title: P23_non-metaplastic tumor


title: P17_non-metaplastic tumor

status: Public on Jun 25 2021

type: SRA

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

country: USA

institute: University of Texas

library_source: transcriptomic

data_processing:
We verified the quality of sequence reads using FastQC.
We aligned the reads to the human transcriptome using the hg19 assembly and a GTF of RefSeq genes.
We estimated the transcripts per million using RSEM with the STAR aligner.
Estimated expression values were used for post-analysis and visualization using custom software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of gene expression transcripts per million for RefSeq protein coding transcriptome

molecule: total RNA

organism: Homo sapiens

source_name: treatment-naïve non-metaplastic tumor

extract_protocol:
To perform deep sequencing of RNA (RNA-seq), total RNA was isolated from tumors, treated with Dnase I, and depleted of cytoplasmic and mitochondrial ribosomal RNA using Ribo-Zero Gold.
TruSeq Stranded Total RNA

tag: subject status

value: triple-negative breast cancer patient

tag: tissue

value: treatment-naive triple negative breast cancer tumor

tag: is metaplastic

value: N

tag: subtype

tag: response

value: RCB - II


title: 519MEF_m6Aseq_techRepl_1_input

city: Rehovot

first: David

last: Dierks

state: Central District

address: Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Library strategy: m6Aseq2
alignment using STAR (V. 2.5.3a)
bam2ReadEnds.R (Garcia-Campos et al. 2019) paired-end alignment to the transcriptome (SK1, mm9 gene annotation)
Genome_build: SK1, NCBI37/mm9

molecule: polyA RNA

organism: Mus musculus

source_name: mus musculus

growth_protocol: MEFs cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Biological industries, 01-052-1A) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
For mEF cells, total RNA was extracted using Nucleozol (Macherey-Nagel, 740404.200).
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)

tag: background

value: WT

tag: antibody


title: 519MEF_m6Aseq_techRepl_2_IP

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: SingleRepA_m6A_IP

data_processing:
Library strategy: m6Aseq
alignment using STAR (V. 2.5.3a)
bam2ReadEnds.R (Garcia-Campos et al. 2019) paired-end alignment to the transcriptome (SK1, mm9 gene annotation)
Genome_build: SK1, NCBI37/mm9

organism: Saccharomyces cerevisiae

source_name: yeast strain

growth_protocol: Yeast total RNA samples were prepared by MasterPure Yeast RNA extraction kit and subsequent 2-time polyA-selection according to manufacturers protocol. m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)

extract_protocol:
Yeast total RNA samples were prepared by MasterPure Yeast RNA extraction kit (Lucigen, MPY03100).
m6A-seq: Fragmentation, 3' adapter ligation, m6A-IP, cDNA synthesis, second adapter ligation and enrichment


title: P13_non-metaplastic tumor


title: SingleRepC_m6A_IP


title: 519MEF_m6Aseq_techRepl_2_Input


title: P16_non-metaplastic tumor

value: UNS


title: SingleRepA_m6A_Input


title: P14_non-metaplastic tumor

value: RCB - III


title: P15_non-metaplastic tumor

value: IM


title: 10A: vax010_063_d21_L4

city: Palo Alto

first: Florian

last: Wimmers

state: CA

address: 1651 Page Mill Road

department: School of Medicine

institute: Stanford University

library_source: genomic

data_processing:
CellRanger-ATAC (v1.1.0) count functionality was used for alignment, deduplication, demultiplexing, and identification of cut sites. All lanes related to each sample were analyzed jointly.
CellRanger-ATAC (v1.1.0)'s aggr function was then used to aggregate samples without depth normalization (--normalize=none)
The resulting fragment file was read into SnapATAC (v1.0). Cells were called as barcodes with at least 1000 UMIs and a promotor ratio (defined as: (fragments in promoter regions + 1) / (total fragments + 1)) of at least 0.1. Reads were mapped into 5kb bins to create a bin-by-cell matrix.
SnapATAC was then used to identify clusters from the cell-by-bin matrix, then peaks were called (MACS2 v2.2.7.1) separately for each cluster and joined for a joined set of peaks.
Fragments were mapped to the joined set of peaks for each cell barcode to create the peak-by-cell matrix.
deeply-sequenced libraries were downsampled to an average of 1500 fragments per barcode by randomly removing counts from these samples at a probability p=1500/(mean fragments per cell in the sample)
Genome_build: hg38
Supplementary_files_format_and_content: TIV_scATAC_counts.mtx.gz: raw count matrix
Supplementary_files_format_and_content: TIV_scATAC_meta.tsv: tab-seperated cell annotations
Supplementary_files_format_and_content: TIV_scATAC_peaks.bed: peaks in bed format

molecule: genomic DNA

source_name: monocytes and dendritic cells

extract_protocol:
Cryopreserved PBMCs were thawed and innate immune cell subsets were isolated using FACS. Within the live gated cells, CD14+ monocytes were identified as CD14+ (fraction A) while a mixture of the remaining monocyte and dendritic cell subsets was identified as CD14-CD56-HLA-DR+ (fraction B). After sorting and depending on the number of isolated cells, fraction A and B were mixed at a 2:1 ratio to yield a solution of monocytes and dendritic cells enriched for CD14- cells.
FACS-purified cells were processed for single nuclei ATAC-seq according to the manufacturer’s instructions (10x Genomics, CG000168 Rev D). Briefly, nuclei were obtained by incubating PBMCs for 3.20 minutes in freshly prepared Lysis buffer following manufacturer’s instructions for Low Cell Input Nuclei Isolation (10x Genomics, CG000169 Rev C). Nuclei were washed and resuspended in chilled diluted nuclei buffer (10x Genomics, 2000153). Next, nuclei were subjected to transposition for 1h at 37C on the C1000 touch PCR instrument (BioRad) prior to single nucleus capture on the 10x Chromium instrument. Samples were subjected to post GEM cleanup, sample index PCR, cleanup and library QC prior to sequencing according to the protocol. Samples were pooled, quantified and sequenced on NovaSeq 6000 instrument (Illumina) with at least minimum recommended read depth (25000 read pairs/nucleus).

tag: subject

tag: time point

tag: experiment

tag: vaccine group

tag: lane

value: monocytes and dendritic cells


title: 10A: vax010_063_d21_L2


title: 10A: vax010_063_d21_L1


title: P12_non-metaplastic tumor

value: MSL


title: 2A: vax010_062_d21_L8


title: 519MEF_m6Aseq2_techRepl_5_IP


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in glycerol and induced with galactose

city: Seattle

first: Monica

middle: S

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

description: Strains were grown in YEP+2% glycerol to OD 0.5, and 2% galactose was added. Cells were grown for 6 hr (maintaining OD <1.0) and RNA was extracted and processed into sequencing libraries as described.

data_processing:
Reads were aligned to SacCer3 using bowtie2 with default parameters with duplicated reads filtered out.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
To calculate mRNA abundance, a pseudocount was added to all positions and the number of reads mapped to a gene was divided by the length of the gene and normalized to yield the mean number of reads per kilobase per million sequencing reads (RPKM).
Genome_build: SacCer3
Supplementary_files_format_and_content: Tab delimited files, columns containing index positions, chromosome, chromosome positions, number of reads, and normalized number of reads. For RNA-seq, two files are provided, one for forward and reverse strand.

source_name: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in exponential phase, grown in glycerol and induced with galactose

growth_protocol: Strains were grown in YEP with indicated carbon souce to specified OD and 2 % galactose was added for 6 hr for GapR induction.

extract_protocol:
RNA was extracted by hot phenol method followed by gDNA removal and mRNA enrichment using poly(dT) pulldown with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were processed as previously reported (Culviner and Laub, 2018).

treatment_protocol: Cells were induced with 2 % galactose for 6 hr.

tag: growth stage

value: exponential phase

tag: strain

tag: media

value: YEP + 2% glycerol


title: 10A: vax010_063_d21_L3


title: 519MEF_m6Aseq2_techRepl_5_Input


title: 2A: vax010_062_d21_L7


title: ML3287 (OAY470), in raffinose and induced with galactose, replicate 1

description: Strains were grown in YEP+2% raffinose to OD 0.05, and 2% galactose was added. Cells were grown for 6 hr (maintaining OD <1.0) and RNA was extracted and processed into sequencing libraries as described.

source_name: ML3287 (OAY470) in exponential phase, grown in raffinose and induced with galactose

value: YEP + 2% raffinose


title: 2A: vax010_062_d21_L6


title: 10A: vax010_063_d21_L5


title: P11_metaplastic tumor

source_name: treatment-naïve metaplastic tumor

value: Y

value: M


title: 519MEF_m6Aseq2_techRepl_4_IP


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in raffinose, alpha-factor arrested, and induced with galactose, replicate 1

description: Strains were grown in YEP+2% raffinose to OD 0.3, alpha-factor was added to 1 μg/mL for 2 hr, and 2% galactose was added. Cells were grown for 6 hr (maintaining OD <1.0) and RNA was extracted and processed into sequencing libraries as described.

source_name: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in exponential phase, grown in raffinose, alpha-factor arrested, and induced with galactose

value: YEP + 2% raffinose + alpha-factor


title: ML3287 (OAY470), in raffinose and induced with galactose, replicate 2


title: 519MEF_m6Aseq_techRepl_1_IP


title: P10_non-metaplastic tumor

value: triple-negative breast cancer patient

value: LAR


title: 2A: vax010_062_d21_L5


title: 519MEF_m6Aseq2_techRepl_4_Input


title: 519MEF_m6Aseq2_techRepl_3_IP


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in raffinose and induced with galactose, replicate 1

source_name: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in exponential phase, grown in raffinose and induced with galactose


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in raffinose and induced with galactose, replicate 2

description: Strains were grown in YEP+2% raffinose to OD 0.05, and 2% galactose was added. Cells were grown for 6 hr (maintaining OD <1.0) and RNA was extracted and processed into sequencing libraries as described


title: P05_non-metaplastic tumor

value: treatment-naive triple negative breast cancer tumor

value: N

value: RCB - I


title: P07_non-metaplastic tumor

value: RCB - 0


title: 519MEF_m6Aseq2_techRepl_3_Input

value: WT


title: 519MEF_m6Aseq2_techRepl_2_IP

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: P08_metaplastic tumor

value: IM

value: RCB - II


title: 2A: vax010_062_d21_L3

value: monocytes and dendritic cells


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG), in raffinose, alpha-factor arrested, and induced with galactose, replicate 2

value: exponential phase


title: 2A: vax010_062_d21_L1


title: P04_metaplastic tumor

value: RCB - III


title: 519MEF_m6Aseq2_techRepl_1_Input


title: 519MEF_m6Aseq2_techRepl_1_IP


title: 2A: vax010_062_d21_L4


title: P03_non-metaplastic tumor


title: P02_non-metaplastic tumor

value: MSL


title: 6A: vax010_061_d21_L6


title: 6A: vax010_061_d21_L7


title: DMQ3: Doxo and MitoQ-treated RNA-seq

city: Fort Collins

first: Alyssa

middle: N

last: Cavalier

state: CO

address: 1582 Campus Delivery, Moby Reception

department: Health and Exercise Science

institute: Colorado State University

data_processing:
Adapters trimmed & file QC by Fastp
Reads aligned with STAR and counting with LiBiNorm
Differential expression analyzed with DESeq2
Genome_build: mm10

source_name: Postmortem hippocampus

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns.
PolyA libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit

value: Postmortem hippocampus

tag: treatment

value: Doxo and MitoQ-treated


title: P09_metaplastic tumor

value: Y

value: UNS


title: DMQ2: Doxo and MitoQ-treated RNA-seq


title: 519MEF_m6Aseq2_techRepl_2_Input


title: P06_non-metaplastic tumor

value: triple-negative breast cancer patient


title: 2A: vax010_062_d21_L2


title: P01_non-metaplastic tumor

value: treatment-naive triple negative breast cancer tumor


title: DMQ1: Doxo and MitoQ-treated RNA-seq


title: 6A: vax010_061_d21_L8


title: 6A: vax010_061_d21_L5


title: 6A: vax010_061_d21_L4


title: DOX_3: Doxo-treated RNA-seq

value: Doxo-treated


title: DOX_1: Doxo-treated RNA-seq


title: RNAseq_HGPS_hMSC_GA_rep3

city: Beijing

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

country: China

institute: institute of zoology, CAS

description: RNA sequencing of GA-treated HGPS hMSCs

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human genome using hisat2 software.
Genome_build: hg19 for Homo sapiens
Supplementary_files_format_and_content: Txt file of read count for RNA-seq.

