title: P15

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description: Raw data access provided at: NGB Nucleotide Sequence Archive (accession code: CNP0000428)

data_processing:
Reads were demultiplexed, converted to FASTQs, and aligned by CellRanger(version 1.3.1)
Then the gene expression matrices for all tumour and normal samples were combined in R and converted to a Seurat object using the Seurat R package (version 3.0.2)
Quality filtering was performed to remove cells with <201 or >9,000 expressed genes or greater than 20% unique molecular identifiers (UMIs) derived from the mitochondrial genome. In the remaining cells, gene expression matrices were log normalized to total cellular read-counts and mitochondrial read-counts by linear regression implemented using the ScaleData function of the Seurat package.
Genome_build: hg19, EBV B95-8 reference genome
Supplementary_files_format_and_content: tab-delimited text files containing gene/barcode matrices  for each Sample

molecule: polyA RNA

source_name: nasopharyngeal carcinoma cell

extract_protocol:
The samples for scRNA-seq were washed with phosphate-buffered saline (PBS; Thermo Fisher Scientific, Waltham, MA, USA), placed on ice, cut into small pieces (<1 mm3) and transferred to 5 ml Dulbecco’s modified Eagle’s medium (DMEM; Thermo Fisher Scientific) containing collagenase IV (1 g/ml) (Thermo Fisher Scientific). The samples were incubated for 40 min at 37°C with manual shaking every 10 min and then filtered twice using a 40-µm nylon mesh (Thermo Fisher Scientific). Following centrifugation (500 × g, 4°C, and 5 min), the supernatant was decanted and discarded before the cell pellet was resuspended in 1 ml foetal bovine serum (FBS; containing 10% DMSO) and transferred to cryogenic vials. Following a 5-min incubation at room temperature, the samples were centrifuged (120 × g, 4℃, and 5 min) using a swing-out rotor. The samples were then resuspended in PBS containing 0.08% bovine serum albumin (BSA; Sigma) and filtered through 40-µm cell strainers (BD) using wide-bore 1-ml low-retention filter tips (Axygen). Next, the cells were counted and assessed for viability using Trypan blue staining with a haemocytometer. Throughout the dissociation procedure, the cells were maintained on ice whenever possible, and the entire procedure was completed in less than 90 min (generally approximately 70 min) to avoid the dissociation-associated artefacts.   A chromium single-cell 3'-library was constructed using the Chromium Single-cell 3'-Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions. Cell suspensions were loaded onto a chromium single-cell chip along with reverse transcription (RT) master mix and single-cell 3'-gel beads, aiming for 2,000–8,000 single cells per reaction.
A chromium single-cell 3'-library was constructed using the Chromium Single-cell 3'-Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions. Cell suspensions were loaded onto a chromium single-cell chip along with reverse transcription (RT) master mix and single-cell 3'-gel beads, aiming for 2,000–8,000 single cells per reaction. The samples were processed using 10x Genomics V2 barcoding chemistry kits. Following cell lysis, first-strand cDNA synthesis and amplification were carried out according to the manufacturer’s instructions with cDNA amplification set for 12 cycles. Libraries were sequenced on an Illumina HiSeq X Ten,  and mapped to the human reference genome (build hg19) and EBV B95-8 reference genome (NC_007605.1) using CellRanger (10x Genomics).

value: tumour tissue

tag: disease state

value: nasopharyngeal carcinoma


title: N01

status: Public on Jul 20 2020

type: SRA

country: China

library_source: transcriptomic

organism: Homo sapiens

source_name: nasopharynx epithelium

tag: tissue

value: nasopharynx tissue

value: chronic nasopharyngitis


title: 4982_CD19 [S27]

city: Amsterdam

first: Brendon

middle: P.

last: Scicluna

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC Locatie AMC

description:
CD19_20161327
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt

data_processing:
Sequence read quality was assessed by means of the FastQC methods and Trimmomatic was used to trim the Illumina adapters containing, poor-quality bases and ambiguous nucleotide-containing sequences.
Reads were used to align against the Genome Reference Consortium Human Genome Build 38 patch release 7 (GRCh38.p7)  (GRCh38.p7) using TopHat 2(vrsion 2.1.1), Count data were generated by means of the featureCounts method.
Sequence reads were analyzed by Mapsplice2. circRNA was called if it was supported by at least four back-spliced reads in at least two different samples.
Genome_build: Genome Reference Consortium Human Genome Build 38 patch release 7 (GRCh38.p7)
Supplementary_files_format_and_content: tab-delimited text files including DESeq2 normalized values for each cell type.

molecule: total RNA

extract_protocol:
Total RNA was isolated from each cell-type by means of the miRNeasy RNA isolation kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions. RNA quality was assessed by bioanalysis (Agilent), with all samples having RNA integrity numbers (RINs) > 7. Total RNA concentrations were determined by Qubit® 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA).
Sequencing libraries were prepared by means of the Ovation® RNA-Seq System V2 (NuGEN) kit as per manufacturer’s instructions

tag: subject status

value: Patient

tag: age

tag: gender

value: female

value: blood

tag: cell type


title: 4195_CD19 [S30]

description:
CD19_20161330
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt


title: P13


title: P12


title: HV65_CD8 [H46]

description:
CD8_20161346
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt

value: Healthy


title: GSS1340_127_F_CD

type: RNA

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

country: USA

institute: Procter and Gamble

description: batch_subjectID_gender_sampling site

hyb_protocol: Biotinylated cRNA was fragmented by limited alkaline hydrolysis and then hybridized overnight to Affymetrix GeneTitan U219 microarray plates using the Affymetrix GeneTitan instrument

scan_protocol: ArrayPlates were scanned using the Affymetrix GeneTitan Instrument utilizing AGCC GeneTitan Instrument Control software version 4.2.0.1566

data_processing: The RMA algorithm was used as the processing protocol to normalize the data for subsequent analysis.

label: biotin

source_name: LCM-separated dermis from human cheek

label_protocol: Biotinylated cRNA were prepared  using the Affymetrix HT 3’ IVT Express kit (Cat. #901253) on a Beckman Biomek FXp Laboratory Automation Workstation (Beckman Cat. #A31842).

extract_protocol: Total RNA from LCM samples was isolated utilizing the Pico Pure RNA Isolation Kit (Life Technologies, Grand Island, NY) according to manufacturer's recommendations

treatment_protocol: Punch biopsy samples were frozen in OCT media. Laser capture microdissection (LCM) was performed to isolate the dermal compartments for gene expression profiling.

value: LCM-separated dermis

tag: collection time


title: HV62_CD8 [H45]

description:
CD8_20161345
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt

value: male


title: P14


title: P11


title: Whole_skin_biopsy_100nMRapamycin_rep5 [203271750037_R08C01]

type: genomic

city: Rio de Janeiro

first: Mariana

last: Boroni

state: RJ

address: Rua André Cavalcanti 37

country: Brazil

institute: Instituto Nacional de Câncer

hyb_protocol: Next the samples were loaded onto the Infinium Human MethylationEPIC BeadChip

scan_protocol: iScan Control Software (ICS) - with the Methylation NXT setting

data_processing: The raw image data was processed using the commands preprocessRaw() followed by preprocessSWAN(). Methylation signals (M-values) were then converted to ratios using the ratioConvert() and next to beta values using getBeta(), all functions implemented in the “minfi” R package. Beta values were normalized using the betaqn() method, which quantile normalizes betas, implemented by the wateRmelon package.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: whole skin biopsy, 100nM Rapamycin

label_protocol: Bisulfite conversion was performed on 750 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research).

growth_protocol: Whole skin samples were maintained in air-liquid interface with DMEM 10%FBS 1%P/S

extract_protocol: DNA extraction was performed using DNeasy Blood and Tissue Kit (Qiagen)

treatment_protocol: The treatment (100nM Rapamycin) was added to the culture media at day 1 and day 3. The skins were harvested for DNA isolation 5 days after first treatment.

tag: Sex

tag: sample/tissue type

value: Normal skin biopsie treated with Rapamycin


title: Whole_skin_biopsy_control_rep2 [203271750037_R02C01]

source_name: whole skin biopsy, control

value: Normal skin biopsie


title: Whole_skin_biopsy_100nMRapamycin_rep4 [203271750037_R07C01]


title: Whole_skin_biopsy_control_rep3 [203271750037_R03C01]


title: Whole_skin_biopsy_100nMRapamycin_rep1 [203271750053_R06C01]


title: Whole_skin_biopsy_control_rep5 [203271750053_R02C01]


title: HV81_CD8 [H43]

description:
CD8_20161343
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt


title: Whole_skin_biopsy_100nMRapamycin_rep2 [203271750053_R07C01]


title: Whole_skin_biopsy_control_rep1 [203271750037_R01C01]


title: Whole_skin_biopsy_control_rep4 [203271750053_R01C01]


title: human_dermal_firboblast_84y_rep3 [201492560033_R06C01]

source_name: human dermal fibroblast from 84y.o. donor

growth_protocol: Cells were grown in T-75 flasks with DMEM 10%FBS 1%P/S and passaged when reached 80-90% confluence

value: human dermal fibroblast

tag: passage


title: human_dermal_firboblast_84y_rep2 [201492560033_R05C01]


title: human_progeria_firbroblast_5uMABT-263_rep3 [203273630137_R07C01]

source_name: human progeria dermal fibroblast, 5uM ABT-263

treatment_protocol: The treatment (1.25uM ABT-263, 5uM ABT-263, 100nM Rapamycin) was added to the culture media and kept for 72 hours. Next, the media was changed, cells maintained for more 72 hours prior to DNA isolation

value: human progeria dermal fibroblast

tag: treatment

value: 5uM ABT-263


title: human_progeria_firbroblast_1.25uMABT-263_rep2 [203273630137_R04C01]

source_name: human progeria dermal fibroblast, 1.25uM ABT-263


title: HV55_CD8 [H44]

description:
CD8_20161344
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt


title: P10


title: human_progeria_firbroblast_5uMABT-263_rep2 [203273630137_R06C01]


title: Whole_skin_biopsy_100nMRapamycin_rep3 [203271750053_R08C01]


title: P08


title: P07


title: 4195_CD8 [S40]

description:
CD8_20161340
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt


title: P06


title: 3919_CD8 [S42]

description:
CD8_20161342
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt


title: 4028_CD8 [S39]

description:
CD8_20161339
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt


title: human_dermal_firboblast_84y_rep1 [201492560033_R04C01]


title: 3938_CD8 [S41]

description:
CD8_20161341
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt


title: P09


title: human_progeria_firbroblast_1.25uMABT-263_rep1 [203273630106_R07C01]


title: human_progeria_firbroblast_control_rep2 [203273630106_R02C01]

source_name: human progeria dermal fibroblast, control

value: control


title: human_progeria_firbroblast_5uMABT-263_rep1 [203273630106_R08C01]


title: human_progeria_firbroblast_100nMRapamycin_rep1 [203273630106_R03C01]

source_name: human progeria dermal fibroblast, 100nM Rapamycin

value: 100nM Rapamycin


title: human_progeria_firbroblast_100nMRapamycin_rep2 [203273630106_R04C01]


title: human_progeria_firbroblast_1.25uMABT-263_rep3 [203273630137_R05C01]


title: human_progeria_firbroblast_control_rep3 [203273630137_R01C01]


title: human_progeria_firbroblast_100nMRapamycin_rep3 [203273630137_R02C01]


title: HV65_CD4 [H45]

description:
CD4_20160345
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt


title: human_dermal_firboblast_29y_rep3 [201492560033_R03C01]

source_name: human dermal fibroblast from 29y.o. donor


title: human_progeria_firbroblast_control_rep1 [203273630106_R01C01]


