title: HCC70 Vehicle 3hr

value: Vehicle 3hr


title: O8

status: Public on Apr 07 2021

type: SRA

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

library_source: genomic

data_processing:
For RRBS, quality control and filtering of low quality reads was performed using “Trim Galore!” (Babraham Bioinformatics). Quality control indicated no relevant problems, so Bismark (v0.9.0, Babraham Bioinformatics) was used in Bowtie2-mode [21] for mapping. Seed length, mismatches and interval during multiseed alignment were set to the default values. The data were subsequently imported using the Bioconductor BiSeq package [22] for extraction and summarization of methylation values per CpG, CHH and CHG. The total methylation counts were used as proxy for DNA methylation since hydroxymethylation was negligible and methylation-specific results were featured by a too low coverage for several samples (see results).  Ensembl (assembly taeGut3.2.4, release 87) and Uniprot annotation (R-package UniProt.ws, v2.14.0) were used for annotation of transcription start site (TSS), start and end positions of genes and obtaining gene symbols for ensembl gene ids throughout all analyses.
Genome_build: taeGut3.2.4
Supplementary_files_format_and_content: .bismark.cov

molecule: genomic DNA

organism: Taeniopygia guttata

source_name: telencephalon

growth_protocol: For RRBS experiments, zebra finches (Taeniopygia guttata) were bred and raised at the University of Liège in an aviary containing 20 nest boxes maintained in a 13:11h light:dark cycle. Birds were provided ad libitum with food, water, grit and cuttlebone, and additional millet branches and egg food. Sprouted sunflower seeds were provided twice and nesting material once per week. The experiment was performed according to the Belgian law on animal experimentation and approved by the Ethical Committee for Animal Experimentation at the University of Liège (protocol 1396).

extract_protocol:
Brains from male and female juvenile and adult zebra finches (age: 1, 20, 65 (± 3 days) and adults (> 170) dph) were used, with birds from one nest randomly assigned to different age groups. Birds were rapidly decapitated, and the brain immediately removed and handled under ribonuclease-free conditions. The telencephalon was separated from the rest of the brain. The brain tissue was rapidly frozen on dry ice and stored at -80°C until further processing.
The combined interphase and organic (phenol) phase fractions of QiazolTM reagent-lysed samples were used for genomic DNA isolation. In short, ethanol was added to precipitate the DNA. The DNA pellet was then washed with sodium citrate solution (0.1M sodium citrate in 10% ethanol). Next, the pellet was incubated with 75% ethanol after which the pellet was dried and resuspended in DNase and RNase free water.
RRBS was performed by NXTGNT. Samples were purified using Zymo’s Genomic DNA Clean & ConcentratorTM-10 to avoid inhibition of enzymatic digestion. The Quant-iT™ PicoGreen™ dsDNA Assay Kit (Invitrogen P11496) was used to assess the concentration of the samples. After pooling the samples per three in equal proportions, the resulting 24 pools were dried and redissolved in water (molecular grade) to obtain a concentration of 2 µg and subsequently digested using MspI (New England BioLabs R0106, 20 000 units/ml). After purification of the digestion product with a GeneJET PCR Purification Kit (ThermoFisher K0701), the Qubit 2.0 Fluorometer (Q32866) was used to determine the concentration.
For the library preparation, the NEBNext® UltraTM DNA Library Prep Kit (New England BioLabs, E7370S) was used. For each sample, half of the DNA was oxidized for oxRRBS, while the other half was subjected to regular RRBS analysis. Subsequently, bisulfite and oxidative bisulfite conversion were performed using the TrueMethyl Seq kit (Cambridge Epigenetix, CEGX). A PCR with TrueMethyl DNA Polymerase was performed as a bisulfite conversion control and showed no aberrations. RRBS sequencing was performed on the Illumina NextSeq500. As initial paired-end experiments (2 x 76nt) demonstrated low quality of reverse reads, only forward reads were used, and subsequent experiments relied on single-end sequencing (1 x 76nt). Also, low-diversity issues led to overclustering and lower sequencing efficiency. Therefore, in collaboration with Illumina, different numbers of dark cycles were used to optimize the resulting useable library size (see Supplementary Information Table S1). Additionally, different concentrations of control PhiX were used as a function of other spiked-in libraries (independent of this project). Given that samples were randomized over different sequencing pools and the optimization particularly focused on increasing yield (forward read data quality was similar and acceptable for all experiments), no bias and at most a limited increase in technical variance is expected due to these variations in the protocol.

tag: tissue

value: telencephalon

tag: age

tag: Sex

value: F


title: O9


title: HCC70 Gefitinib+Vehicle 3hr

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

molecule: total RNA

organism: Homo sapiens

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: HCC70 cells were grown in RPMI1640 supplemented with 10% FBS. Cells were cultured at 37°C  in a humidified 5 % CO2 incubator.

extract_protocol: Cell pellets were harvested and treated with RLT buffer and RNA isolated with Qiagen RNeasy Mini kit following the standard protocol.

treatment_protocol: HCC70 cells were stimulated with IL-26 (30 ng /ml) in the presence or absence of Gefitinib (40μM) for 3 hr.

tag: treatment

value: Gefitinib+Vehicle 3hr


title: N

city: hefei

first: lu

last: zong

state: anhui

address: lujiang road

country: China

institute: Anhui Provincal Hospital

library_source: transcriptomic

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 .Quality control was checked on the raw sequence data using FastQC (https://en.wikipedia.org/wiki/FASTQ_format). Raw data were pre-processed using Solexa CHASTITY and Cutadapt to remove adaptor sequences, ribosomal RNA, and other contaminants that may interfere with clustering and assembly.
The trimmed reads are mapped to the corresponding reference genome using HISAT2 (version 2.0.4) for RNA-seq, and StringTie (version 1.2.3) was used to reconstruct the transcriptome . Then, Ballgown software was applied to calculate the fragments per kilobase of exon per million fragments mapped (FPKM) in RNA-seq data and analyze DEGs
FPKM≥0.5  considered statistically significant.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: adjacent normal endometrium

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adjacent normal endometrium


title: HuPV_042616H_WL13_H1975 DMSO #1

city: Vancouver

first: William

last: Lockwood

state: British Columbia

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: BC Cancer

hyb_protocol: cDNA was hybridized according to manufacturer's instructions at The Centre for Applied Genomics

scan_protocol: GeneChips were scanned according to manufacturer's instructions at The Centre for Applied Genomics

data_processing: Experssion data was RMA normalized by The Centre for Applied Genomics

label: biotin

source_name: H1975 DMSO

label_protocol: 500ng of RNA was converted to cDNA according to manufacturer's instructions and labelled at The Centre for Applied Genomics

growth_protocol: NCI-H23 (H23) and NCI-H1975 (H1975) were cultured in RPMI-1640 medium (Gibco, cat. #11875119) supplemented with 5% (vol/vol) FBS (Sigma), 1% penicillin-streptomycin solution (Gibco), and 1% Glutamax (Gibco) (standard growth media). Cultured cells were incubated in a humidified incubator at 37°C with 5% (vol/vol) CO2 and 95% (vol/vol) air. JQ1 resistant lines were generated by treating parental H23 and H1975 cells with increasing concentrations of JQ1 over a period of 6 months until cells could grow in 10μM JQ1. In parallel, cells were cultured in standard growth media plus 0.1% (vol/vol) DMSO as a control. Resistant lines were maintained in 10μM JQ1 media and the control lines in 0.1% DMSO media. Both resistant and control lines were tested for mycoplasma contamination and authenticated by STR profiling through Genetica.

extract_protocol: Total RNA was extracted from biological triplicates using a RNeasy Mini Kit (Qiagen). Sample quality was assessed using an Agilent Bioanalyzer and subsequent sample preparation, array hybridization, and data acquisition was performed by the Centre for Applied Genomics Microarray Facility (Toronto, Ontario).

treatment_protocol: H23 and H1975 resistant lines were grown in standard growth media with 10μM JQ1 media, control lines were grown in standard growth media with 0.1% DMSO media and control lines were grown in standrd growth media and treated with 10μM JQ1 for 6 hours. All treatments were performed in 6-well plates.

tag: cell line

tag: jq1 status

value: Control

value: DMSO


title: O7


title: A

source_name: thin endometrium

value: thin endometrium


title: O6

value: M


title: HuPV_042616H_WL14_H1975 DMSO #2


title: HuPV_042616H_WL15_H1975 DMSO #3


title: 9d

type: genomic

city: Durham

first: Elaine

last: Guevara

state: North Carolina

address: 130 Science Drive

department: Evolutionary Anthropology

country: USA

institute: Duke University

description: normal brain sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: samples were scanned using an Illumina BeadArrayTM reader

data_processing: .idat files were quality filtered and converted to beta values using the Chimp Analysis Methylation Pipeline R package

label: Cy5 and Cy3

organism: Macaca mulatta

source_name: lateral cerebellum

label_protocol: Standard Illumina Protocol

extract_protocol: silica column

value: lateral cerebellum


title: Total-RNA-seq_168h_rep2

city: Göttingen

first: Jinmi

last: Choi

address: Am Fassberg 11

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

data_processing:
Sequencing data preprocessing. Paired-end reads with additional 6 base reads of barcodes were obtained for each of the samples. Reads from TT-seq/RNA-seq or ChIP-seq/ATAC-seq were demultiplexed and mapped with STAR 2.3.0 (Dobin et al., 2013) or Bowtie2.2.5/Bowtie1.0.0 (Langmead and Salzberg, 2012), respectively, to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). For ATAC-seq, chromosome M was removed. Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
For ChIP-seq , we used the 'callpeak' function of MACS2.1.1 (Zhang et al., 2008) with ‘--BAMPE’ options. To catalogue all the C/EBPα, BRD4 or H3K4me1 binding sites over all the time points, we merged and reduced all peaks, and removed those falling +/- 4Mb of centromeric heterochromatin regions. Duplicates were removed. To obtain the enriched signal (count matrix), read count within the merged peaks were normalized by library size followed by a normalization with counts in corresponding input.
For ATAC-seq, reads were aligned to GRCh38 genome assembly without mitochondrial chromosome (ChrM) using Bowtie1.0.0 (Langmead et al., 2009). Bigwig files were generated by Deeptools 2.3.4 .
For TT-seq, we used a spike-in (RNAs) as described in (Schwalb et al., 2016) to allow antisense bias determination (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) in TT-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015).
For Total RNA-seq, reads were aligned to GRCh38 genome assembly with STAR2.4.2 ((Dobin et al., 2013).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: BRD4allPeaks_reduced.txt:Merged BRD4 peaks from all the time points.; BRD4mat.txt: BRD4 count table for genomic coordinates in BRD4allPeaks_reduced.txt, normalized with size factors and input
Supplementary_files_format_and_content: CEBPallPeaks_reduced.txt:Merged CEBPa peaks from all the time points; CEBPmat.txt: CEBP coverage normalized to size factors and input on the genomic coordinates in CEBPallPeaks_reduced.txt
Supplementary_files_format_and_content: H3K4me1allpeaks_reduced.txt:Merged H3K4me1 peaks from all the time points; H3K4me1mat.txt: H3K4me1 coverage normalized to size factors and input on the genomic coordinates in H3K4me1allPeaks_reduced.txt
Supplementary_files_format_and_content: The bigwig files of ATAC-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X options.
Supplementary_files_format_and_content: Strand specific bigwig files of TT-seq and RNA-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X --filterRNAstrand options.