source_name: Mesenchymal stem cell

extract_protocol: For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: cell type

value: Hutchinson-Gilford progeria syndrome (HGPS) mesenchymal stem cells

value: GA-treated

tag: passage/tissue


title: DOX_2: Doxo-treated RNA-seq

tag: tissue


title: RNAseq_HGPS_hMSC_GA_rep1

description: RNA sequencing of GA-treated HGPS hMSCs


title: RNAseq_HGPS_hMSC_GA_rep2

description: RNA sequencing of GA-treated HGPS hMSCs


title: 6A: vax010_061_d21_L3


title: 6A: vax010_061_d21_L2


title: 6A: vax010_061_d21_L1


title: RNAseq_HGPS_hMSC_DMSO_rep2

description: RNA sequencing of DMSO-treated HGPS hMSCs

value: DMSO-treated


title: 7A: vax010_012_d21_L7


title: DOX_SH3: Sham RNA-seq

value: Sham


title: RNAseq_HGPS_hMSC_DMSO_rep3


title: DOX_SH1: Sham RNA-seq


title: 7A: vax010_012_d21_L6


title: RNAseq_WS_hMSC_GA_rep3

description: RNA sequencing of GA-treated WS hMSCs

value: Werner syndrome (WS) mesenchymal stem cells


title: 7A: vax010_012_d21_L8


title: PreDC-rep3

city: Research Triangle Park

first: Sara

middle: A

last: Grimm

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

data_processing:
Raw reads were filtered to retain only those with average base quality score >20.
Reads were aligned to mm10 via STAR v2.5 (parameters: --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical).
Read counts per gene were determined by Subread featureCounts v1.5.0-p1 (parameters: -s0).
Coverage tracks were generated by STAR v2.5 (parameters: --outWigStrand Unstranded --outWigNorm None), normalized by DESeq2 size factors, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: normalized depth tracks in bigWig format; RNAseq counts per gene in tab-delimited text format

source_name: Lung

extract_protocol:
RNA was isolated via NucleoSpin RNA XS kit (Takara Bio) following the manufacturer's instruction.
Libraries were constructed via Illumina TruSeq RNA sample prep kit.

tag: Sex

value: male

value: FACS-purified bone marrow preDCs

tag: treatment condition

value: Steady state


title: PreDC-rep2


title: 7A: vax010_012_d21_L5

value: monocytes and dendritic cells


title: RNAseq_WS_hMSC_GA_rep2

description: RNA sequencing of GA-treated WS hMSCs


title: RNAseq_WS_hMSC_GA_rep1

description: RNA sequencing of GA-treated WS hMSCs


title: 7A: vax010_012_d21_L4


title: PreDC-rep1


title: RNAseq_HGPS_hMSC_DMSO_rep1


title: DOX_SH2: Sham RNA-seq


title: 7A: vax010_012_d21_L3


title: MONO-rep3

value: FACS-purified lung monocytes


title: RNAseq_WS_hMSC_DMSO_rep2

description: RNA sequencing of DMSO-treated WS hMSCs


title: 7A: vax010_012_d21_L2


title: MONO-rep2


title: RNAseq_WS_hMSC_DMSO_rep3

description: RNA sequencing of DMSO-treated WS hMSCs


title: RNAseq_WS_hMSC_DMSO_rep1

description: RNA sequencing of DMSO-treated WS hMSCs


title: MONO-rep1


title: 8A: vax010_063_d0_L8


title: PI3

city: Chiba City

first: Kazumasa

last: Suzuki

state: Chiba

address: 1-8-1 Inohana

department: Department of Allergy and Clinical Immmunology

country: Japan

institute: Chiba University

data_processing:
Illumina adapters and low-quality reads were trimmed using FASTX-toolkit (ver 0.0.13). Quality-controlled reads were mapped to mouse mm10 genome.
Expression levels were measured and normalized using Strand NGS.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: Vg4+Vd4+gdT cells from NF-kB1 deficient mice treated with imiquimod cream

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-seq libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina (FWD)

value: skin-draining lymph nodes

tag: genotype

value: NF-kB1 deficient mice

value: imiquiod cream


title: MONO-HDE-rep3

value: House dust extract and ovalbumin instillaton, 16 hrs


title: NCH644-KDM5Csh1

type: RNA

city: Heidelberg

first: Violaine

last: GOIDTS

address: IM NEUENHEIMER FELD, 580

country: Germany

institute: DKFZ

description: stable cell line

hyb_protocol: After fragmentation, labeled cRNA was incubated on Human Genome U133 Plus 2.0 chips (Affymetrix) for 16hrs at 45°C according to the manufacturers instructions.

scan_protocol: Microarray scanning was done using an Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The affy R package (from Bioconductor) was used to pre-process the microarray dataset followed by normalization with Robust Microarray Analysis (RMA) approach. Probe sets were filtered based on the MAS5 ‘detection calls’ by the criteria that probe sets flagged as ‘absent’ in all the samples were discarded.

label: biotin

source_name: Gliobastoma stem-like cells (NCH644)

label_protocol: After creating double stranded cDNA reverse transcription of biotin-labeled cRNA was performed according to the GeneChipTM 3' IVT PLUS Reagent Kit Manual

extract_protocol: Cells were havested and RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: NCH644 cells transfected with inducible shRNAs were grown and then induced by incubation with 2 μg ml−1 doxycycline for 5 days

tag: cell line

value: Gliobastoma stem-like cells (NCH644)

value: control


title: NCH644-KDM5Csh2

description: stable cell line


title: NCH644-KDM5Csh2+dox

description: stable cell line

value: KDM5C KD


title: NCH644-nt+dox

description: stable cell line

value: nt+dox


title: NCH644-KDM5Csh1+dox

description: stable cell line


title: NCH644-KDM5Ash2+dox

description: stable cell line

value: KDM5A KD


title: MONO-HDE-rep2


title: PI2


title: 8A: vax010_063_d0_L6


title: NCH644-nt

description: stable cell line

value: nt


title: PI1


title: 8A: vax010_063_d0_L7


title: MONO-HDE-rep1


title: 7A: vax010_012_d21_L1


title: LY6C-HDE-rep3

value: FACS-purified lung CD11b+ Ly-6+ conventional DCs


title: 8A: vax010_063_d0_L4


title: NCH644-KDM5Ash1

description: stable cell line


title: LY6C-HDE-rep2


title: 8A: vax010_063_d0_L5


title: WI1

source_name: Vg4+Vd4+gdT cells from WT mice treated with immiquiod cream

value: wild type


title: 8A: vax010_063_d0_L3


title: LY6C-HDE-rep1

value: male


title: Bo103_5dJQ2_5_days_JQ1_treatment

city: Bochum

first: Stephan

last: Hahn

address: Universitaetsstrasse 150

department: MGO

institute: Ruhr-University Bochum

description: mRNA expression

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions  for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner ( G2505C ) using standard settings

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1 (Agilent) using default parameters (protocol GE1_1200_Jun14_1_3 and Grid: 026652_D_F_20190204) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: patient derived pancreatc cancer xenograft tissue

label_protocol: 100 ng of total RNA were labeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with  cyanine-5-CTP (Cy5)

growth_protocol: Three 1-3 mm tumor pieces of early passage xenograft tumor Bo103 soaked in matrigel were implanted via standard technology subcutaneously on the dorsal flanks of nude mice (two implantation sites per mouse; nu/nu NMRI) to establish treatment and control tumor cohorts.

extract_protocol: Total RNA isolation from 25-30 (20mm) frozen xenograft tumor sections were isolates using the mirVana™ PARIS™ Kit (Applied Biosystems) according to the manufacture`s protocol. RNA integrity was analysed using standard RNA-gel electrophoresis. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: Nude mice were treated  daily with JQ1 (50 mg/kg, MedChem express/ Hycultec) by intra peritoneal (i.p.) injection , treatment was initated when tumor size reached approc. 100-200 mm³

tag: reponse

value: progressive disease

value: JQ1 (50 mg/kg)


title: NCH644-KDM5Ash1+dox

description: stable cell line


title: PC3

source_name: Vg4+Vd4+gdT cells from NF-kB1 deficient mice treated with sham cream

value: sham cream


title: 8A: vax010_063_d0_L1

tag: subject

value: monocytes and dendritic cells


title: PC2

value: skin-draining lymph nodes


title: CD11B-rep2

value: FACS-purified lung CD11b+ Ly-6- conventional DCs

value: Steady state


title: WI3

value: imiquiod cream


title: CD11B-rep1


title: 12A: vax010_062_d0_L8

tag: time point


title: PC1

value: NF-kB1 deficient mice


title: cel-miR-67

city: Klosterneuburg

first: Ryan John

last: Cubero

state: Lower Austria

address: Am Campus 1

country: Austria

institute: IST Austria

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensembl Rattus norvegicus reference genome (GCA_000001895.4 Rnor 6.0.89.6) using STAR 2.7 with default parameters.
Rounded gene counts were normalized to RPKM (reads per kilobase of exon model per million mapped reads) using the rpkm function in the Bioconductor package edgeR  (McCarthy, J. D, Chen, Yunshun, Smyth, K. G (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research, 40(10)).
Genes with RPKM values greater than 2.00 in both miRNA and cel-miR-67 transfected rat CMs were considered as expressed genes.
Fold changes were taken with respect to the expression upon cel-miR-67 transfection (control condition). Genes whose expression fold change were greater than 1.3 were considered as differentially expressed.
Genome_build: Rnor 6.0.89.6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

organism: Rattus norvegicus

source_name: Cardiomyocyte

growth_protocol: Neonatal rat cardiomyocytes were grown in the Dulbecco's modified Eagle medium 4.5 g/l glucose (DMEM, Life Technologies) supplemented with 5% FBS, 20 mg/ml vitamin B12 (Sigma) and with 100 U/ml of penicillin and 100 mg/ml of streptomycin (Sigma) at 37°C in 5% CO2 and humidified atmosphere.

extract_protocol:
Cardiomyocyte cultures were isolated by enzymatic dissociation of 1 day-old neonatal rat hearts. Neonatal cardiomyocytes were seeded on Primaria 10 cm dishes and one day later, cells were transfected with mimics (Life Technologies) of hsa-miR-106b-5p, hsa-miR-93-5p, hsa-miR-25-3p or cel-miR-67 as control (25mM) using (Lipofectamine RNAiMAX, Life Technologies) and 72 hrs later RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ventricular CMs were isolated from neonatal rat. Briefly, ventricles from neonatal rat (day 0) were separated from the atria, cut into pieces and then dissociated in calcium and bicarbonate-free Hanks with HEPES (CBFHH) buffer containing 1.75 mg/ml trypsin (BD Difco) and 10 mg/ml DNase II (Sigma), using a mechanical and physical stirring. Digestion was performed at room temperature in ten-min steps with collection of the surnatant to fetal bovine serum (FBS, Life Technologies) after each step. The surnatant was collected and centrifuged to pellet the cardiomyocytes, which were then resuspended in Dulbecco's modified Eagle medium 4.5 g/l glucose (DMEM, Life Technologies) supplemented with 5% FBS, 20 mg/ml vitamin B12 (Sigma) and with 100 U/ml of penicillin and 100 mg/ml of streptomycin (Sigma). The collected cells were passed through a cell strainer (40mm, BD Falcon) and then plated onto 100-mm plastic dishes for 2 hr at 37C in 5% CO2 and humidified atmosphere. Then, the surnatant, which contains mostly cardiomyocytes, was collected and counted.The cells were plated in 60-cm primary dishes at the concentration of 1,5*10^6 cells.The miRNAs were obtained from Dharmacon, Thermo Scientific. After 24 hr miRNAs were transfected into neonatal rat CMs using a standard transfection protocol, at the final concentration of 25 nM. Briefly, the transfection reagent (Lipofectamine RNAiMAX, Life Technologies) was diluted in OPTI-MEM (Life Technologies) and added to the selected miRNAs; 30 min later, each mix, containing the transfection reagents and the miRNAs, was added to the Dulbecco's modified Eagle medium 4.5 g/l glucose (DMEM, Life Technologies) supplemented with 5% FBS and 20 mg/ml vitamin B12 (Sigma) in absence of antibiotics. Twenty-four hours after transfection, culture medium was replaced by fresh medium.

