)/poly(T) tail trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011. The following 3’ adapter sequences were utilized for generating RNA-Seq libraries and subsequently trimmed: mate1 5’-AGATCGGAAGAGCACACGTC-3’, mate2 5’-AGATCGGAAGAGCGTCGTGT-3’.
Reads shorter than 30 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--rf-stranded” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
Genome_build: As the reference mouse transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCm38 (release 92) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002).
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values at the gene level for each sample.

extract_protocol:
Snap frozen muscles were pulverized and lysed in RLT buffer (Qiagen). RNA was extracted using an AccuPure Tissue RNA Mini Kit (R20096) with an iColumn 24 (AccuBioMed). TruSeq Stranded mRNA HT Sample Prep Kit was used for the library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Soleus muscle


title: PD4_27_PD_hMeDIP_Seq

description: Brain bank Sample code:PD398

value: M

value: Brain prefrontal cortex


title: B lymphocytes, G1_C2

value: B lymphocytes


title: Brain_M12w_4

description: small RNA-deq

value: 12 wph


title: BMDMs control untreated rep 1


title: BMDMs treated Rvd1 6h rep 3

value: bone marrow derived macrophages RvD1 6h treated


title: B lymphocytes, G1_C1


title: PD4_146_PD_hMeDIP_Seq

description: Brain bank Sample code:PD368

value: Parkinson’s UK Brain Bank

value: Biological Sample


title: BMDMs treated Rvd1 6h rep 2


title: T3_90: Treated  Rep3_90min

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

description: Treated Fermenter Replicate3_90min sample (pH 6.0)

data_processing:
Demultiplexing and file conversion performed by bcl2fastq version bcl2fastq-1.8.3
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence and then mapped to reference genome CP001393.1  for DSM6725 strain using CLC Genomics Workbench (CLC bio, Aarhus, Denmark; version 8.0), RNA-sequencing pipeline. Default settings were used for mismatch, insertion, and deletion costs.
Differenential gene expression using the unique gene counts from CLCBio was estimated using DESeq2 .
Supplementary_files_format_and_content: Tab deliminated file includes read counts for each gene across the 30 ( 5 time-points sampled with 3 replicates each for control and treated setup, i.e. 15 per setup. Thus as two setups (control and treated ) used 15x2=30)  samples used in this study

organism: Caldicellulosiruptor bescii

source_name: Treated  Rep3_90min

growth_protocol: Wild-type C. bescii strain DSM6725 was grown anaerobically at 75 °C in batch fermenters with liquid LOD medium with 5 g/L maltose as the carbon source.

extract_protocol:
Briefly, cell pellets from each sample were incubated in 250 µL of 20 mg/mL Lysozyme (Sigma Aldrich part number L-7651, St. Louis, MO) resuspended in SET buffer (50 mM Tris-HCl pH 8.0 50 mM EDTA, 20% w/v Sucrose) followed by incubation at 37oC for eight minutes, vortexing briefly every two minutes.  After incubation, 900 µL of buffer RLT from a Qiagen RNeasy Kit (Qiagen, Hilden, Germany) was added to the lysozyme cell mixture and vortexed.  Then 650 µL of 100% ethanol was added to each aliquot and mixed by pipetting.  Each sample was then applied to a RNeasy spin column (Qiagen, Hilden, Germany) and processed following the manufacturers protocol including the optional on column Dnase I treatment.  Samples were eluted in 35 µL RNAse free water (Qiagen, Hilden, Germany). The quantity and quality of RNA was assessed post-elution using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA). Ribosomal RNA was depleted from the samples using a RiboZero rRNA Removal Kit for bacteria (Illumina Inc. San Diego, CA)
cDNA libraries were prepared and barcoded using a ScriptSeq v2 RNA-Seq library preparation kit (Illumina Inc. San Diego, CA) following the manufacturers protocols.

treatment_protocol: In control fermenters, cells were grown at pH 7.2 throughout whereas, in treated fermenters, cells were grown at pH 7.2 until mid-log phase and pH was then lowered to 6.0 by acid addition.

