title: LNCaP_TR15-MeTA5+Tet_exp1

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LNCaP_TR15-MeTA5+Tet, experiment 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Two cell lines derived from human prostate cancer cell line LNCaP, TR9-MeTA14 and TR15MeTA5, was grown in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: The RNAs from TR9-MeTA14 and TR15-MeTA5 with (4 days treatment) or without tetracycline were prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: parent cell line

value: LNCaP


title: LNCaP_TR15-MeTA5-Tet_exp1

status: Public on Mar 02 2021

type: RNA

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP_TR15-MeTA5-Tet, experiment 1

tag: cell line


title: Double mutant GLAD/TIN of naked mole rat TRF1 in normoxia condition_Sample B

type: SRA

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description:
6-Normo-Dbmut-B
Double mutant GLAD/TIN of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence.
Paired-end reads were mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR software to generate read alignments.
The annotation file Mus_musculus.GRCm38.90.gtf was obtained from the ftp.Ensembl.org server.
Following transcript assembly, gene level counts were obtained using HTSeq.
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: normo-hypo_NMR-TRF1_mutant-wt.csv: Normalized abundance measurements in CPM.

organism: Mus musculus

source_name: tMEF cells

growth_protocol: Cells were grown in DEM with 10% fetal calf serum and antibiotic-antimycotic.

extract_protocol:
Total RNA was extracted with the MicroElute total RNA kit (Omega Bio-Tek) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard TruSeq RNA Illumina protocols.

treatment_protocol: Cells were grown in 1% O2 (hypoxia) or atmospheric oxygen (normoxia).

tag: genotype/variation

value: double mutant GLAD/TIN of naked mole rat TRF1

tag: cell type

value: tMEF cells

tag: treatment

value: Normoxia


title: LNCaP_TR9-MeTA14+Tet_exp1

source_name: LNCaP, TR9-MeTA14+Tet, experiment 1


title: ATAC_3_SW1353_IL1_3

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

library_source: genomic

data_processing:
Quality of raw sequencing reads was checked using FastQC (v0.11.7)
fastq files were aligned to the hg38 reference genome using bowtie2 (v2.3.4.1)
peaks were called using MACS2 (v2.1.1.20160309)
Genome_build: hg38

molecule: genomic DNA

source_name: SW1353 cell line

growth_protocol: SW1353 chondrosarcoma cells were seeded in a standard six-well plate (30 x 10E6 cells/well) in standard growth medium (DMEM/F-12,  10% (v/v) foetal bovine serum (FBS), 100 IU/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine.

extract_protocol:
All protocols described in Buenrostro et al. (PMID 24097267 and  25559105). Nuclei were isolated in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and centrifugation at 500g for 10 minutes at 4oC. Following isolation, the nuclei were resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase TDE1 (Nextera Tn5 Transposase, Illumina) in a total volume of 50  μL  and incubated for 30 minutes at 37oC. DNA from all samples were subsequently purified using Qiagen MinElute PCR Purification Kit.
Transposed DNA was PCR amplified using the NEB Next High-Fidelity PCR Master Mix and primer Ad1_noMX in combination with one of the first six barcoded primers listed in Buenrostro et al. (PMID 24097267 and  25559105). Amplified libraries were purified using a Qiagen MinElute PCR Purification Kit and eluted in 20 μl Elution Buffer before quantitation on an Agilent 4200 TapeStation.  Pooled libraries were sequenced on a High-Output Illumina NextSeq500 generating paired-end 75 bp reads.

treatment_protocol: The next day following seeding, the medium was replaced with medium as described but without the 10% FBS (serum starved).  Approx 20 hours later cells were stimulated as indicated +/- interleukin-1aplha (1 ng/ml) for 6 hours. After this cells were washed in PBS and nuclei isolated.


title: Cel.seq.exp.11

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

country: USA

institute: The Rockefeller University

data_processing:
trim R1 reads to 12 bp and R2 reads to 36 bp using cutadapt
process of trimmed fastq files with UMI-Tools using extract function
mapping reads using STAR
sort bam files using samtools
index bam files using samtools
counting molecules using UMI-Tools using count function
merge all UMI results together using bash join function
Genome_build: mm10
Supplementary_files_format_and_content: UMI count for each cell and sample information for each cell

source_name: liver metastasis and primary tumor

growth_protocol: 6419c5 pancreatic tumor cells were inoculated to the pancreas of C57/Bl6 mice

extract_protocol:
Tumor cells were isolated via photoconversion-based isolation protocol from liver metastasis and primary tumor in a mouse pancreatic cancer model
Libraries were constructed by following the cel-seq2 procedure by the developer’s protocol
Cel-seq2 single cell RNAseq library

tag: cell line for implantation

tag: genetic background


title: ATAC_2_SW1353_IL1_2


title: Mutant TIN of naked mole rat TRF1 in normoxia condition_Sample B

description:
4-Normo-TIN-B
Mutant TIN of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv

value: mutant TIN of naked mole rat TRF1


title: LNCaP_TR9-MeTA14-Tet_exp1

source_name: LNCaP, TR9-MeTA14-Tet, experiment 1


title: Double mutant GLAD/TIN of naked mole rat TRF1 in normoxia condition_Sample A

description:
5-Normo-Dbmut-A
Double mutant GLAD/TIN of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv


title: ATAC_1_SW1353_IL1_1


title: Mutant GLAD of naked mole rat TRF1 in normoxia condition_Sample B

description:
2-Normo-GLAD-B
Mutant GLAD of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv

value: mutant GLAD of naked mole rat TRF1


title: Cel.seq.exp.09


title: Mutant TIN of naked mole rat TRF1 in normoxia condition_Sample A

description:
3-Normo-TIN-A
Mutant TIN of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv


title: ATAC_3_SW1353_Control_3

value: control


title: Cel.seq.exp.06


title: Cel.seq.exp.05


title: Mutant GLAD of naked mole rat TRF1 in normoxia condition_Sample A

description:
1-Normo-GLAD-A
Mutant GLAD of naked mole rat TRF1.
normo-hypo_NMR-TRF1_mutant-wt.csv


title: Cel.seq.exp.10


title: lPC-ENR3

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L23468_Track-53841

data_processing:
Fastq reads were trimmed using Trim Galore 0.4.0 and the function Cutadapt 1.8.1. To remove cytosines that were filled in during ends preparation, an additional 2 bp were cut off from every sequence with detected adapter.
Trimmed reads were mapped against mm10 using Bismark 0.16.1
Base calling was performed using MethylKit 1.5.2.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation percentages of cytosines for individual samples. Txt file exported from Methylkit.

source_name: lPC-ENR_dentate gyrus

growth_protocol: Mice housed in 12:12 light:dark cycle under SPF conditions and given ad libitum access to mouse chow and water.

extract_protocol:
Isolation of cells from the hippocampus by FACS for Nestin-Gfp (NSPCs; nestin::Gfp mice), Dcx-Gfp (lPCs; dcx::Gfp) or Neuro-Fluor.
Genomic DNA was isolated using the QIAamp DNA Micro Kit (QIAGEN) following the manufacturer’s manuals. RRBS libraries were prepared using the Premium RRBS Kit (Diagenode) and purified twice using Agencourt AMPure XP beads (Beckman Coulter; 1X bead volume). Quality and concentration of RRBS libraries were determined using the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical) and a fragment analyzer with capillary size of 33 cm (Advanced Analytical).

treatment_protocol: Mice were housed in either standard cages or in an enriched environment.

tag: strain/genotype

tag: age

value: 3 months

tag: Sex

value: Female

tag: housing

value: enriched environment for five weeks

tag: tissue

value: Dentate gyrus


title: Phc1-KO 4C rep3

city: Hangzhou

first: Li

last: Chen

address: 866 Yuhangtang Rd

department: School of Medicine

country: China

institute: Zhejiang University

data_processing:
Library strategy: 4C-seq
Illumina Casava1.8 software used for basecalling.
The reduced genome (mm9) consisting of only 25 bp sequences flanking the primary restriction enzyme sites was generated using a customized script. 4C-seq reads were trimmed and mapped to this reduced genome by Bowtie2
Each sample’s counts profiles were created from mapped data and removed self-ligated and undigested fragments around bait fragment
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include restriction fragment counts profiles.

source_name: Embryonic stem cells

growth_protocol: mESCs were maintained on 0.1% gelatin-coated plates in DMEM-high glucose, supplemented with 15% FBS, GlutaMAX (Gibco), non-essential amino acids (Gibco), penicillin/streptomycin (Gibco), 0.1mM β-mercaptoethanol (Sigma), and 1000U/ml leukemia inhibitory factor (LIF, Millipore).

extract_protocol:
Washed the cells with PBS and removed supernatant. Then the pellet was resuspended with lysis buffer. The chromatin was digested with 200 units DpnII after pre-treatment with SDS and triton X-100. The reaction was heat-inactivated and then incubated with ligation buffer. Chromatin was reverse crosslinked after Proteinase K and SDS treatment. The DNA was then purified by DNA clean beads followed by the second digestion with NlaIII and ligation in ligation buffer. DNA was precipitated with acetate and ethanol. The precipitation was purified again by DNA clean beads.
Amplified 4C products by PCR and paired-end libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were cross-linked with 1% formaldehyde.