source_name: BLaER

extract_protocol:
ChIP-seq: At each time point, 3x10^7 cells were harvested and fixed with 1% of formaldehyde for 8 minutes (Thermo Scientific, 28908). Formaldehyde was quenched with 0.2M glycine for 5 min. Chromatin was sheared to 200-500 bp in size using the Covaris S220 ultrasonicator (16min for C/EBPα and BRD4, 18min for H3K4me1). A fraction of the resulting chromatin was used as input control. Sheared chromatin (50ug for C/EBPα and BRD4, 30ul for H3K4me1) was incubated with 5 ug of antibodies - anti-C/EBPα (Santa Cruz, sc-61), anti-H3K4me1 (abcam, ab8895), anti-BRD4 (Bethyl Laboratories, A301–985A100)- bound to protein-A beads (Life Technologies, 9999-01). Samples were incubated at 65ºC overnight to reverse the crosslinks, followed by RNase and proteinase K treatments.
ATAC-seq: ATAC-seq was performed as described (Buenrostro et al., 2013). Briefly, 5 x 10^4 cells were harvested and treated with Nextera Tn5 Transposase (Illumina, FC-121-1030) for 45 min at 37°C.
Total RNA-seq: Total RNA was extracted from the cells labelled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min. RNA prepared using QIAzol according to the manufacturer’s instructions was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator before the library preparation.
At each time point, 1-2.2 x 10^8 cells were labeled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min and harvested by centrifuging at 500g for 2 min. Harvested pellets were lysed with QIAzol (Qiagen, 79306). Following addition of 5ng of spike-in mix per 1 x 10^8 cells, total RNA was purified using QIAzol (Qiagen, 79306) according to the manufacturer’s instructions. Total RNA (300ug) was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator. Newly synthesized RNAs were purified as described (Schwalb et al., 2016) with the following modifications. After streptavidin pull down, the resulting RNA was purified with RNeasy Micro Kit (Qiagen, 74004), together with DNase treatment (Qiagen, 79254).
ChIP-seq: NEB Ultra DNA Library kit (NEB, E7370S) ; ATAC-seq:Nextera Tn5 Transposase ((Illumina, FC-121-1030)) 1x NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S) ; Total RNA-seq and TT-seq Ovation Universal RNA-seq System (Nugen, 0343)

tag: cell type

value: RCH-ACV stably expressing estrogen inducible C/EBPa

value: Beta-estradiol (100nM) treatment 168h+ 5 min 4sU labeling


title: 9a

description: normal brain sample

source_name: prefrontal cortex

value: prefrontal cortex


title: HuPV_042616H_WL12_H1975 Resis #3

source_name: H1975 Resis

value: Resistant


title: HuPV_042616H_WL11_H1975 Resis #2


title: HuPV_042616H_WL10_H1975 Resis #1


title: O4


title: Total-RNA-seq_96h_rep2

value: Ovation Universal RNA-seq System (Nugen, 0343)

value: Beta-estradiol (100nM) treatment 96h+ 5 min 4sU labeling


title: O3


title: 15d

description: normal brain sample


title: HuPV_042616H_WL9_H23 6hr #3

source_name: H23 6hr

value: Control Treated


title: 15a

description: normal brain sample


title: 14d

description: normal brain sample


title: 13a

description: normal brain sample


title: Total-RNA-seq_96h_rep1


title: 14a

description: normal brain sample


title: Total-RNA-seq_168h_rep1


title: Total-RNA-seq_72h_rep2


title: O24

value: adult


title: si_Ctr1

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description: Control sample1 transfected with scramble siRNA

data_processing:
Sequenced reads were mapped to hg38 whole genome using STAR Aligner with default parameters
The reads are quantified using featureCounts from Subread package
Picard tools is used to determine the average insert size and standard deviation
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample analyzed

source_name: Lung adenocarcinoma cells

growth_protocol: Cells were grown in DMEM medium supplemented with 10% FBS and 1% pen+strep antibiotics

extract_protocol:
RNA was extracted from 100000 cells using reliaprep rna cell miniprep system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected either with 25 pmol control LNA-GapmeRs or 25 pmol LY6k-AS targeting LNA GapmeRs. For siRNA experiments, Sigma siRNAs were transcfted at 40 pmol concentration. The RNA-iMAX transfection reagent was used in all experiments.

value: A549 cell line


title: 13d

description: normal brain sample


title: Total-RNA-seq_72h_rep1


title: O5

value: telencephalon


title: HuPV_042616H_WL7_H23 6hr #1


title: O22


title: 11d

description: normal brain sample

value: F


title: Total-RNA-seq_48h_rep2


title: O23


title: O21


title: 12a

description: normal brain sample


title: Total-RNA-seq_48h_rep1


title: O20


title: HuPV_042616H_WL8_H23 6hr #2


title: HuPV_042616H_WL6_H23 DMSO #3

source_name: H23 DMSO


title: HuPV_042616H_WL5_H23 DMSO #2


title: Total-RNA-seq_36h_rep2


title: O2


title: Total-RNA-seq_36h_rep1


title: 11a

description: normal brain sample


title: O19


title: AX_2: WT_E14.5_Cortical_Neurospheres_rep2

city: Baltimore

first: Jonathan

middle: Joseph

last: Augustin

state: MD

address: 733 N. Broadway Rm#332

institute: Johns Hopkins Medical Institute

data_processing:
- Fastqs files were used to quantify both spliced and unspliced counts by Alevin (Salmon v1.3.0)
- Abundances matrices were read in by R package tximeta (v1.8.1)
- Removed cells with less than 200 expressed genes, and cells flagged as any outlier deviating more than triple median absolute deviations(MAD) from the median of log2(TotalUMIs),log2(number of expressed genes), percentage of mitochondrial gene counts, and log10(doublet scores)
- Doublet scores were computed using doubletCells function in R package scran (v1.18.1)
- All mitochondrial genes and any genes which were expressed in less than 20 cells werefurther excluded from all subsequent analyses
- Expression abundances were then library size normalized and log2transformed by function normalizeCounts in R package scuttle(v1.0.2)
- The biological samples were integrated together by Seurat (v3.2.2)
- Genome_build: GRCm38
- Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample, and data frame containing UMI, estimated cell cycle stage and tricycle position

organism: Mus musculus

source_name: Neurospheres

growth_protocol: Neuropheres were grown in complete neurosphere media containing a DMEM-F12 base with B27 supplement (no retinoic acid), N2 supplement, 1.42 grams of glucose, 10ng/ml EGF and 10ng/ml bFGF.

extract_protocol:
Neurospheres were dissociated into single cells for use with the Chromium Single Cell 3’ library & GelBead Kit v2 (10x Genomics)
Chromium Single Cell 3’ library & GelBead Kit v2 (10x Genomics)

tag: strain

value: Dorsal Telencephalon

value: Embryonic Day 14.5


title: 12d

description: normal brain sample


title: HuPV_042616H_WL3_H23 Resis #3

source_name: H23 Resis


title: HuPV_042616H_WL2_H23 Resis #2


title: AX_1: WT_E14.5_Cortical_Neurospheres_rep1

data_processing:
- Fastqs files were used to quantify both spliced and unspliced counts by Alevin (Salmon v1.3.0)
- Abundances matrices were read in by R package tximeta (v1.8.1)
- Removed cells with less than 200 expressed genes, and cells flagged as any outlier deviating more than triple median absolute deviations(MAD) from the median of log2(TotalUMIs), log2(number of expressed genes), percentage of mitochondrial gene counts, and log10(doublet scores)
- Doublet scores were computed using doubletCells function in R package scran (v1.18.1)
- All mitochondrial genes and any genes which were expressed in less than 20 cells werefurther excluded from all subsequent analyses
- Expression abundances were then library size normalized and log2transformed by function normalizeCounts in R package scuttle(v1.0.2)
- The biological samples were integrated together by Seurat (v3.2.2)
- Genome_build: GRCm38
- Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample, and data frame containing UMI, estimated cell cycle stage and tricycle position


title: HuPV_042616H_WL4_H23 DMSO #1

value: Control

value: DMSO


title: Total-RNA-seq_30h_rep1


title: O18

value: M


title: 26a

description: normal brain sample


title: Total-RNA-seq_30h_rep2


title: 10d

description: normal brain sample

value: lateral cerebellum


title: HuPV_042616H_WL1_H23 Resis #1


title: 10a

description: normal brain sample


title: O17


title: 24a

description: normal brain sample


title: 26d

description: normal brain sample


title: E1E3-A15

city: Shenzhen

first: JING

last: LUO

email: luoj17@lzu.edu.cn, luojing9520@163.com

address: No 7,Pengfei Road,Dapeng District

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
Hi-C data were mapped to the mm9 with two-step approach incorporated in the Hic-Pro software(v2.10.0)
Homer was used to call TADs at a 10kb resolution while Fit-HiC was used to generate loops at the 10kb resolution
Genome_build: mm9
Supplementary_files_format_and_content: HIC,bed,txt

source_name: mESCs

growth_protocol: The mESCs (ES-E14TG2a, ATCC, CRL_1821) is cultured on 0.1% gelatin-coated plates in ES medium (Knockout-DMEM containing 15% FBS, 100 U/mL Penicillin, 100 ug/mL Streptomycin, 0.1 mM MEM nonessential amino acids, 1 mM sodium pyruvate, 2 mM GlutaMAX, 0.1 mM 2-mercaptoethanol, 1000 U/mL LIF, 3 mM CHIR99021 [GSK3b inhibitor, Selleck], 1 mM PD0325901 [MEK inhibitor, Selleck]) and maintained in a pluripotent state in the absence of a feeder layer

extract_protocol: The exo-Hi-C was coordinated to standard Hi-C with improvement procedure of linear DNA eliminating. Such step was applied following proximity-ligation according to the procedure of reference (Kong S, et al. Exonuclease combinations reduce noises in 3D genomics technologies. Nucleic acids research,  (2020).). LRC or LIC were employed to assess  their effectiveness for eliminating linear interaction noise.