value: Caldicellulosiruptor bescii DSM6725 cells

tag: setup

value: treated

tag: time-point

value: 90 min


title: Brain_M12w_2

description: small RNA-deq


title: T3_60: Treated  Rep3_60min

description: Treated Fermenter Replicate3_60min sample (pH 6.0)

source_name: Treated  Rep3_60min


title: B lymphocytes, G1_P1

tag: genotype

value: PDAP1 KO


title: Brain_M39w_2

description: small RNA-deq

value: 39 wph


title: Brain_M12w_1

description: small RNA-deq


title: BMDMs treated Rvd1 6h rep 1

value: Bone marrow

value: male

value: 2-4 months old


title: T3_30: Treated  Rep3_30min

description: Treated Fermenter Replicate3_30min sample (pH 6.0)

source_name: Treated  Rep3_30min

value: 30 min


title: PD3_20_PD_hMeDIP_Seq

description: Brain bank Sample code:PD028

value: hMeDIP DNA


title: PD3_24_PD_hMeDIP_Seq

description: Brain bank Sample code:PD084

value: M


title: Brain_G5w_4

description: small RNA-deq

value: brain

value: GRZ

value: 5 wph


title: PD6_109_PD_hMeDIP_Seq

description: Brain bank Sample code:AN14569

value: F

value: Brain prefrontal cortex

value: Harvard


title: PD3_18_PD_hMeDIP_Seq

description: Brain bank Sample code:PD041

value: Parkinson’s UK Brain Bank

value: Biological Sample


title: Brain_G5w_3

description: small RNA-deq


title: T3_10: Treated  Rep3_10min

description: Treated Fermenter Replicate3_10min sample (pH 6.0)

source_name: Treated  Rep3_10min

value: Caldicellulosiruptor bescii DSM6725 cells

value: treated

value: 10 min


title: Brain_M12w_3

description: small RNA-deq

value: 12 wph


title: Brain_G5w_2

description: small RNA-deq


title: T2_90: Treated  Rep2_90min

description: Treated Fermenter Replicate2_90min sample (pH 6.0)

source_name: Treated  Rep2_90min

value: 90 min


title: T3_5: Treated  Rep3_5min

description: Treated Fermenter Replicate3_5min sample (pH 6.0)

source_name: Treated  Rep3_5min

value: 5 min


title: PD3_19_PD_hMeDIP_Seq

description: Brain bank Sample code:PD050


title: PD3_68_PD_hMeDIP_Seq

description: Brain bank Sample code:PD081


title: Brain_G5w_1

description: small RNA-deq


title: PD3_31_PD_hMeDIP_Seq

description: Brain bank Sample code:PD079


title: PD3_167_PD_hMeDIP_Seq

description: Brain bank Sample code:PD099


title: CTRL_199_PD_hMeDIP_Seq

description: Brain bank Sample code:732

value: Michigan


title: T2_30: Treated  Rep2_30min

description: Treated Fermenter Replicate2_30min sample (pH 6.0)

source_name: Treated  Rep2_30min

value: 30 min


title: CTRL_162_PD_hMeDIP_Seq

description: Brain bank Sample code:PD034

value: M

value: hMeDIP DNA


title: M5w_15

description: processed data file: counts.txt

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4.
Reads were mapped using TopHat2 v2.1.0 (–no-coverage-search --no-convert-bam --no-novel-juncs –no-novel-indels -T -x 1).
Counting of reads per gene was done using featureCounts v1.5.0 (-s 0).
Genome_build: Genome v20150522 and annotation v20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/).
Supplementary_files_format_and_content: counts.txt: Tab-delimited txt file containing read counts per gene.