value: Mouse embryonic stem cells

tag: genotype


title: Phc1-KO 4C rep4


title: Cel.seq.exp.02


title: Cel.seq.exp.01


title: lPC-ENR2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L23467_Track-53840


title: 12 DUG starving 3

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
Quality control of data was performed using FastQC package
Reads were aligned to Aspergillus nidulans (FGSC A4) genome using hisat2 (version 2.1.0)
Differential gene expression testing was performed using DESeq2 (version 1.20.0)
Genome_build: Genome: http://www.aspergillusgenome.org/download/sequence/A_nidulans_FGSC_A4/current/A_nidulans_FGSC_A4_version_s10-m04-r12_chromosomes.fasta.gz; Genome features file (GFF): http://www.aspergillusgenome.org/download/gff/A_nidulans_FGSC_A4/A_nidulans_FGSC_A4_version_s10-m04-r12_features_with_chromosome_sequences.gff.gz
Supplementary_files_format_and_content: Excel file containing the following collumns: gene ID, BaseMean, log2FoldChange, lfcSE, stat, p-value and adjusted p-value

organism: Aspergillus nidulans

source_name: DUG pathway mutant_carbon starving_fungal mycelia

growth_protocol: Strains were maintained on Barratt’s minimal medium agar plates (Barratt et al. 1965) and conidia collected freshly from plates incubated at 37 °C for 6 d were used in all experiments. For submerged cultivation 50 ml Barratt’s minimal broth supplemented with 5 g/l yeast extract (in 250 ml Erlenmeyer flasks) was inoculated with 50,000,000 conidia and was incubated for 16 h at 37 °C and at 3.7 Hz shaking frequency. Mycelia were collected by filtration and after washing they were transferred into 50 ml fresh medium and the culture was further incubated at 37 °C and at 3.7 Hz shaking frequency.

extract_protocol:
Total RNA was isolated from lyophilized mycelia using TRISOL reagent (Chomczynski 1993). RNA concentration and purity were determined using NanoDrop and capillary electrophoresis.
RNA-Seq libraries were prepared from total RNA using TruSeq RNA Sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: Mycelia were transfered either glucose free Barrat’s minimal broth (starving cultures) or standard Barrat’s minimal broth containing 20 g/l glucose (growing cultures). Samples were taken at 24 h (starving cultures) or at 4 h (growing cultures).

tag: strain

tag: culturing condition

value: carbon starving

value: fungal mycelia


title: Genomic DNA extracted from PBMCs from Patient 3

type: genomic

city: London

first: Samah

last: Alimam

address: Great Maze Pond

department: Cancer Genetics

institute: KCL

hyb_protocol: DNA was bisulfite converted using the EZ DNA Methylation kit (Zymo Research) as per the manufacturer’s protocol

scan_protocol: Standard Illumina protocol

data_processing: The initial quality of data was checked using ENMix. 11984 low quality CpGs were removed. We identified single probe p-values across each array and removed probes with a p value detection > 0.00001 in at least 50% samples; resulting in 869 probes being removed. Data was normalized using the ssNoob approach from the minifi package

label: Cy5 and Cy3

source_name: PBMCs from Patient 3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA extracted from PBMCs

tag: disease state

value: essential thrombocythemia

tag: mutation status

value: CALR (Calreticulin mutation)

value: PBMCs


title: Genomic DNA extracted from PBMCs from Patient 32

source_name: PBMCs from Patient 32

value: TN (Triple negative)


title: WT 4C rep4

value: wild type


title: 11 DUG starving 2


title: Genomic DNA extracted from PBMCs from Patient 11

source_name: PBMCs from Patient 11


title: Genomic DNA extracted from PBMCs from Patient 19

source_name: PBMCs from Patient 19


title: lPC-STD3

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L23465_Track-53838

source_name: lPC-STD_dentate gyrus

value: Standard housing


title: lPC-ENR1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L23466_Track-53839


title: Genomic DNA extracted from PBMCs from Patient 14

source_name: PBMCs from Patient 14


title: Phc1-KO 4C rep2

data_processing:
Library strategy: 4C-seq
Illumina Casava1.8 software used for basecalling.
The reduced genome (mm9) consisting of only 25 bp sequences flanking the primary restriction enzyme sites was generated using a customized script. 4C-seq reads were trimmed and mapped to this reduced genome by Bowtie2.
Each sample’s counts profiles were created from mapped data and removed self-ligated and undigested fragments around bait fragment.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files include restriction fragment counts profiles.

extract_protocol:
Washed the cells with PBS and removed supernatant. Then the pellet was resuspended with lysis buffer. The chromatin was digested with 200 units DpnII after pre-treatment with SDS and Triton X-100. The reaction was heat-inactivated and then incubated with ligation buffer. Chromatin was reverse crosslinked after Proteinase K and SDS treatment. The DNA was then purified by DNA clean beads followed by the second digestion with NlaIII and ligation in ligation buffer. DNA was precipitated with acetate and ethanol. The precipitation was purified again by DNA clean beads.
Amplified 4C products by PCR and paired-end libraries were prepared according to Illumina's instructions.


title: Genomic DNA extracted from PBMCs from Patient 15

source_name: PBMCs from Patient 15


title: 10 DUG starving 1


title: Genomic DNA extracted from PBMCs from Patient 10

source_name: PBMCs from Patient 10


title: lPC-STD2

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L23464_Track-53837


title: WT 4C rep3


title: ATAC_2_SW1353_Control_2


title: Genomic DNA extracted from PBMCs from Patient 12

source_name: PBMCs from Patient 12


title: Genomic DNA extracted from PBMCs from Patient 6

source_name: PBMCs from Patient 6

value: JAK2 (JAK2 mutation)


title: WT 4C rep2


title: Genomic DNA extracted from PBMCs from Patient 21

source_name: PBMCs from Patient 21


title: ATAC_1_SW1353_Control_1

source_name: SW1353 cell line


title: 9 DUG glucose 3

source_name: DUG pathway mutant_growing on glucose_fungal mycelia

value: growing on glucose


title: lPC-STD1

description:
Methylated cytosines converted to uracil by treatment with sodium bisulfite
L23463_Track-53836


title: Genomic DNA extracted from PBMCs from Patient 28

source_name: PBMCs from Patient 28


title: D4 axial progenitors n2

city: PARIS

first: Stephane

last: NEDELEC

address: 17 rue du fer a moulin

country: France

institute: Institut du Fer à Moulin

description: sample 8

data_processing:
Torrent Suite Software was used for basecalling, trimming of adaptator sequence, quality check and to generated FASTQ file
FastQ files were exported to PartekFlow software (v6 Partek Inc) for alignement and quantification step. Briefly sequence were mapped to hg19 reference genome using TOPHAT2 (v2.0.8).  and bowtie 2 (v2.1.0) following the WT Pipeline for Ion Torrent. Mapped reads were annotated on Refseq release 84 and quantified with Partek E/M algorithm , normalised on total count and differential gene were identified using Partek Gene Specific Algorithm (GSA)
Genome_build: hg19
one tab-delimited text files include RPM (read per million)

molecule: polyA RNA

source_name: Axial progenitors

growth_protocol: Human SA001 embryonic stem cell (ESC) line (male, RRID: CVCL_B347)   were cultured at 37 °C on Matrigel (Corning) in mTSER1 medium (Stem Cell Technologies) and amplified using EDTA (Life Technologies) clump-based passaging. hPSC were dissociated with cold Accutase (Life Technologies) for 3 to 5 min at 37°C and resuspended in differentiation medium N2B27 (Advanced DMEM F12, Neurobasal vol:vol (Life Technologies)), supplemented with N2 (Life Technologies), B27 without Vitamin A (Life technologies), penicillin/streptomycin 1%, β-Mercaptoéthanol 0,1% (Life Technologies), with Y-27632 (10μM, Stemgent or Stem Cell Technologies), CHIR-99021 (3 µM Selleckchem) SB431542 (20 μM, Selleckchem) and LDN 193189 (0,1 μM, Selleckchem). 2x105 cells ml-1 were seeded in ultra-low attachment 6 well plates (Corning) to form embryoid bodies (EBs). All conditions of differentiation received the same medium at day 2 and at day 3 but SB431542 was removed at day 3.

extract_protocol:
Medium was remove and 350µl RLTplus were add. Sample were extracted on QIACUBE following the Rneasy Plus Mini kit protocole (Qiagen)
The Ion Ampliseq Transcriptome Human Gene expression kit was used with 50ng of mRNA for the construction of sequencing libraries following the manufacturer protcol.
Ampliseq Transcriptome Human gene expression kit (Termofisher Scientific)

value: hESC derived axial progenitors D4 of differentiation

value: CHIR 3 LDN SB


title: Genomic DNA extracted from PBMCs from Patient 16

source_name: PBMCs from Patient 16


title: WT 4C rep1

source_name: Embryonic stem cells


title: Genomic DNA extracted from PBMCs from Patient 9

source_name: PBMCs from Patient 9


title: 7 DUG glucose 1


title: Genomic DNA extracted from PBMCs from Patient 8

source_name: PBMCs from Patient 8


title: D4 axial progenitors n1

description: sample 7


title: Phc1-KO 4C rep1


title: Mixed WT and KO T cells (gene expression)

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Demultiplexing, alignment, filtering and UMI counting was performed with Cell Ranger 3.1.0 using the cellranger count command.
The filtered_feature_bc_matrix.h5 file (output by Cell Ranger) for both gene expression and hashtag samples were loaded in R merged based on cell barcodes common samples.
WT and cKO cells were labeled with the Biolegend TotalSeq -C0301
anti-mouse Hashtag 1 or TotalSeq -C0302 anti-mouse Hashtag 2
antibodies respectively according to manufacturer s instructions. The
sequenced hashtags are in the IP-HTO-V2_S1_* fastq files. (The other
set of fastq files are the mRNA sequences for the same cells). The
matrix HTO_filtered_feature_bc_matrix.h5 has two rows, "WT" and "KO",
and each column corresponds to a cell barcode. The values in the
matrix are the UMI counts for each hashtag in each cell.
Genome_build: mm10
Supplementary_files_format_and_content: The .h5 files contain a gene or hashtag by cell barcode matrix.

source_name: T cells

extract_protocol:
At day 20 p.i., CD8+CD44int-hi H-2DbGP33-41-tetramer stained cells were isolated by fluorescence activated cell sorting, labelled with hashtags, mixed and then analysed by scRNAseq.
Cell capture and library preparations were performed using the 10x Genomics Chromium system, the Chromium Single Cell 5' Library & Gel Bead Kit (v1.0 chemistry) and the Chromium Single Cell 5' Feature Barcode Library Kit. Single-cell and feature (hashtag) libraries were generated using the Chromium Controller and Single Cell 5’ Library & Gel Bead Kit and Chip A Kit (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol: CD4 depleted WT or cKO mice were infected with 2x10^6 pfu LCMV-Cl13 i.v.