value: embryonic stem cell

tag: genotype/variation


title: O16


title: E1E3-A13


title: O15


title: Total-RNA-seq_12h_rep2

value: RCH-ACV stably expressing estrogen inducible C/EBPa

value: Beta-estradiol (100nM) treatment 12h + 5 min 4sU labeling


title: w326-2


title: Total-RNA-seq_24h_rep1

value: Beta-estradiol (100nM) treatment 24h + 5 min 4sU labeling


title: Total-RNA-seq_24h_rep2

value: Ovation Universal RNA-seq System (Nugen, 0343)

value: Beta-estradiol (100nM) treatment 24h+ 5 min 4sU labeling


title: O14


title: O13


title: 23a

description: normal brain sample

value: prefrontal cortex


title: Total-RNA-seq_0h_rep2

value: Beta-estradiol (100nM) treatment 0h + 5 min 4sU labeling


title: E3-15


title: 24d

description: normal brain sample


title: O12


title: 23d

description: normal brain sample


title: TT_96h_rep2

description: 4sU-labeled RNA

data_processing:
Library strategy: TT-seq (Schwalb et al., 2016)
Sequencing data preprocessing. Paired-end reads with additional 6 base reads of barcodes were obtained for each of the samples. Reads from TT-seq/RNA-seq or ChIP-seq/ATAC-seq were demultiplexed and mapped with STAR 2.3.0 (Dobin et al., 2013) or Bowtie2.2.5/Bowtie1.0.0 (Langmead and Salzberg, 2012), respectively, to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). For ATAC-seq, chromosome M was removed. Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
For ChIP-seq , we used the 'callpeak' function of MACS2.1.1 (Zhang et al., 2008) with ‘--BAMPE’ options. To catalogue all the C/EBPα, BRD4 or H3K4me1 binding sites over all the time points, we merged and reduced all peaks, and removed those falling +/- 4Mb of centromeric heterochromatin regions. Duplicates were removed. To obtain the enriched signal (count matrix), read count within the merged peaks were normalized by library size followed by a normalization with counts in corresponding input.
For ATAC-seq, reads were aligned to GRCh38 genome assembly without mitochondrial chromosome (ChrM) using Bowtie1.0.0 (Langmead et al., 2009). Bigwig files were generated by Deeptools 2.3.4 .
For TT-seq, we used a spike-in (RNAs) as described in (Schwalb et al., 2016) to allow antisense bias determination (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) in TT-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015).
For Total RNA-seq, reads were aligned to GRCh38 genome assembly with STAR2.4.2 ((Dobin et al., 2013).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: BRD4allPeaks_reduced.txt:Merged BRD4 peaks from all the time points.; BRD4mat.txt: BRD4 count table for genomic coordinates in BRD4allPeaks_reduced.txt, normalized with size factors and input
Supplementary_files_format_and_content: CEBPallPeaks_reduced.txt:Merged CEBPa peaks from all the time points; CEBPmat.txt: CEBP coverage normalized to size factors and input on the genomic coordinates in CEBPallPeaks_reduced.txt
Supplementary_files_format_and_content: H3K4me1allpeaks_reduced.txt:Merged H3K4me1 peaks from all the time points; H3K4me1mat.txt: H3K4me1 coverage normalized to size factors and input on the genomic coordinates in H3K4me1allPeaks_reduced.txt
Supplementary_files_format_and_content: The bigwig files of ATAC-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X options.
Supplementary_files_format_and_content: Strand specific bigwig files of TT-seq and RNA-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X --filterRNAstrand options.

value: Beta-estradiol (100nM) treatment 96h+ 5 min 4sU labeling


title: TT_96h_rep1

description: 4sU-labeled RNA


title: E1-6


title: w326-4


title: E1-4


title: 21a

description: normal brain sample


title: 22a

description: normal brain sample


title: w326-3


title: O1

value: telencephalon


title: Total-RNA-seq_0h_rep1


title: 21d

description: normal brain sample


title: WT-A3

value: WT


title: w326-1


title: B8

value: F


title: TT_24h_rep1

description: 4sU-labeled RNA


title: B9


title: 19d

description: normal brain sample


title: TT_12h_rep2

description: 4sU-labeled RNA


title: H-CLP72H-6

city: Hangzhou

first: Xiao

last: Yan

address: No.2318 Yuhangtang Road

institute: Hangzhou Normal University

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Raw counts and Fragments Per Kilobase Million (FPKM) were calculated by stringtie v1.3.3
Genome_build: hg38
Supplementary_files_format_and_content: tab_delimited text files include count and  FPKM values for each Sample

source_name: Heart

extract_protocol:
After collected, the hearts were put in liquid nitrogen quickly, and preserved in low temperature environment. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from heart tissues following a manufacturer’s protocol. Total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running an 1% agarose gel electrophoresis, stained with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

treatment_protocol: C57BL/6J mice were subjected to cecal ligation and puncture (CLP) for 24, 48, and 72 hours.

value: Heart

value: 8–10 weeks old

tag: genotype

value: wild type

value: cecal ligation and puncture (CLP)

tag: time point


title: B7


title: TT_12h_rep1

description: 4sU-labeled RNA


title: H-CLP72H-5


title: O10

value: M


title: 22d

description: normal brain sample

value: lateral cerebellum


title: 20a

description: normal brain sample


title: TT_0h_rep2

description: 4sU-labeled RNA

value: RCH-ACV stably expressing estrogen inducible C/EBPa


title: Total-RNA-seq_12h_rep1

value: Beta-estradiol (100nM) treatment 12h + 5 min 4sU labeling


title: B5


title: 7a

description: normal brain sample

organism: Pan troglodytes


title: H-CLP72H-3


title: 19a

description: normal brain sample


title: H-CLP72H-4


title: H-CLP72H-2


title: 20d

description: normal brain sample


title: Input_18min_96h_rep1_ChIPSeq

description: Chromatin sonication for 18 min with Covaris

value: NEB Ultra DNA Library kit

value: Beta-estradiol (100nM) treatment 96h


title: H-CLP48H-5


title: 6a

description: normal brain sample


title: Input_18min_24h_rep2_ChIPSeq

value: Beta-estradiol (100nM) treatment 24h


title: B3


title: H-CLP48H-4


title: NO3_15mM_2

city: Seville

first: Ana

middle: Belén

last: Romero-Losada

state: Seville

address: St. Américo Vespucio, 49

department: Institute for plant biochemistry and photosynthesis

country: Spain

institute: University of Seville

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor packages ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html) and limma (http://bioconductor.org/packages/release/bioc/html/limma.html)
Genome_build: GCA_011766145.1 available from https://www.ncbi.nlm.nih.gov/genome/67110?genome_assembly_id=839686
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

organism: Haematococcus lacustris

source_name: liquid culture

growth_protocol: Haematococcus lacustris was grown in column photochemostats with two different NO3 concentration.

extract_protocol:
Total RNA was extracted using E.Z.N.A.® Plant RNA Kit (Omega, R6827-01)
Libraries were prepared using 1 μg of total RNA with the VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Vazyme, NR603) according to the manufacturer’s instructions.

treatment_protocol: NO3 2mM and 15mM

value: CCAP 34/8

tag: no3 concentration


title: 8d

description: normal brain sample


title: B24

value: adult


title: B23


title: 5d

description: normal brain sample


title: 7d

description: normal brain sample


title: H-CLP48H-3


title: B22


title: Input_18min_24h_rep1_ChIPSeq


title: Input_18min_12h_rep2_ChIPSeq

value: Beta-estradiol (100nM) treatment 12h


title: 5a

description: normal brain sample

value: prefrontal cortex


title: 6d

description: normal brain sample


title: NO3_15mM_1


title: TT_24h_rep2

description: 4sU-labeled RNA

value: Ovation Universal RNA-seq System (Nugen, 0343)

value: Beta-estradiol (100nM) treatment 24h+ 5 min 4sU labeling


title: NO3_2mM_2


title: Input_18min_12h_rep1_ChIPSeq


title: H-CLP48H-1

value: Heart


title: B6

value: telencephalon


title: O11


title: NO3_2mM_1


title: B21


title: Input_18min_0h_rep2_ChIPSeq

value: Beta-estradiol (100nM) treatment 0h


title: 4d

description: normal brain sample

value: F


title: B2


title: MeRIP-seq-sh-YTHDF1-INPUT-rep3

city: Shanghai

first: Xiao-Yu

last: Chen

state: Shanghai

address: Yishan Road 600, Shanghai, China.

department: Department of Gastroenterology

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

data_processing:
The library establishment and next generation sequencing were performed by Aksomics (Shanghai, China).
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR (2.5.2b)
Genome_build: GRCh37
Supplementary_files_format_and_content: expression transcript and peak text files

source_name: Gastric  cancer cells

growth_protocol: Cells are cultured using Ham's F-12K basic medium

extract_protocol:
RNA was harvested using Trizol reagent. Seq-StarTM poly(A) mRNA Isolation Kit (Arraystar, Rockville, USA) was used to obtain complete mRNA.1 ug of total RNA for the construction of sequencing libraries in RNA-seq. After fragmentating, RNA was incubated with m6A antibody (ABE572, Merck Millipore, Germany) for immunoprecipitation based on the instructions of the MeRIP m6A Kit (Merck Millipore, Germany).  60 ug of total RNA for the construction of sequencing libraries in MeRIP-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AGS cells were infected with lentivirus vectors that encoded either sh-YTHDF1 or an empty vector (sh-NC) according to the manufacturers’ instruction

tag: merip antibody


title: H-CLP24H-6

value: 8–10 weeks old

value: wild type

value: cecal ligation and puncture (CLP)


title: 3a

description: normal brain sample

value: M


title: 4a

description: normal brain sample


title: B19

source_name: telencephalon


title: MeRIP-seq-sh-YTHDF1-INPUT-rep2


title: H-CLP24H-5


title: H3K4me1_96h_rep2_ChIPSeq

value: RCH-ACV stably expressing estrogen inducible C/EBPa

value: NEB Ultra DNA Library kit

tag: chip antibody

value: anti-H3K4me1 (abcam, ab8895)


title: 2a

description: normal brain sample


title: 3d

description: normal brain sample

value: lateral cerebellum


title: Input_18min_0h_rep1_ChIPSeq


title: H-CLP24H-3


title: MeRIP-seq-sh-YTHDF1-INPUT-rep1


title: H3K4me1_96h_rep1_ChIPSeq

value: Beta-estradiol (100nM) treatment 96h


title: B18


title: H-CLP24H-2


title: MeRIP-seq-sh-NC-INPUT-rep3

description: sh-NC


title: Input_18min_96h_rep2_ChIPSeq


title: 1a

description: normal brain sample


title: H-CLP24H-1


title: MeRIP-seq-sh-NC-INPUT-rep2

description: sh-NC


title: B17


title: 2d

description: normal brain sample


title: H3K4me1_24h_rep1_ChIPSeq

value: Beta-estradiol (100nM) treatment 24h


title: B16


title: H-CON-5

value: Sham operation


title: MeRIP-seq-sh-NC-INPUT-rep1

description: sh-NC


title: H-CON-4


title: B15


title: H3K4me1_12h_rep2_ChIPSeq

value: Beta-estradiol (100nM) treatment 12h


title: B14


title: MeRIP-seq-sh-YTHDF1-rep3

value: m6A antibody (ABE577, Merck Millipore, Germany)