extract_protocol:
RNA from each sample was extracted from protein lysates using Qiazol lysis reagent (Qiagen). In brief, 1ml of Qiazol reagent was added to 100 µL of lysate, followed by the addition of 200 µL of chloroform. Samples were mixed vigorously and centrifuged at 12000x g for 20 min at 4°C, after 3 min incubation at room temperature. The upper aqueous phase was carefully transferred into a fresh tube and mixed with 1 volume of isopropyl alcohol, 0.16 volumes of Sodium acetate (2M; pH 4.0) and 1µL of GlycoBlue (InvitrogenTM) in order to precipitate RNA. After 10 min of incubation at room temperature, samples were centrifuged at 12000x g for 30 min at 4°C. The supernatant was completely removed and RNA pellets were washed by adding 80% (v/v) ethanol and centrifuging at 7500x g for 5 min at 4°C. Washing step was performed twice. The resulting pellets were air-dried for no more than 5 min and dissolved in 10 µL nuclease-free water. To ensure full dissolution of RNA in water, samples were then incubated at 65°C for 5 min, before storage at -80°C.
Total RNA library preparation was done by use of Illumina’s TruSeq Stranded Total RNA Library Prep Kit (RiboZero Gold), following the manufacturer’s instructions.

value: brain


title: M5w_14

description: processed data file: counts.txt

value: 5 wph


title: T2_10: Treated  Rep2_10min

description: Treated Fermenter Replicate2_10min sample (pH 6.0)

source_name: Treated  Rep2_10min


title: T2_60: Treated  Rep2_60min

description: Treated Fermenter Replicate2_60min sample (pH 6.0)

source_name: Treated  Rep2_60min


title: CTRL_200_PD_hMeDIP_Seq

description: Brain bank Sample code:1338


title: M5w_11

description: processed data file: counts.txt


title: Pituitary, P7_T2

city: Hadano

first: Tomoki

last: Takeda

address: Hirasawa 2445

country: Japan

institute: Japan Bioassay Research center

description: replicate 2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray 4x44K v3 (Probe Name version) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Pituitary, P7_T

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Pituitary of lactating Wistar rats at postpartum day 7

extract_protocol: Total RNA was extracted using RNeasy kits (QIAGEN).

treatment_protocol: The tissues were immediately immersed in RNAlater stabilization reagent (QIAGEN).

value: Wistar

tag: developmental stage

value: postpartum day 7

tag: agent

value: TCDD

value: pituitary


title: Pituitary, P7_T4

description: replicate 4


title: Pituitary, P7_C3

description: replicate 3

source_name: Pituitary, P7_C

value: control


title: T1_90: Treated  Rep1_90min

description: Treated Fermenter Replicate1_90min sample (pH 6.0)

source_name: Treated  Rep1_90min

value: Caldicellulosiruptor bescii DSM6725 cells


title: CTRL_116_PD_hMeDIP_Seq

description: Brain bank Sample code:C075

value: Brain prefrontal cortex

value: Parkinson’s UK Brain Bank

value: Biological Sample


title: T2_5: Treated  Rep2_5min

description: Treated Fermenter Replicate2_5min sample (pH 6.0)

source_name: Treated  Rep2_5min

value: treated


title: Pituitary, P7_T3

description: replicate 3


title: Pituitary, P7_C4

description: replicate 4


title: M5w_12

description: processed data file: counts.txt


title: CTRL_42_PD_hMeDIP_Seq

description: Brain bank Sample code:C037


title: CTRL_192_PD_hMeDIP_Seq

description: Brain bank Sample code:5657

value: Maryland


title: Pituitary, P7_C1

description: replicate 1


title: Pituitary, P7_T1

description: replicate 1


title: T1_30: Treated  Rep1_30min

description: Treated Fermenter Replicate1_30min sample (pH 6.0)

source_name: Treated  Rep1_30min


title: T1_10: Treated  Rep1_10min

description: Treated Fermenter Replicate1_10min sample (pH 6.0)

source_name: Treated  Rep1_10min

value: 10 min


title: Hypothalamus, P7_T4_Th

description: replicate 4

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray 4x44K v3 (Probe Name version) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