value: LCMV H-2Kb GP33-41-specific CD8+ T cells

value: Mixture of CD4-cre+ Egr2 flox/flox and CD4-cre+ Egr2+/+ littermate cells


title: D3 axial progenitors n2

description: sample 6

value: hESC derived axial progenitors D3 of differentiation


title: Genomic DNA extracted from PBMCs from Control 2

source_name: PBMCs from Control 2

value: healthy control

value: CTRL (Healthy Control)


title: Insl3_3

city: Bergen

first: Diego

last: Crespo

address: Nordnesgaten 50

department: Reproduction and Developmental Biology

country: Norway

institute: Institute of Marine Research

data_processing:
Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using CASAVA software (v1.8; Illumina, Inc.)
Reads were aligned to the zebrafish genome (GRCz10) using TopHat2 (v2.0.12)
Data were filtered using SAMtools (v0.1.18)
The read counts were extracted using the Python package HTSeq (v.0.6.1)
Differential expression analysis was performed using the R/Bioconductor package DESeq (v1.18.1)
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text files include gene ID and raw counts for each sample

organism: Danio rerio

source_name: Testis

extract_protocol:
Total RNA was isolated from testis tissue using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio-analyzer 2100 total RNA Nano series II chip (Agilent)
Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.) according to the manufacturer’s instructions

value: Testis

value: Adult

value: Wild type


title: 5 reference starving 2

value: carbon starving

value: fungal mycelia


title: Insl3_2


title: 4 reference starving 1


title: D3 axial progenitors n1

description: sample 5


title: Genomic DNA extracted from PBMCs from Patient 26

source_name: PBMCs from Patient 26

value: essential thrombocythemia

value: TN (Triple negative)

value: PBMCs


title: D2 axial progenitors n2

description: sample 4

value: hESC derived axial progenitors D2 of differentiation


title: Genomic DNA extracted from PBMCs from Patient 13

source_name: PBMCs from Patient 13


title: 8 DUG glucose 2

value: growing on glucose


title: Insl3_1


title: Genomic DNA extracted from PBMCs from Patient 5

source_name: PBMCs from Patient 5

value: JAK2 (JAK2 mutation)


title: 3 reference glucose 3

source_name: reference_growing on glucose_fungal mycelia


title: 6 reference starving 3


title: 2 reference glucose 2


title: Basal_3

value: control


title: hESC SA001 mTser n2

description: sample 2

value: Human ES cells

value: mTESR1 matrigel culture


title: D2 axial progenitors n1

description: sample 3

value: CHIR 3 LDN SB


title: Basal_2


title: 1 reference glucose 1


title: Basal_1


title: pit_2

status: Public on Mar 01 2021

city: Baltimore

first: Isabelle

last: Coppens

state: Maryland

address: 615 N. Wolfe St

department: MMI

institute: Johns Hopkins University

data_processing:
Base-calls performed by Illumina CASAVA 1.8 software
Raw sequencing reads were filtered to remove reads containing adapters or reads of low quality using in-house scripts (Novogene Corp)
TopHat2 was used to align reads to the reference genome
HTSeq software was used to analyze gene expression levels using the union mode.
Read counts were normalized using DESeq. The p-value estimation model was a negative binomial distribution and the FDR estimation method was the Benjamini-Hochberg (BH) procedure.
Genome_build: ToxoDB-39_TgondiiGT1_Genome
Supplementary_files_format_and_content: tab-delimited text file including readcounts, log2FoldChange, pvalue, and adjusted pvalue per sample for each gene in reference.

organism: Toxoplasma gondii

source_name: TgPIT KO derived from RH∆ku80∆hxg clone

growth_protocol: Parasites were grown in human foreskin fibroblasts for 24h, scraped, washed with PBS,  syringed, and collected by centrifugation

extract_protocol:
Total RNA was extracted using a Qiagen Rneasy kit. Total RNA shipped to Novogene Corporation was processed and analyzed. Toral RNA was converted to sequencing read libraries using the NEB Next Ultra kit (Illumina). The libraries were subjected to paired-end sequencing using the Novaseq 6000 with a read length of 150 bp. Each sample was sequenced to a depth of at least 20 million reads
Library construction was by Novogene Corporation (Sacamento, CA), using a NEB Next Ultra by Illumina

value: TgPiT-deficient

tag: Stage

value: tachyzoite

tag: habitat

value: intracellular


title: Ku80_2

source_name: Type I RH∆ku80∆hxg clone

tag: genotype/variation

value: wild type


title: Ku80_1


title: Genomic DNA extracted from PBMCs from Patient 2

source_name: PBMCs from Patient 2

value: CALR (Calreticulin mutation)

tag: cell type


title: Genomic DNA extracted from PBMCs from Patient 1

source_name: PBMCs from Patient 1


title: Genomic DNA extracted from PBMCs from Patient 25

source_name: PBMCs from Patient 25


title: Genomic DNA extracted from PBMCs from Patient 18

source_name: PBMCs from Patient 18


title: Genomic DNA extracted from PBMCs from Patient 31

source_name: PBMCs from Patient 31


title: BIL_10081_inflorescence meristem

city: Nagoya

first: Fanmiao

last: Wang

address: Furo-cho

department: Bioscience and Biotechnology Center

institute: Nagoya University

description: Gene expression profiling in the rice inflorescence meristem, collected by RNeasy plant mini kit (QIAGEN)

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 277 - 1500ng of labeled and fragmented cRNA was hybridized to Agilent Rice 44K custom array (G2519F) using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2565BA according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent). Obtained background subtracted Signal intensities(gProcessedSignal) were normalized by variance stabilization (VSN) using R software (http://www.r-project.org/).

organism: Oryza sativa

source_name: inflorescence meristem, 1-1.5mm

label_protocol: Cy3-labeled cRNA were prepared from total RNA using Low RNA Linear Amplification Kit (Agilent) in accordance with the manufacturer's protocol with slight modification. The cDNA synthesis reaction time was extended to 6 hrs.

growth_protocol: 79 individual Backcross inbred lines (BILs) from a cross between Koshihikari (japonica) and Habataki (indica) were grown in a paddy field in the farm of Nagoya University in the middle of June, 2010. The planting density was 25 cm between rows and 15 cm between plants per row.

extract_protocol: Total RNA was extracted from the inflorescence meristem of 1-1.5mm long using RNeasy plant mini kit (QIAGEN).

value: inflorescence meristem

tag: developmental stage

value: at the secondary panicle branch developmental stage

tag: cultivar

value: Backcross inbred line


title: BIL_10076_inflorescence meristem


title: Genomic DNA extracted from PBMCs from Patient 27

source_name: PBMCs from Patient 27

value: essential thrombocythemia

value: TN (Triple negative)


title: BIL_10077_inflorescence meristem


title: BIL_10082_inflorescence meristem


title: BIL_10080_inflorescence meristem


title: BIL_10078_inflorescence meristem


title: BIL_10079_inflorescence meristem


title: BIL_10074_inflorescence meristem


title: BIL_10072_inflorescence meristem


title: BIL_10073_inflorescence meristem


title: BIL_10075_inflorescence meristem


title: hESC SA001 mTser n1

description: sample 1

source_name: Embryonic stem cells

tag: cell line

tag: treatment


title: BIL_10071_inflorescence meristem


title: Genomic DNA extracted from PBMCs from Patient 17

source_name: PBMCs from Patient 17

value: PBMCs


title: BIL_10070_inflorescence meristem


title: Genomic DNA extracted from PBMCs from Patient 4

source_name: PBMCs from Patient 4


title: BIL_10063_inflorescence meristem


title: pit_1


title: BIL_10062_inflorescence meristem


title: BIL_10060_inflorescence meristem


title: BIL_10067_inflorescence meristem


title: BIL_10065_inflorescence meristem


title: BIL_10069_inflorescence meristem


title: BIL_10055_inflorescence meristem


title: BIL_10054_inflorescence meristem


title: Genomic DNA extracted from PBMCs from Control 1

source_name: PBMCs from Control 1

value: healthy control

value: CTRL (Healthy Control)


title: BIL_10052_inflorescence meristem


title: BIL_10059_inflorescence meristem


title: BIL_10058_inflorescence meristem


title: BIL_10051_inflorescence meristem


title: BIL_10053_inflorescence meristem


title: BIL_10066_inflorescence meristem


title: Genomic DNA extracted from PBMCs from Patient 24

source_name: PBMCs from Patient 24


title: Genomic DNA extracted from PBMCs from Patient 30

source_name: PBMCs from Patient 30


title: BIL_10068_inflorescence meristem


title: Genomic DNA extracted from PBMCs from Patient 23

source_name: PBMCs from Patient 23


title: BIL_10049_inflorescence meristem


title: BIL_10050_inflorescence meristem


title: Genomic DNA extracted from PBMCs from Patient 7

source_name: PBMCs from Patient 7

value: JAK2 (JAK2 mutation)