title: H3K4me1_12h_rep1_ChIPSeq


title: H3K4me1_24h_rep2_ChIPSeq


title: H-CON-3

value: Heart


title: B13

value: telencephalon


title: MeRIP-seq-sh-YTHDF1-rep2

value: m6A antibody (ABE576, Merck Millipore, Germany)


title: 8a

description: normal brain sample

value: F

value: prefrontal cortex


title: H3K4me1_0h_rep2_ChIPSeq

value: Beta-estradiol (100nM) treatment 0h


title: 1d

description: normal brain sample


title: H-CON-2

value: 8–10 weeks old

value: wild type


title: MeRIP-seq-sh-YTHDF1-rep1

value: m6A antibody (ABE575, Merck Millipore, Germany)


title: B12

value: M


title: H3K4me1_0h_rep1_ChIPSeq

value: RCH-ACV stably expressing estrogen inducible C/EBPa

value: NEB Ultra DNA Library kit

value: anti-H3K4me1 (abcam, ab8895)


title: B11


title: H-CON-1


title: B10


title: MeRIP-seq-sh-NC-rep3

description: sh-NC

value: m6A antibody (ABE574, Merck Millipore, Germany)


title: MeRIP-seq-sh-NC-rep2

description: sh-NC

value: m6A antibody (ABE573, Merck Millipore, Germany)


title: B1


title: MeRIP-seq-sh-NC-rep1

description: sh-NC

value: m6A antibody (ABE572, Merck Millipore, Germany)


title: JD-9

data_processing:
FastQC (v0.10.1) was used to assess RNA-seq data quality, indicating no relevant problems. Therefore, no additional trimming was performed.  STAR (v2.5.2b) was used to align and map reads to the reference genome [20]. Samtools (v0.1.18) and htseq-count (v0.6.0) (based on GTF file, Ensembl, assembly 3.2.4, release 87) were used for downstream analysis and data summary, respectively.
Genome_build: taeGut3.2.4
Supplementary_files_format_and_content: htseq-count

growth_protocol: For RNA-seq, zebra finches (Taeniopygia guttata) were bred and raised at the University of Liège in an aviary containing 20 nest boxes maintained in a 13:11h light:dark cycle. Birds were provided ad libitum with food, water, grit and cuttlebone, and additional millet branches and egg food. Sprouted sunflower seeds were provided twice and nesting material once per week. The experiment was performed according to the Belgian law on animal experimentation and approved by the Ethical Committee for Animal Experimentation at the University of Liège (protocol 1396).

extract_protocol:
Brains from male and female juvenile and adult zebra finches (age: 1, 20, 65 (± 3 days) and adults (> 170) dph) were used, with birds from one nest randomly assigned to different age groups. Birds were rapidly decapitated, and the brain immediately removed and handled under ribonuclease-free conditions. The telencephalon was separated from the rest of the brain. The brain tissue was rapidly frozen on dry ice and stored at -80°C until further processing.
Telencephalon samples were lysed in QiazolTM lysis reagent (Qiagen 79306) using a TissueLyser instrument (Qiagen 85300). RNA was extracted using the RNeasy mini kit (Qiagen 74106), according to the manufacturer’s instructions.
Quality control and library preparation for RNA sequencing was performed by the NXTGNT sequencing facility of Ghent University (Ghent, Belgium). RNA samples were quantified, and quality controlled using the Quant-iTTM Ribogreen® RNA Assay (Invitrogen R11491) kit and Agilent RNA 6000 Nano (Agilent 5067-1511; on Agilent Bioanalyzer). Upon DNase treatment, library preparation (Truseq stranded mRNA, Illumina RS-122-2101 and RS-122-2102) was performed on 1µg of each sample. As recommended by Illumina, fragmentation was performed for 8 minutes at 94°C. Samples were pooled and subsequently multiplex identifiers were added to each pool. To increase uniformity of the protocol, library preparation was performed using the IP-star® Compact Automated System (Diagenode B03000002). Bioanalyzer QC after library preparation (Agilent, High Sensitivity DNA kit) demonstrated no relevant batch effects. Single-end 75 bp sequencing was performed three times for each of the pooled libraries on the Illumina NextSeq500 (over four lanes).

tag: age (days post hatching)


title: RNA-seq-sh-YTHDF1-rep3


title: JD-6


title: RNA-seq-sh-NC-rep3

description: sh-NC


title: RNA-seq-sh-YTHDF1-rep2


title: JD-8


title: RNA-seq-sh-NC-rep2

description: sh-NC


title: JD-5


title: RNA-seq-sh-YTHDF1-rep1


title: JD-7


title: RNA-seq-sh-NC-rep1

description: sh-NC


title: B20

value: adult


title: JD-4


title: Gpos_Ppos_Q73_C

city: Rochester

first: John

last: Mariani

state: NY

address: 601 Elmwood Avenue

department: Neurology

institute: University of Rochester

description: Gene expression from transduced Lateral Ganglionic Eminence Astrocytes and Neurons

hyb_protocol: Hybridization was processed according ot manufacturer instructions

scan_protocol: GeneChips were scanned according to manufacturer instructions

data_processing: Following import of raw data into R with the oligo package (R Core Team ; Gautier et al. 2004) robust multiarray analysis (RMA) was utilized for pre-processing and normalization (Irizarry et al. 2003). Probe annotations were fetched using biomaRt (Durinck et al. 2009) and probes targeting multiple enesmbl IDs were removed. . For removal of unwanted variance, SVA determined 4 surrogate variables to be added to the design formula (Leek et al. 2012) prior to differential expression analysis in limma (Richieet al. 2015) where an adjusted p-value of < 0.1 was deemed significant.

label_protocol: Total RNA was labeled with biotin according to manufacturer instructions

growth_protocol: LGE tissue was minced and dissociated using papain and DNase as previously described, always within 2 h of extraction. The dissociated cells were maintained in DMEM/F12/N2-based medium supplemented with 2% PD-FBS and 10 ng ml−1 FGF2 until ready for lentiviral transduction.

extract_protocol: Transduced cells were isolated by FACS for EGFP in combination with antigenic selection of PSA-NCAM to isolate neuronal and astrocytic populations. RNA was extracted from the FACS-isolated cells and then used for microarray profiling.

treatment_protocol: To express mutant or control HTT in LGE cells, the cells were transduced with lentivirus at 0.5 multiplicities of infection expressing EGFP in tandem with the first exon of either wild type HTT (Q23), mHTT (Q73), or control expressing reporter only (pTank) (see (Benraiss et al., 2016) for viral constructs and amplification).

tag: sort

tag: lentivirus

tag: sampleID

value: C


title: JD-3


title: JD-2


title: Gpos_Pneg_Q73_C


title: Gpos_Pneg_Q23_C


title: Gpos_Pneg_pTANK_C

value: pTANK


title: Gpos_Ppos_pTANK_C


title: Gpos_Ppos_Q23_C


title: Gpos_Ppos_Q73_B

value: B


title: SK-N-AS RNA shIGF2BP1 replicate B

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. BBDuk was used to trim/filter low-quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome (GRCh38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCh38.78). EdgeR was used to fit the read counts to the negative binomial model along with generalized linear model (GLM) and differentially expressed genes were determined by the likelihood ratio test method implemented in the edgeR package. Significance was defined to be those with q-value < 0.01 calculated by the Benjamini-Hochberg method to control the false discovery rate (FDR) and log2 fold change is greater than 1 or smaller than -1. The list of differentially expressed genes was analyzed with Ingenuity Pathway Analysis (Qiagen).
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file containing the result of edgeR differential expression analysis and CPM (copy per million) values for each sample

source_name: SK-N-AS

growth_protocol: IGF2BP1 was knocked down using doxycycline inducible SMARTvector Inducible TurboGFP shRNA Lentiviral constructs (Cat. No. V3SH11252- 227953809 GE Dharmacon) shRNA SMARTvector Inducible Non-targeting Control construct (VSC11653 GE Dharmacon). Lentivirus particles were produced from above plasmids in Lenti-X 293T cells (Takara) and where used to transduce SK-N-AS cells to make stable cell lines. Cells were then subjected to 7 days of puromycin selection (1mg/ml) in growth media.

extract_protocol:
Three biological replicates of control and IGF2BP1 knockdown cells were collected and RNA was isolated using RNeasy Mini Kit (Qiagen) before being subjected to total RNA sequencing (RNAseq)
RNA-seq libraries were generated using KAPA RNA HyperPrep Kits with RiboErase (HMR) (Roche), which targets and depletes rRNA using DNA probes and RNase H

treatment_protocol: Cells transduced with shRNA constructs were induced with docycyclin (1-2 mg/ml) for 6 days prior to harvesting.

value: SK-N-AS

value: neuroblastoma

value: pLenti shRNA IGF2BP1 (GFP) positive


title: B4

data_processing:
For RRBS, quality control and filtering of low quality reads was performed using “Trim Galore!” (Babraham Bioinformatics). Quality control indicated no relevant problems, so Bismark (v0.9.0, Babraham Bioinformatics) was used in Bowtie2-mode [21] for mapping. Seed length, mismatches and interval during multiseed alignment were set to the default values. The data were subsequently imported using the Bioconductor BiSeq package [22] for extraction and summarization of methylation values per CpG, CHH and CHG. The total methylation counts were used as proxy for DNA methylation since hydroxymethylation was negligible and methylation-specific results were featured by a too low coverage for several samples (see results).  Ensembl (assembly taeGut3.2.4, release 87) and Uniprot annotation (R-package UniProt.ws, v2.14.0) were used for annotation of transcription start site (TSS), start and end positions of genes and obtaining gene symbols for ensembl gene ids throughout all analyses.
Genome_build: taeGut3.2.4
Supplementary_files_format_and_content: .bismark.cov

tag: tissue

value: telencephalon

tag: age


title: Gpos_Ppos_Q23_B


title: SK-N-AS RNA shIGF2BP1 replicate C


title: H-CLP48H-2

value: Heart

value: 8–10 weeks old

value: wild type

tag: treatment

value: cecal ligation and puncture (CLP)


title: JD-24

tag: Sex

value: M


title: SK-N-AS RNA shIGF2BP1 replicate A

tag: cell line


title: SK-N-AS RNA shScramble control replicate C

tag: cell type

value: pLenti shRNA Scramble (GFP) positive


title: NMYC_RB_M3490 [scRNA-seq]

city: New York

first: Nicholas

last: Brady

address: 1188 York Ave

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

data_processing:
scRNA-seq reads were aligned to mm10 reference genome using the cellranger count pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 file containing per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode.

source_name: Mouse tumor

extract_protocol:
Prostate tumors were digested using 1 mg/mL collagenase and 0.2 mg/mL hyaluronidase for 1 hour at 37C followed by additional digestion with TrypLE for 15 minutes at 37C. Digestions were inactivated with media containing 1x B-27 supplement.
Libraries were generated using the 10x Genomics Chromium Single Cell RNA Library Kit following the manufacturer's recommended protocol.