value: Wistar

value: heart

tag: age

value: post natal day 1

value: ventricular cardiomyocytes

value: transfected with cel-miR-67


title: hsa-miR-25-3p

value: transfected with hsa-miR-25-3p


title: CD11B-HDE-rep2

value: House dust extract and ovalbumin instillaton, 16 hrs


title: CD11B-rep3

value: male


title: WI2

value: wild type


title: Bo103_K2_vehicle control

description: mRNA expression

value: progressive disease

value: vehicle


title: 12A: vax010_062_d0_L6

tag: experiment

tag: vaccine group

value: monocytes and dendritic cells


title: WC2

source_name: Vg4+Vd4+gdT cells from WT mice treated with sham cream

value: skin-draining lymph nodes

value: sham cream


title: NCH644-KDM5Ash2

description: stable cell line

value: Gliobastoma stem-like cells (NCH644)

value: control


title: WC3


title: Bo103_5dJQ1_5_days_JQ1_treatment

description: mRNA expression

value: JQ1 (50 mg/kg)


title: CD11B-HDE-rep3

value: FACS-purified lung CD11b+ Ly-6- conventional DCs


title: RNA-Seq Pre_340_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
The RNA-seq reads were aligned to human genome hg19 using Spliced Transcripts Alignment to a Reference (STAR) software version 2.4.0j
featureCounts (v1.4.6-p5) were used to create gene counts
Differential expression analysis of gene counts was performed using the DESeq2 version 1.26.0
Genome_build: human genome hg19
Supplementary_files_format_and_content: text file

source_name: cultured fetal lung fibroblast

growth_protocol: WI-38 fibroblasts were plated in a six-well plate at a density of 1 x 10^5 cells for 24h in DMEM + 20% FBS.

extract_protocol:
RNA was isolated from cells using the TriPure isolation reagent (Roche) and the Direct-zol Mini Kit (Zymo) following the manufacturers’ protocols.
Samples were quantified on a NanoDrop ND-1000 instrument. Agarose electrophoresis was used to check the integrality of total RNA samples. 1 ∼ 2 µg total RNA of each sample was taken for RNA-seq library preparation. Briefly, rRNA is removed from the total RNA with a RiboZero Magnetic Gold Kit; The enriched rRNA depleted RNA was used for RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The library preparation procedure included: 1) Fragmentation of the RNA molecules; 2) Reverse transcription to synthesis first strand cDNA; 3) Second strand cDNA synthesis incorporating dUTP; 4) End-repair and A-tailing of the double stranded cDNA; 5) Illumina compatible adapter ligation; 6) PCR amplification and purification for the final RNA-seq library. The completed libraries were qualified on Agilent 2100 Bioanalyzer for concentration, fragment size distribution between 400 ∼ 600 bp, and adapter dimer contamination. The amount was determined by absolute quantification qPCR method. The barcoded libraries were mixed in equal amounts and used for sequencing on the instrument.

treatment_protocol: Cells were transfected with 50 nM control miRNA or pre-miR-340-5p and cultured for an additional four days, changing media every 48h (DMEM with 20% FBS).

value: Fibroblast

tag: cell culture


title: Bo103_K1_vehicle control

description: mRNA expression


title: hsa-miR-106b-5p

tag: strain

value: Wistar

value: heart

value: post natal day 1

value: transfected with hsa-miR-106b-5p


title: WC1


title: 12A: vax010_062_d0_L7

source_name: monocytes and dendritic cells

tag: lane


title: 12A: vax010_062_d0_L5


title: 12A: vax010_062_d0_L4


title: RNA-Seq Pre_340_2

tag: treatment


title: EXP2.KO.3

city: Iowa City

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

institute: University of Iowa

data_processing:
Reads were aligned to the mm10 genome build using STAR version 020201, with default parameters from bcbio-nextgen version 1.0.7
BAM files were indexed and sorted using SAMtools version 1.6, with default parameters from bcbio-nextgen version 1.0.7
Gene-level counts were quantified using featureCounts version 1.4.4, with default parameters from bcbio-nextgen version 1.0.7
Genome_build: mm10, GENCODE release M14
Supplementary_files_format_and_content: CSV text file containing gene-level counts for all samples

source_name: P35 cortex

extract_protocol:
E10.5 embryonic telencephalon were quickly removed and stored in RNA later at 4C for a maximum of 1 week.  P35 cortex was quickly dissected in cold PBS and RNA immediately extracted.  RNA was extracted using Trizol and purified using mirVana miRNA Isolation Kit (Ambion/Life technologies )
RNA libraries were prepared for sequencing using Illiumina TruSeq Stranded mRNA library prep kit following standard Illumina protocols

value: cortex

value: CAMK

value: KO

tag: group

tag: replicate


title: RNA-Seq Pre_340_1

tag: cell type


title: 12A: vax010_062_d0_L3

tag: tissue


title: CD103-rep3

tag: Sex

value: male

value: FACS-purified lung CD103+ conventional DCs

tag: treatment condition

value: Steady state


title: CD11B-HDE-rep1

value: House dust extract and ovalbumin instillaton, 16 hrs


title: EXP2.KO.2

tag: genotype


title: RNA-Seq Control3

value: control miR


title: EXP2.KO.1


title: 12A: vax010_062_d0_L2

value: monocytes and dendritic cells


title: RNA-Seq Control2


title: EXP2.CONTROL.4

value: CONTROL


title: CD103-rep1


title: CD103-HDE-rep3


title: EXP2.CONTROL.3


title: 1A: vax010_061_d0_L8


title: 1A: vax010_061_d0_L7


title: CD103-rep2


title: 1A: vax010_061_d0_L6


title: EXP2.CONTROL.2


title: 12A: vax010_062_d0_L1


title: EXP2.CONTROL.1

value: WT


title: RNA-Seq Control1


title: 1A: vax010_061_d0_L5


title: 414_m6A_IP_clones_W10H

source_name: mus musculus

tag: background

value: Wtap -/-

tag: antibody

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: KO_3

city: Wuhan

first: Zhuzhen

last: Zhang

state: Hubei

address: 6015Shengke Building, College of life sciences, 299 Bayi Road, Wuchang

department: Biochemistry

institute: Wuhan University

data_processing:
Raw image data file from high-throughout sequencing was transformed to sequenced reads (called raw data or raw reads) by CASAVA base recognition (Base Calling), Q30≥80%
Raw data is atored in FASTQ(fq) format files,Fastq files were checked for quality using fastqc and fastq_screen
Reads were quality filtered. Filtered fastq files were aligned to mouse genome using STAR (v2.5). STAR used the method of maximal mappable prefix (MMP) which can generate a precise mapping result for junction reads.
Htseq v0.6.1 was used to count the read numbers mapped of each gene.
FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effects of sequencing depth and gene length for the reads count at the same time
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited txt files that includes normalized read counts for each sample per gene

source_name: epididymal adipose tissue

extract_protocol:
Epididymal adipose tissues were harvested from Tfrcfl/fl and TfrcAKO mice after 10 weeks HFD feeding. RNA was extracted using Trizol reagent, and purified with the Qiagen RNA purification kit. 1 µg of total DNAse treated RNA is then prepared for the library construction.
RNA libraries were prepared for sequencing using NEBNext UltraTM RNA library Prep Kit.

treatment_protocol: Mice were on 60% high fat diet for 10 weeks

value: epididymal adipose tissue

tag: diet

value: high fat diet for 10 weeks

value: TfrcAKO

value: 4.5 months


title: CD103-HDE-rep1


title: RNA-Seq miR_Control_2

extract_protocol:
RNA was isolated from cells using the TriPure isolation reagent (Roche) and the Direct-zol Mini Kit (Zymo) following the manufacturers’ protocols.
The total RNA purity and quantity were analyzed by RNA 6000 Nano LabChip Kit (Agilent, Palo Alto, CA, USA) and Bioanalyzer 2100 with RIN number >7.0. About 1 μg of RNA was used to construct small RNA library according to the protocol of Illumina’s TruSeq small RNA sample preparation Kits (San Diego, CA, USA). Sequencing was performed on Illumina HiSeq2500 with single-end mode (36bp SE).

treatment_protocol: Cells were transfected with 50 nM control miRNA or anti-miR-340-5p and cultured for an additional four days, changing media every 48h (DMEM with 20% FBS).

value: Fibroblast


title: RNA-Seq miR Control_1

description: miR Control_1


title: 1A: vax010_061_d0_L4

tag: subject

tag: time point


title: 413_m6A_IP_clones_W9A

growth_protocol: Commonly used V6.5 51 mouse embryonic stem cell line was kept in DMEM (Gibco) supplemented with penicillin-streptomycin, 1 mM L-glutamin, 1% non-essential amino acids, 20% high-grade fetal bovine serum, beta-mercaptoethanol and 10 µg recombinant leukemia inhibiting factor (LIF). Cells were kept on tissue culture plates covered by 0.2% gelatin in co-culture with in-house generated, radiation-inactivated mouse embryonic fibroblasts (MEF). For ESCs cells, total RNA was extracted using Nucleozol and subsequent 2-time polyA-selection according to manufacturers protocol.  m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)

extract_protocol:
For mESCs cells, total RNA was extracted using Nucleozol (Macherey-Nagel, 740404.200).
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)


title: 8A: vax010_063_d0_L2

tag: experiment

tag: vaccine group


title: KO_2

tag: strain

tag: age


title: KO_1


title: 412_m6A_IP_clones_M10G

value: Mettl3 -/-


title: ATAC-Seq siLBR_3

data_processing:
The reads were aligned to the hg38 human genome using Bowtie2 version 2.1.0
Data were filtered to remove mitochondrial and non-unique reads
Peaks were called using MACS2 in the BAMPE mode and annotated with ChipSeeker package from Bioconductor
Differential peaks were identified using the EdgeR GLM algorithm in DiffBind and annotated by CHIPpeakAnno package from Bioconductor
Significant Peaks are used to do further Functional Analysis by ChipSeeker on GeneOntology/Reactom Pathway/Kegg Pathway
Genome_build: human genome hg38
Supplementary_files_format_and_content: .xls text file

extract_protocol:
Using 50,000 intact cells as input. Cells were washed and lysed to generate a crude nuclei preparation.
Library for ATAC-seq was prepared according to a published protocol (Buenrostro et al., 2013). Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters.  DNA fragments were PCR amplified and subsequently purified using Qiagen MinElute PCR Purification Kit (Qiagen, Maryland, USA). Final library quality and quantity were analyzed and measured by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) and Life Technologies Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA), respectively. The final libraries were sequenced using 150 bp paired-end reads on Illumina HiSeq Sequencer (Illumnia Inc., San Diego, CA).

treatment_protocol: Cells were transfected with 50 nM control miRNA, pre-miR-340-5p, or siLBR and cultured for an additional four days, changing media every 48h (DMEM with 20% FBS). Cells exposed to 10 Gy of IR were cultured for an additional 10 days.

tag: cell culture

tag: treatment

tag: treatment duration

value: 4 days


title: ATAC-Seq siLBR_2

tag: cell type


title: WT_3

tag: tissue

value: Tfrcfl/fl


title: CD103-HDE-rep2

tag: Sex

value: male

value: FACS-purified lung CD103+ conventional DCs


title: RNA-Seq anti_miR-340-5p_2


title: 1A: vax010_061_d0_L3

tag: lane


title: 1A: vax010_061_d0_L1


title: ATAC-Seq pre-miR-340-5p_4


title: WT_1

tag: genotype


title: RNA-Seq anti_miR-340-5p_1


title: 1A: vax010_061_d0_L2


title: 411_m6A_IP_clones_M10D

tag: background


title: 410_m6A_IP_clones_WT

tag: antibody


title: ATAC-Seq pre-miR-340-5p_3


title: 409_m6A_input_clones_W10H


title: WT_2

tag: diet


title: 3A: vax010_012_d0_L8

tag: subject


title: ATAC-Seq IR_1

value: IR _10 Gy

value: 10 days


title: 407_m6A_input_clones_M10G


title: ATAC-Seq IR_2

value: IR_10 Gy


title: ATAC-Seq miR Control_2

description: miR Control_2

value: control miR


title: C39 M01 WT rep1 Fibroblast

city: Indianapolis

first: Monte

last: Willis

address: 635 Barnhill Street Drive

institute: University of Indiana School of Medicine

description: Sample 17

data_processing:
Kallisto (v0.44.0) count abundance over GENCODE ‘comprehensive gene annotation’ (Release M18) with 50x bootstrap
tximport (v1.6.0) read count input
DESeq2 (v1.18.1) read count normalzation and differential expression analysis
R (v3.4.4) for all other analyses
genome build: GRCm38.p6
processed data files format and content: TSV, raw and normalized counts

source_name: Fibroblast

extract_protocol:
Cardiomyocytes and cardiac fibroblasts were isolated from hearts of 16-month Bag3-P209L Tg+ and age matched Bag3-WT mice. Total RNA was extracted from isolated cardiomyocytes and cardiac fibroblasts using an RNEASY kit (Qiagen).
mRNA was enriched using oligo(dT) beads and randomly fragmented by adding fragmentation buffer. cDNA was then synthesized using an (Illumina) RNA library construction kit. Completed libraries, containing unique Illumina adaptors, were then pooled and fed into HiSeq/MiSeq sequencers. Following initial sequencing, cardiomyocyte samples underwent an additional second round of sequencing to increase the total data output.