title: BIL_10047_inflorescence meristem


title: BIL_10046_inflorescence meristem


title: BIL_10061_inflorescence meristem


title: Genomic DNA extracted from PBMCs from Patient 29

source_name: PBMCs from Patient 29


title: BIL_10041_inflorescence meristem


title: BIL_10040_inflorescence meristem


title: BIL_10042_inflorescence meristem


title: BIL_10048_inflorescence meristem


title: BIL_10039_inflorescence meristem


title: Genomic DNA extracted from PBMCs from Patient 20

source_name: PBMCs from Patient 20


title: BIL_10034_inflorescence meristem


title: BIL_10038_inflorescence meristem


title: BIL_10033_inflorescence meristem


title: BIL_10036_inflorescence meristem


title: BIL_10032_inflorescence meristem


title: BIL_10035_inflorescence meristem


title: BIL_10045_inflorescence meristem


title: BIL_10031_inflorescence meristem


title: BIL_10028_inflorescence meristem


title: BIL_10030_inflorescence meristem


title: BIL_10029_inflorescence meristem


title: BIL_10013_inflorescence meristem


title: BIL_10024_inflorescence meristem


title: BIL_10022_inflorescence meristem


title: BIL_10019_inflorescence meristem


title: BIL_10016_inflorescence meristem


title: BIL_10018_inflorescence meristem


title: BIL_10026_inflorescence meristem


title: BIL_10057_inflorescence meristem


title: BIL_10064_inflorescence meristem


title: BIL_10012_inflorescence meristem


title: BIL_10014_inflorescence meristem


title: BIL_10043_inflorescence meristem


title: BIL_10015_inflorescence meristem


title: BIL_10023_inflorescence meristem


title: BIL_10011_inflorescence meristem


title: BIL_10021_inflorescence meristem


title: BIL_10017_inflorescence meristem


title: BIL_10010_inflorescence meristem


title: BIL_10027_inflorescence meristem


title: HMRHL SiRNA knockdown Rep1

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

description: silenced

data_processing:
GRCh38 (hg38) Genome was downloaded from GENCODE and indexed using Bowtie2-build with default parameters. Adapter ligation was done using Trim Galore (v0.4.4) and each of the raw Fastq files were passed through a quality check using the Fast QC. PCR duplicates were  removed using the Samtools 1.3.1 with the help of rmdup option.
Each of the raw files was then aligned to GRCh38 (hg38) genome assembly using TopHat with default parameters for paired end sequencing as described in Trapnell et al. After aligning, quantification of transcripts was performed using Cufflinks and then Cuffmerge was used to create merged transcriptome annotation.
Finally, differentially expressed (DE) genes were identified using Cuffdiff. The threshold for DE genes was log2 (fold change) >1.5 for up-regulated genes and log2 (fold change) <1.5 for down-regulated genes. GO enrichment analysis Gene Ontology (GO) analysis was performed in PANTHER (48). Significant enrichment test was performed with the set of differentially expressed genes in PANTHER.
Genome_build: GRCh38 (hg38)

source_name: K562 cell line

growth_protocol: K562 cells were cultured in RPMI medium with 10% FBS and 1% penecillin/streptomycin at 37.C in a humidified chamber with 5% CO2

extract_protocol:
Total RNA was isolated using Trizol after 36 hours of post transfection from both scramble control siRNA and HMRHL siRNA
Libraries were prepared according toTruseq stranded RNA library prep kit

treatment_protocol: K562 cells were transfected with scramble control siRNA and HMRHL siRNA

value: lymphoblast

tag: passages

tag: sirna

value: HMRHL siRNA


title: Scramble control Rep2

description: control

value: Scramble siRNA


title: HMRHL SiRNA knockdown Rep2

description: silenced


title: Genomic DNA extracted from PBMCs from Patient 22

source_name: PBMCs from Patient 22


title: BIL_10009_inflorescence meristem


title: Macrophage_C

city: Westmead

first: J

middle: Dinny

last: Graham

state: NSW

address: 176 Hawkesbury Rd

department: Westmead Institute for Medical Research

institute: University of Sydney

description: Donor C : Dermis Macrophage

data_processing:
Raw sequence data was aligned to the UCSC human reference genome (hg19) using TopHat2 v2.0.9
Aligned sequencing reads were summarised to counts per gene using the RAEM procedure using SAMMate v2.6.1
RPKM values were calculated from read counts using SAMMate v 2.6.1
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing normalized read counts for each sample replicate

source_name: Abdominal skin dermal tissue

extract_protocol:
Primary cell populations isolated by flow cytometry were lysed and total RNA was extracted.  mRNA transcripts were reverse transcribed and amplified from 1ng total RNA, using the Smart-seq2 protocol of Picelli et al (Nature Methods. 2013;10(11):1096-8).
Sequencing libraries were prepared from 1ng cDNA product using Illumina Nextera XT reagents, in accordance with the supplier’s protocol, except that PCR was limited to 8 cycles to minimize read duplicates, and final library elution was performed using 17.5μl elution buffer EB.
Libraries were sequenced as pools over 1 or 2 lanes on an Illumina HiSeq 2500 sequencer.

value: Macrophage

tag: biological replicate/donor number

tag: sample number


title: Langerin+ cDC2_C

description: Donor C : Dermis Langerin+ cDC2

value: Langerin+ cDC2


title: CD14+ CD1c+ MDDC_C

description: Donor C : Dermis CD14+ CD1c+ MDDC

value: ex vivo CD14+ CD1c+ MDDC


title: CD14+ CD1c- MDM_C

description: Donor C : Dermis CD14+ CD1c- MDM

value: ex vivo CD14+ CD1c- MDM


title: Langerin- cDC2_C

description: Donor C : Dermis CD1a+ cDC2

value: Langerin- cDC2


title: BIL_10007_inflorescence meristem

tag: tissue

value: inflorescence meristem


title: BIL_10020_inflorescence meristem

value: at the secondary panicle branch developmental stage


title: BIL_10008_inflorescence meristem

value: Backcross inbred line


title: BIL_10004_inflorescence meristem


title: BIL_10056_inflorescence meristem


title: Koshihikari2_inflorescence meristem

value: Koshihikari


title: BIL_10005_inflorescence meristem


title: Koshihikari3_inflorescence meristem


title: BIL_10001_inflorescence meristem


title: BIL_10002_inflorescence meristem


title: Scramble control Rep1

description: control


title: Habataki1_inflorescence meristem

value: Habataki


title: Habataki3_inflorescence meristem


title: Koshihikari1_inflorescence meristem


title: Habataki2_inflorescence meristem


title: Langerin+ cDC2_B

description: Donor B : Dermis Langerin+ cDC2


title: Langerhans cells_C

description: Donor C : Epidermis Langerhan cells

source_name: Abdominal skin epidermal tissue

value: Langerhans cell


title: Macrophage_B

description: Donor B : Dermis Macrophage


title: CD14+ CD1c+ MDDC_B

description: Donor B : Dermis CD14+ CD1c+ MDDC


title: Langerin- cDC2_B

description: Donor B : Dermis CD1a+ cDC2


title: CD14+ CD1c- MDM_B

description: Donor B : Dermis CD14+ CD1c- MDM


title: Langerin+ cDC2_A

description: Donor A : Dermis Langerin+ cDC2


title: Langerin- cDC2_A

description: Donor A : Dermis CD1a+ cDC2


title: CD14+ CD1c+ MDDC_A

description: Donor A : Dermis CD14+ CD1c+ MDDC


title: Macrophage_A

description: Donor A : Dermis Macrophage


title: CD14+ CD1c- MDM_A

description: Donor A : Dermis CD14+ CD1c- MDM


title: Control vs Telaprevir treatment

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

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

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Tel+

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

growth_protocol: Normal human epidermal keratinocytes were cultured in HuMedia-KG2 medium.

extract_protocol: Total RNA was extracted from NHEK by Torizol reagent kit and then purified by Qiagen RNeasy Mini Kit.

treatment_protocol: After incubation with or without teraprevir 3.96 µg/ml for 24 hours, cells were harvested, and total RNA was extracted immediately.

value: Keratinocytes (NHEKs)

source_name: Tel-


title: K562_HPLM+dS_rep1

city: Madison

first: Jason

middle: R

last: Cantor

state: WI

address: 330 North Orchard Street

institute: Morgridge Institute for Research

data_processing:
Base calls were performed by the instrument control software and further processed using the Offline Base Caller version 1.9.4 (Illumina).
Reads were aligned to the human genome (GRCh37) with Ensembl annotation v. 75 using Tophat version 2.1.1 (parameters '--solexa1.3-quals', '--no-novel-juncs' and '--segment-length' of 20)
featureCounts was used to obtain counts with -s 2 (reversely stranded) and using Ensembl gtf annotation (v75).
Genome_build: GRCh37
Supplementary_files_format_and_content: Counts (text)

source_name: K562 cells

growth_protocol: Following at least two passages in the culture medium of interest, cells were pelleted and then seeded at a density of 200,000 cells/mL in 6 cm culture dishes containing 6 mL fresh medium.

extract_protocol:
After 24 hr incubation, RNA was harvested using the miRNeasy Mini Kit (QIAGEN 217004) according to manufacturer instructions.
700 ng total RNA was used to generate mRNA libraries using the TruSeq Stranded mRNA Library Preparation Kit (Illumina 20020594). Libraries prepared from each sample were quantified using the KAPA Library Quantification Kit (Roche KK4824) and then pooled at equimolar ratios. Following denaturation, 40 bp single-end reads were generated on a HiSeq 2500 (Illumina).

tag: cell line subtype

value: CML

tag: culture conditions

value: 24-hr culture in HPLM+dS


title: BIL_10044_inflorescence meristem

source_name: inflorescence meristem, 1-1.5mm


title: K562_RPMI+dS_rep2

value: 24-hr culture in RPMI+dS


title: K562_HPLM+dS_rep2


title: Langerhans cells_A

description: Donor A : Epidermis Langerhans cells


title: K562_RPMI+dS_rep1


title: BIL_10006_inflorescence meristem


title: Langerhans cells_B

description: Donor B : EpidermisLangerhans cells


title: 30033_ES-I_0

city: Minnespolis

first: Irina

last: Vlasova-St. Louis

state: MN

address: 2001 6th St SE

department: Medicine

institute: University of Minnesota

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastq files were processed using the Minnesota Supercomputing Institute Unix interface: the qualities of raw reads were assessed and trimmed (in Trimmomatic), if necessary.
The alignment and mapping of sequencing reads to a reference transcriptome (hg38) was performed with HISAT2 (hierarchical indexing for spliced alignment of transcripts).
Transcript expression was normalized to FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and quantified using Cuffquant (Cufflinks workflow).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samoles ...

source_name: Blood

extract_protocol:
Total ribonucleic acid (RNA) was extracted from whole blood using PAXgene Blood RNA kits (QIAGEN Inc.) according to the manufacturer’s protocol, and quantity was measured by RiboGreen RNA Quantification.
The Clontech StrandedRNA Pico Mammalian kit was used for library creation.  Paired-end (2x125bp or x50bp) sequencing was done on a HiSeq2500 instrument, for 125 cycles, using v4 chemistry (Illumina).