value: Pb-Cre+; Pten f/f; Rb1 f/f; MYCN+

value: 6 weeks

value: Mouse tumor

tag: status

value: Intact


title: JD-22

value: adult


title: NMYC_RB_M3489 [scRNA-seq]


title: Gpos_Pneg_Q23_B


title: SK-N-AS RNA shScramble control replicate B


title: JD-21

value: F


title: SK-N-AS RNA shScramble control replicate A


title: JD-23


title: Gpos_Pneg_Q73_B

value: B


title: NMYC_RB_M3056 [scRNA-seq]

value: 8 weeks


title: Gpos_Ppos_pTANK_B

value: pTANK


title: Gpos_Pneg_pTANK_B


title: RB_M3032 [scRNA-seq]

value: Pb-Cre+; Pten f/f; Rb1 f/f


title: Gpos_Pneg_Q73_A

value: A


title: LNCaP_NMYC_shRB1_R2

data_processing:
Quality control of raw sequencing reads was performed using FastQC
Trimming and adapter removal using Trim Galore in non-directional mode with default parameters
Single-end bisulfite converted reads were aligned using Bismark with default parameters
MethylKit was used for identifying differentially methylated sites and annotating them to promoters (±1000bp from TSS), exons, introns, CpG islands and CpG shores (±2000bp from CpGi). Sites covered by at least 10X coverage were considered for methylation analysis
Sites with at least 25% difference in methylation between poorly differentiated and adenocarcinomas mice tumors with 5% False Discovery Rate (FDR) were considered as significantly differentially methylated
Genome_build: GEMM:GRCm38. LNCap: GRCh38
Supplementary_files_format_and_content: Differentially methylated sites with annotations

source_name: LNCaP cells

growth_protocol: GEMM were created by crossing mice carrying an integrated CAG-LSL-MYCN gene at the Rosa26 locus with mice harboring homozygously-floxed Pten alleles and expressing Cre recombinase under the control of the probasin promoter. All LNCaP cells were grown in in RPMI 1640 (Gibco) supplemented with 10% FBS (Gemini), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco).

extract_protocol:
DNA extraction was performed using the NucleoSpin Tissue Extraction Kit (Macherey-Nagel) following the manufacturer’s recommendation.
Library preparation for reduced representation of bisulfite sequencing (RRBS) libraries, sequencing and post-processing of the raw data was performed at the Epigenomics Core at Weill Cornell Medicine

treatment_protocol: All LNCaP cells were maintained in androgen deprived media (phenol-red free RPMI medium (Gibco, 11835-030) supplemented with 5% charcoal stripped serum (Gibco, A33821-01) and 1% penicillin/streptomycin (Gibco, 15140-122)) for 96 hours.

value: MYCN+; shRB1

value: Androgen deprived


title: Gpos_Ppos_Q73_A


title: LNCaP_NMYC_shRB1_R1


title: JD-18


title: JD-20


title: RB_M3031 [scRNA-seq]


title: JD-19


title: NMYC_RB_M2872 [scRNA-seq]


title: NMYC_RB_M2861 [scRNA-seq]


title: LNCaP_NMYC_shCTL_R2

value: MYCN+; shCTL


title: RB_M2822 [scRNA-seq]


title: XPO6(RNAi-Res)_shXPO6_rep2

city: Saint Louis

first: Jieya

last: Shao

address: 660 South Euclid Ave

institute: Washington University in St. Louis

data_processing:
Basecalling and demultiplexing were perforemd using Illumina's bcl2fastq software
Read alignment was performed using STAR version 2.5.1a
Gene counts were dervied from the number of uniquely aligned ambiguous reads by Subread:featureCount version 1.4.6-p5
Genome_build: Ensembl release 76 primary assembly (hg38)
Supplementary_files_format_and_content: Tab-delimited text file containing Ensembl gene id, chromosome, star and end positions, strand, length, read count, CPM, and RPKM

growth_protocol: MCF-7 cells were cultured on plastic at 50-80% confluence in RPMI 1640 medium supplemented with 10% FBS, 50 μg/mL gentamycin, 1mM sodium pyruvate, 10 mM HEPES and 4.5 g/L glucose.

extract_protocol:
Cells grown in 10cm dishes were rinsed by PBS, gently scraped, and harvested by centrifugation at 1000rpm for 5 min. Pellets were lysed by TRIzol, and further purified by RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF-7 cells were infected with lentiviruses expressing wild type or RNAi-resistant exportin-6, selected with G418 at 0.2-0.4 mg/ml for 2 weeks, subsequently infected with lentiviruses expressing shRNAs targeting firefly luciferase or exportin-6, followed by puromycin selection at 1-2 ug/ml for 3-4 days.

value: breast cancer cell line

tag: passages

tag: shRNA


title: JD-16

value: M


title: JD-15


title: TT_0h_rep1

description: 4sU-labeled RNA

value: RCH-ACV stably expressing estrogen inducible C/EBPa

value: Ovation Universal RNA-seq System (Nugen, 0343)

value: Beta-estradiol (100nM) treatment 0h + 5 min 4sU labeling


title: Gpos_Pneg_Q23_A


title: JD-17


title: Gpos_Ppos_pTANK_A


title: LNCaP_NMYC_shCTL_R1

tag: genotype


title: XPO6(RNAi-Res)_shXPO6_rep1


title: Gpos_Pneg_pTANK_A


title: Gpos_Ppos_Q23_A


title: 2266_Adenocarcinoma

value: Pb-Cre+; Pten f/f; Rb1 f/f; MYCN+

tag: histology

value: Adenocarcinoma


title: NMYC_RB_3489

data_processing:
scATAC-seq reads were aligned to mm10 reference genome using the cellranger-atac count pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered HDF5 feature barcode and transcription factor matrix files generated using the cellranger-atac count pipeline.

extract_protocol:
Prostate tumors were digested using 1 mg/mL collagenase and 0.2 mg/mL hyaluronidase for 1 hour at 37C followed by additional digestion with TrypLE for 15 minutes at 37C. Digestions were inactivated with media containing 1x B-27 supplement.
Libraries were generated using the 10x Genomics Chromium Single Cell ATAC Library Kit following the manufacturer's recommended protocol.

value: 6 weeks

value: Intact


title: JD-14

value: F


title: JD-13


title: XPO6(RNAi-Res)_shLUC_rep1

value: shLUC


title: 9_aIRS2KD3

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: Hybridization was using the Affymetrix MoGene 2.0ST arrays on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G.

data_processing: Data were analyzed using Robust Multi-Array Average (RMA).

label_protocol: Biotin-labeling was performed following the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol.

extract_protocol: RNA was extracted from cells using RNeasy Mini Kit (QIAGEN).

tag: replicate

value: alpha cells

tag: genotype/variation

value: IRS2 KD


title: XPO6(RNAi-Res)_shLUC_rep2


title: XPO6(WT)_shXPO6_rep2


title: XPO6(WT)_shXPO6_rep1


title: 2266_PoorDifferentiation

value: Poorly Differentiated


title: JD-11

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

institute: Ghent University

tag: age (days post hatching)


title: JD-10


title: 1845_Adenocarcinoma

value: Pb-Cre+; Pten f/f; Rb1 f/+; MYCN+


title: XPO6(WT)_shLUC_rep2


title: JD-1


title: 1715_PoorDifferentiation


title: 6_aIRS1KD3

value: IRS1 KD


title: NMYC_RB_3490


title: XPO6(WT)_shLUC_rep1


title: NMYC_RB_3056

value: 8 weeks

value: prostate tumors


title: JD-12

value: M


title: 5_aIRS1KD2


title: 7_aIRS2KD1


title: 4_aIRS1KD1


title: 3_Control3

source_name: Control

value: control


title: 2_Control2


title: neonatal mouse exposed to hyperoxia_2

status: Public on Apr 06 2021

city: Fukushima

first: Hayato

last: Go

state: Fukushima

address: Hikarigaoka 1

department: Pediatrics

institute: Fukushima Medical University

description: SAMPLE 5

data_processing: SDS software (Applied Biosystems) was used to collect data.  Threshold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems). Data were processed using Expression Suite Software (Applied Biosystems).

label: FAM

source_name: day7 lung after 168h hyperoxia

label_protocol: Five ul total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, sets A and B (Applied Biosystems), then diluted to 100 ul. Manufacturer's protocol was followed throughout.

extract_protocol: Lung samples were obtained from two groups, day7 neonatal mice control, day7 neonatal mice exposed to hyperoxia. The mice were anesthetized with an intraperitoneal injection of ketamine hydrochloride and xylazine hydrochloride. After the pulmonary artery was perfused with PBS, the right lung was excised and snap-frozen with liquid nitrogen for protein and RNA analyses.

treatment_protocol: Newborn mice (<12 h old) were exposed to room air (RA) or hyperoxia (95%) for 7 day. Hyperoxic exposure was conducted in chamber, which allows for continuous monitoring and regulation of oxygen and carbon dioxide. Ambient carbon dioxide was maintained at <1,500 ppm by adjustment of the chamber's ventilation. The dams were switched every 24 h between room air and hyperoxia to avoid injury.

tag: developmental stage

value: neonate

tag: stress

value: hyperoxia

value: lung


title: neonatal mouse exposed to hyperoxia_1

description: SAMPLE 4


title: neonatal mouse control_1

description: SAMPLE 1

source_name: day7 lung


title: neonatal mouse control_3

description: SAMPLE 3


title: neonatal mouse control_2

description: SAMPLE 2


title: neonatal mouse exposed to hyperoxia_3

description: SAMPLE 6


title: 1_Control1


title: P9_12D

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

data_processing:
Reads were trimmed and quality-filtered using Trim Galore v.0.4.1 and aligned using STAR v.2.7.1a. Reads from Col- Cvi crosses were mapped to a Col-Cvi 'metagenome' (TAIR10 sequence appended to a Cvi 'pseudogenome' generated by substituting the Cvi allele at 576,697 Col-Cvi SNPs). Reads from Col-Ler crosses were mapped to a Col-Ler 'metagenome'. Sequences from ThermoFisher ERCC RNA spike-ins were also appended to the metagenome. Reads that mapped uniquely to the ERCC sequences were extracted and omitted from the rest of the analysis. Procedures and scripts for mapping with the metagenome are available in Picard and Gehring (Methods Mol Biol 2020). Reads overlapping a SNP were identified  using a custom script (Picard and Gehring, 2020) and assigned to parent- of-origin. PCR duplicates were removed using MarkDuplicates from the Picard Toolkit (Broad Institute). Total and allele-specific counts over genes were then obtained using htseq-count v.0.9.1 and the Araport11 gene annotations (excluding new Araport11 annotations antisense to existing TAIR10 genes). Single-nuclei samples with a total of at least 1,500 genes detected (≥ 1 overlapping read) and 1,000 genes well-detected (≥ 5 overlapping reads) prior to removing PCR duplicates were considered high quality and kept for subsequent analyses. Raw total expression counts were normalized to CPM (counts per million) while allelic count data for Col,Cvi reciprocal crosses at 4 DAP were normalized using the same procedure used in DESingle (Miao et al. 2018, Bioinformatics).
Genome_build: Araport 11 (excluding new Araport11 annotations antisense to existing TAIR10 genes)
Supplementary_files_format_and_content: Processed files for each library are tab-delimited with four fields: locus_name, all_counts, [parent1]_counts, [parent2]_counts, corresponding to raw counts of total reads, parent1-derived reads, and parent2-derived reads respectively. Additionally, three matrices are provided: CPM_total_expression.txt contains CPM-normalized total expression data for all 1,437 libraries that passed QC checks (and were not controls). norm_maternal_counts.txt and norm_paternal_counts.txt contain maternal and paternal counts for the 4 DAP Col, Cvi dataset (excluding libraries with few allelic counts; N=748 total), respectively; this subset of the data was used for imprinting analyses. Maternal and paternal counts were normalized according to the procedure used in DESingle (Miao et al. 2018, Bioinformatics), separately for the Col x Cvi and the Cvi x Col dataset.