tag: replicate


title: C40 M00 WT rep1 Fibroblast

description: Sample 18


title: 3A: vax010_012_d0_L6

tag: time point

tag: experiment

value: monocytes and dendritic cells


title: 3A: vax010_012_d0_L5

tag: vaccine group


title: 406_m6A_input_clones_M10D


title: C37 M10 Tg+ rep1 Fibroblast

description: Sample 15

value: Bag3-P209L Tg+


title: ATAC-Seq miR Control_1

description: miR Control_1


title: 405_m6A_input_clones_WT

value: WT


title: C36 F03 WT rep1 Fibroblast

description: Sample 14


title: 3A: vax010_012_d0_L3


title: Col-0 leaves P120-L

city: Berlin

first: Margarete

last: Baier

address: Königin-Luise-Straße 12-16

department: Institute of Biology

institute: Freie Universität Berlin

description: harvested after 120 min of excess light exposure

data_processing:
All raw reads obtained by cDNA library sequencing were quality controlled with the help of the SOAPnuke software (Chen et al. 2017). Residual adaptor sequences and reads with more than 5 % unclear base pairs were assigned as unclean reads.
The remaining clean reads were aligned to the Arabidopsis reference genome TAIR10 with a phred-value of 64 using HISAT v. 2.1.0 (Kim et al. 2015)
The number of reads for each transcript were normalized against the transcript length and the total number of reads per treatment (Fragments Per Kilobase Million - FPKM).
Genome_build: Arabidopsis genome annotation TAIR10
Supplementary_files_format_and_content: Excell-file including the FPKM values for all samples and all indentified genes

organism: Arabidopsis thaliana

source_name: complette rosette (vegetative state)

growth_protocol: Arabidopsis thaliana (Col-0) plants were grown for 28 days individually in round pots (6 cm diameter) in soil at 20 ± 2 °C at a day - night regime of 10 h light / 14 h dark and an illumination rate of 100-110 μmol quanta m−2 s−1 (Lumilux Cool White fluorescence stripes).

extract_protocol:
For the RNASeq samples, entire rosettes of at least 5 plants were harvested per treatment , combined and immediately frozen in liquid N2 to stabilize the RNA against degradation.
For RNA library construction, the mRNA was enriched using oligo (dT) magnetic beads and depleted from rRNA by DNA/rRNA hybridization according to standard procedures of the Beijing Genomics Institute (Beijing, China). Afterwards, the mRNA was transcribed into cDNA and the second DNA strand was generated with random N6 primer. The double stranded cDNA was then 5´-end repaired, 3´-poly-A-tailed and ligated with an oligo-dT-adapter.

treatment_protocol: For priming, a 24 h cold stimulus was imposed to half of the 4-week-old plants by transferring them 2.5 h after the onset of light to a 4 ± 2 °C cold chamber with the same aeration, illumination and air humidity setting as the 20 °C chamber. Afterwards the primed plants were placed back to 20 °C and further cultivated side-by-side with non-primed plants in a randomized pattern. Cold triggering was started after a lag-phase of 5 days at 20 °C with 40 % of the primed and 40 % of the control plants by transfer of the plants to 4 °C (cold triggering) . For high light triggering, 40 % of the primed and 40 % of the control plants were exposed a photon flux density of 800 µmol quanta m-2 s-1. Samples were harvested after 30, 60 and 120 min of stress exposure. The remaining 20 % of the control and of the cold primed plants were harvested directly at the end of the 5 days lag-phase (C0 and P0) as a control group

tag: ecotype

value: leaves

tag: 1. treatment

value: cold-primed

tag: 2. treatment

value: light-triggered


title: C40 M00 WT rep2 Cardiomyocyte

description: Sample 12


title: mRNA

first: Hideki

last: Nakano

address: 111 TW Alexander Drive

department: Immunity, Inflammation and Disease Laboratory

data_processing:
Alignment, barcode assignment and unique molecular identifier (UMI) counting Alignment, barcode assignment and unique molecular identifier (UMI) counting was performed using Cell Ranger 3.0.1 and the “cellranger count” command. Alignment was performed with the mouse mm10-1.2.0 reference.
The following feature libraries were included for antibody sequencing: Ly6C (sequence: AAGTCGTGAGGCATG) and CD11b (sequence: TGAAGGCTCATTTGT).
Outputs from filtered count matrices were used for subsequent analyses. From Cell Ranger an estimated 3,891 cells, 144076 mean reads per cells, and 2653 median genes per cell were recovered. 90% of reads mapped to genome and 97.7% barcodes were valid in antibody sequencing.
Genome_build: mm10
Supplementary_files_format_and_content: raw and filtered matrices in h5 format
Supplementary_files_format_and_content: raw and filtered matrices in matrix market format

extract_protocol:
CD11b+ cDCs from C57BL/6 mice inhaled house dust extract together with ovalbumin were purified by flow cytometry, and stained with Total A-Seq oligo-conjugated antibodies against CD11b and Ly-6C according to manufacturer’s instruction (BioLegend). The cells were counted and examined for viability using a TC-20 cell counter (Bio-Rad). 7000 live cells at 7×105 cells/mL concentration with 98% viability were loaded into the Single Cell Chip followed by forming single cell emulsion in Chromium Controller (10x Genomics). The cDNA for antibody derived transcripts (ADT) and gene derived transcripts was generated and amplified according to manufacturer’s instructions (10x Genomics and BioLegend).
The Gene Expression library and the ADT Library were prepared using the Chromium single cell 3′ v2 library and gel bead kit (10x Genomics) and additional reagents recommended in the protocol of Total A-seq (Biolegend). The two libraries were mixed at 10:1 molar ratio (Gene Expression library to ADT library).

tag: strain

value: CD11b+ conventional dendritic cells

tag: assay

value: gene expression


title: 3A: vax010_012_d0_L7

extract_protocol:
Cryopreserved PBMCs were thawed and innate immune cell subsets were isolated using FACS. Within the live gated cells, CD14+ monocytes were identified as CD14+ (fraction A) while a mixture of the remaining monocyte and dendritic cell subsets was identified as CD14-CD56-HLA-DR+ (fraction B). After sorting and depending on the number of isolated cells, fraction A and B were mixed at a 2:1 ratio to yield a solution of monocytes and dendritic cells enriched for CD14- cells.
FACS-purified cells were processed for single nuclei ATAC-seq according to the manufacturer’s instructions (10x Genomics, CG000168 Rev D). Briefly, nuclei were obtained by incubating PBMCs for 3.20 minutes in freshly prepared Lysis buffer following manufacturer’s instructions for Low Cell Input Nuclei Isolation (10x Genomics, CG000169 Rev C). Nuclei were washed and resuspended in chilled diluted nuclei buffer (10x Genomics, 2000153). Next, nuclei were subjected to transposition for 1h at 37C on the C1000 touch PCR instrument (BioRad) prior to single nucleus capture on the 10x Chromium instrument. Samples were subjected to post GEM cleanup, sample index PCR, cleanup and library QC prior to sequencing according to the protocol. Samples were pooled, quantified and sequenced on NovaSeq 6000 instrument (Illumina) with at least minimum recommended read depth (25000 read pairs/nucleus).

tag: tissue


title: C36 F10 Tg+ rep1 Fibroblast

description: Sample 13


title: 408_m6A_input_clones_W9A

data_processing:
Library strategy: m6Aseq2
alignment using STAR (V. 2.5.3a)
bam2ReadEnds.R (Garcia-Campos et al. 2019) paired-end alignment to the transcriptome (SK1, mm9 gene annotation)
Genome_build: SK1, NCBI37/mm9

value: Wtap -/-


title: ADT

tag: Sex

tag: cell type

value: antibody capture


title: C40 M00 WT rep1 Cardiomyocyte

description: Sample 11

tag: genotype


title: Col-0 leaves C120-L

value: non-primed


title: Col-0 leaves P120-C

description: harvested after 120 min of cold exposure

value: cold-triggered


title: 3A: vax010_012_d0_L2

data_processing:
CellRanger-ATAC (v1.1.0) count functionality was used for alignment, deduplication, demultiplexing, and identification of cut sites. All lanes related to each sample were analyzed jointly.
CellRanger-ATAC (v1.1.0)'s aggr function was then used to aggregate samples without depth normalization (--normalize=none)
The resulting fragment file was read into SnapATAC (v1.0). Cells were called as barcodes with at least 1000 UMIs and a promotor ratio (defined as: (fragments in promoter regions + 1) / (total fragments + 1)) of at least 0.1. Reads were mapped into 5kb bins to create a bin-by-cell matrix.
SnapATAC was then used to identify clusters from the cell-by-bin matrix, then peaks were called (MACS2 v2.2.7.1) separately for each cluster and joined for a joined set of peaks.
Fragments were mapped to the joined set of peaks for each cell barcode to create the peak-by-cell matrix.
deeply-sequenced libraries were downsampled to an average of 1500 fragments per barcode by randomly removing counts from these samples at a probability p=1500/(mean fragments per cell in the sample)
Genome_build: hg38
Supplementary_files_format_and_content: TIV_scATAC_counts.mtx.gz: raw count matrix
Supplementary_files_format_and_content: TIV_scATAC_meta.tsv: tab-seperated cell annotations
Supplementary_files_format_and_content: TIV_scATAC_peaks.bed: peaks in bed format

tag: lane


title: C52 F00 Tg+ rep1 Fibroblast

description: Sample 16


title: Col-0 leaves C120-C


title: 8R: vax010_063_d42_polyA RNA

data_processing:
Alignment, demultiplexing, cell-calling and filtering were performed using the count pipeline from 10x Genomics' CellRanger (v3.1.0) on each sample
Filtered count matrices were concatendated along the feature-axis without any normalization and analyzed jointly in all downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: *_matrix.mtx: raw counts in Matrix Market format
Supplementary_files_format_and_content: *_genes.mtx: gene identifiers
Supplementary_files_format_and_content: *_barcodes.tsv: cell barcodes

extract_protocol:
Cryopreserved PBMCs were thawed and innate immune cell subsets were isolated using FACS. Within the live gated cells, CD14+ monocytes were identified as CD14+ (fraction A) while a mixture of the remaining monocyte and dendritic cell subsets was identified as CD14-CD56-HLA-DR+ (fraction B). After sorting and depending on the number of isolated cells, fraction A and B were mixed at a 2:1 ratio to yield a solution of monocytes and dendritic cells enriched for CD14- cells.
FACS-purified cells were resuspended in PBS supplemented with 1% BSA (Miltenyi), and 0.5 U/μL RNase Inhibitor (Sigma Aldrich). About 9,000 cells were targeted for each experiment. Cells were mixed with the reverse transcription mix and subjected to partitioning along with the Chromium gel-beads using the 10X Chromium system to generate the Gel-Bead in Emulsions (GEMs) using the 3' V3 chemistry (10X Genomics). The RT reaction was conducted in the C1000 touch PCR instrument (BioRad). Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was subjected to 0.6x SPRI beads cleanup (Beckman, B23318). 25% of the amplified cDNA was subjected to enzymatic fragmentation, end-repair, A tailing, adapter ligation and 10X specific sample indexing as per manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) analysis. Libraries were pooled and sequenced on an NovaSeq 6000 instrument (Illumina) using the recommended sequencing read lengths of 28 bp (Read 1), 8 bp (i7 Index Read), and 91 bp (Read 2).