tag: patient id

tag: grouping

tag: timing

tag: outcome

value: survived

value: Early

tag: treatment-outcome code

value: ES

tag: baseline cd4+

tag: baseline lfa (crag)

tag: baseline hiv_rna

tag: age

tag: read length


title: 30028_ES-N_0

tag: treatment


title: 30028_ES-N_8


title: 30023_ED-I_0

value: died

value: ED


title: 30023_ED-I_1


title: 30033_ES-I_4i

value: survived-IRIS


title: 30012_ED-N_1


title: 30015_ED-I_0


title: 30006_ES-I_8


title: 30033_ES-I_1


title: 30015_ED-I_1


title: 30012_ED-N_0


title: 30006_ES-I_1_S55


title: 30006_ES-I_1_S40


title: 30004_ED-I_4i

value: died-IRIS


title: 30004_ED-I_0


title: 30028_ES-N_1


title: 30004_ED-I_1


title: 30023_ED-I_4i


title: 20090_DS-N_8

value: deferred

value: DS


title: 20086_DS-N_0


title: 20090_DS-N_1


title: 20090_DS-N_4


title: 20090_DS-N_0


title: 20082_DD-N_1

value: DD


title: 20086_DS-N_1


title: 20086_DS-N_4


title: 20082_DD-N_0


title: 30006_ES-I_4i


title: 20063_ES-I_4i


title: 20062_ES-N_8


title: 30006_ES-I_0


title: 20063_ES-I_1


title: 20063_ES-I_0


title: 20057_ES-N_0


title: 20059_ES-N_0


title: 20057_ES-N_8


title: 20057_ES-N_1


title: 20050_DS-N_1


title: 20049_DS-N_4


title: 20049_DS-N_1


title: 20049_DS-N_0


title: 20041_DS-I_8


title: 20050_DS-N_4


title: 20041_DS-I_0


title: 20049_DS-N_8


title: 20041_DS-I_4i


title: 20032_ED-N_0


title: 20023_ED-I_4i


title: 20032_ED-N_1


title: 20062_ES-N_1


title: 20050_DS-N_0


title: 20062_ES-N_0


title: 20011_ES-N_4


title: 20011_ES-N_1


title: 20011_ES-N_0


title: 10243_ED-N_1


title: 10243_ED-N_0


title: 10242_ED-N_1


title: 20041_DS-I_1


title: 10234_ED-I_1


title: 20023_ED-I_0


title: 20059_ES-N_1


title: 10234_ED-I_0


title: 20050_DS-N_8


title: 10229_ES-I_8


title: 10242_ED-N_0


title: 10229_ES-I_4i


title: 10229_ES-I_1


title: 10229_ES-I_0


title: 10222_DD-N_1


title: 10222_DD-N_0


title: 10219_ED-I_4i


title: 10219_ED-I_0


title: 20023_ED-I_1


title: 10218_DS-N_8


title: 10218_DS-N_0


title: 10213_ES-I_8


title: 10218_DS-N_1


title: 10213_ES-I_4i


title: 10213_ES-I_1


title: 10234_ED-I_4i


title: 10211_DS-I_1


title: 10211_DS-I_4i


title: 10211_DS-I_8


title: 10211_DS-I_0


title: 10201_DD-N_1


title: 10191_DS-I_8


title: 10191_DS-I_4i


title: 10213_ES-I_0


title: 10201_DD-N_0


title: 10191_DS-I_0


title: 10191_DS-I_1


title: 10189_ED-N_1


title: 10219_ED-I_1


title: 10180_DD-N_1


title: 10180_DD-N_0


title: 10176_DS-I_8


title: 10189_ED-N_0


title: 10218_DS-N_4


title: 10176_DS-I_1


title: 10176_DS-I_4i


title: 10165_DD-N_0


title: 10158_DS-I_8


title: 10158_DS-I_4i


title: 10176_DS-I_0


title: 10158_DS-I_0


title: 10150_DD-N_0


title: 10150_DD-N_1


title: 10145_DS-N_8


title: 10145_DS-N_0


title: 10145_DS-N_1


title: 10123_ES-N_8


title: 10123_ES-N_0


title: 10123_ES-N_1


title: 10145_DS-N_4


title: 10120_DS-I_8


title: 10123_ES-N_4


title: 10120_DS-I_1


title: 10120_DS-I_0


title: 10117_ES-N_4


title: 10117_ES-N_0


title: 10114_DS-N_8


title: 10114_DS-N_4


title: 10165_DD-N_1


title: 10112_DS-I_4i


title: 10114_DS-N_1


title: 10114_DS-N_0


title: 10112_DS-I_8


title: 10112_DS-I_1


title: 10158_DS-I_1


title: 10112_DS-I_0


title: 10111_ED-N_1


title: 10109_DS-I_8


title: 10111_ED-N_0


title: 10109_DS-I_0


title: 10109_DS-I_4i


title: 10106_ED-I_4i


title: 10109_DS-I_1


title: 10106_ED-I_1


title: 10106_ED-I_0


title: 10117_ES-N_1


title: 10092_ED-N_1


title: 10096_DS-N_8


title: 10096_DS-N_0


title: 10092_ED-N_0


title: 10099_ED-I_1


title: 10099_ED-I_0


title: 10083_ES-N_8


title: 10090_DD-N_1


title: 10090_DD-N_0


title: 10083_ES-N_1


title: 10080_ES-I_4i


title: 10083_ES-N_4


title: 10083_ES-N_0


title: 10099_ED-I_4i


title: 10080_ES-I_0


title: 10075_ED-N_0


title: 10072_DS-N_1


title: 10096_DS-N_4


title: 10096_DS-N_1


title: 10075_ED-N_1


title: 10058_ES-I_4i


title: 10072_DS-N_0


title: 10058_ES-I_8


title: 10066_ES-I_0


title: 10066_ES-I_4i


title: 10072_DS-N_4


title: 10058_ES-I_0


title: 10051_DS-N_8


title: 10080_ES-I_8


title: 10051_DS-N_0


title: 10047_ES-N_4


title: 10047_ES-N_0


title: 10051_DS-N_4


title: 10051_DS-N_1


title: 10046_ES-I_8


title: 10058_ES-I_1


title: 10046_ES-I_1


title: 10046_ES-I_0


title: 10044_DD-N_1


title: 10044_DD-N_0


title: 10020_ED-N_1


title: 10066_ES-I_8


title: 10015_DD-N_0


title: 10013_ED-I_0


title: 10015_DD-N_1


title: 10012_ES-N_8


title: 10012_ES-N_4


title: 10012_ES-N_0


title: 10013_ED-I_1


title: 10011_ES-I_8


title: 10011_ES-I_4i


title: 10047_ES-N_1


title: 10010_DS-I_4i


title: 10010_DS-I_8


title: 10006_DS-I_8


title: 10010_DS-I_0


title: 10011_ES-I_1


title: 10046_ES-I_4i


title: 10011_ES-I_0


title: 10006_DS-I_0


title: 10006_DS-I_1


title: 10010_DS-I_1


title: 10006_DS-I_4i


title: 10080_ES-I_1


title: 10002_ED-I_1


title: 10002_ED-I_0


title: 10002_ED-I_4i


title: 10020_ED-N_0


title: 10012_ES-N_1


title: U937_stim_2-Tag-30_ATAC

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description: ATAC-Seq of U937 in condition: LPS 4hr

data_processing:
Aligned reads using BWA (v0.7.17)
Removed PCR duplicates using the MarkDuplicates function from Picard (v1.731)
filtered to uniquely aligning reads using samtools (MAPQ >= 30)
tdf files computed using igvtools
Genome_build: hg19
Supplementary_files_format_and_content: tdf

source_name: monocytic cell line

growth_protocol: We maintained cells at a density between 100K and 1M per ml in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA) with 10% heat-inactivated FBS (HIFBS, Thermo Fisher Scientific), 2mM L-glutamine, and 100 units/ml streptomycin and 100 mg/ml penicillin by diluting cells 1:8 in fresh media every three days.