title: P02

value: tumour tissue


title: 4982_CD8 [S37]

description:
CD8_20161337
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt


title: HV62_CD4 [H39]

description:
CD4_20160339
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt


title: HV55_CD4 [H37]

description:
CD4_20160337
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt


title: P01

value: nasopharyngeal carcinoma


title: human_dermal_firboblast_29y_rep1 [201492560033_R01C01]


title: Huh-7

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 16
The first 4 and the last 4 bases were trimmed off  using Cutadapt (v 1.14) with parameters  -m 16 -u 4/-4
Trimmed reads were mapped against the human genome (hg38 UCSC) using Bowtie2 (v 2.3.3) with parameters  -p 6 -N 1
aligned reads were sorted using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -s 1 -T 6  -t miRNA -g ID and miRBase annotations (v21)
gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

source_name: liver cancer derived cell line

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

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

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

tag: cell line

value: parental cell line

tag: passages

value: harvested 48h upon seeding


title: ES-2

source_name: ovarian cancer derived cell line


title: HV81_CD4 [H38]

description:
CD4_20160338
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt


title: P03


title: P05


title: C643

source_name: thyroid cancer derived cell line


title: 3919_CD4 [S33]

description:
CD4_20160333
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt

value: Patient


title: 3938_CD4 [S32]

description:
CD4_20160332
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt

value: female


title: 6641_CD8 [S38]

description:
CD8_20161338
processed data file:
CD8-circRNA-normalized.txt
CD8-linear-normalized.txt

value: blood


title: P04

description: Raw data access provided at: NGB Nucleotide Sequence Archive (accession code: CNP0000428)


title: mSTARR_HeLa_SG4_1

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

data_processing:
Library strategy: STARR-seq
STARR-seq reads were mapped to mm9 build of the mouse genome using BWA (Li et al., Bioinformatics 2009).
For visualization purposes, bam files were converted to bigwig files using bamCoverage (Ramirez et al., Nucleic Acids Research 2016) and visualized using the UCSC genome browser (Kent et al., Genome Research 2002).
We compared bam files of m/hSTARR_SG4/Wnt to m/hSTARR_pcDNA using bamCompare (Ramirez et al., Nucleic Acids Research 2016) with bin sizes of 50 bases to compute the log2 of the number of reads ratio. Bins were filtered to exclude regions with a read count <75.
Flanking bins were merged using mergeBED (overlaps on either strand; maximum distance between features: 0) (Quinlan et al., Bioinformatics 2010). Merged bins with a log2 fold change of >0.585 (fold change >1.5) were included for further analysis.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: STARR-seq .bigwig files: Normalized read count of sequencing reads mapped to mm9 reference genome.
Supplementary_files_format_and_content: STARR-seq .bed files: Coordinates of genomic regions with a log2 fold ratio of >1.5 of SG4-/Wnt- over pcDNA sequence read signal.

organism: Mus musculus

source_name: BAC DNA spanning Tbx3 locus

growth_protocol: 15*10^6 COS7 or HeLa cells were cultured in DMEM (ThermoFisher Scientific; 31966-021) supplemented with 10% FBS (ThermoFisher Scientific; 10270-106) and 1% Pen/Strep (ThermoFischer Scientific; 15070-063).

extract_protocol:
48 hours after transfection, total RNA was isolated using the Qiagen RNeasy maxi prep kit (Qiagen; 75162). polyA+ RNA was isolated using Dynabeads Oligo-dT25 (ThermoFisher Scientific; 61002) and treated with Ambion turboDNase (ThermoFisher Scientifc; AM2238) for 30min at a maximum concentration of 150ng/μl. RNA was purified using the Qiagen RNeasy MinElute kit (Qiagen; 74204).
First-strand cDNA synthesis and library preparation was performed as described (Arnold et al., Science 2013). Library quality and concentration were assessed by Bioanalyzer (Agilent) and KAPA Library Quantification Kit (KAPA Biosystems; KK4824). Libraries were pooled equimolarly before sequencing on a Miseq (PE150).

treatment_protocol: Cells were transfected with 150μg library DNA and 75μg of pcDNA (control), SG4 (15μg Smad1, 15μg Smad4, 30μg Alk3 and 15μg Gata4 expression vectors) or Wnt (15μg Tcf4 expression vector, 60μg pcDNA, and 0.4M LiCl) using Polyethylenimine 25 kDa (PEI; Sigma-Aldrich; 408727) in a ratio of 1:3 (DNA:PEI). Medium was refreshed 6 hours after transfection. 48 hours after transfection, total RNA was isolated.

tag: strain

value: FVB/N

tag: transfection

value: Murine Tbx3 STARR-seq library transfected in HeLa cells

tag: co-transfection

value: STARR-seq library co-transfected with SG4


title: 4195_CD4 [S50]

description:
CD4_20161350
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt


title: mSTARR_HeLa_pcDNA_1

value: STARR-seq library co-transfected with pcDNA


title: 4028_CD4 [S49]

description:
CD4_20161349
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt

value: male


title: human_dermal_firboblast_29y_rep2 [201492560033_R02C01]

value: human dermal fibroblast


title: 6641_CD4 [S44]

description:
CD4_20160344
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt


title: 4982_CD4 [S43]

description:
CD4_20160343
processed data file:
CD4-circRNA-normalized.txt
CD4-linear-normalized.txt


title: mSTARR_SG4_2

value: Murine Tbx3 STARR-seq library transfected in COS7 cells


title: mSTARR_HeLa_input_1

description:
mSTARR_HeLa_Transfection input control_1
Plasmid DNA


title: mSTARR_Wnt_1

value: STARR-seq library co-transfected with Wnt


title: mSTARR_SG4_1


title: mSTARR_pcDNA_3


title: HV62_CD14 [H40]

description:
CD14_20160340
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt

value: Healthy


title: HV65_CD14 [H47]

description:
CD14_20160347
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt


title: HV55_CD14 [H41]

description:
CD14_20160341
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt


title: mSTARR_pcDNA_2


title: HV81_CD14 [H42]

description:
CD14_20160342
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt


title: mSTARR_pcDNA_1


title: 3938_CD14 [S36]

description:
CD14_20160336
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt


title: mSTARR_input_2

description:
mSTARR_input_2
Plasmid DNA


title: MA033

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Methylation EPIC BeadChip using standard protocols

scan_protocol: Arrays were imaged using Illumina iScan Microarray System

data_processing: R package RnBeads was used for quality control and preprocessing of the arrays

source_name: Whole blood

label_protocol: Standard Illumina protocol

extract_protocol: DNA was prepared from 0.5 ml - 3 ml of anticoagulated whole blood (EDTA) by erythrocyte lysis in 70 μg of NH4H2CO3/ml and 7.0 mg of NH4Cl/ml followed by lysis of leukocytes  in 1% sodium dodecyl sulfate, 100 mM EDTA, and 200 mM Tris (pH 8.5) and precipitation in isopropanol

tag: group

value: Exposed

value: Male

tag: batch

value: Whole blood


title: 3919_CD14 [S35]

description:
CD14_20160335
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt

tag: tissue


title: mSTARR_input_1

description:
mSTARR_input_1
Plasmid DNA


title: MA032


title: 4195_CD14 [S47]

description:
CD14_20161347
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt

tag: subject status


title: NGP_ARID1A_heter_input

city: Hangzhou

first: Ting

last: Tao

state: Zhejiang

address: 3333 Binsheng Road

institute: Children's Hospital, Zhejiang University School of Medicine

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.2.9 with configuration -p 8 -x $SHARED_DATABASES/bowtie2_indexes/hg19 -U. For ARID1A and its corresponding input ChIP-Seq, configuration -p 8 -x $SHARED_DATABASES/bowtie2_indexes/hg19  was used.
Data were filtered using SAMtools version 1.3.1 with configuration samtools view -bS -q 20
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files represent counts of aligned reads within 20 bp bins with each read being extended 75 (50 for ARID1A and its corresponding input ChIP-Seq) in the direction of alignment. Counts are in reads-per-million.

source_name: Neuroblastoma

growth_protocol: The NGP neuroblastoma cell line was maintained in RPMI 1640 Medium (GIBCO) supplemented with 10% fetal bovine serum (Sigma) and 1X penicillin-streptomycin (GIBCO),and 0.5ug/ml puromycin (Sigma #P8833).

extract_protocol:
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: NGP

tag: genotype

tag: chip antiboy


title: JN354

value: Control

tag: gender


title: 4028 CD14 [S48]

description:
CD14_20161348
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt

value: Patient

tag: age

tag: cell type


title: JN329

value: Case


title: 6641_CD14 [S46]

description:
CD14_20160346
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt

value: female

value: blood


title: JN311


title: Progeria_fibroblast_passage19_rep2 [201492560178_R05C01]

source_name: human progeria dermal fibroblast passage19

tag: Sex

value: human progeria dermal fibroblast


title: NGP_ARID1A_mut#2_repeat

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT2 version 2.1.0 with defalt parameters for single end reads.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using GFold version 1.1.2
Genome_build: hg19

extract_protocol:
Total RNA was depleted of ribosomal RNA with the KAPA mRNA HyperPrep Kit (Roche). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a Illumina NextSeq 500 with 75bp single-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: NGP_ARID1A_heter


title: JN267


title: JN283

value: Female


title: 4982_CD14 [S34]

description:
CD14_20160334
processed data file:
CD14-circRNA-normalized.txt
CD14-linear-normalized.txt


title: NGP_ctrl_repeat

value: control


title: NGP_ARID1A_heter_BRG1


title: MA028


title: JN352


title: JN350


title: Progeria_fibroblast_passage11_rep1 [201492560178_R01C01]

source_name: human progeria dermal fibroblast passage11

tag: passage


title: Progeria_fibroblast_passage19_rep3 [201492560178_R06C01]


title: BM_MLL-AF9 [I19R031a17]

city: Tuebingen

first: Corina

last: Schneidawind

address: Otfried-Mueller-Str. 10

department: Hematology and Oncology

institute: University Hospital Tuebingen

data_processing:
Single-end reads were cleaned up and trimmed with BBduk (BBMap suite v38.67) and parameters: k=13,ktrim=r,useshortkmers=t,mink=5,qtrim=r,trimq=10,minlength=20
Cleaned-up and trimmed fastq files were alined with STAR (v2.7.0a) against the Ensembl H.sapiens genome with parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD
Read counts for all genes were determined using Rsubread (v2.0.0) with parameters: GTF.featureType = "exon",GTF.attrType = "gene_id",useMetaFeatures = TRUE,allowMultiOverlap = FALSE,strandSpecific = 1,countMultiMappingReads = FALSE
Genome_build: Ensembl v95 H.sapiens
Supplementary_files_format_and_content: CVS file with raw read counts per gene identified by Ensembl gene ID

source_name: CD34+ HSPCs from bone marrow

growth_protocol: Cells were cultured in StemSpan II media (StemCell Technologies) including 10% fetal bovine serum (FBS, Biochrom) and 100 IU/ml penicillin-streptomycin (Lonza) supplemented with cytokines: stem cell factor (SCF), thrombopoietin (TPO), FLT3-L, interleukin-6 (IL-6), interleukin-3 (IL-3) (50 ng/mL each, PeproTech) and StemRegenin1 (SR1; 0.75 mM) and UM729 (0.75 mM; both StemCell Technologies). Cells were maintained at a cell density of 7.5-20x105/ml, at 37°C and 5% CO2 and subcultured every second day.

extract_protocol:
Total RNA was isolated with Macherey Nagel NucleoSpin RNA Kit.
Libraries were generated using QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina.
Poly(A)-selected sequencing libraries were generated according to manufacturer instructions and sequenced on a NextSeq 500 at 75bp paired-end resolution at a depth of ~5 million reads.