source_name: Hypothalamus, P7_T

growth_protocol: Hypothalamus of lactating Wistar rats at postpartum day 7

value: Hypothalamus


title: CTRL_201_PD_hMeDIP_Seq

description: Brain bank Sample code:899

value: M

value: Michigan


title: M39w_10

description: processed data file: counts.txt

source_name: N. furzeri brain

value: brain

value: 39 wph


title: M39w_6

description: processed data file: counts.txt


title: M39w_9

description: processed data file: counts.txt


title: CTRL_139_PD_hMeDIP_Seq

description: Brain bank Sample code:PD030

value: hMeDIP DNA


title: Hypothalamus, P7_T3_Th

description: replicate 3

value: Wistar

value: postpartum day 7


title: T1_60: Treated  Rep1_60min

description: Treated Fermenter Replicate1_60min sample (pH 6.0)

source_name: Treated  Rep1_60min


title: T1_5: Treated  Rep1_5min

description: Treated Fermenter Replicate1_5min sample (pH 6.0)

source_name: Treated  Rep1_5min

value: 5 min


title: M39w_8

description: processed data file: counts.txt


title: CTRL_195_PD_hMeDIP_Seq

description: Brain bank Sample code:5661


title: C3_90: Control  Rep3_90min

description: Control Fermenter Replicate3_90min sample (pH 7.2)

source_name: Control  Rep3_90min

value: control

value: 90 min


title: C3_60: Control  Rep3_60min

description: Control Fermenter Replicate3_60min sample (pH 7.2)

source_name: Control  Rep3_60min

value: Caldicellulosiruptor bescii DSM6725 cells


title: CTRL_196_PD_hMeDIP_Seq

description: Brain bank Sample code:5824

value: Brain prefrontal cortex


title: M12w_5

description: processed data file: counts.txt

value: 12 wph


title: M12w_3

description: processed data file: counts.txt


title: M12w_4

description: processed data file: counts.txt


title: C3_30: Control  Rep3_30min

description: Control Fermenter Replicate3_30min sample (pH 7.2)

source_name: Control  Rep3_30min

value: 30 min


title: Hypothalamus, P7_T2_Th

description: replicate 2

value: TCDD


title: CTRL_184_PD_hMeDIP_Seq

description: Brain bank Sample code:HctZZJ

value: Miami

value: Biological Sample


title: M12w_1

description: processed data file: counts.txt


title: CTRL_108_PD_hMeDIP_Seq

description: Brain bank Sample code:AN10592

value: M

value: Harvard


title: PEC CD102+F4/80+ Male 1

source_name: Peritoneal exudate cells

value: single CD45+ SiglecF- CD19- CD3- Ly6G- CD102+


title: C3_10: Control  Rep3_10min

description: Control Fermenter Replicate3_10min sample (pH 7.2)

source_name: Control  Rep3_10min

value: 10 min


title: G5w_4

description: processed data file: counts.txt

value: GRZ

value: brain

value: 5 wph


title: C3_5: Control  Rep3_5min

description: Control Fermenter Replicate3_5min sample (pH 7.2)

source_name: Control  Rep3_5min

value: 5 min


title: G5w_3

description: processed data file: counts.txt


title: G5w_2

description: processed data file: counts.txt


title: Hypothalamus, P7_C4_Th

description: replicate 4

source_name: Hypothalamus, P7_C

value: Wistar

value: postpartum day 7

value: control

value: Hypothalamus


title: G5w_1

description: processed data file: counts.txt


title: CTRL_36_PD_hMeDIP_Seq

description: Brain bank Sample code:C008

value: F

value: Brain prefrontal cortex

value: hMeDIP DNA

value: UK Multiple Sclerosis Tissue Bank


title: PANC1

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence ends using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 16
The fist and the last 4 bases were trimmed off, since the manufacturer’ protocol appended 4 bases at the beginning and the end of the miRNA sequences. This was performed using Cutadapt (v 1.14) with parameters -m 16 -u 4/-4
Trimmed reads were mapped against the human genome (hg38 UCSC) usingBowtie2 (v 2.3.2) with parameters -N 1 --un-gz -p 6
alignments were sorted using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -s 1 -t miRNA -g ID and miRBase annotations (v 21, GRCh 38)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file containing CPM values

source_name: pancreas cancer derived cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
50ng of total RNA served as input using the NEXTflex Small RNA Library Prep Kit v3 (Bioo Scientific). Sequencing was performed on the Illumina HighSeq 2000 platform
small RNA-Seq

treatment_protocol: 48 hours upon seeding cells were harvested for RNA extraction.