extract_protocol: ATAC-seq. We applied ATAC-seq as previously described [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/], with modifications. Briefly, we washed 50,000 cells once with 50 μl of cold 1x PBS and added 50 μl of Nuclei Isolation EZ Lysis Buffer (SIGMA NUC101-1KT) to resuspend gently, immediately centrifuging at 500xg for 10 minutes at 4°C. The lysis buffer was decanted away from the nuclei pellet. Afterwards, we resuspended the nuclei in 100 μl of Nuclei Isolation EZ Lysis Buffer again and centrifuged at 500xG for 5 minutes at 4°C and re-decant the lysis buffer, which we found to decrease mitochondrial reads although at the cost of library complexity. We then resuspended the nuclear pellet in 50 µl of transposition reaction mix (25 µl Buffer TD, 2.5 µl TDE1 (Illumina 15028212);  7.5 μl water, 15 μl PBS, to increase salinity which we found to increase signal-to-noise) and incubated the mix at 37°C for 30 minutes in a PCR block. Immediately following the transposition reaction, we split the 50 uL reaction volume into two and we added 25 uL of guanidine hydrochloride (Buffer PB, Qiagen 28606) to each as a chaotropic agent to stop the reaction and dissociate the proteins and transposase from the DNA. Keeping one of the reactions as backup, we proceeded with one by adding 1.8X SPRI beads (Agencourt A63881), waiting 5 minutes for the DNA to associate to the beads, and then washing the beads twice using 80% EtOH. We then eluted the DNA from the beads using 10 uL of water and added to it 25 uL NEBNext HiFi 2x PCR MasterMix (NEB M0541), with 2.5 uL of each of the dual-indexed Illumina Nextera primers (25 uM). We amplified the PCR reaction to 15 cycles, as previously described. We purified amplified libraries and removed adapters using two clean-ups with 1.8x volume SPRI (Agencourt A63881). We sequenced these libraries on an Illumina HiSeq 2500. We filtered, aligned, and processed the data to generate BAM files as previously described. [https://www.nature.com/articles/s41588-019-0538-0?proof=true1]    H3K27ac ChIP-seq. We generated and analyzed ChIP-seq data from 5 million cells in each cell line and stimulation state, following protocols previously described[]. Before harvesting for ChIP-seq, cells at 1 million cells per mL were replenished by a 1:2 (v/v) split in fresh media and allowed to grow for 4 hours. 10 million cells were harvested from each cell type at 500K cells/mL and washed 2x in cold PBS. Cells were resuspended in warm PBS with 1% formaldehyde (Cat #28906, Thermo Scientific) and incubated at 37°C for 10 minutes. Crosslinking was quenched by adding glycine to a concentration of 250 mM and incubating for 5 minutes at 37°C. Cells were placed on ice for 5 minutes, then washed 2x in ice-cold PBS and snap-frozen in liquid nitrogen and stored. Later, crosslinked cells were lysed in 1 mL cell lysis buffer (20 mM Tris pH 8.0, 85 mM KCl, 0.5% NP40) and incubated on ice for 10 minutes. The nuclear pellet was isolated by spinning the cell lysis mix at 5,600xg at 4°C for 3.5 minutes and discarding the supernatant. Nuclear pellets were lysed by adding 1 mL nuclear lysis buffer (10 mM Tris-HCl pH 7.5 ml, 1% NP-40 alternative (CAS 9016-45-9), 0.5% Na Deoxycholate, 0.1% SDS) with protease inhibitors on ice for 10 minutes. The chromatin-containing nuclear lysate was sonicated 3x using a Branson sonifier (ON 0.7s, OFF 1.3s, TIME 2 minutes, WATTS 10-12), with 1 minute rest between sonifications. Sonicated chromatin was spun down at maximum speed. 300 µL of the clarified supernatant was diluted 1:1 with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.1, 1.1% Triton X-100, and 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS). To immunoprecipitate H3K27ac, 3 uL of H3K27ac monoclonal antibody (Cat #39685, Active Motif) was added to each sample and rotated overnight at 4°C. The following morning, 50 uL of a 1:1 mix of Protein A (Cat #10008D, Invitrogen) and Protein G Dynabeads magnetic beads (Cat #10004D, Life Technologies) were washed with blocking buffer (PBS, 0.5% Tween20, 0.5% BSA with protease inhibitors), resuspended in 100 uL blocking buffer, and added to each sample. The samples were rotated end-over-end for 1 h at 4°C to capture antibody complexes, then washed as follows: once with 200 uL Low-Salt RIPA buffer (0.1% SDS, 1% Triton X-100, 1 mM EDTA, 20 mM Tris-HCl pH 8.1, 140 mM NaCl, 0.1% Na Deoxycholate), once with 200 µL High-Salt RIPA buffer (0.1% SDS, 1% Triton X-100, 1 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl, 0.1% Na Deoxycholate), twice with 200 µL LiCl buffer (250 mM LiCl, 0.5% NP40, 0.5% Na Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), and twice with 200 µL TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0). Chromatin was then eluted from the beads with 60 µL ChIP elution buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS). Crosslinking was reversed by adding 8 µL of reverse cross-linking enzyme mix (250 mM Tris-HCl pH 6.5, 62.5 mM EDTA pH 8.0, 1.25 M NaCl, 5 mg/ml Proteinase K (Cat #25530-049, Invitrogen), 62.5 µg/ml RNAse A (Cat #111199150001, Roche)) to each immunoprecipitated sample, as well as to 10 µL of the sheared chromatin input for each sample brought to volume of 60 µL ChIP elution buffer. Reverse crosslinking reactions were incubated 2 h at 65°C and cleaned using Agencourt Ampure XP SPRI beads (Cat #A63880, Beckman Coulter) with a 2x bead:sample ratio. Sequencing libraries were prepared with KAPA Library Preparation kit (Cat #KK8202, KAPA Biosystems). ChIP libraries were sequenced using single-end sequencing on an Illumina Hiseq 2500 machine (Read 1: 76 cycles, Index 1: 8 cycles), to a depth of >30 million reads per ChIP sample.

treatment_protocol: We stimulated BJAB cells with 4 µg/ml anti-CD40 (Invitrogen-140409-82) and 10 µg/ml anti-IgM (Sigma-I0759) for 4 hours. We stimulated Jurkat cells with 5 µg/ml anti-CD3 (Biolegend-317315) and 100 ng/ml phorbol 12-myristate 13-acetate (PMA, Sigma-P1585) for 4 hours. We stimulated U937 cells with 200 ng/ml LPS for 4 hours. We stimulated THP1 cells with 1 µg/ml bacterial lipopolysaccharide (LPS) from E. coli K12 (LPS-EK Invivogen tlrl-peklps) for 4 hours.     For THP1 cells, we generated epigenomic data examining a longer time-course, by stimulating with PMA (100 ng/mL) for 12 hours, then removing PMA and adding LPS (1 µg/mL) and profiling at 0, 1, 2, 6, 12, 24, 48, 72, 96, and 120 hours after addition of LPS. Because THP1 cells adhere when stimulated with PMA (changing into a more macrophage-like state), we harvested cells by taking out the media, washing twice, adding TrypLE for 5 minutes at 37°C, then supplementing with 100 µL of media, removing cells from the round-bottom plate and pelleting.

tag: cell line

tag: stimulation

value: LPS 4hr

tag: assay

value: ATAC-Seq


title: U937-stim-2_H3K27ac

description: H3K27ac ChIP-Seq of U937 in condition: LPS 4hr

value: H3K27ac ChIP-Seq


title: U937_stim_1-Tag-30_ATAC

description: ATAC-Seq of U937 in condition: LPS 4hr


title: U937-stim-1_H3K27ac


title: U937-ctrl-2_H3K27ac

description: H3K27ac ChIP-Seq of U937 in condition: no stimulation


title: U937_ctrl_1-Tag-30_ATAC

description: ATAC-Seq of U937 in condition: no stimulation


title: THP1pmaLPS_K27ac_18_96h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  96h

value: pma 4h LPS  96h


title: THP_pmaLPS_ATAC_17_96h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  96h


title: U937_ctrl_2-Tag-30_ATAC


title: U937-ctrl-1_H3K27ac


title: THP1pmaLPS_K27ac_17_96h_H3K27ac


title: THP1pmaLPS_K27ac_15_72h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  72h

value: pma 4h LPS  72h


title: THP1pmaLPS_K27ac_16_72h_H3K27ac


title: THP_pmaLPS_ATAC_14_48h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  48h

value: pma 4h LPS  48h


title: THP1pmaLPS_K27ac_7_6h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  6h

value: pma 4h LPS  6h


title: THP_pmaLPS_ATAC_13_48h_ATAC


title: THP_pmaLPS_ATAC_12_24h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  24h

value: pma 4h LPS  24h


title: THP_pmaLPS_ATAC_7_6h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  6h


title: THP_pmaLPS_ATAC_5_2h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  2h

value: pma 4h LPS  2h


title: THP1pmaLPS_K27ac_5_2h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  2h


title: THP_pmaLPS_ATAC_6_2h_ATAC


title: THP_pmaLPS_ATAC_11_24h_ATAC


title: THP1pmaLPS_K27ac_14_48h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  48h


title: THP1pmaLPS_K27ac_13_48h_H3K27ac


title: THP1pmaLPS_K27ac_12_24h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  24h


title: THP1pmaLPS_K27ac_4_1h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  1h

value: pma 4h LPS  1h


title: THP_pmaLPS_ATAC_4_1h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  1h


title: THP1pmaLPS_K27ac_3_1h_H3K27ac


title: THP1pmaLPS_K27ac_11_24h_H3K27ac


title: THP_pmaLPS_ATAC_9_12h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  12h

value: pma 4h LPS  12h


title: THP_pmaLPS_ATAC_15_72h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  72h


title: THP_pmaLPS_ATAC_10_12h_ATAC


title: THP1pmaLPS_K27ac_9_12h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  12h


title: THP1pmaLPS_K27ac_8_6h_H3K27ac


title: THP1pmaLPS_K27ac_6_2h_H3K27ac


title: THP1pmaLPS_K27ac_10_12h_H3K27ac


title: THP1pmaLPS_K27ac_20_120h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  120h

value: pma 4h LPS  120h


title: THP_pmaLPS_ATAC_20_120h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  120h


title: THP_pmaLPS_ATAC_19_120h_ATAC


title: THP1pmaLPS_K27ac_19_120h_H3K27ac


title: THP_pmaLPS_ATAC_2_0h_ATAC

description: ATAC-Seq of THP1 in condition: pma 4h LPS  0h

value: pma 4h LPS  0h


title: THP_pmaLPS_ATAC_1_0h_ATAC


title: THP1pmaLPS_K27ac_2_0h_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: pma 4h LPS  0h


title: THP_stim_2-Tag-30_ATAC

description: ATAC-Seq of THP1 in condition: LPS 4hr


title: THP1pmaLPS_K27ac_1_0h_H3K27ac


title: THP-stim-1_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: LPS 4hr


title: THP_stim_1-Tag-30_ATAC

description: ATAC-Seq of THP1 in condition: LPS 4hr


title: THP1_ctrl_2-Tag-30_ATAC

description: ATAC-Seq of THP1 in condition: no stimulation


title: THP-stim-2_H3K27ac


title: THP1_ctrl_1-Tag-30_ATAC


title: THP-ctrl-2_H3K27ac

description: H3K27ac ChIP-Seq of THP1 in condition: no stimulation


title: Jurkat_stim_2-Tag-30_ATAC

description: ATAC-Seq of Jurkat in condition: anti-CD3 PMA 4hr

source_name: T cell line

value: Jurkat

value: anti-CD3 PMA 4hr


title: Jurkat-stim-2_H3K27ac

description: H3K27ac ChIP-Seq of Jurkat in condition: anti-CD3 PMA 4hr


title: Jurkat_stim_1-Tag-30_ATAC


title: Jurkat-ctrl-1_H3K27ac

description: H3K27ac ChIP-Seq of Jurkat in condition: no stimulation


title: Jurkat_ctrl_2-Tag-30_ATAC

description: ATAC-Seq of Jurkat in condition: no stimulation


title: Jurkat-ctrl-2_H3K27ac


title: Jurkat_ctrl_1-Tag-30_ATAC


title: Jurkat-stim-1_H3K27ac


title: BJAB_stim_1-Tag-30_ATAC

description: ATAC-Seq of BJAB in condition: anti-IgM anti-CD40 4hr

source_name: B cell line

value: BJAB

value: anti-IgM anti-CD40 4hr


title: BJAB_stim_2-Tag-30_ATAC


title: BJAB-stim-2_H3K27ac

description: H3K27ac ChIP-Seq of BJAB in condition: anti-IgM anti-CD40 4hr


title: BJAB-stim-1_H3K27ac


title: BJAB_ctrl_2-Tag-30_ATAC

description: ATAC-Seq of BJAB in condition: no stimulation


title: BJAB-ctrl-2_H3K27ac

description: H3K27ac ChIP-Seq of BJAB in condition: no stimulation


title: BJAB_ctrl_1-Tag-30_ATAC


title: S18-Over-01

city: Guangzhou

first: Qi

last: Zhao

state: Guangdong

address: No. 651, Dongfengdong Road

department: Medical Oncology

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina HiSeq2500 software used for basecalling.
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.xls: Excel files include FPKM values for each Sample.