title: 3A: vax010_012_d0_L1


title: RNA-Seq CASE6

city: Cambridge

first: Weifeng

last: Xu

state: Massachusetts

address: The Picower Institute of Learning and Memory

institute: MIT

description: polyribosomal RNA

data_processing:
RNA-seq data analysis: The generated fastq files were first trimmed by cutadapt tool to remove thr first 5 bases at the 5' end that were poorly mapped (possbily resulting from bias of the random priming). The trimmed data were aligned to the UCSC mouse reference genome assembly mm10 using TopHat2.0. The TopHat program uses high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by HTSeq tool to measure gene counts at gene exonic regions.  The GTF annotation file for UCSC mm10 was used for gene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Text table format for RNA-Seq gene counts

source_name: hippocampus

growth_protocol: 5 week old C57/Bl6 mice were ordered from Charles River and allowed to acclimate for one week to the animal facility (acclimate from day -7 to day 0). After acclimating, the mice were individually housed for 2 days (separated at day 0). For the two days following the intial separation of the mice, the mice are allowed to acclimate to the room where they will be tested (acclimate on day 1 and day 2). On day 3, the mice were exposed to a novel context and then sacrificed 15 minutes after the initial exposure (exposure on day 3). The novel context exposure lasts 8 minutes and then the mice is placed back in their homecage for 7 more minutes until a total time of 15 minutes has elapsed since placing the mouse in the novel context. The mouse is then sacrificed for tissue collection.

extract_protocol:
Once the mouse is ready to be sacrificed for tissue extraction, the mice undergo a sacrifice and the head is cooled in liquid nitrogen. The brain is then dissected to isolate the hippocampus brain region and homogenize it in a lysis buffer. The homogenized hippocampus tissue is then kept on ice until all samples are ready to be processed for the next step. After homogenizing all hippocampi, the samples are spun at 2,000xg for 10min and supernatant removed. This supernatant is combined with detergents (NP-40 and DHPC) to help isolate polysomes. The samples are then spun again at 20,000g for 10min and supernatant removed. One aliquot of this supernatant is put aside to serve as a representative sample of total RNA for each homogenized hippocampus sample. The remaining supernatant is loaded onto a sucrose cushion (1M sucrose) and spun in an ultracentrifuge at 266,000xg for 4h. The resulting pellets were re-suspended in TRIzol and processed accordingly. Samples were then column-purified (Qiagen) to remove residual salts and genomic contamination. Next, RNA integrity was assessed using a BioAnalyzer (Agilent) at the MIT BioMicro Center.
Following polysome enrichment, all RNA samples were prepared for RNA-seq using the SMARTer total RNA-seq kit (Clontech). The quality of prepared bar-coded libraries was assessed using a BioAnalyzer (Agilent) before mixing for sequencing on the Illumina NextSeq500 (Illumina) platform at the MIT BioMicro Center to generate 40bp paired-end fastq files generated from Illumina NextSeq500 platform.

tag: age

value: 6 weeks

tag: sample group

value: fear case


title: RNA-Seq CASE5

description: polyribosomal RNA


title: C39 M01 WT rep2 Cardiomyocyte

description: Sample 10


title: Col-0 leaves P60-L

description: harvested after 60 min of excess light exposure


title: RNA-Seq CASE4

description: polyribosomal RNA


title: C39 M01 WT rep1 Cardiomyocyte

description: Sample 9


title: 3A: vax010_012_d0_L4

tag: subject


title: C52 F00 Tg+ rep2 Cardiomyocyte

description: Sample 8

tag: replicate


title: 4R: vax010_012_d42_polyA RNA

tag: time point


title: C52 F00 Tg+ rep1 Cardiomyocyte

description: Sample 7


title: 9R: vax010_063_d21_polyA RNA

tag: experiment


title: Col-0 leaves P60-C

description: harvested after 60 min of cold exposure


title: Col-0 leaves P30-L

description: harvested after 30 min of excess light exposure


title: C37 M10 Tg+ rep1 Cardiomyocyte

description: Sample 5


title: 2R: vax010_062_d21_polyA RNA

tag: vaccine group


title: C37 M10 Tg+ rep2 Cardiomyocyte

description: Sample 6


title: Col-0 leaves C30-L

tag: ecotype


title: 6R: vax010_012_d21_polyA RNA


title: 10R: vax010_062_d42_polyA RNA


title: 7R: vax010_063_d0_polyA RNA


title: Col-0 leaves P30-C

description: harvested after 30 min of cold exposure

tag: 1. treatment


title: RNA-Seq CASE1

description: polyribosomal RNA


title: C36 F03 WT rep1 Cardiomyocyte

description: Sample 3


title: RNA-Seq CTRL6

description: polyribosomal RNA

value: control


title: C36 F03 WT rep2 Cardiomyocyte

description: Sample 4


title: RNA-Seq CTRL5

description: polyribosomal RNA


title: Col-0 leaves C60-L

tag: 2. treatment


title: RNA-Seq CTRL4

description: polyribosomal RNA

tag: strain


title: 11R: vax010_062_d0_polyA RNA


title: Col-0 leaves C30-C

description: harvested after 30 min of cold exposure


title: RNA-Seq CTRL3

description: polyribosomal RNA


title: C36 F10 Tg+ rep2 Cardiomyocyte

description: Sample 2


title: RNA-Seq CASE2

description: polyribosomal RNA


title: RNA-Seq CASE3

description: polyribosomal RNA


title: Col-0 leaves P0

description: harvested at the end of the 5 day long lag phase between priming and triggering

value: non-triggered


title: Col-0 leaves C60-C

description: harvested after 60 min of cold exposure


title: 5R: vax010_061_d21_polyA RNA


title: C36 F10 Tg+ rep1 Cardiomyocyte

description: Sample 1


title: Col-0 leaves C0


title: MS3_transcriptome

status: Public on Jun 24 2021

city: Fu Yang

first: Min

last: Zhong

state: Hang Zhou

address: Rice research road NO.28

institute: China National Rice Research Institute

description:
MS3_MS_FPKM
MS3_Clean_Data1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: 100 μΜ cadmium_shoot

growth_protocol: Germinating seedlings were removed to a hydroponics solution consisting of Hoagland’s solution (pH 5.5) in a climate chamber (relative humidity 80%, 30/28℃ day/night temperature)

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Once the first leaf was fully expanded, seedlings were subjected to CdCl2•2.5H2O in different concentrations, including 0 µM (the control, MC) and 100 µM (MS) for 12 days, in triplicate.

tag: cultivar

value: Zhong Jiazao-17

value: Shoot

tag: cadmium treatment

value: 100 μΜ cadmium treatment for 12 days

tag: development stage

value: rice at one leaf stage


title: RNA-Seq CTRL1

description: polyribosomal RNA


title: MS2_transcriptome

description:
MS2_MS_FPKM
MS2_Clean_Data1

tag: tissue


title: MS1_transcriptome

description:
MS1_MS_FPKM
MS1_Clean_Data1


title: 3R: vax010_012_d0_polyA RNA

first: Florian

last: Wimmers

address: 1651 Page Mill Road

value: monocytes and dendritic cells


title: MC2_transcriptome

description:
MC2_MC_FPKM
MC2_Clean_Data1

source_name: 0 μΜ cadmium_shoot

value: 0 μΜ cadmium treatment for 12 days


title: hsa-miR-93-5p

value: Wistar

value: heart

value: post natal day 1

tag: genotype

value: wild type

tag: cell type

value: ventricular cardiomyocytes

tag: treatment

value: transfected with hsa-miR-93-5p


title: MC3_transcriptome

description:
MC3_MC_FPKM
MC3_Clean_Data1


title: 1R: vax010_061_d0_polyA RNA


title: MC1_transcriptome

description:
MC1_MC_FPKM
MC1_Clean_Data1


title: RNA-Seq CTRL2

description: polyribosomal RNA

tag: age

tag: sample group


title: noTF-condition_ZNF598_siRNA_Rep1

first: Ryan

middle: Lehman

last: McCarthy

address: 1900 9th Ave

department: Pediatrics

data_processing:
Samples were demultiplexed to produce FASTQ files using cutadapt (v.1.15) with Python  (v.2.7.14)
Reads with low quality, adapter, high N rate or poly-A sequences were filtered out from the raw FASTQ data before alignment using SOAPnuke (v.2.0.2)
Clean reads were aligned to the hg38 reference and gene expression levels were quantified using RSEM (v.1.3.2)
Genome_build: hg38

source_name: Human BJ Fibroblast

growth_protocol: Human BJ foreskin fibroblasts were obtained from Stemgent (08-0027) at passage 6 and cultured in Eagle's Minimum Essential Medium (Sigma M2279) supplemented with 10% fetal bovine serum (FBS, Hyclone SH30071) and 2mM L-glutamine (Gibco) at 37°C and 5% CO2

extract_protocol:
RNA was purified using the ZR-96 Quick-RNA kit (Zymo Research R1052) and was polyA-selected using Oligo(dT)25 Dynabeads (Thermo Fisher Scientific, #61002).
75-100 ng of isolated RNA was used to prepare RNA-seq libraries for sequencing. All custom primers used in cDNA synthesis are listed below. An oligo-dT primer was used to perform poly-A enrichment and was incubated with the sample for 5 minutes. First-stand cDNA synthesis was performed with Superscript II Reverse Transcriptase (Invitrogen 18064022) and a template switch oligo by incubating for 1.5 hours. Second-strand cDNA synthesis was performed with the KAPA HiFi HotStart Ready Mix (Roche 7958927001) and an IS primer with 3 cycles of PCR amplification. 5ng of cDNA was fragmented using the Tn5 enzyme-adaptor compound. 15 cycles of PCR were then carried out with barcoded primers compatible with the BGISEQ-500. The 300-500bp DNA fragments were selected and purified. The fragments were then heat-denatured and one of the single strands was circularized with DNA ligase to obtain a single strand circular DNA library. The remaining single strand was digested with the exonuclease. The sequencing process was conducted according to the BGISEQ-500 protocol

treatment_protocol: Cells were treated with two rounds of transfection with 10nM Silencer Silect siRNAs (Thermo Fisher Scientific) and 2.5 μl Lipofectamine RNAiMAX (Thermo Fisher #13778150), for 3 days per transfection. RNA was harvested at day 6 after the first transfection. For samples in the "hepatic TF" protocol, cells were first infected with lentiviruses delivering the human hepatic transcription factors FOXA3, HNF1A, and HNF4A (MOI 1.25 per virus) the day before the first siRNA transfection (day -1), or 7 days before RNA harvest.