organism: Arabidopsis thaliana

source_name: seed nuclei

growth_protocol: All parent plants were grown in a growth chamber under 16h light at 50% relative humidity (16h at 22°C and 120μm light, 8h at 20°C and 0μm light).

extract_protocol:
Seeds were manually removed from siliques (~ 2 siliques per sample) into 50 uL Partec nuclei extraction buffer (Partec CyStain UV Precise P system), ground to release nuclei, DAPI stained by adding 400 uL Partec staining buffer, and filtered through a 30 um mesh. For the last four batches, nuclei were then washed 2x in 1:8 Partec extraction buffer:Partec staining buffer. Other batches did not include this was step. Single nuclei from the 3C or 6C peaks were sorted into a 96 well plate using fluorescence-activated nuclei sorting (FANS); each plate also included at least one negative control (no nucleus sorted into the well).
Libraries were prepared according the Smart-seq v2 protocol with a few minor variations and carried out at reduced volume. Nuclei were sorted into 1 μL lysis buffer (0.19% vol/vol Triton-X 100, 2U SUPERase RNase inhibitor, ERCC RNA spike-ins (ThermoFisher). 1 μL poly-A hybridization mix (final conc. 2.5mM/ea. dNTPs + 2.5 μM oligo-dT primer) was added to each well and the plate was incubated at 72°C 3 min before putting back on ice. 2.85 μL RT reaction mix (final concentration 1μM TSO, 1x Maxima RT buffer (Life Technologies), 1M betaine, 5 mM DTT, 6 mM MgCl2, 0.5 U SUPERase RNase-inhibitor, 2 U Maxima RT) was added and RT reaction was performed either in thermocycler with program 42°C 90', 10 x [50°C 2', 42°C 2'], 70°C 15' or in thermomixer. 7.5 μL pre-amp PCR mix (final conc. 1x KAPA HiFi HotStart Readymix (Kapa Biosystems), 0.1 μM IS PCR primer) was added and plate was incubated in thermocycler: 3' 98°C, [cycle #] x [98°C 20'', 67°C 15'', 72°C 6'], 72°C 5'. Number of pre- amplification cycles used varied between 18-21. cDNA was cleaned up using a 0.8x Ampure XP protocol (Beckman Coulter). Final libraries were built from successful cDNA preps using the Nextera XT kit (Illumina) with reduced volume (1/4 or 1/5 standard volumes). Up to 384 libraries were multiplexed together and sequenced on an Illumina HiSeq 2000 using a 40bp single-end protocol, or on an Illumina NextSeq using a 40x40bp paired-end protocol.

treatment_protocol: Plants were emasculated in the afternoon or evening, and pollinated in the morning two days later. Seeds were harvested either 2, 3, 4 or 5 days after pollination, at approximately the same time in the morning.

tag: female parent

value: Ler

tag: male parent

value: Col

tag: days after pollination

tag: number of nuclei

tag: fans peak

tag: plate/batch

tag: extra wash steps?

value: no

tag: control?


title: P9_11F


title: P9_11E


title: P9_11G


title: P9_10H


title: P9_12E


title: P9_10G


title: P9_11A


title: P9_11C


title: P9_11D


title: P9_12H


title: P9_12A


title: P9_12G


title: P9_10F


title: P9_12C


title: P9_10D


title: P9_12F


title: P9_12B


title: P9_9H


title: P9_10E


title: P9_10B


title: P9_9F


title: P9_9G


title: P9_9E


title: P9_9D


title: P9_11B


title: P9_11H


title: P9_9C


title: P9_8H


title: P9_9B


title: P9_7F


title: P9_10C


title: P9_8C


title: P9_7G


title: P9_8E


title: P9_8G


title: P9_7E


title: P9_8F


title: P9_8D


title: P9_7H

value: yes - two nuclei sorted in same well


title: P9_7D


title: P9_7B


title: P9_8B


title: P9_9A


title: P9_6H


title: P9_6G


title: P9_7A

value: yes - no nucleus sorted


title: P9_8A


title: P9_6E


title: P9_7C


title: P9_6D


title: P9_6A


title: P9_6B


title: P9_5H


title: P9_6F


title: P9_5G


title: P9_5C


title: P9_5A


title: P9_4D


title: P9_5E


title: P9_4G


title: P9_4B


title: P9_4F


title: P9_4E


title: P9_5D


title: P9_5B


title: P9_4C


title: P9_4H


title: P9_3E


title: P9_6C


title: P9_3G


title: P9_3C


title: P9_3F


title: P9_3B


title: P9_3D


title: P9_2F


title: P9_2C


title: P9_2D


title: P9_2E


title: P9_2B


title: P9_5F


title: P9_3H


title: 8_aIRS2KD2

tag: cell type

value: alpha cells


title: P9_2G


title: P9_1G


title: P9_1B


title: P9_1E


title: P9_1H


title: P9_2H


title: P8_12F


title: P9_1C


title: P9_1A


title: P8_12E


title: P9_1F


title: P9_2A


title: P8_12H


title: P8_12B


title: P9_1D


title: P8_12D


title: P8_12G


title: P8_12A


title: P8_11H


title: P8_12C


title: P8_11C


title: P8_11D


title: P8_11E


title: P8_11F


title: P8_10H


title: P8_11A


title: P8_10G


title: P8_10F


title: P8_10D


title: P8_11G


title: P8_9F

value: Cvi


title: P8_9H


title: P8_10B


title: P8_10E


title: P9_3A


title: P8_9B


title: P8_10C


title: P8_8G


title: P8_8H


title: P8_11B


title: P8_9G


title: P8_9A


title: P8_8D


title: P8_8B


title: P8_8A


title: P8_8C


title: P8_8E


title: P8_7F


title: P8_8F


title: P8_7E


title: P8_7D


title: P8_7G


title: P8_7H


title: P8_9D


title: P8_9E


title: P8_7C


title: P8_9C


title: P8_7A


title: P8_7B


title: P8_6H


title: P8_6G


title: P8_6F


title: P8_6B


title: P8_6C


title: P8_6D


title: P8_6A


title: P8_5G


title: P8_5H


title: P8_5E


title: P8_5D


title: P8_5C


title: P8_5F


title: P8_5B


title: P8_5A


title: P8_4H


title: P8_4E


title: P8_4C


title: P8_4F


title: P8_4D


title: P8_4B


title: P8_3H


title: P8_3F


title: P8_3G


title: P8_3E


title: P8_6E


title: P8_3D


title: P8_3B


title: P8_3C


title: P8_3A


title: P8_2G


title: P8_2H


title: P8_2F


title: P8_2A


title: P8_1G


title: P8_2B


title: P8_2D


title: P8_1E


title: P8_1D


title: P8_4G


title: P8_1C


title: P8_1B


title: P7_12H


title: P7_12G


title: P7_12F


title: P7_12D


title: P8_1A


title: P7_12E


title: P7_12A


title: P7_11G


title: P7_12C


title: P7_11F


title: P7_11H


title: P8_2E


title: P8_2C


title: P8_1H


title: P7_11E


title: P7_11D


title: P7_12B


title: P7_11B


title: P7_11C


title: P8_1F


title: P7_11A


title: P7_10C


title: P7_10G


title: P7_10F


title: P7_10B


title: P7_10D


title: P7_10H


title: P7_9G


title: P7_9E


title: P7_9F


title: P7_9D


title: P7_9C


title: P7_9A


title: P7_9B


title: P7_8H


title: P7_7H


title: P7_8B


title: P7_8G


title: P7_8C


title: P7_8E


title: P7_8F


title: P7_10E


title: P7_10A

value: yes - only water used for Nextera library prep


title: P7_7G


title: P7_7F


title: P7_8A


title: P7_7E


title: P7_8D


title: P7_7D


title: P7_7C


title: P7_6G


title: P7_9H


title: P7_6F


title: P7_6H


title: P7_7B


title: P7_6E


title: P7_6A


title: P7_6B


title: P7_6C


title: P7_6D


title: P7_5G


title: P7_5F


title: P7_5D


title: P7_5C


title: P7_5H


title: P7_5E


title: P7_5A


title: P7_4H


title: P7_7A


title: P7_5B


title: P7_4E


title: P7_4F


title: P7_4G


title: P7_4B


title: P7_4A


title: P7_3G


title: P7_3F


title: P7_3H


title: P7_3D


title: P7_3E


title: P7_3C


title: P7_3B


title: P7_3A


title: P7_2H


title: P7_2F


title: P7_2E


title: P7_2D


title: P7_2G


title: P7_4C


title: P7_2A


title: P7_1H


title: P7_1A


title: P7_1D


title: P7_1F


title: P6_12H


title: P7_1G


title: P7_1C


title: P7_1E


title: P6_12G


title: P7_1B


title: P6_12E


title: P6_12C


title: P6_12B


title: P6_12D


title: P6_12A


title: P6_11H


title: P6_11F


title: P6_11G


title: P7_4D


title: P6_11D


title: P6_11C


title: P6_11A


title: P7_2C


title: P6_11B


title: P6_10H


title: P7_2B


title: P6_10G


title: P6_12F


title: P6_10F


title: P6_10E


title: P6_10B


title: P6_11E


title: P6_9H


title: P6_10C


title: P6_9D


title: P6_10D


title: P6_9C


title: P6_9B


title: P6_9G


title: P6_9F


title: P6_8H


title: P6_9A


title: P6_9E


title: P6_8E


title: P6_8F


title: P6_8G


title: P6_7G


title: P6_7E


title: P6_7F


title: P6_8C


title: P6_8B


title: P6_7B


title: P6_7C


title: P6_7A


title: P5_6H


title: P5_6E


title: P5_6C


title: P5_6D


title: P5_6F


title: P5_6G


title: P5_6A


title: P6_8D


title: P6_8A


title: P5_6B


title: P5_5F


title: P5_5G


title: P5_5E


title: P6_7H


title: P5_5D


title: P5_5H


title: P5_5B


title: P5_5A


title: P5_4G


title: P6_7D


title: P5_4F


title: P5_4E


title: P5_4D


title: P5_4C


title: P5_4A


title: P5_4B


title: P5_3H


title: P5_3G


title: P5_3F


title: P5_3D


title: P5_5C


title: P5_3E


title: P5_3A


title: P5_3C


title: P5_2H


title: P5_3B


title: P5_2G


title: P5_2B


title: P5_2D


title: P5_2E


title: P5_1B


title: P5_2C


title: P5_1A


title: P5_1E


title: P5_2A


title: P5_1G


title: P5_1D


title: P5_1F


title: P4_6E


title: P4_6D


title: P5_2F


title: P5_1C


title: P4_6B


title: P4_6H


title: P4_6A


title: P4_5H


title: miRNAs in CLD neonates on day 28_2

data_processing: SDS software (Applied Biosystems) was used to collect data.  Threshold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems). Data were processed using Expression Suite Software(Applied Biosystems).