tag: cell line

tag: sirna

value: parental cell line

tag: passages

value: harvested 48h upon seeding


title: MV3

source_name: melanoma derived cell line


title: CTRL_152_PD_hMeDIP_Seq

description: Brain bank Sample code:C054

tag: Sex

value: M

value: Parkinson’s UK Brain Bank

value: Biological Sample


title: C2_90: Control  Rep2_90min

description: Control Fermenter Replicate2_90min sample (pH 7.2)

source_name: Control  Rep2_90min

value: Caldicellulosiruptor bescii DSM6725 cells

value: 90 min


title: CTRL_176_PD_hMeDIP_Seq

description: Brain bank Sample code:AN14074

tag: pmi

value: Harvard


title: MB_FLI_22_IV_brain_RNAseq

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step.
Reads were mapped using STAR (2.4.1d).
Reads per gene were counted using featureCounts (1.4.6-p4).
Counts were normalized to RPKM values as described in Mortazavi et al. (2008).
Genome_build: genome v20150522 and annotation v20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
Supplementary_files_format_and_content: The Excel files include raw counts (sample_counts.xls) and RPKM values (sample_rpkms.xls) of all genes for each sample.

source_name: brain

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.

value: brain

value: 26 weeks

value: male


title: C2_60: Control  Rep2_60min

description: Control Fermenter Replicate2_60min sample (pH 7.2)

source_name: Control  Rep2_60min

value: control


title: CTRL_50_PD_hMeDIP_Seq

description: Brain bank Sample code:AN19145

tag: braak stage


title: Hypothalamus, P7_T1_Th

description: replicate 1

value: Wistar

value: postpartum day 7

value: TCDD

value: Hypothalamus


title: CTRL_173_PD_hMeDIP_Seq

description: Brain bank Sample code:AN10329

value: F

value: Brain prefrontal cortex

tag: molecule subtype

value: hMeDIP DNA


title: C2_10: Control  Rep2_10min

description: Control Fermenter Replicate2_10min sample (pH 7.2)

source_name: Control  Rep2_10min

value: 10 min


title: Hypothalamus, P7_C2_Th

description: replicate 2


title: MB_FLI_22_III_brain_RNAseq


title: C2_30: Control  Rep2_30min

description: Control Fermenter Replicate2_30min sample (pH 7.2)

source_name: Control  Rep2_30min

value: 30 min


title: Hypothalamus, P7_C3_Th

description: replicate 3


title: Hypothalamus, P7_C1_Th

description: replicate 1


title: RV

last: Dong

address: 30 Shuangqing Rd

institute: Tsinghua University

description: TH1 cells infected with empty retrovirus vector

hyb_protocol: Arrays were hybridized for 17 hours at 65 degrees Celsius.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2505C US91203659. Numerical results were extracted with Feature Extraction version 10.7.1.Grid: 028005_D_F_20140728; Protocol: GE1_107_Sep09.

data_processing: Feature extraction data processing (version 10.7.3.1)

growth_protocol: Infected CD4+ T cells were cultured in TH1 polarizing condition (20 ng/ml IL-12, 5 μg/ml anti-IL-4, and 40 U/ml IL-2) for 72 hours.

extract_protocol: Total RNA was extracted from sorted GFP positive cells using a RNeasy Mini kit from Qiagen.