value: human BJ Fibroblast

tag: sirna


title: noTF-condition_ZNF598_siRNA_Rep2


title: noTF-condition_ZNF622_siRNA_Rep1


title: noTF-condition_ZNF622_siRNA_Rep2


title: noTF-condition_ZNF207_siRNA_2_Rep1


title: noTF-condition_ZNF638_siRNA_Rep2


title: noTF-condition_ZNF207_siRNA_2_Rep2


title: noTF-condition_ZNF207_siRNA_1_Rep1


title: noTF-condition_ZNF207_siRNA_1_Rep2


title: noTF-condition_ZC3H13_siRNA_Rep2


title: noTF-condition_ZNF438_siRNA_Rep2


title: noTF-condition_ZNF326_siRNA_Rep2


title: noTF-condition_YY2_siRNA_Rep2


title: noTF-condition_ZNF512_siRNA_Rep1


title: noTF-condition_ZC3H13_siRNA_Rep1


title: noTF-condition_ZNF326_siRNA_Rep1


title: noTF-condition_ZNF638_siRNA_Rep1


title: noTF-condition_ZNF438_siRNA_Rep1


title: noTF-condition_YY2_siRNA_Rep1


title: noTF-condition_ZNF512_siRNA_Rep2


title: noTF-condition_YTHDC1_siRNA_Rep1


title: noTF-condition_YLPM1_siRNA_Rep2


title: noTF-condition_YTHDC1_siRNA_Rep2


title: noTF-condition_YBX3_siRNA_Rep2


title: noTF-condition_YBX1_siRNA_Rep2


title: noTF-condition_YLPM1_siRNA_Rep1


title: noTF-condition_YBX3_siRNA_Rep1


title: noTF-condition_YBX1_siRNA_Rep1


title: noTF-condition_XRN2_siRNA_2_Rep1


title: noTF-condition_XRN2_siRNA_1_Rep1


title: noTF-condition_UTP3_siRNA_Rep2


title: noTF-condition_XRN2_siRNA_1_Rep2


title: noTF-condition_WDR46_siRNA_Rep2


title: noTF-condition_THRAP3_siRNA_Rep2


title: noTF-condition_WDR46_siRNA_Rep1


title: noTF-condition_SUV39H2_siRNA_Rep2


title: noTF-condition_THRAP3_siRNA_Rep1


title: noTF-condition_TCF25_siRNA_Rep1


title: noTF-condition_TRA2B_siRNA_Rep1


title: noTF-condition_TRA2B_siRNA_Rep2


title: noTF-condition_TRA2A_siRNA_Rep2


title: noTF-condition_TAF15_siRNA_Rep1


title: noTF-condition_UBE2I_siRNA_Rep1


title: noTF-condition_TAF15_siRNA_Rep2


title: noTF-condition_UBE2I_siRNA_Rep2


title: noTF-condition_TARDBP_siRNA_Rep2


title: noTF-condition_TRA2A_siRNA_Rep1


title: noTF-condition_SUZ12_siRNA_Rep1


title: noTF-condition_SUV39H2_siRNA_Rep1


title: noTF-condition_SUV39H1_siRNA_1_Rep2


title: noTF-condition_SUZ12_siRNA_Rep2


title: noTF-condition_XRN2_siRNA_2_Rep2


title: noTF-condition_SUV39H1_siRNA_1_Rep1


title: noTF-condition_SUMO2_siRNA_Rep2


title: noTF-condition_SUV39H1_siRNA_2_Rep1


title: noTF-condition_TARDBP_siRNA_Rep1


title: noTF-condition_SUV39H1_siRNA_2_Rep2


title: noTF-condition_UTP3_siRNA_Rep1


title: noTF-condition_TCF25_siRNA_Rep2


title: noTF-condition_SLTM_siRNA_Rep2


title: noTF-condition_SFPQ_siRNA_Rep2


title: noTF-condition_SETDB1_siRNA_Rep2


title: noTF-condition_RPS19BP1_siRNA_Rep1


title: noTF-condition_RPS19BP1_siRNA_Rep2


title: noTF-condition_RPF1_siRNA_Rep1


title: noTF-condition_RIF1_siRNA_Rep1


title: noTF-condition_SFPQ_siRNA_Rep1


title: noTF-condition_RIF1_siRNA_Rep2


title: noTF-condition_SAFB2_siRNA_Rep1


title: noTF-condition_SETDB1_siRNA_Rep1


title: noTF-condition_RPF2_siRNA_Rep1


title: noTF-condition_SAFB_siRNA_Rep2


title: noTF-condition_RELA_siRNA_Rep2


title: noTF-condition_SAFB_siRNA_Rep1


title: noTF-condition_RPF2_siRNA_Rep2


title: noTF-condition_RPF1_siRNA_Rep2


title: noTF-condition_RELA_siRNA_Rep1


title: noTF-condition_RBMX_siRNA_2_Rep2


title: noTF-condition_RBMX_siRNA_1_Rep2


title: noTF-condition_RBMX_siRNA_1_Rep1


title: noTF-condition_RBM26_siRNA_Rep2


title: noTF-condition_RBM26_siRNA_Rep1


title: noTF-condition_RBM15_siRNA_Rep2


title: noTF-condition_RBM15_siRNA_Rep1


title: noTF-condition_SUMO2_siRNA_Rep1


title: noTF-condition_SLTM_siRNA_Rep1


title: noTF-condition_RBM12B_siRNA_Rep2


title: noTF-condition_RBM12B_siRNA_Rep1


title: noTF-condition_QKI_siRNA_Rep1


title: noTF-condition_SAFB2_siRNA_Rep2


title: noTF-condition_PTBP1_siRNA_Rep2


title: noTF-condition_QKI_siRNA_Rep2


title: noTF-condition_PRDM15_siRNA_Rep2


title: noTF-condition_PPHLN1_siRNA_Rep2


title: noTF-condition_PTBP1_siRNA_Rep1


title: noTF-condition_PRDM15_siRNA_Rep1


title: noTF-condition_PPAN_siRNA_Rep2


title: noTF-condition_PRMT1_siRNA_Rep1


title: noTF-condition_PPAN_siRNA_Rep1


title: noTF-condition_PHB_siRNA_Rep2


title: noTF-condition_PIAS2_siRNA_Rep1


title: noTF-condition_PES1_siRNA_Rep2


title: noTF-condition_PPHLN1_siRNA_Rep1


title: noTF-condition_PRMT1_siRNA_Rep2


title: noTF-condition_PIAS2_siRNA_Rep2


title: noTF-condition_POLDIP3_siRNA_Rep2


title: noTF-condition_POLDIP3_siRNA_Rep1


title: noTF-condition_PHB_siRNA_Rep1


title: noTF-condition_NONO_siRNA_Rep1


title: noTF-condition_NCOA7_siRNA_Rep2


title: noTF-condition_NONO_siRNA_Rep2


title: noTF-condition_NCOA5_siRNA_Rep2


title: noTF-condition_NCOA7_siRNA_Rep1


title: noTF-condition_RBMX_siRNA_2_Rep1


title: noTF-condition_PRRX2_siRNA_Rep2


title: noTF-condition_PRRX2_siRNA_Rep1


title: noTF-condition_NCOA5_siRNA_Rep1


title: noTF-condition_MYEF2_siRNA_Rep1


title: noTF-condition_MYBBP1A_siRNA_Rep2


title: noTF-condition_MYBBP1A_siRNA_Rep1


title: noTF-condition_PES1_siRNA_Rep1


title: noTF-condition_MBNL1_siRNA_Rep2


title: noTF-condition_MRTO4_siRNA_2_Rep2


title: noTF-condition_MRTO4_siRNA_2_Rep1


title: DNMT3A/3B double KO mouse embryonic stem cells with WT DNMT3A induction-WGBS

city: Stanford

first: Yung-Hsin

last: Huang

address: CCSR 2155, 269 Campus drive

data_processing:
RNA-seq:
STAR v2.5.4a was used to map to the mouse genome GRCm38 and calculate the raw read counts using default parameter settings.
edgeR_3.26.8 was used to normalize the read count data and generate the gene expression matrix (Reads per Kilobase per Million).
WGBS (human):
Raw reads of whole genome bisulfite sequencing data were mapped to genome using BSMAP (v2.90) with default parameters.
Duplicated reads were removed and only properly paired reads that uniquely mapped to genome were used.
CpG methylation ratios on both strands were combined and CpG loci with sequencing depth less than 5 were excluded.
WGBS (mouse):
Raw reads of whole genome bisulfite sequencing data were mapped to genome using BSMAP (v2.90) with default parameters.
Duplicated reads were removed and only properly paired reads that uniquely mapped to genome were used.
CpG methylation ratios on both strands were combined and CpG loci with sequencing depth less than 5 were excluded.
Genome_build: GRCm38; hg19
Supplementary_files_format_and_content: raw read counts for each genes; CpG location and methylation ratio

source_name: Embryonic stem cells

growth_protocol: DKO mESCs and their DNMT3A mutant-expressing derivatives were cultured in 12.5% Foundation ES serum, 1X Glutamax, 100 μM b-mercaptoethanol, 1X NEAA and 1000U/mL leukemia inhibitory factor (LIF) and Knockout DMEM. LCLs are cultured in RPMI 1640 medium (containing 10% fetal calf serum and 5% L -glutamine)

extract_protocol:
DNA is extracted using purelink genomic DNA extraction kit. RNA is extracted using Rneasy kit.
WGBS is generated using Truseq DNA methylation kit. RNAseq is generated using Truseq stranded mRNA kit.

treatment_protocol: 1uM MG132 and 2ug/ml doxycycline are treated for 30 days

tag: dnmt3a genotype

value: WT

value: doxycycline


title: noTF-condition_MBD3_siRNA_1_Rep2


title: DNMT3A/3B double KO mouse embryonic stem cells with  DNMT3A W297Del  induction-WGBS


title: noTF-condition_MPHOSPH10_siRNA_Rep2


title: DNMT3A/3B double KO mouse embryonic stem cells with DNMT3A E756A induction-WGBS


title: noTF-condition_MRTO4_siRNA_1_Rep1


title: noTF-condition_MYEF2_siRNA_Rep2


title: noTF-condition_MBD3_siRNA_2_Rep2


title: noTF-condition_MBD3_siRNA_1_Rep1


title: DNMT3A/3B double KO mouse embryonic stem cells-WGBS

value: KO


title: 16_E18_fetalBrain_WT_7556-F9_M

city: Scarborough

first: Arturo

last: Hernandez

state: ME

address: 81 Research Drive

department: Center for Molecular Medicine

institute: Maine Medical Center Research Institute

description: E18.5-Wild type

data_processing:
FASTQC and multiQC v1.9 were used to determine the quality of sequencing data. The adaptor sequences were trimmed using cutadapt 3.1 with Phython 3.6.2 with -m 1 option. The STAR version 2.5.3a (Spliced Transcripts Alignment to a Reference was used to align the reads to the reference genome (GRCm38/mm10) using the default settings, and the genome index was built based on the GENCODE VM22 annotation (GRCm38/mm10). rRNA and tRNA were filtered using bedtools version 2.26.0, using the GTF files downloaded from the UCSC Table Browser (GRCm38/mm10). HTSeq was used to count the reads per transcript (HTseq counts) with a default setting over the union with -s no option. For differential gene expression analysis, DESeq2 version 1.30.1 was performed in the R environment (Version 4.0.3), using the HTseq counts and the significance cutoff set as adjusted p-values <0.05 . ComBat-seq was utilized to adjust the batch effects between the two batches of samples.
Genome_build: GRCm38/mm10

source_name: Fetal brain

extract_protocol:
Qiagen RNAeasy mini kit
Standard Illumina protocols

tag: background strain

value: fetal brain

tag: embryonic age

tag: Sex

value: male


title: 11_E13_fetalBrain_KO_7377-F5_M


title: noTF-condition_MBD3_siRNA_2_Rep1

city: Seattle


title: noTF-condition_MATR3_siRNA_Rep2


title: 2_E13_fetalBrain_WT_7376-F11_M

description: E13.5-Wild type


title: noTF-condition_MATR3_siRNA_Rep1


title: 7_E18_fetalBrain_KO_7940-F9_M


title: 1_E13_fetalBrain_WT_7376-F10_M

description: E13.5-Wild type


title: noTF-condition_LTBP2_siRNA_Rep2


title: noTF-condition_LTBP2_siRNA_Rep1


title: noTF-condition_MRTO4_siRNA_1_Rep2


title: noTF-condition_LOXL2_siRNA_Rep2


title: noTF-condition_MBNL1_siRNA_Rep1


title: myc-inth2b2b-wt-async-x32

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

institute: Weizmann Institute

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-170 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: *.out.txt file contains genome coverage for all 12,157,105 bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)

source_name: budding yeast

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for 6 hours at 30deg before fixation