source_name: Serum extracellular vesicles

label_protocol: Five ul total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Megaplex Pre-Amp primers, sets A and B (Applied Biosystems), then diluted to 100 ul. Manufacturer's protocol was followed throughout.

extract_protocol: Serum were obtained from 4 groups, day0 and day28 neonates with CLD and non-CLD.  Serum samples (250ul) from cord blood at birth and venous blood of neonates at 28 DAYS were transferred to sterile tubes containing 63 μl of ExoQuick precipitation solution (System Bioscience, Mountain View, CA, USA), and mixed.  The mixtures were incubated for 30 min at 4℃, and centrifuged at 1500×g for 30 min.  Then, the supernatants were removed, the pellets (extracellular vesicles) were diluted to 60 μl with phosphosaline buffer, and then thawed on dry ice for total RNA extraction with a miRvana isolation kit (Ambion). 3pM synthetic ath-miR159a was spiked into each sample to correct for technical differences.   FAM

tag: disease state

value: CLD

tag: age

tag: tissue

value: serum


title: P4_5E


title: P4_5G


title: P4_5F


title: miRNAs in non-CLD neonates on day 28_3

value: non-CLD


title: P4_5D


title: miRNAs in non-CLD neonates on day 28_2


title: P4_6G


title: P4_6F


title: P4_5B


title: H3; Tet2H1795R+LPS

city: Chapel Hill

first: Yue

last: Xiong

state: NC

address: 450 West Dr

department: Linebeger Cancer Center

institute: UNC-Chapel Hill

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie HISAT v2.04 with parameters -p 8 --phred64 --sensitive -I 1 -X 1000
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads and FPKM values for each Sample …

source_name: BMDM

growth_protocol: macrophages were caultured in DMEM with 10% FBS and antibiotics

extract_protocol:
Medium was removed, cells were collected, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 250μM octyl-itaconic acid were pretreated for 12 hours and then 100 ng/LPS were added for 4hours

value: BMDM

tag: strain

value: 6 weeks

tag: genotype

value: Tet2H1795R  knock in

tag: treatment

value: LPS 4 hours


title: P4_5A


title: H2; Tet2H1795R+LPS


title: H1; Tet2H1795R+LPS


title: miRNAs in non-CLD neonates on day 28_1

tag: developmental stage

value: neonate


title: P4_4E


title: P4_4F


title: G3; Tet2H1795R

value: control


title: miRNAs in non-CLD neonates at birth_2


title: miRNAs in CLD neonates at birth_1


title: miRNAs in CLD neonates on day 28_1


title: P4_4D


title: miRNAs in non-CLD neonates at birth_1


title: P4_4B


title: G2; Tet2H1795R


title: P4_4C


title: P4_5C


title: G1; Tet2H1795R


title: C3; WT+LPS+ITA

value: WT

value: ITA pretreat 12 hours + LPS 4hours


title: miRNAs in CLD neonates at birth_2


title: C2; WT+LPS+ITA


title: P4_3H

value: Col

value: no


title: P4_3G


title: C1; WT+LPS+ITA


title: P4_3E


title: P4_3D


title: miRNAs in non-CLD neonates at birth_3


title: B1; WT+LPS


title: P4_3C


title: B3; WT+LPS


title: B2; WT+LPS


title: A3; WT


title: P4_3A


title: P4_3B


title: P4_2G


title: P4_4G

value: yes - two nuclei sorted in same well


title: F3: Tet2 Knockout+LPS+ITA

description: cell lines with CRISPR

growth_protocol: macrophages were cultured in DMEM with 10% FBS and antibiotics

tag: cell line

value: Tet2 knock out


title: P4_2E

tag: female parent

value: Cvi


title: A1; WT


title: A2; WT


title: P4_2F

tag: male parent


title: F2: Tet2 Knockout+LPS+ITA

description: cell lines with CRISPR


title: P4_2H

tag: days after pollination


title: P4_3F

tag: number of nuclei


title: P4_2D

tag: fans peak


title: P4_2C

tag: plate/batch


title: E3: Tet2 Knockout+LPS

description: cell lines with CRISPR


title: P4_2A

tag: extra wash steps?


title: E1: Tet2 Knockout+LPS

description: cell lines with CRISPR


title: E2: Tet2 Knockout+LPS

description: cell lines with CRISPR


title: D3: Tet2 Knockout

description: cell lines with CRISPR


title: P4_1F

tag: control?


title: P4_1G


title: D2: Tet2 Knockout

description: cell lines with CRISPR


title: P4_1E


title: C3: WT+LPS+ITA

description: cell lines with CRISPR


title: P4_1D


title: D1: Tet2 Knockout

description: cell lines with CRISPR


title: P4_1C


title: P4_1B


title: P3_6H


title: C1: WT+LPS+ITA

description: cell lines with CRISPR


title: B1: WT+LPS

description: cell lines with CRISPR


title: P3_6G


title: F1: Tet2 Knockout+LPS+ITA

description: cell lines with CRISPR


title: B2: WT+LPS

description: cell lines with CRISPR


title: B3: WT+LPS

description: cell lines with CRISPR


title: P3_6E


title: P3_6F


title: P4_2B


title: A3: WT

description: cell lines with CRISPR


title: A2: WT

description: cell lines with CRISPR


title: P3_6D


title: A1: WT

description: cell lines with CRISPR


title: P3_6C


title: P3_6A


title: P3_6B


title: P3_5H


title: P4_1A

value: yes - no nucleus sorted


title: C2: WT+LPS+ITA

description: cell lines with CRISPR


title: P3_5E


title: P3_5G


title: P3_5F


title: P3_5B


title: P3_5D


title: P3_5C


title: P3_5A


title: P3_4G


title: P3_4F


title: P3_4E


title: SFM22_8

city: Rijswijk

first: Raissa

last: Timmerman

address: Lange Kleiweg 161

department: Alternatives

country: Netherlands

institute: Biomedical Primate Research Centre

data_processing:
Clustering and sequencing: Illumina NextSeq 500 was used for sample 1-40, Illumina NextSeq 6000 was used for sample 41-52
Reads were trimmed for adapter sequences using Trimmomatic v0.30
Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters) with 2 or less mismatches and an alignment score of at least 12
The Macaca mulatta genomic reference (Macaca_mulatta.Mmul_8.01.dna.toplevel.fa) was used for alignment of the reads for each sample.
The reads were mapped to the reference sequence using a short read aligner based on Burrows-Wheeler Transform (Tophat v2.0.14) with default settings.
SAMtools v1.3 package was used to sort and index the BAM files. Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.6.1p1.
Genome_build: Macaca_mulatta.Mmul_8.01.dna.toplevel.fa
Supplementary_files_format_and_content: .count files containing raw gene counts for each sample
Supplementary_files_format_and_content: .tsv files containing FPKM values for each sample

source_name: Primary cultured microglia

growth_protocol: Primary microglia were cultured for 8 days in serum and exposed to M-CSF or IL-34, with or without TGF-b (sample1-16). Primary microglia were cultured for 8 days in serum+M-CSF or 4 days in serum followed by a serum-free washout of 4, 11 and 18 days, or cultured in serum-free medium for 22 days (sample21-40). Primary microglia were cultured for 8 days in serum+M-CSF, or cultured in serum for 4 days followed by a serum-free washout for 11 days, or co-cultured with oligodendrocytes and progenitor cells in serum for 4 days followed by a serum-free washout for 11 days (sample 41-52).

extract_protocol:
Total cellular RNA was isolated using the RNeasy minikit (Qiagen, Cat#74104) according to manufacturer’s protocol
For sample 1-40 the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat#E7420L) was used to prepare and process the samples, For sample 41-52 The NEBNext Low Input RNA Library Prep Kit (New England Biolabs, Cat#E6420L) for Illumina was used to process the samples

value: Primary cultured microglia

tag: brain area

value: Subcortical white matter

tag: donor nr

tag: gender

value: Male


title: SM4-SFM18_8

tag: tissue

tag: age


title: SM4-SFM11_8


title: P3_4C


title: SM4-SFM4_8


title: SM M-CSF_8


title: P3_4B


title: P3_4A


title: SM4-SFM18_7


title: SK-LMS-1 HDAC4 KO (cl. 1231) RepB

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

description: HDAC4KO achieved through Cas9+sgRNA1 Rep B

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with the Lumi package in R.

source_name: Leiomyosarcoma cells

label_protocol: Aliquots of RNAs were amplified and labelled according to the specifications of the Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: SK-LMS-1 cells (HDAC4KO or wt) were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine and penicillin–streptomycin (Euroclone, Milan, Italy). For each experiment 0.5*10^6 cells were used.

extract_protocol: Total RNA was purified with Quick-RNA Miniprep (ZymoResearch), amplified according to the specifications of the Illumina TotalPrep RNA Amplification Kit (Ambion) and hybridized on Illumina whole-genome HumanHT-12 v 4.0 chip (Illumina)

treatment_protocol: CRISPR/Cas9 technology was applied to obtain HDAC4-/- clones. The KO clones were screened by PCR, immunoblot and validated by Sanger sequencing.Cells were seeded in 35 mm plates. 48h later RNA was extracted.