source_name: nasopharyngeal carcinoma cells

growth_protocol: The S18 and 5-8F cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells and tissue specimens using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: nasopharyngeal carcinoma cells

tag: genotype/variation

tag: metastatic ability

value: lowly metastatic


title: BJAB-ctrl-1_H3K27ac

value: H3K27ac ChIP-Seq


title: 5-8F-Vector-01

description: Vector

value: Wild type

value: highly metastatic


title: AlkB-PLCStem_m1Aseq

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

description:
Using TGIRT to capture m1A-induced mismatch information
AlkB-PLCStem_m1Aseq.mismatch.xls

data_processing:
Raw sequencing reads produced from m1A-seq were firstly subjected to Trim_galore (version 0.3.7. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming. The minimum quality threshold was set to 20, and the minimum length required for reads after trimming was 30 nt. The remaining reads were further processed by removing the first 10 nt random barcode in the 5’ end. As for the ribosome profiling (Ribo-seq) data and the corresponding RNA-seq data, reads with a quality lower than 20 were discarded, and the adaptor in 3’ end was trimmed. Processed reads with a length ranging from 25 nt to 35 nt in the ribosome profiling sample were kept for further analysis.
Processed reads from m1A-seq were mapped to tRNA sequences, which was downloaded from UCSC Table Browser, using BWA-MEM (version 0.7.17-r1188) with default parameters. The processed reads from Ribo-seq were mapped to human transcriptome (Refseq annotation, downloaded from UCSC Table Browser) using BWA-MEM (version 0.7.17-r1188) with default parameters.
For m1A-seq analysis, reads mapping to an identical position of reference were considered as PCR duplications if their 10 nt random barcodes were the same, and only one of these reads was kept.
Samtools mpileup (1.8) was used to extract the reads mapping of every nucleotide in the tRNA transcriptome.
Mismatch rate was calculated using in-house scripts. RPKM was calculated using in-house scripts following the definition of RPKM, translation efficiency (TE) were then calculated following: TE=RPKM(Riboseq)/RPKM(RNAseq).
Genome_build: hg19
Supplementary_files_format_and_content: Mismatch rate file in tab-delimited format; containing the mismatch rate for every nucleotide in the tRNA transcriptome; For Riboseq data, the processed files are translation efficiency file in tab-demilited format.
Supplementary_files_format_and_content: PLC_m1Aseq.mismatch.xls: Mismatch rate file in tab-delimited format
Supplementary_files_format_and_content: PLCStem_m1Aseq.mismatch.xls: Mismatch rate file in tab-delimited format
Supplementary_files_format_and_content: AlkB-PLC_m1Aseq.mismatch.xls: Mismatch rate file in tab-delimited format
Supplementary_files_format_and_content: AlkB-PLCStem_m1Aseq.mismatch.xls: Mismatch rate file in tab-delimited format
Supplementary_files_format_and_content: PLC.TE.xls: Translation efficiency file in tab-demilited format
Supplementary_files_format_and_content: PLC_stem.TE.xls: Translation efficiency file in tab-demilited format

source_name: human PLC cell line

growth_protocol: Human hepatocellular carcinoma (HCC) cell line PLC/PRF/5 was maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 100 μg/ml penicillin G, and 100 U/ml streptomycin (Invitrogen, NY, USA).

extract_protocol:
For m1A-seq, total RNA was isolated from cell lines by Trizol(invitrogen).<200 nt fraction RNA was enriched from total RNA with size selection using Megaclear kit (invitrogen), then was collected from the flow through.
For m1A-seq, RNA samples were dephosphorylated with PNK (NEB) and ligated to 3’ RNA linker using T4 RNA ligase2, truncated KQ (NEB). Reverse transcription was carried using different reverse transcriptase for different samples.  5’ adaptor was ligated to cDNA and then amplified by PCR. PCR products were purified by 8% TBE gel

treatment_protocol: We sorted liver CSCs (CD13+CD133+) and non-CSCs (CD13-CD133-). For cell sorting, cocktail PE-conjugated anti-human CD133 and FITC-conjugated anti-human CD13 antibodies were incubated with HCC PLC/PRF/5 cells, followed by sorting with FACS Aria III (BD Immunocytometry Systems, San Jose, CA, USA).

value: PLC stem cells

tag: library strategy

value: small RNA (<200)

value: AlkB demethylation


title: S18-Vector-01


title: PLCStem_m1Aseq

description:
Using TGIRT to capture m1A-induced mismatch information
PLCStem_m1Aseq.mismatch.xls


title: AlkB-PLC_m1Aseq

description:
Using TGIRT to capture m1A-induced mismatch information
AlkB-PLC_m1Aseq.mismatch.xls

value: Normal PLC cells


title: 5-8F-Over-01

description: Over


title: SV20

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the hg19 reference genome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: hg19
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: Heart

extract_protocol:
Total RNA was extracted using the miRNeasy Kit (Qiagen) including DNAse treatment. RNA concentration and quality was determined using the NanoVue Plus™ spectrophotometer (GE Healthcare) and the Agilent 2100 RNA Nano Chip (Agilent)
RNA sequencing libraries were prepared using the Illumina TruSeq stranded mRNA kit followed by the Nugen Ovation amplification kit.

tag: ethnicity

value: EUR

tag: Sex

value: male

tag: batch


title: 427

value: AA

value: female


title: 312


title: PLC_m1Aseq

description:
Using TGIRT to capture m1A-induced mismatch information
PLC_m1Aseq.mismatch.xls


title: 321


title: 285


title: 16-1174


title: 44-1336


title: 225


title: 86-1380


title: 89-1342


title: 555


title: 233


title: 661


title: 486-1460-080


title: 521


title: 93-1385


title: 30-135


title: 679


title: 113-1138


title: 719


title: 603


title: 76-1544


title: 245


title: 697


title: 41-1282


title: 633-1310-003


title: 38-1298


title: 134


title: 127-1188


title: 56-061


title: 24-1311


title: 415


title: 136


title: 316


title: 37-1189


title: 120-1042


title: 258


title: 781


title: 23-1346-028


title: 96-1592


title: 50-1394


title: 78-045


title: 560


title: 114-1160


title: 57-1673


title: 72-1677


title: 60-099


title: 90-1481


title: 384


title: 749


title: 444


title: 802


title: 108-1665


title: 271


title: 588


title: 111-1008


title: 366


title: 262


title: 63-1622


title: 442


title: 61-1559-060


title: 28-1619


title: 286


title: 106-1231


title: 370


title: 408


title: PR0334_70_a

city: Fukuoka

first: Michitaka

last: Nakano

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Biosystemic Sciences

institute: Kyushu University

data_processing:
Sequencing was performed on Illumina HiSeq2500 (Illumina) to achieve an average of 8.5 million reads per cell.
Raw sequence data were converted to FASTQ format.
Reads were mapped to the reference genome (GRCh37/hg19).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Colon cancer organoid

growth_protocol: A single CD44+ colon cancer stem cell is sorted into 96 well plate, and cultured in the condition as we previously published.

extract_protocol:
The isolated cells from a single organoid were washed and resuspended at a concentration of 500 cells/μL and put into Fluidigm C1 Single Cell Auto Prep system.
Single-cell RNA isolation and amplification were performed using Fluidigm C1 Single Cell Auto Prep IFC, according to the manufacturer’s protocol.