treatment_protocol: Before genome editing, cells were maintained without FCS for 48h. For CRISPR/Cas9-directed engineering, cells were nucleofected with sgRNAs and CAs9 protein as RNPs. Thereafter, cells were cultured with z-Vad (20µM) for 48h and subsequently 10% FCS were added to the culture.

tag: genetics

value: CD34+ HSPCs


title: Progeria_fibroblast_passage19_rep1 [201492560178_R04C01]


title: JN347


title: BM_MLL-AF4 [I19R031a36]


title: BM_MLL-AF9 [I19R031a23]


title: Progeria_fibroblast_passage11_rep3 [201492560178_R03C01]


title: Ctrl [I19R031a14]

source_name: CD34+ HSPCs

value: normal karyotype


title: JN262


title: JN257


title: CB_MLL-AF9 [I19R031a03]

source_name: CD34+ HSPCs from cord blood


title: CB_MLL-AF4 [I19R031a02]


title: JN252


title: CB_MLL-AF9 [I19R031a04]


title: NGP_ARID1A_mut#1_repeat

tag: cell line


title: MA021


title: CB_MLL-AF4 [I19R031a01]


title: Ctrl [I19R031a13]


title: Whole_skin_biopsy_rep_10 [201516320041_R02C01]

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Infinium Human MethylationEPIC BeadChip

source_name: whole skin biopsy

tag: sample type

value: Normal skin biopsie


title: NGP_ARID1A_mut#2

extract_protocol:
Total RNA was depleted of ribosomal RNA with the SMARTer Universal Low Input RNA Kit (Clontech). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on aIllumina NextSeq 500 with 75bp single-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: NGP_ARID1A_mut#1


title: NGP_ctrl


title: JN250


title: JN198


title: Whole_skin_biopsy_rep_16 [201516320041_R08C01]


title: leuS_27_relA

city: Cambridge

first: Darren

middle: John

last: Parker

state: MA

address: 31 Ames Street

department: Biology

institute: MIT

description:
Ribosome protected mRNA
Inducible leuS with 27 μM IPTG + relA D264G mutation

data_processing:
Library strategy: ribosome profiling
Bam files were converted to fastq files using bedtools command bamtofastq
fastq files were stripped of Linker-1 sequence (CTGTAGGCACCATCAAT)
Stripped fastq files were aligned to B. subtilis 168 chromosome NC_000964.3 using bowtie with options -v 2 -k 1 --best
Footprint reads with sizes between 20 to 40 nucleotides were stripped of the first and last 8 nucleotides and a count of 1/n where n equals the remaining read length was assigned to the remaining positions. One wig file for each strand
Genome_build: NC_000964.3
Supplementary_files_format_and_content: 2 wig files for each raw fastq file

organism: Bacillus subtilis

growth_protocol: Overnight cultures in MCCG media (see Methods in publication for details) were backdiluted 1:1000 into fresh media and grown to OD600 0.3 in shaking flasks at 37°C with the listed [IPTG]

extract_protocol:
Cell collection & lysis was performed as described in detail previously (Lalanne et al., 2018 Cell)
Library preparation was done as described in detail previously (Lalanne et al., 2018 Cell) with the following modification. Final cDNA was amplified using Q5 DNA polymerase (New England Biolabs) instead of Phusion DNA polymerase (New England Biolabs). Sequencing was performed on an Illumina HiSeq 2000 or NextSeq500.

tag: strain


title: JN344


title: NGP_ARID1A_mut#2_input

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.2.9 with configuration -p 8 -x $SHARED_DATABASES/bowtie2_indexes/hg19 -U
Data were filtered using SAMtools version 1.3.1 with configuration samtools view -bS -q 20
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files represent counts of aligned reads within 20 bp bins with each read being extended 75 in the direction of alignment. Counts are in reads-per-million.


title: Whole_skin_biopsy_rep_14 [201516320041_R06C01]


title: leuS_25

description:
Ribosome protected mRNA
Inducible leuS with 25 μM IPTG Ribosome profiling

source_name: Inducible leuS with 25 μM IPTG


title: JN233


title: NGP_ARID1A_mut#2_H3K27ac

value: H3K27ac (Abcam, #ab4729)


title: Whole_skin_biopsy_rep_13 [201516320041_R05C01]


title: JN172


title: Whole_skin_biopsy_rep_4 [201516320034_R04C01]


title: BM_MLL-AF4 [I19R031a05]


title: ileS_500

description:
Ribosome protected mRNA
Inducible ileS with 500 μM IPTG Ribosome profiling

source_name: Inducible ileS with 500 μM IPTG


title: Whole_skin_biopsy_rep_8 [201516320034_R08C01]


title: NGP_ARID1A_mut#2_H3K4me3

value: H3K4me3 (Abcam, #ab8580)


title: MA018

value: Exposed


title: JN264


title: ileS_30

description:
Ribosome protected mRNA
Inducible ileS with 30 μM IPTG Ribosome profiling

source_name: Inducible ileS with 30 μM IPTG


title: NGP_ARID1A_mut#2_ARID2

value: ARID2 (Santa Cruz Biotechnology, #sc166117X)


title: ileS_15_WT

description:
Ribosome protected mRNA
Inducible ileS with 15 μM IPTG Ribosome profiling

source_name: Inducible ileS with 15 μM IPTG


title: Whole_skin_biopsy_rep_5 [201516320034_R05C01]


title: Whole_skin_biopsy_rep_11 [201516320041_R03C01]


title: NGP_ARID1A_mut#2_BRG1


title: Progeria_fibroblast_passage11_rep2 [201492560178_R02C01]


title: Whole_skin_biopsy_rep_7 [201516320034_R07C01]


title: JN046

value: Male

value: Whole blood


title: JN202

value: Control


title: ileS_15_relA

description:
Ribosome protected mRNA
Inducible ileS with 15 μM IPTG + relA D264G mutation Ribosome profiling


title: NGP_ARID1A_mut#1_input

value: NGP


title: ileS_10

description:
Ribosome protected mRNA
Inducible ileS with 10 μM IPTG Ribosome profiling

source_name: Inducible ileS with 10 μM IPTG


title: Whole_skin_biopsy_rep_3 [201516320034_R03C01]


title: control_500

description:
Ribosome protected mRNA
168 Wildtype with 500 μM IPTG Ribosome profiling

source_name: 168 Wildtype with 500 μM IPTG


title: Whole_skin_biopsy_rep_2 [201516320034_R02C01]


title: Whole_skin_biopsy_rep_15 [201516320041_R07C01]


title: JN126

value: Case


title: argS_500

description:
Ribosome protected mRNA
Inducible argS with 500 μM IPTG Ribosome profiling

source_name: Inducible argS with 500 μM IPTG


title: NGP_ARID1A_mut#1_H3K4me3


title: JN120


title: argS_30

description:
Ribosome protected mRNA
Inducible argS with 30 μM IPTG Ribosome profiling

source_name: Inducible argS with 30 μM IPTG


title: JN110


title: NGP_ARID1A_mut#1_ARID2


title: argS_15

description:
Ribosome protected mRNA
Inducible argS with 15 μM IPTG Ribosome profiling

source_name: Inducible argS with 15 μM IPTG


title: NGP_ARID1A_mut#1_BRG1


title: Whole_skin_biopsy_rep_12 [201516320041_R04C01]

value: female


title: JN094

source_name: Whole blood


title: 168_WT

description:
Ribosome protected mRNA
168 Wildtype Ribosome profiling

source_name: 168 Wildtype


title: JN083


title: MA005


title: NGP_ARID1A_mut#1_H3K27ac

source_name: Neuroblastoma


title: NGP_ctrl_input


title: 168_relA

description:
Ribosome protected mRNA
168 relA D264G Ribosome profiling

source_name: 168 relA D264G


title: NGP_ctrl_H3K27ac


title: Whole_skin_biopsy_rep_9 [201516320041_R01C01]


title: JN071


title: JN077


title: MA010


title: NGP_ctrl_H3K4me3


title: NGP_ctrl_ARID2


title: JN052


title: NGP_ctrl_BRG1


title: NGP_ARID1A_mut#1_SS18


title: JN048


title: Whole_skin_biopsy_rep_6 [201516320034_R06C01]


title: Whole_skin_biopsy_rep_1 [201516320034_R01C01]

value: Normal skin biopsy


title: NGP_ctrl_SS18


title: MA002


title: JN038


title: JN034


title: serS_500

description:
Ribosome protected mRNA
Inducible serS with 500 μM IPTG Ribosome profiling

source_name: Inducible serS with 500 μM IPTG


title: JN027


title: serS_20

description:
Ribosome protected mRNA
Inducible serS with 20 μM IPTG Ribosome profiling

source_name: Inducible serS with 20 μM IPTG


title: Plus-NMB1

city: Newark

first: Juan

middle: C.

last: Inclan Rico

state: New Jersey

address: 205 South Orange Avenue, Rutgers Cancer Institute of New Jersey at University Hospital

department: Medicine/CII

institute: Rutgers New Jersey Medical School

data_processing:
Base calling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and Alignment (Cutadapt v2.5, STAR vSTAR_2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 output with normalized counts

source_name: NMB-treated ILC2s

growth_protocol: Wildtype mice were infected with 500 larvae of the hookworm Nippostrongylus brasiliensis 7 days prior sort-purification

extract_protocol:
RNA was extracted using Qiagen RNeasy plusTM micro kit (Cat. #74034), and amplified using Ambion MessageAmp II aRNATM Amplification Kit (Cat. #AM1751).
Illumina compatible libraries were generated using the NEBNext Ultra II kit (NEB E7645S)

treatment_protocol: Lung-resident ILC2s from 5 wildtype Nb-infected mice were sort-purified on live CD45+CD3-CD19-CD11b-CD11c-NK1.1-B220-CD5-Ter-119-gdTCR-FceR1–CD90+CD127+ cells and pooled into 1 biological replicate. Then, three biological replicates per experimental group were treated as indicated above. Purity for all cell populations were determined to be 98% or greater.

tag: strain background

tag: genotype/variation

value: wild type

tag: infection

value: hookworm Nippostrongylus brasiliensis

value: Lung-resident sort-purified ILC2s

tag: treatment

value: recombinant Neuromedin B (NMB) for 24 h


title: Plus-NMB2


title: No-NMB2

source_name: vehicle-treated ILC2s

value: vehicle for 24 h


title: serS_10_WT

description:
Ribosome protected mRNA
Inducible serS with 10 μM IPTG Ribosome profiling

source_name: Inducible serS with 10 μM IPTG


title: JN013

tag: group

tag: batch

tag: tissue


title: adipocyte specific TFG KO, biological rep2

city: Hiroshima

first: Takeshi

last: Yamamotoya

address: 1-2-3, Kasumi, Minami-ku

country: Japan

institute: Hiroshima University

hyb_protocol: Samples were hybridized using GeneChip Hybridization, Wash, and Stain Kit (Thermo Fisher).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were processed using Transcriptome Analysis Console (TAC) ver.4.0.

source_name: subcutaneous inguinal WAT

label_protocol: Samples were biotinylated using GeneChip WT pico Reagent Kit (Thermo Fisher).

growth_protocol: Subcutaneous inguinal WAT isolated from 2-month-old mice.

extract_protocol: Samples were snap flozen in liquid N2 and total RNA was extracted using NucleoSpin RNA (Takara Bio).