treatment_protocol: Isolated naive CD4+CD25−CD62LhiCD44lo T cells from 8-week-old C57BL/6 mice were activated with plate-bound anti-CD3 and anti-CD28 (2μg/ml each). 20 hours later, the supernatant with virus particle (RV or RV-FoxO4) was added, and spin transduction was performed in the presence of polybrene (8μg/ml) at 2,000 rpm for 90 minutes at 30℃

value: Spleen and lymph nodes

tag: cell type

value: TH1 cells


title: RV-FoxO4

description: TH1 cells infected with retrovirus expressing FoxO4


title: C2_5: Control  Rep2_5min

description: Control Fermenter Replicate2_5min sample (pH 7.2)

source_name: Control  Rep2_5min

value: Caldicellulosiruptor bescii DSM6725 cells

value: 5 min


title: CTRL_57_PD_hMeDIP_Seq

description: Brain bank Sample code:PD026

tag: brain bank

value: Parkinson’s UK Brain Bank

tag: replicate

value: Biological Sample


title: MB_FLI_22_II_brain_RNAseq

tag: strain

tag: tissue

value: brain

value: 26 weeks

value: male


title: A549

source_name: lung cancer derived cell line

value: parental cell line

value: harvested 48h upon seeding


title: PCV2-3

city: Hangzhou

first: Jin

last: He

address: Yuhangtang Road No.866

institute: Zhejiang University

description:
PCV2 infected cells
processed data file: Normalized dataset.xls

data_processing:
Reads were trimmed to remove the bases with low quality and adapter sequences.
The trimmed reads were aligned to the pig reference genome using Hisat2.
Gene expression levels were quantified using the featureCounts.
Differentially expressed genes between NC and PCV2 infection group were selected by DESeq2 with Padj. <0.05 and fold change (FC) of >1.2 or <0.0.83.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Normalized dataset.xls: Excel file includes FPKM for each sample.

organism: Sus scrofa

source_name: PK-15 cell line

extract_protocol:
Total RNA was isolated using the Mini Best Universal RNA Extraction kit (Takara, Dalian, China).
rRNAs were depleted with RNA sample purification beads, which employ an RNaseH-based method. Then, the RNA was fragmented and reverse transcribed. The cDNA library was subjected to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.

value: Kidney cell line

tag: infection

value: Porcine Circovirus type 2 (PCV2)


title: C1_90: Control  Rep1_90min

description: Control Fermenter Replicate1_90min sample (pH 7.2)

source_name: Control  Rep1_90min

tag: setup

value: control

tag: time-point

value: 90 min


title: CTRL_22_PD_hMeDIP_Seq

description: Brain bank Sample code:PD700

value: F

tag: age

value: Brain prefrontal cortex

value: hMeDIP DNA


title: MB_FLI_22_I_brain_RNAseq


title: PCV2-2


title: CTRL_32_PD_hMeDIP_Seq

description: Brain bank Sample code:PD023


title: MB_FLI_6_IV_brain_RNAseq

value: 6 weeks


title: MB_FLI_6_III_brain_RNAseq


title: con-3

description:
Negative Control
processed data file: Normalized dataset.xls

value: Mock


title: C1_60: Control  Rep1_60min

description: Control Fermenter Replicate1_60min sample (pH 7.2)

source_name: Control  Rep1_60min

value: Caldicellulosiruptor bescii DSM6725 cells


title: CTRL_194_PD_hMeDIP_Seq

description: Brain bank Sample code:5572

value: Maryland


title: CTRL_149_PD_hMeDIP_Seq

description: Brain bank Sample code:C022

value: UK Multiple Sclerosis Tissue Bank

value: Biological Sample


title: C1_10: Control  Rep1_10min

description: Control Fermenter Replicate1_10min sample (pH 7.2)

source_name: Control  Rep1_10min

value: 10 min


title: MB_FLI_6_II_brain_RNAseq

value: brain

value: male


title: CTRL_166_PD_hMeDIP_Seq

description: Brain bank Sample code:4431

value: Sepulveda


title: MB_FLI_6_I_brain_RNAseq


title: con-2

value: Kidney cell line


title: C1_5: Control  Rep1_5min

description: Control Fermenter Replicate1_5min sample (pH 7.2)

source_name: Control  Rep1_5min

value: 5 min


title: con-1


title: MEF_WT_3

status: Public on Jun 18 2020

city: Houston

first: Margarida

last: Almeida Santos

state: Texas

address: 1515 Holcombe Blvd Mail code 1000

department: Epigenetics and Molecular Carcinogenesis

institute: UT MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
The reads were mapped to the mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENECODE Release M17 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.18.0).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq) for all the samples.