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.
SLIM-Chip, as per Gutin et al, Cell Reports 2019

treatment_protocol: For h2o2 samples: exponentially growing cultures were exposed to 0.3 mM H2O2 and samples taken at indicated timepoints (in minutes)

tag: antibody

value: myc

tag: background

value: wt

value: async

tag: sensor

value: H2B-TEV, H2B-Fast

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV, HTB1-GGS-HA-Fast-MYC, bar1


title: noTF-condition_MPHOSPH10_siRNA_Rep1

institute: University of Washington


title: myc-inth2b1b-wt-async-x33

tag: strain


title: noTF-condition_LOXL2_siRNA_Rep1


title: myc-inth2b1a-wt-async-x33


title: noTF-condition_LOXL1_siRNA_Rep2


title: noTF-condition_LLPH_siRNA_Rep2


title: noTF-condition_KHDRBS3_siRNA_Rep2


title: myc-inth2b1b-wt-async-x32


title: myc-inth2b1a-wt-async-x32


title: noTF-condition_KHDRBS1_siRNA_2_Rep2


title: noTF-condition_LOXL1_siRNA_Rep1


title: noTF-condition_KHDRBS3_siRNA_Rep1


title: noTF-condition_KHDRBS1_siRNA_2_Rep1


title: myc-hhf11b-wt-async-x30

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV, HHF1-GGS-HA-Fast-MYC, bar1


title: myc-hht21a-wt-async-x30

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC, bar1


title: noTF-condition_KHDRBS1_siRNA_1_Rep1


title: myc-h42a-wt-async-x28

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV, HHF2-GGS-HA-Fast-MYC


title: myc-h42a-asf-async-x28

value: asf

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHF2-GGS-HA-Fast-MYC bar1 , asf1::KANMX


title: myc-inth2b2a-wt-async-x32


title: noTF-condition_KHDRBS1_siRNA_1_Rep2


title: noTF-condition_KAP1_siRNA_2_Rep2


title: myc-hhf11a-wt-async-x30


title: myc-hht22-wt-async-x30


title: noTF-condition_KAP1_siRNA_2_Rep1


title: noTF-condition_KAP1_siRNA_1_Rep2


title: myc-h41b-asf-async-x28


title: myc-hhf12-wt-async-x30


title: myc-h41b-wt-async-x28


title: noTF-condition_KAP1_siRNA_1_Rep1


title: noTF-condition_LLPH_siRNA_Rep1


title: myc-hht21b-wt-async-x30


title: noTF-condition_HP1BP3_siRNA_Rep2


title: myc-h41a-asf-async-x28


title: myc-h41a-wt-async-x28


title: myc-h32x2-wt-async-x30

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: myc-h32x1b-wt-async-x30


title: noTF-condition_HP1BP3_siRNA_Rep1

value: human BJ Fibroblast


title: myc-h32x-wt-async-x31


title: myc-h32x1a-wt-async-x30


title: myc-h32a-wt-alpha2hr-x28


title: myc-h32b-wt-alpha2hr-x28


title: noTF-condition_HNRNPK_siRNA_Rep1


title: noTF-condition_HNRNPL_siRNA_Rep1


title: noTF-condition_HNRNPA2B1_siRNA_Rep2


title: noTF-condition_HNRNPL_siRNA_Rep2


title: myc-h31b-wt-alpha2hr-x28


title: myc-fast1b-wt-alpha2hr-x26

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: myc-h31a-wt-alpha2hr-x28


title: noTF-condition_HNRNPA2B1_siRNA_Rep1


title: noTF-condition_HMGA1_siRNA_Rep2


title: myc-fast1a-wt-alpha2hr-x26


title: myc-fast-wt-alpha2hr-x28


title: noTF-condition_HDLBP_siRNA_Rep2


title: myc-fast1a-wt-alpha2hr-x27


title: noTF-condition_HMGA1_siRNA_Rep1


title: noTF-condition_HDLBP_siRNA_Rep1


title: noTF-condition_GLTSCR2_siRNA_Rep2


title: ha-inth2b2b-wt-async-x32

value: ha


title: ha-inth2b2a-wt-async-x32


title: noTF-condition_GLTSCR2_siRNA_Rep1


title: noTF-condition_GATAD2B_siRNA_Rep2


title: noTF-condition_HNRNPK_siRNA_Rep2


title: noTF-condition_GATAD2B_siRNA_Rep1


title: ha-inth2b1b-wt-async-x33


title: noTF-condition_FYTTD1_siRNA_Rep2


title: noTF-condition_GATAD2A_siRNA_Rep1


title: ha-inth2b1b-wt-async-x32


title: ha-inth2b1a-wt-async-x33


title: noTF-condition_FYTTD1_siRNA_Rep1


title: ha-hht22-wt-async-x30


title: noTF-condition_EXOSC10_siRNA_Rep2


title: ha-inth2b1a-wt-async-x32


title: ha-hhf12-wt-async-x30


title: ha-hht21b-wt-async-x30


title: noTF-condition_FUS_siRNA_Rep2


title: noTF-condition_FUS_siRNA_Rep1


title: noTF-condition_EXOSC10_siRNA_Rep1


title: noTF-condition_ERH_siRNA_2_Rep2


title: ha-hhf11b-wt-async-x30


title: ha-hht21a-wt-async-x30


title: ha-h41b-wt-async-x28


title: ha-h42a-asf-async-x28


title: noTF-condition_ERH_siRNA_1_Rep2


title: noTF-condition_ERH_siRNA_1_Rep1


title: noTF-condition_GATAD2A_siRNA_Rep2


title: noTF-condition_EBNA1BP2_siRNA_Rep2


title: noTF-condition_EBNA1BP2_siRNA_Rep1


title: ha-h41a-asf-async-x28


title: ha-h41a-wt-async-x28


title: noTF-condition_DDX5_siRNA_Rep2


title: ha-h41b-asf-async-x28


title: ha-h32x2-wt-async-x30


title: noTF-condition_DDX5_siRNA_Rep1


title: noTF-condition_DDX17_siRNA_Rep2


title: noTF-condition_DDX17_siRNA_Rep1


title: ha-h32x1a-wt-async-x30


title: ha-h42a-wt-async-x28


title: ha-h32b-wt-alpha2hr-x28


title: noTF-condition_ERH_siRNA_2_Rep1


title: ha-h32x-wt-async-x31


title: noTF-condition_CHTOP_siRNA_Rep2


title: noTF-condition_CHTOP_siRNA_Rep1


title: ha-h31b-wt-alpha2hr-x28


title: noTF-condition_CHAF1A_siRNA_Rep2


title: ha-h32a-wt-alpha2hr-x28


title: ha-hhf11a-wt-async-x30


title: ha-fast1b-wt-alpha2hr-x26


title: ha-h31a-wt-alpha2hr-x28


title: noTF-condition_CHAF1A_siRNA_Rep1


title: ha-fast1a-wt-alpha2hr-x27


title: noTF-condition_CEBPZ_siRNA_Rep2


title: ha-fast-wt-alpha2hr-x28


title: noTF-condition_CEBPZ_siRNA_Rep1


title: ha-fast1a-wt-alpha2hr-x26


title: noTF-condition_CCDC86_siRNA_Rep2


title: myc-fast1b-wt-alpha2hr-x22


title: noTF-condition_CCDC86_siRNA_Rep1


title: ha-h32x1b-wt-async-x30


title: myc-fast1a-wt-alpha2hr-x24


title: noTF-condition_CCDC59_siRNA_Rep2


title: myc-fast1a-wt-alpha2hr-x22


title: noTF-condition_CUX1_siRNA_Rep2


title: noTF-condition_CUX1_siRNA_Rep1


title: ha-fast1b-wt-alpha2hr-x22


title: noTF-condition_CCDC137_siRNA_Rep2


title: noTF-condition_CBX5_siRNA_Rep2


title: ha-fast1a-wt-alpha2hr-x22


title: noTF-condition_CCDC137_siRNA_Rep1


title: noTF-condition_CBX5_siRNA_Rep1


title: noTF-condition_CBX1_siRNA_Rep2


title: noTF-condition_CBX3_siRNA_Rep1


title: noTF-condition_CBX1_siRNA_Rep1


title: myc-h31a-wt-async-x28

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64  with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-170 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: *.out file contains gneome coverage for all 12,157,105   bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)

growth_protocol: yeast cells were grown to saturation overnight in YPD  and then dilute in fresh,pre-warmed YPD and incubated for 6 hours at 30deg before fixation


title: myc-h32b-wt-async-x28


title: myc-h31b-wt-async-x28


title: myc-h32a-wt-async-x28


title: myc-fast1a-wt-async-x27


title: myc-h2a2-hir1-async-x26

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1 , hir1::NAT


title: myc-h2a1-hir1-async-x26


title: noTF-condition_C5orf41_siRNA_Rep2


title: myc-fast-wt-async-x28


title: noTF-condition_C5orf41_siRNA_Rep1


title: noTF-condition_CCDC59_siRNA_Rep1


title: noTF-condition_BCLAF1_siRNA_Rep1


title: ha-h31b-wt-async-x28


title: ha-h32b-wt-async-x28


title: noTF-condition_Control_siRNA_2_Rep1


title: noTF-condition_Control_siRNA_2_Rep2


title: noTF-condition_CBX3_siRNA_Rep2


title: noTF-condition_Control_siRNA_1_Rep2


title: hepaticTF-condition_ZNF638_siRNA_Rep2


title: ha-fast1a-wt-async-x27


title: ha-h2a2-hir1-async-x26


title: ha-fast-wt-async-x28


title: hepaticTF-condition_ZNF638_siRNA_Rep1


title: hepaticTF-condition_ZNF622_siRNA_Rep2


title: hepaticTF-condition_ZNF622_siRNA_Rep1


title: myc-h2a2a-spt16DAmp-async-x21

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1 , DAmP-SPT16::NAT


title: hepaticTF-condition_ZNF598_siRNA_Rep1


title: noTF-condition_BCLAF1_siRNA_Rep2


title: ha-h32a-wt-async-x28


title: hepaticTF-condition_ZNF512_siRNA_Rep1


title: myc-h2a1b-spt16DAmp-async-x21


title: hepaticTF-condition_ZNF512_siRNA_Rep2


title: ha-h31a-wt-async-x28


title: hepaticTF-condition_ZNF438_siRNA_Rep2


title: myc-h2a1a-spt16DAmp-async-x21


title: myc-h2a1a-wt-async-x25

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1


title: myc-fast2a-asf-async-x21

value: myc

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , asf1::KANMX


title: myc-fast2a-spt16DAmp-async-x21

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , DAmP-SPT16::NAT


title: myc-fast1b-spt16DAmp-async-x21


title: ha-h2a1-hir1-async-x26


title: hepaticTF-condition_ZNF326_siRNA_Rep2


title: hepaticTF-condition_ZNF438_siRNA_Rep1


title: myc-fast1b-htz1-async-x22

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , htz1::NAT


title: noTF-condition_Control_siRNA_1_Rep1


title: myc-fast1b-hir2-async-x25

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , hir2::NAT


title: hepaticTF-condition_ZNF326_siRNA_Rep1


title: myc-fast1b-asf-async-x22


title: myc-fast1b-hir1-async-x25

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1 , hir1::NAT


title: myc-fast1b-asf-async-x21


title: hepaticTF-condition_ZNF207_siRNA_2_Rep1


title: hepaticTF-condition_ZNF207_siRNA_2_Rep2


title: hepaticTF-condition_ZNF598_siRNA_Rep2


title: h3-fast1a-wt-async-x27

value: wt


title: hepaticTF-condition_ZNF207_siRNA_1_Rep2


title: hepaticTF-condition_ZC3H13_siRNA_Rep1


title: hepaticTF-condition_ZC3H13_siRNA_Rep2


title: hepaticTF-condition_ZNF207_siRNA_1_Rep1


title: hepaticTF-condition_YY2_siRNA_Rep2


title: myc-fast1a-htz1-async-x22


title: hepaticTF-condition_YY2_siRNA_Rep1


title: myc-fast1a-hir2-async-x25


title: myc-fast1a-hir1-async-x25


title: myc-fast1a-spt16DAmp-async-x21


title: myc-fast1a-asf-async-x22

value: asf


title: myc-fast1a-asf-async-x21


title: hepaticTF-condition_YTHDC1_siRNA_Rep2


title: ha-h2a2a-spt16DAmp-async-x21


title: hepaticTF-condition_YLPM1_siRNA_Rep1


title: hepaticTF-condition_YTHDC1_siRNA_Rep1


title: hepaticTF-condition_YLPM1_siRNA_Rep2


title: hepaticTF-condition_YBX3_siRNA_Rep2


title: ha-h2a1a-wt-async-x25


title: ha-fast2a-spt16DAmp-async-x21


title: ha-h2a1b-spt16DAmp-async-x21


title: hepaticTF-condition_YBX1_siRNA_Rep2


title: ha-h2a1a-spt16DAmp-async-x21


title: ha-fast2a-asf-async-x21


title: hepaticTF-condition_XRN2_siRNA_2_Rep2


title: hepaticTF-condition_XRN2_siRNA_2_Rep1


title: ha-fast1b-spt16DAmp-async-x21


title: ha-fast1b-htz1-async-x22


title: hepaticTF-condition_XRN2_siRNA_1_Rep2


title: ha-fast1b-hir2-async-x25


title: ha-fast1b-asf-async-x22


title: hepaticTF-condition_XRN2_siRNA_1_Rep1


title: ha-fast1b-asf-async-x21


title: hepaticTF-condition_WDR46_siRNA_Rep2


title: hepaticTF-condition_UTP3_siRNA_Rep1


title: ha-fast1a-htz1-async-x22


title: hepaticTF-condition_UTP3_siRNA_Rep2


title: ha-fast1b-hir1-async-x25


title: ha-fast1a-spt16DAmp-async-x21


title: hepaticTF-condition_YBX3_siRNA_Rep1


title: hepaticTF-condition_UBE2I_siRNA_Rep1


title: hepaticTF-condition_UBE2I_siRNA_Rep2


title: hepaticTF-condition_YBX1_siRNA_Rep1


title: ha-fast1a-hir2-async-x25


title: hepaticTF-condition_TRA2B_siRNA_Rep1


title: hepaticTF-condition_TRA2A_siRNA_Rep2


title: hepaticTF-condition_TRA2A_siRNA_Rep1


title: hepaticTF-condition_THRAP3_siRNA_Rep2


title: ha-fast1a-asf-async-x21


title: hepaticTF-condition_THRAP3_siRNA_Rep1


title: ha-fast1a-asf-async-x22


title: hepaticTF-condition_TCF25_siRNA_Rep2


title: myc-h2a2-wt-async-x26

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64  with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-170 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: *.out.txt file contains genome coverage for all 12,157,105 bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)