value: male

tag: genotype

value: adipocyte specific TFG KO

value: subcutaneous inguinal WAT


title: WT, biological rep3

tag: gender


title: adipocyte specific TFG KO, biological rep3


title: adipocyte specific TFG KO, biological rep1


title: WT, biological rep2


title: WT, biological rep1


title: JN011


title: serS_5

description:
Ribosome protected mRNA
Inducible serS with 5 μM IPTG Ribosome profiling

source_name: Inducible serS with 5 μM IPTG


title: MA025

value: Female


title: SCC Macrophage FceRIa_Pos1

city: Portland

first: Naoki

last: Oshimori

state: OR

address: 2720 S Moody Ave

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

description: Transcriptome data from FceRIa-pos macrophages

data_processing:
The FastQC software was used for basecalling.
The STAR aligner was used to align the trimmed reads to the mouse reference genome mm10 (GRCm38).
A counts per mellion (CPM) value were calculated, and only genes that have a CPM value greater than 1 in at least 3 samples were included.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include a counts per million (CPM) value

source_name: Macrophages in SCC

extract_protocol:
RNA in FACS-purified cells were isolated using Trizol reagent. Illumina TruSeq v2 library prep was used with 100 ng of total RNA for the construction of sequence libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cutaneous squamous cell carcinoma (SCC)

value: macrophages

value: FVB


title: no_insert_500

description:
Ribosome protected mRNA
Inducible no insert construct with 500 μM IPTG Ribosome profiling


title: hSTARR_Wnt_1

source_name: BAC DNA spanning TBX3 locus

tag: transfection

value: Human TBX3 STARR-seq library transfected in COS7 cells

tag: co-transfection

value: STARR-seq library co-transfected with Wnt


title: SCC Macrophage FceRIa_Pos2

tag: cell type


title: leuS_500

description:
Ribosome protected mRNA
Inducible leuS with 500 μM IPTG Ribosome profiling

source_name: Inducible leuS with 500 μM IPTG


title: JN007

value: Control

value: Whole blood


title: SCC Macrophage FceRIa_Neg3

description: Transcriptome data from FceRIa-neg macrophages


title: No-NMB1


title: SCC Macrophage FceRIa_Neg2


title: SCC Macrophage FceRIa_Neg1


title: SCC Macrophage FceRIa_Pos3


title: leuS_35

description:
Ribosome protected mRNA
Inducible leuS with 35 μM IPTG Ribosome profiling

source_name: Inducible leuS with 35 μM IPTG


title: serS_10_relA

description:
Ribosome protected mRNA
Inducible serS with 10 μM IPTG + relA D264G mutation Ribosome profiling


title: leuS_30

description:
Ribosome protected mRNA
Inducible leuS with 30 μM IPTG Ribosome profiling

source_name: Inducible leuS with 30 μM IPTG


title: hSTARR_pcDNA_2

value: STARR-seq library co-transfected with pcDNA


title: hSTARR_SG4_1

value: STARR-seq library co-transfected with SG4


title: hSTARR_SG4_2


title: hSTARR_pcDNA_1


title: Basophil-depleted ILC2s 3

description:
Baso3
diffexpr-results.csv

data_processing:
Base calling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and Alignment (Cutadapt v2.5, STAR vSTAR_2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: diffexpr-results.csv (DESeq2 output with normalized counts).

source_name: Lung-resident sort-purified ILC2s

growth_protocol: Wildtype or basophil-depleted mice were infected with the hookworm Nippostrongylus brasiliensis 5 days prior sort-purification

treatment_protocol: Lung-resident ILC2s from control and basophil-depleted mice were sort-purified on live CD45+CD3-CD19-CD11b-CD11c-NK1.1-B220-CD5-Ter-119-gdTCR-FceR1–CD90+CD127+ cells from six biological replicates and pooled into two samples per group. Purity for all cell populations were determined to be 98% or greater.

tag: condition

value: Basophil-depleted

value: hookworm Nippostrongylus brasiliensis

value: Lung-resident ILC2s


title: hSTARR_input_3

description:
hSTARR_input_3
Plasmid DNA


title: leuS_27_WT

description:
Ribosome protected mRNA
Inducible leuS with 27 μM IPTG Ribosome profiling

source_name: Inducible leuS with 27 μM IPTG


title: Basophil-depleted ILC2s 2

description:
Baso2
diffexpr-results.csv


title: hPSC miR-29a Replicate 3

city: Indianapolis

first: Janaiah

last: Kota

state: Indiana

address: 975 W. Walnut Street, IB 244C

department: Medical & Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts and analysis (excel) from edgeR

source_name: pancreas

growth_protocol: hPSC cells were  grown using DMEM High Glucose Culture Media supplemented with 10% FBS in a humidified 5% CO2 incubator at 37degreesC.

extract_protocol:
RNA was isolated using RNeasy Plus Mini Kit (74134, Qiagen)  following manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequence library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: origin

value: Fibroblastic

value: miR-29a overexpressing

value: human pancreatic stellate cells (hPSCs)


title: wildtype ILC2s 3

description:
WT3
diffexpr-results.csv

value: control


title: hPSC miR-29a Replicate 2


title: wildtype ILC2s 1

description:
WT1
diffexpr-results.csv


title: hPSC Control Replicate 3

value: Wildtype


title: hSTARR_input_1

description:
hSTARR_input_1
Plasmid DNA


title: hSTARR_input_2

description:
hSTARR_input_2
Plasmid DNA


title: hPSC Control Replicate 2


title: B3-CK

city: Nanjing

first: Wenran

last: Wang

address: Weigang

institute: Nanjing Agricultural University

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house peri scripts. In this step, clean data(clean data) were obtained by removing reads cotaining adapter.
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 iscurrently the most commonly used method for estimating gene expression levels.
Genome_build: https://genomes.cribi.unipd.it/grape/search_form.php
Supplementary_files_format_and_content: FPKM

organism: Vitis vinifera

source_name: Grapevine berry at 10 DAF

growth_protocol: Three-year-old ‘Fujiminori’ grape trees grown in Nanjing, China (N32°02′12.77′′, E118°37′33.25′′) were chosen as the experimental material. The plant materials were grown under common field conditions at the Jiangsu Vocational College of Agriculture and Forestry grape farm, Jurong, China.

extract_protocol:
Total RNA of the berry samples at GBS was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and the processed RNA was checked for purity and integrity using Nanodrop-2000spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. 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 NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: In order to investigate a demonstrative biological selection of transcripts at green-berry stage, RNA for Illumina sequencing was filtered from tissues comprised of three biological replicated for this stage.

value: Grapevine berry

tag: age

value: at  10 DAF


title: leuS_40

description:
Ribosome protected mRNA
Inducible leuS with 40 μM IPTG Ribosome profiling

source_name: Inducible leuS with 40 μM IPTG


title: hPSC Control Replicate 1


title: Madena.HMO

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

data_processing:
Library strategy: WGS
All gibbon genomic shot-gun data were aligned to the gibbon genome reference (Nleu3.0) using BWA
MELT v2.1.3 was used to predict de novo LAVA insertions and deletions (indels) from each of the 23 whole genome shot-gun alignments
We characterized all LAVA inserts based on information such as genomic location, length, and insertion position relative to closest gene [intergenic, exonic, intronic, promoter (<3Kb upstream of gene) or terminator (<3Kb downstream of gene)]
The initial set of LAVA predictions was next filtered to remove: 1) low quality inserts, as assessed by MELT, 2) single copy inserts in the population, 3) inserts shorter than 290bp (the minimum length required to discriminate a composite LAVA from its non-SVA subunits), and 4) inserts found on unplaced Nleu3.0 contigs.
We generated binary LAVA genotype profiles for all gibbon individuals (heterozygous or homozygous LAVA insertion=1, homozygous absence of LAVA= 0)
Genome_build: Nleu3.0
Supplementary_files_format_and_content: an excel spreadsheet containing position, genomic and genotype information for all LAVA insertions across 23 gibbons

organism: Hylobates moloch

source_name: blood

extract_protocol:
Total gDNA was extracted from blood of gibbons and randomly sheared
sheared gDNA was used to generate illumina libraries using the NEBNext Ultra II library contruction kit (NEB)

value: blood


title: Karenina.SSY

organism: Symphalangus syndactylus


title: Monty.SSY


title: SCC Tumor TGF-beta Pos_3

description: Transcriptome data from TGFb reporter-pos SCC basal cells

source_name: SCC epithelial basal cells

value: cutaneous squamous cell carcinoma (SCC)

value: tumor epithelial cell

value: FVB


title: HEK293T_CT

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

data_processing:
Unpaired sequencing reads were trimmed and subjected to proprietary quality filtration for the Ion Torrent platform (minimum quality threshold 20).
Reads were mapped using Bowtie2 (with default options) against repeat-unmasked (hg38.fa) human genome. Reads were mapped end-to-end with default option.
Mapped reads were subjected to variant calling across the sequenced locations in all datasets using BCFtools. A minimum coverage of 5 reads was used as a threshold to filter the variants.
Genome_build: hg38

growth_protocol: HEK293T and human fibroblasts cells were grown in DMEM supplemented with 10 % FBS at 37˚C and 5% CO2.

extract_protocol:
DNA isolated from HEK293T and GM02639 cells were sonicated. The lysates were clarified and subjected to MeDIP by anti-5-methylcytosine antibody cocktail. MeDIP DNA was purified using PCR cleanup kit. Genomic DNA was isolated from GM02640 and GM02641 cells.
The Ion Xpress(TM) Plus Fragment Library Kit (Cat. no. 4471269) was used for library preparation. All the steps were performed as per manufacturer’s instructions for sequencing on Ion Torrent S5 platform without any barcoding.

treatment_protocol: HEK293T cells were transduced with following shRNA lentiviruses: non-targeting (CT), CGGBP1-targeting (KD). For stable transduction, control- and CGGBP1-shmiR transduced cells were selected with 10 ug/ml puromycin for a week. GM02639 cells were transfected twice with following siRNA: non-targeting (CT) and CGGBP1-targeting (KD). Genomic DNA was isolated from GM02640 and GM02641 cells without any treatment.

tag: antibody

value: MABE146 and SAB2702243 (Sigma) ; NBP2-42813 (Novus Biologicals)

tag: cell line

tag: sirna

value: non-targeting RNAi


title: HEK293T_KD

value: CGGBP1 knocked-down by RNAi


title: SCC Tumor TGF-beta Pos_2

tag: strain


title: F. novicida PmrA mutant [2845-D-mRNA]

city: Columbus

first: John

last: Gunn

address: 700 Children’s Drive

department: Center for Microbial Pathogenesis

institute: Abigail Wexner Research Institute at Nationwide Children’s Hospital

description:
processed data file: 1819_vs_2845_annotated_results_deseq2.csv
2845-D-mRNA

data_processing:
F. tularensis samples were aligned to the GCA_000009245.1_ASM924v1 assembly of the Francisella tularensis LVS reference from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000009245.1) using v0.7.15 of the BWAMEM aligner. F. novicida samples were aligned to the GCF_000014645.1 assembly of the Francisella tularensis U112 reference from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000014645.1) using v0.7.5a the BWAMEM aligner.
Features were identified from the GFF files that came with the assembly from NCBI.
Feature coverage counts were calculated using version 0.6.1p1 of HTSeq -count
Differentially expressed features were calculated using DESeq2.
Genome_build: Francisella tularensis LVS & Francisella tularensis U112
Supplementary_files_format_and_content: Excel spreadsheet and CSV files containing read counts for each sample and differential expression data for each feature.