tag: Sex

value: female

value: vulva

tag: cell type

value: Leiomyosarcoma cells

tag: grade

tag: genotype

value: HDAC4KO achieved through Cas9+sgRNA1


title: SK-LMS-1 HDAC4 KO (cl. 1254) RepB

tag: cell line


title: SK-LMS-1 HDAC4 KO (cl. 76) RepA

description: HDAC4KO achieved through Cas9+sgRNA2 Rep A

value: HDAC4KO achieved through Cas9+sgRNA2


title: SK-LMS-1 Cas9 RepA

description: Control expressing Cas9 Rep A

value: Control expressing Cas9


title: SFM22_7


title: SK-LMS-1 HDAC4 KO (cl. 76) RepB

description: HDAC4KO achieved through Cas9+sgRNA2 Rep B


title: SK-LMS-1 HDAC4 KO (cl. 1231) RepA

description: HDAC4KO achieved through Cas9+sgRNA1 Rep A


title: SK-LMS-1 HDAC4 KO (cl. 205) RepB


title: P3_3G

tag: female parent

tag: male parent


title: P3_3F

tag: days after pollination

tag: number of nuclei


title: SK-LMS-1 Cas9 RepB

description: Control expressing Cas9 Rep B


title: SK-LMS-1 HDAC4 KO (cl. 205) RepA


title: SK-LMS-1 HDAC4 KO (cl. 1254) RepA


title: SK-LMS-1 Control RepB

description: Control expressing Cas9+sgRNA2 Rep B

value: Control expressing Cas9+sgRNA2


title: P3_4D

tag: fans peak

tag: plate/batch


title: P3_3E

tag: extra wash steps?

tag: control?


title: SK-LMS-1 Control RepA

description: Control expressing Cas9+sgRNA1 Rep A

value: Control expressing Cas9+sgRNA1


title: SM4-SFM18_6

tag: brain area

tag: donor nr

value: Female


title: SM4-SFM4_6

tag: tissue

tag: gender


title: P3_3C

value: Col

value: no


title: SM M-CSF_7

tag: age


title: SM4-SFM11_7


title: P3_3B


title: SFM22_6


title: P3_3D


title: P3_2H


title: P3_3A


title: P3_3H


title: SM4-SFM11_6


title: SM4-SFM4_7


title: P3_2G


title: SM M-CSF_6


title: SM4-SFM18_5


title: SFM22_5


title: P3_2F


title: SM4-SFM11_5


title: P3_2D


title: SM4-SFM4_5


title: Ex vivo_8

source_name: Freshy isolated microglia

value: Freshy isolated microglia


title: P3_2E

value: Cvi


title: P3_2B


title: P3_2C


title: P3_2A


title: SM M-CSF + TGF-b_4


title: Ex vivo_7


title: SM IL-34 + TGF-b_4


title: Ex vivo_6


title: SM M-CSF_4


title: Ex vivo_5


title: SM IL-34 + TGF-b_3


title: P3_1C


title: P2_6H


title: P3_1D


title: P3_1E


title: SM IL-34_4


title: P3_1F

value: yes - two nuclei sorted in same well


title: P3_1B


title: SM M-CSF_5

value: Primary cultured microglia


title: P2_6F


title: P2_6E


title: P2_6D


title: SM M-CSF_3

value: Subcortical white matter


title: SM IL-34_3


title: P3_1G


title: P3_1A

value: yes - no nucleus sorted


title: SM M-CSF + TGF-b_2

value: Male


title: P2_6C


title: P2_6B


title: SM M-CSF_2


title: SM IL-34_2


title: SM IL-34 + TGF-b_1


title: P2_5H


title: SM M-CSF + TGF-b_1


title: P2_6G


title: SM M-CSF + TGF-b_3


title: P2_6A


title: P2_5G


title: SM IL-34_1


title: SM IL-34 + TGF-b_2


title: SM M-CSF_1


title: P2_5F


title: P2_5D


title: P2_5C


title: P2_5B


title: P2_5A


title: P2_5E


title: P2_4E


title: P2_4G


title: P2_4C


title: P2_3H


title: P2_4A


title: P2_3G


title: P2_4F


title: P2_4D


title: P2_3E


title: P2_3C


title: P2_3D


title: skeletal muscle, standard-care nutritional supplement, subject 261, post-intervention

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).

source_name: m. vastus lateralis, non-fasted morning sample

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The ProMO-Study (PROtein supplementation in Malnourished Older adults) was a randomized, standard-care controlled, open-label trial conducted at Wageningen University, The Netherlands between July 2016 and August 2017. The study was approved by the medical and ethical committee of Wageningen University and registered at clinicaltrials.gov under NCT02683720. Participants (n=81, mean age 74±7, BMI 22±3) were recruited via dieticians, geriatric outpatient clinics of two hospitals (Rijnstate, Arnhem, The Netherlands and Gelderse Vallei, Ede, The Netherlands), the volunteer database of Wageningen University, and via advertisements in local and online media. Interested participants were, after obtaining informed consent, screened for eligibility during a home visit. We included participants aged 65 y and older, with a score below 12 on the Mini Nutritional Assessment Tool – Short form (MNA-sf). Exclusion criteria were an expected life-expectancy of <12 months, performing over 2 h / w of resistance exercise, planned increase in exercise during the study, impaired kidney function (estimated glomerular filtration rate (eGRF) <30 ml / min / 1.73m², measured at baseline), lactose intolerance or milk protein allergy, use of corticosteroids (unless administered via inhaler or topically), use of diabetes medication, consumption of >19 portions of ONS in the previous month or >9 in the previous week and use of >21 alcohol units per week.

extract_protocol: RNA was purified from muscle biopsies using TRIzol (Life Technologies, Bleiswijk, the Netherlands) followed by an additional round of purification with RNeasy Microkit columns (Qiagen, Venlo, the Netherlands). RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands). RNA was considered suitable for array hybridization only if RNA integrity number exceeded 7.0.

treatment_protocol: Vastus Lateralis tissue biopsies were taken under local anaesthesia, by using a Bergström needle, in a subgroup of  n=36 participants who were willing to undergo a muscle biopsy and not using anti-coagulants. Collected tissue was immediately rolled until dry, checked for quantity and type of tissue, and snap frozen in liquid nitrogen for analysis. Samples were frozen in -80 degrees until analysis. In n=21 participants, the tissue collection was successfully completed both at baseline and after 12 weeks.

tag: sex (female=1, male=0)

tag: subjectid

tag: age (yrs)

tag: moment of sampling (pre/post intervention)

value: post-intervention (after 12 wks)

tag: time of sampling (hr

tag: experimental condition

value: standard-care nutritional supplement

value: skeletal muscle

tag: sample type

value: non-fasted morning sample


title: skeletal muscle, standard-care nutritional supplement, subject 265, post-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 258, post-intervention

value: novel oral nutritional supplement


title: skeletal muscle, novel oral nutritional supplement, subject 266, post-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 264, pre-intervention

value: pre-intervention (at baseline)


title: P2_4B

tag: female parent

tag: male parent

tag: days after pollination

tag: number of nuclei


title: skeletal muscle, novel oral nutritional supplement, subject 266, pre-intervention


title: P2_3B

tag: fans peak

tag: plate/batch

tag: extra wash steps?

tag: control?


title: skeletal muscle, standard-care nutritional supplement, subject 259, pre-intervention

tag: tissue


title: skeletal muscle, standard-care nutritional supplement, subject 265, pre-intervention


title: P2_3A


title: skeletal muscle, standard-care nutritional supplement, subject 261, pre-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 258, pre-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 259, post-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 253, pre-intervention


title: P2_3F


title: skeletal muscle, standard-care nutritional supplement, subject 250, post-intervention


title: P2_2G


title: P2_2A


title: P2_2E


title: skeletal muscle, standard-care nutritional supplement, subject 252, pre-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 264, post-intervention


title: P2_2C


title: P2_2D


title: skeletal muscle, novel oral nutritional supplement, subject 253, post-intervention


title: P2_2B


title: P2_2H


title: skeletal muscle, standard-care nutritional supplement, subject 245, post-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 250, pre-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 245, pre-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 231, post-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 243, post-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 252, post-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 231, pre-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 238, post-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 219, pre-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 243, pre-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 238, pre-intervention


title: P2_1E


title: P2_1F


title: P2_2F


title: P2_1G


title: P2_1D


title: skeletal muscle, standard-care nutritional supplement, subject 215, post-intervention


title: P2_1B


title: P2_1A


title: skeletal muscle, novel oral nutritional supplement, subject 219, post-intervention


title: P2_1C


title: P1_3H


title: P1_3G


title: P1_3F


title: P1_3E


title: P1_3B


title: P1_3C


title: P1_3A


title: P1_3D


title: P1_2H


title: skeletal muscle, novel oral nutritional supplement, subject 214, pre-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 215, pre-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 212, post-intervention


title: P1_2G


title: P1_2E


title: skeletal muscle, standard-care nutritional supplement, subject 205, post-intervention


title: P1_2F


title: skeletal muscle, standard-care nutritional supplement, subject 211, post-intervention


title: P1_2D


title: skeletal muscle, novel oral nutritional supplement, subject 214, post-intervention


title: HP_Serum_Con4

city: Guangzhou

first: Xiaoxia

last: Zhu

state: Guangdong

address: No. 253 Gongye Street

department: Radiation Oncology Department

institute: Zhujiang Hospital, Southern Medical University

description: miRNA expression in serum of healthy people

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: Serum, Healthy People, Control Group, 04

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRI reagent BD (MRCgene, TB-126) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies).

value: Serum

tag: pathology

tag: tnm

tag: Stage

tag: disease state

value: healthy


title: HP_Serum_Con5

source_name: Serum, Healthy People, Control Group, 05


title: skeletal muscle, standard-care nutritional supplement, subject 212, pre-intervention

tag: sex (female=1, male=0)

tag: subjectid

tag: age (yrs)

tag: moment of sampling (pre/post intervention)


title: HP_Serum_Con6

source_name: Serum, Healthy People, Control Group, 06

tag: sample type


title: skeletal muscle, standard-care nutritional supplement, subject 211, pre-intervention

tag: time of sampling (hr

tag: experimental condition


title: skeletal muscle, standard-care nutritional supplement, subject 203, pre-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 205, pre-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 202, post-intervention


title: skeletal muscle, standard-care nutritional supplement, subject 203, post-intervention


title: skeletal muscle, novel oral nutritional supplement, subject 202, pre-intervention


title: P1_2A

tag: female parent

value: Col

tag: male parent

tag: days after pollination

tag: number of nuclei


title: P1_2C

tag: fans peak

tag: plate/batch

tag: extra wash steps?

value: no

tag: control?


title: B1

first: Haipeng

last: Xiao

address: 58 Zhangshan er Road

institute: The First Affiliated Hospital of Sun yat-sen University

data_processing:
 Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.

extract_protocol:
After treatment, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
 Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: KHM-5M cells were treated with DMSO and YK-4-279 at different dosage (0.3 μM and 1 μM) for 24 hours

tag: cell type

value: Thyroid cancer

tag: cell line

tag: treatment


title: A3


title: B2


title: B3


title: HP_Serum_Con3

source_name: Serum, Healthy People, Control Group, 03

tag: pathology

tag: tnm

tag: Stage

tag: disease state


title: A1


title: P1_2B

value: Cvi


title: C3

source_name: DMSO rep3

value: DMSO


title: C1

source_name: DMSO rep1


title: C2

source_name: DMSO rep2


title: A2