title: hepaticTF-condition_TCF25_siRNA_Rep1


title: hepaticTF-condition_TRA2B_siRNA_Rep2


title: hepaticTF-condition_TARDBP_siRNA_Rep2


title: ha-fast1a-hir1-async-x25


title: hepaticTF-condition_TARDBP_siRNA_Rep1


title: myc-h2a1-wt-async-x26


title: hepaticTF-condition_TAF15_siRNA_Rep2


title: myc-fast1b-wt-async-x26


title: hepaticTF-condition_TAF15_siRNA_Rep1


title: hepaticTF-condition_SUZ12_siRNA_Rep2


title: hepaticTF-condition_SUZ12_siRNA_Rep1


title: ctrc-4

city: jinan

first: Bing

last: Li

address: Wenhua Xi Road 107

institute: Qilu Hospital

description: gene expression of colonic mucosa

hyb_protocol: 0.6 ug of cy3-labelled cRNA was fragmented at 60 ℃ for 30 minutes in a rection wolume of 22,5ul containing 1* Agilent fragmentation buffer and 2* Agilent blocking agent following the  manufacuturer's instructions. On completion of the fragmentation reaction, 22.5ul of 2* Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Scanner G5761A for 17 hours at 65 ℃ in a rotation Agilent hybridization oven.After hybridization, microarrays were washed 1 minute at roon temperature with GE wash buffer 1(Agilent) and 1 minute with 37 ℃ GE wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediatedly after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4*180k array slides (Scan area 61*21.6mm, scan resolution 3um, dye channel is set to green and green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction sofeware (version12.0.3.1,Agilent Technologies) using default paremeters to obtain background subtracted and spatially detrended processed signal intensities as the raw data. Raw data were nornalized in quantile algorithm with Genespring sofeware (version14.8,Agilent Technologies). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: colonic mucosa

label_protocol: Cyanine-3 (cy3) labeled cRNA was prepared from 0.2ug 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, Valencla, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from tissue samples using RNA Isolation Kit following the manufacturer's instructions

tag: subject status

value: Healthy control

tag: gender

value: female

value: colonic mucosa


title: myc-fast1a-wt-async-x26

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: ucnof-5

description: gene expression of colonic mucosa

source_name: non-inflamed colonic mucosa

value: UC patient

value: male

tag: tissue

value: non-inflamed colonic mucosa


title: ctrc-2

description: gene expression of colonic mucosa


title: hepaticTF-condition_SUV39H2_siRNA_Rep1

value: human BJ Fibroblast


title: hepaticTF-condition_SUV39H2_siRNA_Rep2


title: hepaticTF-condition_SUV39H1_siRNA_2_Rep2


title: ha-h2a2-wt-async-x26

value: ha

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1


title: ucnof-4

description: gene expression of colonic mucosa


title: hepaticTF-condition_SUV39H1_siRNA_2_Rep1

tag: cell type


title: ha-h2a1-wt-async-x26

tag: treatment

value: async


title: ucnof-3

description: gene expression of colonic mucosa

tag: age


title: hepaticTF-condition_SUV39H1_siRNA_1_Rep1


title: ctrc-1

description: gene expression of colonic mucosa


title: hepaticTF-condition_SUV39H1_siRNA_1_Rep2


title: ucnof-2

description: gene expression of colonic mucosa


title: hepaticTF-condition_SUMO2_siRNA_Rep2


title: hepaticTF-condition_SLTM_siRNA_Rep2


title: ha-fast1b-wt-async-x26


title: hepaticTF-condition_SUMO2_siRNA_Rep1


title: ha-fast1a-wt-async-x26


title: hepaticTF-condition_WDR46_siRNA_Rep1


title: hepaticTF-condition_SFPQ_siRNA_Rep2


title: myc-slow1b-wt-async-x22

value: myc

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT1-GGS-HA-Slow-MYC


title: hepaticTF-condition_SFPQ_siRNA_Rep1


title: myc-slow1a-wt-async-x22


title: hepaticTF-condition_SAFB2_siRNA_Rep1


title: hepaticTF-condition_SETDB1_siRNA_Rep1


title: myc-notag2-wt-async-x22

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0


title: myc-notag1-wt-async-x22


title: hepaticTF-condition_RPS19BP1_siRNA_Rep2


title: hepaticTF-condition_SAFB_siRNA_Rep2


title: scATAC-seq Inner POD14

first: Michael

last: Januszyk

address: 257 Campus Dr

department: Surgery

institute: Stanford University

description: Inner POD14

data_processing:
Fastq files were aligned to the mm10 mouse genome, peaks were called, fragements filtered, and peacks annoted in a single step using the 10X Genomics software CellRanger with the command "cellranger-atac count" using default parameters
genome build: mm10 v3.0.0
processed data files format and content: Standard 10X Genomics scATAC-seq filtered_peak_bc_matrix files

source_name: Dorsal wound

extract_protocol:
scATAC-seq:  Single cell ATAC-seq was performed following 10x Genomics protocols. Rainbow mouse wound healing fibroblasts were FACS-isolated as previously described. Spatial Transcriptomics: Wound specimens were rapidly harvested and flash frozen in OCT. Using the Visium Tissue Optimization Slide & Reagent kit, permeabilization time was optimized at a thickness of 10um per section and 37 minutes for mouse cutaneous scar tissue. Wound tissues were cryosectioned at -20 degrees onto gene expression slides.
scATAC-seq: For nuclei isolation, 10x genomics protocol CG000169 Rev D was followed using the low cell input modifications. Transposition, GEM generation and barcoding, post GEM Incubation Cleanup, library construction, and quantification was conducted following the 10x genomics protocol CG000169 Rev D. Pooled libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Spatial transcriptomics: The Gene Expression Slide & Reagent kit was followed per protocol, and used to produce sequencing libraries.
scATAC-seq: cDNA libraries were sequenced on a NextSeq 500 Illumina platform. In total, we generated scATAC-seq profiles from 5,353 cells, which yielded on average 13.0 × 10^3 unique fragments mapping to the nuclear genome. Spatial transcriptomics: The libraries were then sequenced using NextSeq (Illumina).

treatment_protocol: Skin tissue from mouse specimens was minced on ice and digested in DMEM-F12 (GIBCO®) with 0.5mg/ml LiberaseTM (Roche) for 30 minutes at 37º in an orbital shaker. The digests were quenched with quench media (DMEM-F12 with 10% Fetal Bovie Serum (FBS, Sigma)), centrifuged at 300 x G for 5 minutes at 4 deg C, resuspended in quench media, filtered through 100, 70, and 40um cell strainers (Falcon cell strainer, ThermoFisher), centrifuged once more, and resuspended in FACS buffer.

value: Rainbow

value: Dorsal wound

value: Splinted excisional wound healing

value: Fibroblasts


title: scATAC-seq Outer POD7

description: Outer POD7


title: scATAC-seq Outer POD14

description: Outer POD14


title: myc-h4b-wt-async-x25

value: wt

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV, HHF2-GGS-HA-Fast-MYC


title: scATAC-seq Inner POD7

description: Inner POD7


title: hepaticTF-condition_RPS19BP1_siRNA_Rep1


title: hepaticTF-condition_SAFB_siRNA_Rep1


title: ucinf-4

description: gene expression of colonic mucosa

source_name: inflamed colonic mucosa

value: inflamed colonic mucosa


title: ucinf-2

description: gene expression of colonic mucosa

value: UC patient

value: female


title: ucinf-5

description: gene expression of colonic mucosa

value: male


title: ucinf-3

description: gene expression of colonic mucosa


title: hepaticTF-condition_RPF2_siRNA_Rep1

value: human BJ Fibroblast


title: hepaticTF-condition_SAFB2_siRNA_Rep2


title: hepaticTF-condition_SLTM_siRNA_Rep1


title: scATAC-seq Inner POD2

description: Inner POD2


title: hepaticTF-condition_SETDB1_siRNA_Rep2


title: ucinf-1

description: gene expression of colonic mucosa


title: hepaticTF-condition_RPF2_siRNA_Rep2


title: hepaticTF-condition_RPF1_siRNA_Rep1


title: myc-h2b1b-wt-async-x25

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC


title: hepaticTF-condition_RBMX_siRNA_2_Rep2


title: myc-fast2b-wt-async-x22

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: ctrc-5

description: gene expression of colonic mucosa

value: Healthy control

value: colonic mucosa


title: hepaticTF-condition_RPF1_siRNA_Rep2


title: scATAC-seq Outer POD2

description: Outer POD2


title: hepaticTF-condition_RIF1_siRNA_Rep2


title: hepaticTF-condition_RIF1_siRNA_Rep1


title: hepaticTF-condition_RELA_siRNA_Rep2


title: myc-h2b1a-wt-async-x25

value: myc

value: async


title: myc-h2a1-wt-async-x19

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1


title: hepaticTF-condition_RELA_siRNA_Rep1


title: hepaticTF-condition_RBMX_siRNA_1_Rep2


title: hepaticTF-condition_RBMX_siRNA_2_Rep1


title: hepaticTF-condition_RBMX_siRNA_1_Rep1


title: myc-h4a-wt-async-x25


title: myc-fast2a-wt-async-x22


title: myc-fast2a-wt-async-x21


title: myc-fast1b-wt-async-x22


title: hepaticTF-condition_RBM26_siRNA_Rep1


title: hepaticTF-condition_RBM15_siRNA_Rep2


title: hepaticTF-condition_RBM26_siRNA_Rep2


title: hepaticTF-condition_RBM15_siRNA_Rep1


title: hepaticTF-condition_RBM12B_siRNA_Rep2


title: hepaticTF-condition_RBM12B_siRNA_Rep1


title: myc-fast1b-wt-async-x21


title: hepaticTF-condition_QKI_siRNA_Rep2


title: ucnof-1

description: gene expression of colonic mucosa

value: non-inflamed colonic mucosa


title: hepaticTF-condition_QKI_siRNA_Rep1


title: hepaticTF-condition_PTBP1_siRNA_Rep2


title: myc-fast1b-wt-async-x16


title: myc-fast1a-wt-async-x25


title: myc-fast1a-wt-async-x23


title: hepaticTF-condition_PRRX2_siRNA_Rep2


title: hepaticTF-condition_PTBP1_siRNA_Rep1


title: myc-fast1a-wt-async-x22


title: hepaticTF-condition_PRRX2_siRNA_Rep1


title: hepaticTF-condition_PRMT1_siRNA_Rep2


title: hepaticTF-condition_PRMT1_siRNA_Rep1


title: hepaticTF-condition_PRDM15_siRNA_Rep2


title: myc-fast1a-wt-async-x21


title: hepaticTF-condition_PRDM15_siRNA_Rep1


title: hepaticTF-condition_PPHLN1_siRNA_Rep1


title: hepaticTF-condition_PPHLN1_siRNA_Rep2


title: k56ac-fast2a-wt-async-x25