organism: Francisella tularensis subsp. novicida

source_name: F. novicida PmrA mutant sample

extract_protocol:
rRNA was removed with Illumina ScriptSeq Gram Negative rRNA removal kit
libraries were constructed from first strand cDNA using ScriptSeq v2 kit (Illumina,CA)

tag: genotype/variation

value: PmrA mutant

tag: growth phase

value: exponential phase


title: F. novicida PmrA mutant [2845-C-mRNA]

description:
processed data file: 1819_vs_2845_annotated_results_deseq2.csv
2845-C-mRNA


title: SCC Tumor TGF-beta Pos_1


title: hPSC miR-29a Replicate 1


title: SCC Tumor TGF-beta Neg_3

description: Transcriptome data from TGFb reporter-neg SCC basal cells


title: F. novicida PmrA mutant [2845-B-mRNA]

description:
processed data file: 1819_vs_2845_annotated_results_deseq2.csv
2845-B-mRNA


title: F. novicida PmrA mutant [2845-A-mRNA]

description:
processed data file: 1819_vs_2845_annotated_results_deseq2.csv
2845-A-mRNA


title: MA007

source_name: Whole blood

tag: group

value: Exposed

value: Male

value: Whole blood


title: F. novicida WT [1819-D-mRNA]

description:
processed data file: 1819_vs_2845_annotated_results_deseq2.csv
1819-D-mRNA

source_name: F. novicida WT sample

value: WT


title: SCC Tumor TGF-beta Neg_2


title: Lionel.HMO


title: SCC Tumor TGF-beta Neg_1


title: Domino.HPI

organism: Hylobates pileatus


title: F. novicida WT [1819-C-mRNA]

description:
processed data file: 1819_vs_2845_annotated_results_deseq2.csv
1819-C-mRNA


title: F. novicida WT [1819-B-mRNA]

description:
processed data file: 1819_vs_2845_annotated_results_deseq2.csv
1819-B-mRNA


title: Scrambled control transfection replicate 3

city: Heidelberg

first: Arlou Kristina

last: Angeles

state: BW

address: Im Neuenheimer Feld 460

institute: DKFZ/NCT

description: replicate 3

hyb_protocol: Standard Illumina Hybridization Protocol

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol.

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore.

label: Biotin

source_name: PC-3 cell line

label_protocol: Biotin-labeled cRNA

growth_protocol: Cells were seeded at 80% confluency into 6-well plates 24 h prior to transfection. Maintenance media: F-12K medium (ATCC) suplemented with 10% fetal bovine serum (Gibco, Thermo Fisher Scientific)

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer's protocol, including the DNase I digestion step. RNA quality was assessed by Bioa

treatment_protocol: Cells were transfected using Lipofectamine RNAiMax (Thermo Fisher Scientific) with 10 nM siRNA targeting LINC00920 (si2_LINC920 and si3_LINC920) or a scrambled, non-targeting control (NTC). Cells were harvested for RNA isolation 48 h after transfection.

value: scrambled control

tag: passage


title: LINC00920 knockdown by siRNA2 replicate 2

description: replicate 2

value: LINC00920 knockdown by siRNA2


title: Scrambled control transfection replicate 2

description: replicate 2


title: LINC00920 knockdown by siRNA2 replicate 3

description: replicate 3


title: LINC00920 knockdown by siRNA3 replicate 1

description: replicate 1

value: LINC00920 knockdown by siRNA3


title: LINC00920 knockdown by siRNA2 replicate 1

description: replicate 1


title: LINC00920 knockdown by siRNA3 replicate 2

description: replicate 2


title: LINC00920 knockdown by siRNA3 replicate 3

description: replicate 3


title: S16 ΔSOX10 2-1

city: Ann Arbor

first: Elizabeth

last: Fogarty

state: MI

address: 1105 N. University Ave

institute: University of Michigan

description: Cells were maintained in standard growth medium containing 10% FBS, glutamine, and pen-strep.

data_processing:
Sequenced reads were trimmed of adapter sequences using Cutadapt (v 1.14)
Read 1 from each sample was mapped to the rn5 genome using STAR (v 2.5.2a)
BAM files were generated using Samtools (v 1.9)
Per-base start site counts were generated using the Make_CTSS script from Takahashi and colleagues (Nature Protocols, 2012). TSS clustering was performed using Paraclu (v 9).
Per-cluster read counts were generated using featureCounts (subread v 1.6.1). Statistical analysis was performed using edgeR (v 3.24.3).
Genome_build: rn5
Supplementary_files_format_and_content: Tab-delimited text file includes 4,993 TSSs associated with SOX10-bound promoters in sciatic nerve. For each TSS, genomic coordinates, id number, strand, associated gene symbol, and coordinates of H3K4me3 and SOX10 ChIP-Seq peaks are provided (ChIP-Seq peaks from previously published datasets). Following are the reads per million (RPM) values for each TSS in each sample as measured by Tn5Prime. Statistical values (log2 fold change and FDR-corrected p-values) are provided for cAMP versus control-treated primary Schwann cells and ΔSOX10 versus parental S16 cells.

organism: Rattus norvegicus

source_name: S16 cells

extract_protocol:
Total RNA was isolated using the Qiagen Rneasy Mini Kit (Catalog Number 74104) with on-column Dnase treatment (Catalog Number 79254) according to manufacturer protocol.
Tn5Prime libraries were constructed essentially as described by Cole and colleagues (NAR, 2018). Briefly, RNA was reverse-transcribed by SMARTScribe RT in the presence of an oligo-dT primer and template-switching oligo. The reaction was treated with RNase and Exonuclease. The resulting DNA was subjected to an indexing PCR, tagmentation by purified Tn5 enzyme pre-loaded with Tn5ME-B/R adapters, and another round of PCR. Size selection to 400-1000bp was performed on a 0.8% low-melt agarose TAE gel. DNA was purified using the Qiagen Gel Extraction Kit (Catalog Number 28704). Libraries were sequenced on Illumina HiSeq or NovaSeq sequencers. Read 1 (corresponding to 5' end of mRNAs) was used for subsequent analyses.

tag: treatment


title: S16 Parental 2

tag: genotype

value: wild type


title: S16 ΔSOX10 1-1


title: Knockout mouse 5 8 weeks

city: Shreveport

first: Matthew

last: Woolard

state: LA

address: 1501 Kings Hwy

department: Microbiology and Immunology

institute: Louisiana State University Health Science Center Shreveport

description:
Male mice on high fat diet for 12 weeks
1418 8 wk KO

hyb_protocol: Canopy biosciences received RNA and perfromed hybridization

scan_protocol: Canopy biosciences performed direct digital counting

data_processing: Canopy biosciences normalized all data via log2 count data

source_name: aortic root tissue section

label_protocol: Extracted RNA samples were shipped to Canopy Biosciences for labeling with a capture probe and a reporter probe https://canopybiosciences.com/nanostring/

growth_protocol: Male mice 7-14 weeks of age were given an AAV8-PCSK9 retroorbital injection and fed a high fat diet for 8-12 weeks to induce atherosclerosis. After 8 or 12 weeks, mice were euthanized and aortic roots were extracted, formalin-fixed, deydated, and sectioned into 5um tissue sections before RNA islaation

extract_protocol: RNA Storm kit was used to extract RNA from tissue sections

tag: tissue

value: aortic root

tag: Sex

value: male

tag: diet

value: high fat

tag: time on diet

value: 12 weeks

value: lipin-1 KO


title: Wild type mouse 4 8 weeks

description:
Male mice on high fat diet for 12 weeks
1438 8wk Con


title: Wild type mouse 6 8 weeks

description:
Male mice on high fat diet for 12 weeks
1470 8 wk Con


title: S16 ΔSOX10 1-2


title: Knockout mouse 6 8 weeks

description:
Male mice on high fat diet for 12 weeks
1471 8 wk KO


title: Sciatic Nerve 2

source_name: sciatic nerve


title: Wild type mouse 5 8 weeks

description:
Male mice on high fat diet for 12 weeks
1441 8 wk Con


title: Knockout mouse 4 8 weeks

description:
Male mice on high fat diet for 12 weeks
1324 8wk KO


title: Scrambled control transfection replicate 1

description: replicate 1

tag: transfection


title: Knockout mouse 3 8 weeks

description:
Male mice on high fat diet for 12 weeks
1322 8 wk KO


title: F. novicida WT [1819-A-mRNA]

description:
processed data file: 1819_vs_2845_annotated_results_deseq2.csv
1819-A-mRNA


title: 89428: 314C_R_DT_442R

city: Vienna

first: Anna

last: Obenauf

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Institute of Molecular Pathology

data_processing:
Adapter and polyA sequences are clipped with bbduk (v38.06).
Abundant sequences (iGenomes GRCm38) are removed with bbmap (v38.06).
Cleaned reads are aligned against the genome (GRCm38, primary_assembly) with STAR (v2.6.0c).
Reads are counted towards their corresponding gene (Ensembl 94) with featureCounts (v1.6.2).
Genome_build: GRCm38
Supplementary_files_format_and_content: featureCounts standard output (TXT)

source_name: YUMM1.7 cell line from tumor

extract_protocol:
Whole tumours, tumours were dissected, cut into small pieces and dissociated for 1.5 hours using Collagenase A (1 mg/ml) in PBS. Single cell suspensions were strained through a 70 µm nylon mesh, washed in FACS buffer (0.5% BSA, 2 mM EDTA) and incubated for 10 min on 4 °C with anti-mouse Fc-Block CD16/CD32 antibody (clone 2.4G2, BD Pharmingen, 1:10). Cells were subsequently stained with a live-dead stain (Fixable viability dye eFluor 780, eBioscience, 1:1000) and a pan mouse immune-cell antibody CD45 PECy7 (clone 30-F11, BD Pharmingen, 1:500) in FACS buffer for 30 min on 4 °C. Injected CaTCH-isolated cancer cells were further identified by their strong GFP expression signal. Whole RNA was isolated from cells using a magnetic bead-based purification kit (in-house).
Quantseq libraries were generated using the Lexogen Quantseq 3’ mRNA seq kit using 250 ng input RNA, according to manufacturer’s instructions.

tag: cell type

value: RAFi/MEKi

tag: clone name


title: Wild type mouse 2 8 weeks

description:
Male mice on high fat diet for 12 weeks
1320 8wk Con


title: Wild type mouse 3 8 weeks

description:
Male mice on high fat diet for 12 weeks
1321 8 wk Con


title: S16 ΔSOX10 2-2


title: Wild type mouse 1 8 weeks

description:
Male mice on high fat diet for 12 weeks
1311 8 wk Con


title: Sciatic Nerve 1


title: Primary Schwann Cell cAMP 3

description: Cells were maintained in medium containing 10% FBS, 10nM neuregulin, and 2uM forskolin, in addition to glutamine, pen-strep, and gentamicin. Cells were plated on poly-L-lysine- and laminin-coated dishes. The next day medium was replaced with medium lacking neuregulin and forskolin. The following day medium was replaced with medium containing 5% FBS. The following day medium was replaced with medium containing 5% FBS and supplemented with 250 uM CPT-cAMP. CPT-cAMP medium was replenished each day for 3 days.