growth_protocol: Cells were grown in 10cm plates with RPMI 1640 media and corresponding treatment for 6 days

extract_protocol:
RNA was purified using a QIAGEN Rneasy mini kit
Libraries were made using an Illumina TruSeq stranded mRNA kit

treatment_protocol: Cells were treated for 6 days before harvest. CARM1 inhibitor was used at 1uM concentrations. 4-OHT was used at 2uM concentrations.

value: mouse embryonic fibroblast

tag: genotype

value: CARM1f/f ER-Cre

tag: treatment


title: MEF_KO_1


title: MEF_CARM1i_3

value: CARM1 inhibitor TP-064


title: MEF_WT_1


title: MEF_KO_2


title: MEF_KO_3


title: MEF_WT_2


title: MEF_CARM1i_2


title: MEF_CARM1i_1


title: bladder_881s_K9

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using SingleCellExperiment, pagoda2 and monocle packages in R-software
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

source_name: male mouse

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse bladder in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard SmartSeq2 protocol

value: bladder

value: PdgfrbGFP

value: 10-20 weeks

tag: cluster


title: Pituitary, P7_C2

description: replicate 2

source_name: Pituitary, P7_C

value: Wistar

tag: developmental stage

value: postpartum day 7

tag: agent

value: control

value: pituitary


title: C1_30: Control  Rep1_30min

description: Control Fermenter Replicate1_30min sample (pH 7.2)

source_name: Control  Rep1_30min

value: Caldicellulosiruptor bescii DSM6725 cells

value: 30 min


title: bladder_881s_K22

tag: Sex


title: bladder_881s_K6


title: bladder_881s_K4


title: bladder_881s_K7


title: bladder_881s_K5


title: bladder_881s_K21


title: bladder_881s_K3


title: bladder_881s_K23


title: PCV2-1

tag: cell line

value: Porcine Circovirus type 2 (PCV2)


title: bladder_881s_K24

value: male


title: bladder_881s_K2


title: bladder_881s_K20


title: bladder_881s_K18


title: bladder_881s_K19


title: bladder_881s_K16


title: bladder_881s_K14


title: bladder_881s_K10


title: bladder_881s_K8


title: bladder_881s_K17


title: bladder_881s_K1


title: bladder_881s_J24


title: bladder_881s_J21


title: bladder_881s_J4


title: bladder_881s_K13


title: bladder_881s_K15


title: bladder_881s_J19


title: bladder_881s_J15


title: bladder_881s_J7


title: bladder_881s_J16


title: bladder_881s_J9


title: bladder_881s_J17


title: bladder_881s_J5


title: bladder_881s_K11


title: bladder_881s_J2


title: bladder_881s_J6


title: bladder_881s_J3


title: bladder_881s_J11


title: bladder_881s_J10


title: bladder_881s_J23


title: bladder_881s_J22


title: bladder_881s_J18


title: bladder_881s_J20


title: bladder_881s_I7


title: bladder_881s_J13


title: bladder_881s_J8


title: bladder_881s_I6


title: bladder_881s_J12


title: bladder_881s_K12


title: bladder_881s_J1


title: bladder_881s_I8


title: bladder_881s_I3


title: bladder_881s_I4


title: bladder_881s_I23


title: bladder_881s_I24


title: bladder_881s_J14


title: bladder_881s_I2


title: bladder_881s_I5


title: bladder_881s_I19


title: bladder_881s_I18


title: bladder_881s_I16


title: bladder_881s_I20


title: bladder_881s_I21


title: bladder_881s_I15


title: bladder_881s_I9


title: bladder_881s_I22


title: bladder_881s_I14


title: bladder_881s_I12