source_name: primary Schwann cell

value: CPT-cAMP


title: 89427: 314C_R_DT_440R


title: 89426: 314C_R_DT_438L


title: NGP_ARID1A_mut#2_SS18

source_name: Neuroblastoma

extract_protocol:
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: NGP

tag: chip antiboy


title: JN195

data_processing: R package RnBeads was used for quality control and preprocessing of the arrays

extract_protocol: DNA was prepared from 0.5 ml - 3 ml of anticoagulated whole blood (EDTA) by erythrocyte lysis in 70 μg of NH4H2CO3/ml and 7.0 mg of NH4Cl/ml followed by lysis of leukocytes  in 1% sodium dodecyl sulfate, 100 mM EDTA, and 200 mM Tris (pH 8.5) and precipitation in isopropanol

value: Control

tag: gender

value: Female

tag: batch


title: Primary Schwann Cell cAMP 2


title: 89425: 314C_R_UT_441L

tag: strain

value: untreated


title: Knockout mouse 2 8 weeks

description:
Male mice on high fat diet for 12 weeks
1299 8 wk KO


title: S16 Parental 1


title: Knockout mouse 1 8 weeks

description:
Male mice on high fat diet for 12 weeks
1298 8 wk KO


title: 89424: 314C_R_UT_439R


title: Primary Schwann Cell Control 3

description: Cells were maintained in medium containing 10% FBS, 10nM neuregulin, and 2uM forskolin, in addition to glutamine, pen-strep, and gentamicin. Cells were plated on poly-L-lysine- and laminin-coated dishes. The next day medium was replaced with medium lacking neuregulin and forskolin. The following day medium was replaced with medium containing 5% FBS. 5% FBS-containing medium was replenished each day for 4 days.

value: Vehicle


title: Primary Schwann Cell cAMP 1


title: 89422: Depleted1_DT_408R


title: Johannes.NLE

organism: Nomascus leucogenys

value: blood


title: 89420: Depleted1_DT_400R


title: Khao.NLE


title: Primary Schwann Cell Control 2


title: Wild type mouse 4 12 weeks

description:
Male mice on high fat diet 8 weeks
703 12 wk Con

value: 8 weeks

value: WT


title: Wild type mouse 5 12 weeks

description:
Male mice on high fat diet 8 weeks
882 12 wk Con


title: Primary Schwann Cell Control1


title: Asia.NLE


title: 89417: 312A_R_DT_418L


title: Phyllis.NLE (RNA-Seq)

data_processing:
Reads were trimmed with Trimmomatic (Bolger et al. 2014)
Trimmed reads were aligned to Nleu3.0 using STAR (Dobin et al. 2013)
We counted high-quality uniquely mapping reads (MAPQ>25) aligning to each gene
We used edgeR (Robinson et al. 2010) to remove genes for which fewer than two individuals had >0.5 read counts per million (CPM)
We used the Conditional Quantile Normalization package (CQN; Hansen et al, 2012) to normalize gene counts based on gene length, GC content and RNA-seq library size
The normalized read counts were regularized log (rlog) transformed using DEseq2 (Love et al. 2014) to stabilize the variance
Lastly, genes located on unassembled contigs in the genome were excluded
Genome_build: Nleu3.0
Supplementary_files_format_and_content: A table in txt format with the normalized gene counts for each individual

source_name: EBV-transformed lymphocyte cell line

extract_protocol:
Total RNA was extracted from EBV-transformed lymphocyte cell lines using the RNeasy Mini kit (Qiagen) and RNA integrity scores were assessed on the Bioanalyzer with the RNA 6000 Pico kit (Agilent Genomics)
RNA libraries were prepared for sequencing using the illumina Truseq kit protocol

value: EBV-transformed lymphocyte cell line


title: Wild type mouse 6 12 weeks

description:
Male mice on high fat diet 8 weeks
885 12 wk Con


title: Knockout mouse 4 12 weeks

description:
Male mice on high fat diet 8 weeks
643 12 wk KO


title: 89415: 312A_TN_DT_411R


title: Wild type mouse 2 12 weeks

description:
Male mice on high fat diet 8 weeks
597 12 wk Con


title: Knockout mouse 6 12 weeks

description:
Male mice on high fat diet 8 weeks
865 12 wk KO


title: 89421: Depleted1_DT_404L


title: Melouprey.NLE (RNA-Seq)


title: 89418: 312A_R_DT_421L


title: 89419: 312A_R_DT_422R


title: Knockout mouse 3 12 weeks

description:
Male mice on high fat diet 8 weeks
611 12 wk KO


title: F. tularensis LVS PmrA mutant [18-0401_3233-4]

description:
processed data file: AllData_180328_RNAseq_Gunn_Results.xlsx
18-0401_3233-4_S8_L006

organism: Francisella tularensis

source_name: F. tularensis LVS PmrA mutant sample

tag: genotype/variation

value: LVS PmrA mutant

value: exponential phase


title: Ricky.NLE (RNA-Seq)


title: China.NLE (RNA-Seq)


title: Knockout mouse 1 12 weeks

description:
Male mice on high fat diet 8 weeks
578 12 wk KO

value: aortic root

value: male


title: Knockout mouse 2 12 weeks

description:
Male mice on high fat diet 8 weeks
610 12 wk KO

value: high fat


title: Bobby.NLE (RNA-Seq)


title: 89416: 312A_TN_DT_415L


title: Wild type mouse 3 12 weeks

description:
Male mice on high fat diet 8 weeks
598 12 wk Con


title: F. tularensis LVS PmrA mutant [18-0399_3233-2]

description:
processed data file: AllData_180328_RNAseq_Gunn_Results.xlsx
18-0399_3233-2_S6_L006

tag: growth phase


title: Nancy.NLE (RNA-Seq)


title: Asia.NLE (RNA-Seq)


title: 89411: 314C_TN_DT_428L


title: 89410: Depleted1_UT_407L


title: Knockout mouse 5 12 weeks

description:
Male mice on high fat diet 8 weeks
649 12 wk KO

value: lipin-1 KO


title: 89423: 314C_R_UT_436L


title: 89414: 312A_TN_DT_409R

value: RAFi/MEKi


title: Khao.NLE (RNA-Seq)


title: 89413: 314C_TN_DT_432L


title: Wild type mouse 1 12 weeks

description:
Male mice on high fat diet 8 weeks
596 12 wk Con


title: Vok.NLE.H3K9me3

data_processing:
All reads were aligned to Nleu3.0 using BWA with default single-end settings, and low-quality and multi-mapping read alignments (MAPQ<30) were removed
The Pearson correlation of ChIP-seq signal across biological replicates and histone marks was calculated using deepTools
ChromHMM tool (21) was used to identify and characterize 9 chromatin states based on the histone ChIP-seq alignments
Genome_build: Nleu3.0
Supplementary_files_format_and_content: a bedgraph containing genome-wide chromatin state annotations

extract_protocol:
We fixed 5x106 cells per ChIP assay, with 1% formaldehyde for 5min on ice and then quenched fixation by adding glycine to a final concentration of 0.1M. After washing the cells twice with cold 1X PBS, we lysed the fixed cells at a concentration of 3x106cells/100ul in Lysis buffer (0.1% SDS, 0.5% Triton X-100, 20mM Tris-HCl pH=8.0, 150mM NaCl, 1x Proteinase inhibitor (Roche)) for 5min on ice. Using the Bioruptor Pico sonicator (Diagenode), we sheared lysates in 1.5mL tubes with 7 cycles (30sec on/off). We spun the sonicated lysates at max speed for 10min at 4°C to remove cell debris and then rotated them for 2hr at 4°C with 20ul ChIP-grade Protein A/G Magnetic Beads (Pierce) to preclear the lysate. From each chromatin preparation, we set aside a 1% volume aliquot as chromatin input, and the rest we divided equally into each histone mark ChIP reactions. We diluted the reactions to 1.6x106cells/100ul with Lysis buffer and then added the corresponding antibodies in the following amounts: 2ug H3K4me1 (ab8895, Abcam), 1ug H3K4me3 (ab8580, Abcam), 1ug H3K27ac (ab4729, Abcam), 2ug H3K27me3 (39155, Active Motif) and 2ug H3K9me3 (ab9263, Abcam), and let reactions rotate overnight at 4°C. Next, we added 20ul Pierce ChIP-grade Protein A/G Magnetic Beads (Pierce) and let samples rotate for 2hrs at 4°C. We then washed the beads consecutively (rotating at 4°C) with TBST buffer (3 times for 15min), Lysis buffer (once for 1hr), 1xTE pH=8 (once for 1hr, then once for 10min). Following washes, we eluted chromatin in 250ul fresh Elution buffer (1% SDS, 0.1M NaHCO3). We incubated the ChIP and input samples overnight at 65°C in presence of NaCl to reverse crosslinks and then digested them consecutively with 8ug RNAse A (30 minutes at 37°C) and 80ug Proteinase K (2 hour at 55°C). Lastly, we purified the samples using traditional phenol:chloroform extraction and ethanol precipitation. We quantified all samples using the Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific).
All sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) for 1-5ng of starting material and without size selection. The Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 were used to QC the libraries.

tag: antibody

value: anti-H3K9me3, (ab9263, Abcam)


title: 89412: 314C_TN_DT_431L


title: F. tularensis LVS WT [18-0396_2086-3]

description:
processed data file: AllData_180328_RNAseq_Gunn_Results.xlsx
18-0396_2086-3_S3_L006

source_name: F. tularensis LVS WT sample

value: LVS WT


title: F. tularensis LVS PmrA mutant [18-0400_3233-3]

description:
processed data file: AllData_180328_RNAseq_Gunn_Results.xlsx
18-0400_3233-3_S7_L006


title: F. tularensis LVS WT [18-0397_2086-4]

description:
processed data file: AllData_180328_RNAseq_Gunn_Results.xlsx
18-0397_2086-4_S4_L006


title: Vok.NLE.H3K27me3

value: anti-H3K27me3 (39155, Active Motif)


title: Vok.NLE.H3K4me1

value: anti-H3K4me1, (ab8895, Abcam)


title: F. tularensis LVS WT [18-0394_2086-1]

description:
processed data file: AllData_180328_RNAseq_Gunn_Results.xlsx
18-0394_2086-1_S1_L006


title: 89407: 312A_R_UT_426L

value: untreated


title: 89405: 312A_R_UT_420R


title: Vok.NLE.H3K27ac

value: anti-H3K27ac, (ab4729, Abcam)


title: 89404: 314C_TN_UT_434R


title: 89406: 312A_R_UT_424L


title: X044_WT_N3

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University

data_processing:
Raw reads were trimmed for low quality reads and miscalled nucleotides using Trimmomatic v. 0.39.
Reads that passed the trimming step were aligned to rhesus macaque genome (Ensembl Mmul_8.0.1 release 88) using the STAR aligner (version 2.7.0e).
Aligned reads were counted using HTSeq (version 0.9.1).
Genome_build: Ensembl Mmul_8.0.1 release 88.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

organism: Macaca mulatta

source_name: Blood Natural Killer cells

extract_protocol:
Total RNA was extracted from sorted NK cells and enriched for polyadenylated species by two sequential rounds of binding to oligo-dT dynabeads (Life Technologies), chemically fragmented in the presence of Mg2+, and reverse transcribed using Superscript III reverse transcriptase (Life Technologies).
Second strand cDNA synthesis, end repair, A-tailing, and sequencing adaptor ligation were performed using NEBNext enzyme modules (New England Biolabs). Libraries were amplified using universal and indexed primers from the NEBNext system with Kapa 2x Hot Start Readymix (Kapa Biosystems). Amplified libraries were size-selected using Beckman-Coulter Ampure XP beads, quantified by qPCR using the Kapa Library Quantification Kit for Illumina (Kapa Biosystems), and checked for sizing by electrophoresis on a BioAnalyzer (Agilent). Completed libraries were loaded on Illumina Truseq Paired-End v2 Cluster Kits and sequenced in 2 x 150 base paired-end runs on an Illumina HiSeq 4000 sequencer with an average of 20 million reads per sample.

value: Blood Natural Killer cells

tag: animal id

tag: timepoint

value: wild-type neutralizing monoclonal antibody VRC07-523LS


title: Ricky.NLE.H3K9me3


title: X044_WT_N2

tag: treatment


title: Vok.NLE.input-3


title: Vok.NLE.input-1


title: 89408: Depleted1_UT_402L


title: F. tularensis LVS PmrA mutant [18-0398_3233-1]

description:
processed data file: AllData_180328_RNAseq_Gunn_Results.xlsx
18-0398_3233-1_S5_L006


title: X044_WT_N1


title: 89409: Depleted1_UT_405R


title: V187_LALA_N1

value: antibody with LALA mutation


title: 89399: 312A_TN_UT_410L


title: 89402: 314C_TN_UT_427R


title: V187_LALA_N3


title: Ricky.NLE.H3K4me3

value: EBV-transformed lymphocyte cell line

value: anti-H3K4me3, (ab8580, Abcam)


title: Ricky.NLE.H3K27ac


title: Ricky.NLE.H3K4me1


title: Ricky.NLE.H3K27me3-1


title: Ricky.NLE.H3K27me3-2


title: V187_LALA_N2


title: 89401: 312A_TN_UT_416R


title: F. tularensis LVS WT [18-0395_2086-2]

description:
processed data file: AllData_180328_RNAseq_Gunn_Results.xlsx
18-0395_2086-2_S2_L006

value: exponential phase


title: Vok.NLE.PU1

data_processing:
Raw reads were QC’d using FastQC and trimmed with Trimmomatic
We then used bowtie2 to align processed reads from gibbon and human ChIP-seq replicates to Nleu3.0
RepEnrich2  and edgeR  were next used to calculate number of aligned reads to each repeat family and to test enrichment of repeat families in PU.1 ChIP-seq data compared to input.
low quality and multi-mapping read alignments using samtools and peak calling was performed using MACS2
MACS2 was used to generate fold-enrichment tracks after combining alignments from biological replicates
Genome_build: Nleu3.0
Supplementary_files_format_and_content: Enrichment of transposable element families in gibbon PU.1 relative to input appears in an xlsx spreadsheet
Supplementary_files_format_and_content: Significant PU.1 peaks for two gibbon individuals (Ricky and Vok) appear in two separate xls spreadsheets
Supplementary_files_format_and_content: Fold-Enrichment tracks for PU.1 (merged between two individuals) apear in a bedgraph file

extract_protocol:
10x106 fixed cells were used per ChIP assay. After washing the cells twice with cold 1X PBS, we lysed the fixed cells in Lysis buffer (0.1% SDS, 0.5% Triton X-100, 20mM Tris-HCl pH=8.0, 150mM NaCl, 1x Proteinase inhibitor (Roche)) and used the Bioruptor Pico sonicator (Diagenode) to shear lysates. Each ChIP assay was incubate with 6ul of the PU.1 antibody (MA5-15064, ThermoFisher Scientific) overnight. Next, we added 20ul Pierce ChIP-grade Protein A/G Magnetic Beads (Pierce) and let samples rotate for 2hrs at 4°C. We then washed the beads consecutively (rotating at 4°C) with TBST buffer (3 times for 15min), Lysis buffer (once for 1hr), 1xTE pH=8 (once for 1hr, then once for 10min). Following washes, we eluted chromatin in 250ul fresh Elution buffer (1% SDS, 0.1M NaHCO3). We incubated the ChIP and input samples overnight at 65°C in presence of NaCl to reverse crosslinks and then digested them consecutively with 8ug RNAse A (30 minutes at 37°C) and 80ug Proteinase K (2 hour at 55°C). Lastly, we purified the samples using traditional phenol:chloroform extraction and ethanol precipitation. We quantified all samples using the Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific).
libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs)

value: anti-PU.1 (MA5-15064, ThermoFisher Scientific)


title: V165_DEL_N3

value: antibody with DEL mutation


title: 89403: 314C_TN_UT_429L


title: V165_DEL_N1


title: V165_DEL_N2


title: V151_DEL_N3


title: Ricky.NLE.PU1


title: Vok.NLE.input


title: Asia.NLE.H3K9me3


title: Ricky.NLE.input


title: 89400: 312A_TN_UT_412R


title: Andrea.NGA

organism: Nomascus gabriellae

tag: tissue

value: blood


title: Asia.NLE.H3K4me1


title: V151_DEL_N2


title: Melouprey.NLE


title: V151_DEL_N1


title: Asia.NLE.H3K27me3


title: Bobby.NLE


title: Asia.NLE.H3K27ac


title: Asia.NLE.input-3


title: Ricky.NLE.input-2


title: Ricky.NLE.input-1


title: Asia.NLE.input-1


title: V149_DEL_N2


title: V108_DEL_N3


title: Cavefish_singlecell_10x

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Cavefish Liver

data_processing:
Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline (version 2.1.1). Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using cavefish genome astMex1, ensembl 87 gene model. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters.
Genome_build: astMex1
Supplementary_files_format_and_content: cellranger output raw count matrix in hdf5 format

organism: Astyanax mexicanus

source_name: Pachon Cavefish

extract_protocol:
Single cell suspension from freshly dissected headkidney tissue from cave and surface morphotypes of A. mexicanus were produced by forcing tissue through 40 µM cell strainer into L-15 media (Sigma), containing 10 % water and 5 mM HEPES buffer (pH 7.2) and 20 U/mL heparin (L-90). The strainer was washed once with L-90 and cells were washed once by spinning cells at 500 x g at 4 ºC for 5 mins. Supernatant was discarded and cells were resuspended in 1 mL of L-90 media (L-15 containing 10 % water, 5 mM HEPES (7.2 pH), 5 % fetal calf serum, 4 mM L-glutamin, Penicillin-Streptomycin mix with 10000 U/mL each). Mature Erythrocytes were reduced via flowcytometric sorting (Influx System) of hematopoietic tissue based on scatter characteristics. Sorted cells were washed once in L-90 media  and run again on Influx system to ensure removal of mature erythrocyte cluster and measure cell viability (percentage live cells after sorting: surface fish 82.2 % and cavefish 88.9 %).
Single Cell 3' Reagent kits v2 User Guide Rev D (10X Genomics)
scRNA-seq (10x Genomics)

tag: morphotype

value: cave

tag: age

value: Adult

tag: Sex

value: Female

value: headkidney


title: V108_DEL_N2


title: V149_DEL_N3


title: V108_DEL_N1


title: V077_WT_N2


title: V077_WT_N3


title: Surfacefish_singlecell_10x

description: Surfacefish Liver

source_name: Surfacefish

value: surface


title: V149_DEL_N1


title: smallRNAs_se2_rep3

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

description: smallRNA

data_processing:
adapter sequence was removed with fastx_clipper
clean reads were mapped to Arabidopsis thialana TAIR10 genome using bowtie with -v 0 parameter
fasta file with sequences which mapped to the genome was generated with samtools view with -h -F 4 parameter
genereted fasta file was collapsed with fastx_collapser
TAIR10
collapsed fasta file with counts and sequences for all mapped reads from one library

organism: Arabidopsis thaliana

source_name: aerial tIssue

growth_protocol: Plants were grown in soil under 16 hour light/8 hour dark cycle at 20°C

extract_protocol:
Aerial parts of 4 weeks plants were collected and immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using Direct-zol kit (Zymo Research) according to manufacturers instructions. Total RNA integrity was analyzed on Agilent 2100 Bioanalyzer. 10ug of RNA was resolved on denaturing 15%PAA gel and small RNA fraction was cout out from the gel
Libraries were constructed using the TruSeq SmallRNA Library Preparation Kit (Illumina) as described in the manual.

tag: ecotype background


title: V077_WT_N1

tag: cell type


title: smallRNAs_hen2-2_x_se2_rep1

description: smallRNA

value: hen2-2 x se2


title: Input_EV_2_SetC

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: ChIP-seq (Input chromatin for SetC ChIP samples) performed on A375 cells expressing empty vector. Replicate 2 of 2.

data_processing:
Base Calling. Basecalling, quality scoring and de-multiplexing was performed directly using the NextSeq 550 software (RTAv2). Alignment. For each de-multiplexed sample, multiple fastq files were merged using the ‘cat’ function (four raw files per sample). Merged files were aligned to the human genome (GRCh38 build) using bowtie2 v2.2.6 for single end sequence data (default options) to generate .SAM files. Aligned read data was processed using HOMER v4.8. Using the HOMER suite of tools, SAM files were converted into tag directories and multi-mapping reads were removed using makeTagDirectory -unique -fragLength 150. Mapped regions which, due to fragment processing, extended beyond the end of the chromosomes were removed using removeOutOfBoundsReads.pl with chromosome lengths for GRCh38.  Replicate data, was combined at this stage and genome browser files (.bw) were generated using makeUCSCfile with the following options: -bigWig -fsize 1e20 -strand both -norm 10e7. Supplementary files format and content. Processed files are in bigwig format representing mapped tag densities across the mappable portion of the genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: .bigWig files contain information on both the genomic distribution and signal strength of the mapped reads (representative of the sample composition).  .bigWig files are in an indexed binary format.

source_name: Cultured A375 melanoma cells

growth_protocol: A375 cells (ATCC) were cultured in DMEM media supplemented with 2 mM L-glutamine (Life Technologies) and 10% fetal calf serum (Life Technologies) and grown at 37°C in a 5% CO2 humidified incubator. The HA-tagged PRL3 plasmid (Addgene) was linearized and transfected with Attractene transfection reagent according to manufacturer's instructions (Qiagen). Targeted A375 cells were maintained in hygromycin containing media at concentration of 100 μg/ml.

extract_protocol:
Empty vector and PRL3 stable overexpressing cells were cultured to 80% confluency and harvested by dissociation with trypsin in PBS/EDTA. Cells were resuspended in PBS and immediately fixed in 1% formaldehyde in PBS for 10 minutes at room temperature. The fixation was neutralised by the addition of glycine and incubated for an additional 5 minutes. The cells were washed in cold PBS. Cell pellets were resuspended in 150 µl cold lysis buffer (1% SDS, 10mM EDTA, 50 mM Tris-HCl pH8.1, 1x protease inhibitor cocktail, 1x PhosSTOP phosphatase inhibitors (Roche) and fresh 1mM DTT) and supplemented with 1350 µl 1% Triton X IP dilution buffer (1% Triton X, 20mM Tris-HCl pH8.1, 150mM NaCl, 2mM EDTA, 1x protease inhibitor cocktail (Roche), 1x PhosSTOP phosphatase inhibitors (Roche) and fresh 1mM DTT and 1mM PMSF) and incubated on ice for 10 min. Lysed cells were sonicated on ice for 5x30 seconds with a probe sonicator followed by 50-60 cycles (30 sec on / 30 sec off) in a chilled bioruptor (Diagenode) to yield chromatin fragments ranging between 200 – 800 bp in length. For MITF ChIP, lysed cells were sonicated in a chilled SoniPrep150 probe sonicator for 15x30 seconds with a 30 seconds gap between burst. Sheared chromatin was centrifuged at max speed for 10 minutes at 4°C and the soluble supernatant transferred to new tubes. 500 ml chromatin samples were supplemented with 5 ml (5mg/ml) BSA. 10% of the input was stored and the rest was used for the immunoprecipitation. Anti-DDX21 (Proteintech; cat no. 10528-1-AP), RNA-POLII tot, RNA-POLII PS2, PS5 (Novus Biologicals) and MITF (Atlas Antibodies) were pre-bound to proteinG dynabeads (ThermoFisher) in 10% w/v BSA in PBS according to the manufacturer’s instructions (Life Technologies) for approximately 1 h at 4°C with rotation following which free antibody was removed with 3 washes of cold 10% w/v BSA in PBS. Chromatin and proteinG beads were combined and incubated over night at 4°C (at a ratio of 500 ng of bead bound antibody per 1M cell equivalents of chromatin). Samples were washes at 4°C with rortation through the following series: 2 times in 1% Triton X IP dilution buffer, 2 times with ChIP wash A (50mM Hepes ph7.9, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS. 1x protease inhibitor cocktail, 1x PhosSTOP phosphatase inhibitors (Roche) and fresh 1mM DTT) and 2 times with ChIP wash B (20mM Tris pH 8.0, 1mM EDTA, 250mM LiCl, 1% NP-40, 0.1% Na-deoxycholate, 1x protease inhibitor cocktail, 1x PhosSTOP phosphatase inhibitors (Roche) and fresh 1mM DTT). Finally, the samples were washed with TE (1mM EDTA ,10mM Tris pH8.0). The samples were resuspended in TE and supplemented with preheated 37°C Extraction buffer (0.1M NaHCO3 and 1%SDS), vortexed and incubated for 15 minutes at 37°C on a vibrating platform. The pH of the extracted chromatin was adjusted by adding 6ml 2M Tris-HCl pH6.8 following which both the ChIP and input samples were incubated with 20mg RNAseA at 65°C for 1 hour. Cross-links were reversed and the protein degraded by the addition of 20mg Proteinase K and incubation at 65°C for 6-8 h. Following removal of the dynabeads from the ChIP samples, DNA was purified using a Qiagen PCR cleanup kit following manufacturer’s instructions.
DNA libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) following manufacturer’s instructions.

tag: cell line

value: A375 cells expressing empty vector

value: Input


title: Input_PRL3_2_SetC

description: ChIP-seq (Input chromatin for SetC ChIP samples) performed on A375 cells expressing HA-tagged PRL3. Replicate 2 of 2.

value: A375 cells expressing HA-tagged PRL3


title: smallRNAs_hen2-2_x_se2_rep3

description: smallRNA


title: Input_EV_1_SetC

description: ChIP-seq (Input chromatin for SetC ChIP samples) performed on A375 cells expressing empty vector. Replicate 1 of 2.


title: smallRNAs_se2_rep2

description: smallRNA


title: V064_LALA_N3

value: Blood Natural Killer cells


title: smallRNAs_se2_rep1

description: smallRNA


title: smallRNAs_hen2-2_x_se2_rep2

description: smallRNA


title: Input_PRL3_1_SetC

description: ChIP-seq (Input chromatin for SetC ChIP samples) performed on A375 cells expressing HA-tagged PRL3. Replicate 1 of 2.


title: smallRNAs_hen2-2_rep2

description: smallRNA


title: smallRNAs_hen2-2_rep3

description: smallRNA


title: V064_LALA_N2

value: antibody with LALA mutation


title: MITF-EV_2_SetC

description:
ChIP-seq (anti MITF) performed on A375 cells expressing empty vector. Replicate 2 of 2.
MITF_EV.bigWig

value: anti-MITF (Atlas Antibodies cat no. HPA003259)


title: V064_LALA_N1


title: smallRNAs_hen2-2_rep1

description: smallRNA


title: MITF-EV_1_SetC

description:
ChIP-seq (anti MITF) performed on A375 cells expressing empty vector. Replicate 1 of 2.
MITF_EV.bigWig


title: V052_DEL_N3


title: MITF-PRL3_2_SetC

description:
ChIP-seq (anti MITF) performed on A375 cells expressing HA-tagged PRL3. Replicate 2 of 2.
MITF_PRL.bigWig


title: smallRNAs_wt_rep2

description: smallRNA

value: wild-type (WT)


title: V052_DEL_N2


title: smallRNAs_wt_rep3

description: smallRNA


title: V052_DEL_N1


title: smallRNAs_wt_rep1

description: smallRNA


title: MITF-PRL3_1_SetC

description:
ChIP-seq (anti MITF) performed on A375 cells expressing HA-tagged PRL3. Replicate 1 of 2.
MITF_PRL.bigWig


title: HJR_WT_N3

value: HJR

value: wild-type neutralizing monoclonal antibody VRC07-523LS


title: HJR_WT_N2


title: hen2_x_se2_rep2

data_processing:
Raw reads where trimmed (first 10 nucleotides) with FASTX-Toolkit
Adapters were removed using Trimmomatic
Clean reads were aligned to the Arabidopis TAIR10 reference genome using HISAT2
StringTie and prepDE.py script was used to create gene_count_matrix with count reads
TAIR10
Gene raw counts matrix

extract_protocol:
Leaves of 4 weeks old Arabidopsis plants were harvested then flash frozen in Liquid Nitrogen. RNA was isolated using Trizol and Direct-zol RNA Kit from Zymo Research. rRNA from samples was removed with RiboMinus Plant
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®


title: HJR_WT_N1


title: Input_EV_2_SetB

description: ChIP-seq (Input chromatin for SetB ChIP samples) performed on A375 cells expressing empty vector. Replicate 2 of 2.


title: Input_PRL3_2_SetB

description: ChIP-seq (Input chromatin for SetB ChIP samples) performed on A375 cells expressing HA-tagged PRL3. Replicate 2 of 2.


title: se2_rep3


title: HF7_WT_N3


title: Input_PRL3_1_SetB

description: ChIP-seq (Input chromatin for SetB ChIP samples) performed on A375 cells expressing HA-tagged PRL3. Replicate 1 of 2.


title: hen2_x_se2_rep3


title: hen2_x_se2_rep1


title: se2_rep2


title: DDX21_IP_EV_1_SetB

description:
ChIP-seq (anti DDX21) performed on A375 cells expressing empty vector. Replicate 1 of 2.
DDX21_EV.bigWig

value: anti-DDX21 (Proteintech cat no. 10528-1-AP)


title: HF7_WT_N1


title: DDX21_IP_EV_2_SetB

description:
ChIP-seq (anti DDX21) performed on A375 cells expressing empty vector. Replicate 2 of 2.
DDX21_EV.bigWig


title: HF7_WT_N2


title: DDX21_IP_PRL3_1_SetB

description:
ChIP-seq (anti DDX21) performed on A375 cells expressing HA-tagged PRL3. Replicate 1 of 2.
DDX21_PRL.bigWig


title: se2_rep1


title: DGVK_WT_N3

value: DGVK


title: Input_EV_1_SetB

description: ChIP-seq (Input chromatin for SetB ChIP samples) performed on A375 cells expressing empty vector. Replicate 1 of 2.


title: hen2-2_rep3


title: DDX21_IP_PRL3_2_SetB

description:
ChIP-seq (anti DDX21) performed on A375 cells expressing HA-tagged PRL3. Replicate 2 of 2.
DDX21_PRL.bigWig


title: DGVK_WT_N2


title: hen2-2_rep1


title: wt_rep3


title: DG96_LALA_N3


title: DG96_LALA_N2


title: wt_rep2


title: B3

city: Hong Kong

first: Qian

last: Yu

address: 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: Hong Kong University

data_processing:
Raw fastq sequences were treated with Trimmomatic tools(v 0.36) using the following options: : TRAIL- ING:20, MINLEN:235 and CROP:235, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the rat reference genome m6 with HISAT2. HTSeq vret0. 6.0 was used to count the reads numbers mapped to each gene.
The whole samples expression levels were presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced), which is the recommended and most common method to estimate the level of gene expression using a protocol from Mortazavi A et al., Nat Methods, 2008
The statistically significant different expression genes were obtained by an adjusted P-value threshold of <0.05 and |log2(fold change)| > 1 using the DEGseq software.
Genome_build: m6
Supplementary_files_format_and_content: counts, RPKM

source_name: liver

extract_protocol:
Total RNA was isolated from the liver using Trizol (Invitrogen).RNA was purified by the removal of ribosomal RNA using EpicentreRibo-Zero rRNA Removal Kit (illumina, USA) and then subjected to cDNA synthesis followed by adaptor ligation and enrichment according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA) and paired-end sequenced (PE150, Sequencing reads were 150 bp) using IlluminaHiSeq 3000 platform. The clean reads were aligned to the rat reference genome using HISAT2 and then converted into read counts for each gene model by HTSeq. DEseq was applied to assess the differential expression using read counts as input.

value: Sprague Dawley

value: liver

value: HFD+SAMC co-administration


title: DG96_LALA_N1


title: B2


title: DFN3_LALA_N3


title: RNA fraction from wild type plants rep3

data_processing:
Raw reads where trimmed (first 12 nucleotides) with FASTX-Toolki
Adapters were removed using Trimmomatic
rRNA sequences where removed with Bowtie
Clean reads were aligned to the Arabidopis TAIR10 reference genome using HISAT2
Transcript-level abundance for RNA clean reads where estimated using Salmon. Multifasta file with Arabidopsis thaliana reference transcripts (cdna and ncrna) for quasi-mapping was additionally supplemented with pri-miRNA transcirpts described in mirEX2 database.
Genome_build: TAIR10
Supplementary_files_format_and_content: transcript abundance, output format from Salmon software .sf extension

source_name: wild type plants_aerial tissue

growth_protocol: Plants were grown in soil under 16 hour light/8 hour dark cycle at 22°C

extract_protocol:
Leaves of 4 weeks old Arabidopsis plants were harvested then flash frozen in Liquid Nitrogen. RNA was isolated using Trizol and Direct-zol RNA Kit from Zymo Research. rRNA from samples was removed with RiboMinus Plant Kit for RNA-seq (Thermo Fisher Scientific)
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

value: wild type

value: 4 weeks

value: aerial tussue


title: RNA fraction from wild type plants rep2


title: DFN3_LALA_N2


title: B1


title: F4

value: HFD (high fat diet)


title: DFN3_LALA_N1


title: RNA fraction from wild type plants rep1


title: hen2-2_rep2


title: RNAPII-Total_EV_1_SetA

description:
ChIP-seq (anti Total RNAPII) performed on A375 cells expressing empty vector. Replicate 1 of 2.
RNAPII_EV.bigWig

value: A375 cells expressing empty vector

value: anti-RNA-POLII (Novus Biologicals cat no. C15200004)


title: DGVK_WT_N1

value: Blood Natural Killer cells


title: Input_PRL3_2_SetA

description: ChIP-seq (Input chromatin for SetA ChIP samples) performed on A375 cells expressing HA-tagged PRL3. Replicate 2 of 2.

value: A375 cells expressing HA-tagged PRL3

value: Input


title: RNAPII-Total_PRL3_1_SetA

description:
ChIP-seq (anti Total RNAPII) performed on A375 cells expressing HA-tagged PRL3. Replicate 1 of 2.
RNAPII_PRL3.bigWig


title: Input_EV_2_SetA

description: ChIP-seq (Input chromatin for SetA ChIP samples) performed on A375 cells expressing empty vector. Replicate 2 of 2.


title: RNAPII-Total_EV_2_SetA

description:
ChIP-seq (anti Total RNAPII) performed on A375 cells expressing empty vector. Replicate 2 of 2.
RNAPII_EV.bigWig


title: Input_EV_1_SetA

description: ChIP-seq (Input chromatin for SetA ChIP samples) performed on A375 cells expressing empty vector. Replicate 1 of 2.


title: Input_PRL3_1_SetA

description: ChIP-seq (Input chromatin for SetA ChIP samples) performed on A375 cells expressing HA-tagged PRL3. Replicate 1 of 2.


title: F3


title: F2


title: RNAPII-Total_PRL3_2_SetA

description:
ChIP-seq (anti Total RNAPII) performed on A375 cells expressing HA-tagged PRL3. Replicate 2 of 2.
RNAPII_PRL3.bigWig


title: RNA fraction from hen2-2 mutant plants rep3

source_name: hen2-2 mutant plants_aerial tissue