tag: sample type

value: single cell

tag: tissue

value: Colon cancer organoid


title: PR0334_71_a


title: PR0334_72_a

value: bulk control


title: 15-1203-024


title: PR0334_69_a


title: 88-1451


title: 161


title: 35-1360-010


title: PR0334_64_a


title: PR0334_63_a


title: 854


title: PR0334_62_a


title: PR0334_65_a


title: PR0334_61_a


title: PR0334_57_a


title: PR0334_59_a


title: PR0334_56_a


title: PR0334_60_a


title: PR0334_55_a


title: PR0334_54_a


title: PR0334_53_a


title: PR0334_48_a


title: PR0334_49_a


title: PR0334_51_a


title: PR0334_50_a


title: PR0334_52_a


title: PR0334_68_a


title: PR0334_66_a


title: PR0334_45_a


title: PR0334_46_a


title: PR0334_42_a


title: PR0334_47_a


title: PR0334_67_a


title: PR0334_44_a


title: PR0334_43_a


title: PR0334_40_a


title: PR0334_41_a


title: PR0334_58_a


title: PR0334_38_a


title: PR0334_37_a


title: PR0334_34_a


title: PR0334_33_a


title: PR0334_28_a


title: PR0334_32_a


title: PR0334_30_a


title: PR0334_31_a


title: PR0334_29_a


title: PR0334_27_a


title: PR0334_26_a


title: PR0334_25_a


title: PR0334_23_a


title: PR0334_22_a


title: PR0334_21_a


title: PR0334_39_a


title: PR0334_20_a


title: PR0334_19_a


title: PR0334_13_a


title: PR0334_36_a


title: PR0334_11_a


title: PR0334_12_a


title: PR0334_17_a


title: PR0334_10_a


title: PR0334_15_a


title: PR0334_16_a


title: PR0334_09_a


title: PR0334_18_a


title: PR0334_14_a


title: PR0334_35_a


title: PR0334_08_a


title: PR0334_06_a


title: PR0334_07_a


title: PR0334_03_a


title: PR0334_04_a


title: PR0334_05_a


title: PR0334_01_a


title: PR0334_24_a


title: PR0334_02_a


title: 7_PFC_neuron primary cohort: P2A9

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

data_processing:
Low quality reads and adapters were removed using TrimGalore (v0.4.4)
Bismark (v0.17.0) was used to align bisulfite sequencing reads to a masked reference genome and the base pair specific methylation calls were extracted
Methylation calls overlapping padlock probe arms were removed using Bedtools
Methylation calls were only considered for cytosines with at least a 30× read depth. For technical replicate samples, methylation calls and counts were averaged for each site. Sites with less than 70% of samples containing methylation calls and/or sites with all samples having a methylation call of 0 were removed from further analysis. Sites overlapping common SNPs in the population (minor allele frequency ≥ 0.05), as identified by the 1000 Genomes Project (phase 3 v5a 20130502 release for chr1-chr22, v1b 20130502 for chrX; all populations and European populations) were also removed from further analysis
We next explored the data using principal component analysis (PCA) of beta values defined as B = M / (M+U). PCA of all datasets was computed and sample projection onto the first two principal components was plotted, which served to identify outlying samples. Samples deviating from the center of either of the first two principal components by more than 3 standard deviations were deemed outliers and removed from further analysis. Next, the distribution of U and M read counts across experimental batches was used to determine whether sample cohort should be normalized. Normalized B values for appendix datasets were obtained from quantile normalized and rounded M and U read count matrices. Sites with stable DNA methylation calls (0%, 100%, and/or missing) in 50% or more of the samples were excluded from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Each txt file contain the following information in order: chromosome #, genomic coordinate, strand, unmethylation count, methylation count, CHH/CHG/CG context of cytosine, exact sequence of the previous context

source_name: PFC

extract_protocol:
Neurons from prefrontal cortex were isolated using an antibody (NeuN) and flow cytometry-based approach. Neuronal nuclei (NeuN and 7-AAD stained) were isolated using a MoFlo Astrios (Beckman Coulter) running Summit 6.3. Genomic DNA was extracted using standard phenol-chloroform extraction methods from prefrontal cortex neurons of PD patients and controls.
DNA methylation fine-mapping was performed using the bisulfite padlock probe technique. Bisulfite conversion of gDNA and purification was done using the EZ DNA Methylation-Lightning Kit (Zymo Research) and quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). For each sample, the bisulfite-converted DNA (200 ng) was hybridized to the padlock probes (1.5 ng) at 55ºC for 20 h. Target regions flanked by the hybridized padlock probes were extended using PfuTurbo Cx (Agilent Technologies) and circularization was completed using Ampligase (Epicentre). The non-targeted, non-circularized DNA was digested using exonuclease (Exonuclease I and III; New England Biolabs). The target circularized DNA was amplified using a common linker sequence within the padlock probe. Libraries were then PCR amplified, pooled in equimolar amounts, and purified by QIAquick Gel Extraction kit (Qiagen). Libraries were quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems). Next-generation sequencing of the libraries was performed on an Illumina HiSeq 2500 machine

value: prefrontal cortex neurons

tag: subject id

tag: replicate

value: TR

tag: group

value: PD

value: M

tag: pmi

tag: proportionglu


title: 7_PFC_neuron primary cohort: P2A8

tag: age


title: 7_PFC_neuron primary cohort: P2A6

value: No

value: CTRL


title: 7_PFC_neuron primary cohort: P2A5


title: 7_PFC_neuron primary cohort: P2A4


title: 7_PFC_neuron primary cohort: P2A3


title: 7_PFC_neuron primary cohort: H12

value: F


title: 7_PFC_neuron primary cohort: P2A2


title: 7_PFC_neuron primary cohort: H9


title: 7_PFC_neuron primary cohort: H8


title: 7_PFC_neuron primary cohort: H6


title: 7_PFC_neuron primary cohort: H1


title: 7_PFC_neuron primary cohort: H2


title: 7_PFC_neuron primary cohort: G12


title: 7_PFC_neuron primary cohort: H10


title: 7_PFC_neuron primary cohort: H4


title: 7_PFC_neuron primary cohort: H5


title: 7_PFC_neuron primary cohort: H3


title: 7_PFC_neuron primary cohort: G7


title: 7_PFC_neuron primary cohort: G9


title: 7_PFC_neuron primary cohort: G8


title: 7_PFC_neuron primary cohort: G6


title: 7_PFC_neuron primary cohort: G11


title: 7_PFC_neuron primary cohort: G10


title: 7_PFC_neuron primary cohort: P2A1


title: 7_PFC_neuron primary cohort: G4


title: 7_PFC_neuron primary cohort: G3


title: 7_PFC_neuron primary cohort: P2A7


title: 7_PFC_neuron primary cohort: P2A12


title: 7_PFC_neuron primary cohort: F10


title: 7_PFC_neuron primary cohort: F11


title: 7_PFC_neuron primary cohort: F12

value: BR


title: 7_PFC_neuron primary cohort: G1


title: 7_PFC_neuron primary cohort: F9


title: 7_PFC_neuron primary cohort: F8


title: 7_PFC_neuron primary cohort: F6


title: 7_PFC_neuron primary cohort: F3


title: 7_PFC_neuron primary cohort: F5


title: 7_PFC_neuron primary cohort: F4


title: 7_PFC_neuron primary cohort: G5


title: 7_PFC_neuron primary cohort: F2


title: 7_PFC_neuron primary cohort: F7


title: 7_PFC_neuron primary cohort: E10


title: 7_PFC_neuron primary cohort: E12


title: 7_PFC_neuron primary cohort: E8


title: 7_PFC_neuron primary cohort: E7


title: 7_PFC_neuron primary cohort: G2


title: 7_PFC_neuron primary cohort: E6


title: 7_PFC_neuron primary cohort: E3


title: 7_PFC_neuron primary cohort: F1


title: 7_PFC_neuron primary cohort: E1


title: 7_PFC_neuron primary cohort: D12


title: 7_PFC_neuron primary cohort: D11


title: 7_PFC_neuron primary cohort: D9


title: 7_PFC_neuron primary cohort: D8


title: 7_PFC_neuron primary cohort: E2


title: 7_PFC_neuron primary cohort: D7


title: 7_PFC_neuron primary cohort: D5


title: 7_PFC_neuron primary cohort: D4


title: 7_PFC_neuron primary cohort: D6


title: 7_PFC_neuron primary cohort: D2


title: 7_PFC_neuron primary cohort: D1


title: 7_PFC_neuron primary cohort: E11


title: 7_PFC_neuron primary cohort: C12


title: 7_PFC_neuron primary cohort: C10


title: 7_PFC_neuron primary cohort: C9


title: 7_PFC_neuron primary cohort: E4


title: 7_PFC_neuron primary cohort: C8


title: 7_PFC_neuron primary cohort: C11


title: 7_PFC_neuron primary cohort: C7


title: 7_PFC_neuron primary cohort: C6


title: 7_PFC_neuron primary cohort: C4


title: 7_PFC_neuron primary cohort: B7


title: 7_PFC_neuron primary cohort: B8


title: 7_PFC_neuron primary cohort: C2


title: 7_PFC_neuron primary cohort: B10


title: 7_PFC_neuron primary cohort: B11


title: 7_PFC_neuron primary cohort: B6


title: 7_PFC_neuron primary cohort: D3


title: 7_PFC_neuron primary cohort: B1


title: 7_PFC_neuron primary cohort: A10


title: 7_PFC_neuron primary cohort: B5


title: 7_PFC_neuron primary cohort: A12


title: 7_PFC_neuron primary cohort: B4


title: 7_PFC_neuron primary cohort: B3


title: 7_PFC_neuron primary cohort: A11


title: 7_PFC_neuron primary cohort: B2


title: 7_PFC_neuron primary cohort: A9


title: 7_PFC_neuron primary cohort: A7


title: 7_PFC_neuron primary cohort: A4


title: 7_PFC_neuron primary cohort: A6


title: 7_PFC_neuron primary cohort: C3


title: 7_PFC_neuron primary cohort: B12


title: 7_PFC_neuron primary cohort: A1


title: 7_PFC_neuron primary cohort: A3


title: 6_PFC_neuron replication cohort: PFC_6_PD3518


title: 6_PFC_neuron replication cohort: PFC_32_CON3446


title: 6_PFC_neuron replication cohort: PFC_8_CON3512


title: 6_PFC_neuron replication cohort: PFC_4_PD3389


title: 6_PFC_neuron replication cohort: PFC_9_CON3363


title: 6_PFC_neuron replication cohort: PFC_31_PD3374


title: 6_PFC_neuron replication cohort: PFC_5_PD3459


title: 6_PFC_neuron replication cohort: PFC_3_CON3511


title: 6_PFC_neuron replication cohort: PFC_30_PD3525


title: 7_PFC_neuron primary cohort: B9


title: 6_PFC_neuron replication cohort: PFC_29_CON3557


title: 6_PFC_neuron replication cohort: PFC_27_CON3454


title: 6_PFC_neuron replication cohort: PFC_25_PD3370


title: 6_PFC_neuron replication cohort: PFC_21_CON3460


title: 6_PFC_neuron replication cohort: PFC_2_PD_3531


title: 6_PFC_neuron replication cohort: PFC_26_PD3369


title: 6_PFC_neuron replication cohort: PFC_24_PD3440


title: 7_PFC_neuron primary cohort: A5


title: 6_PFC_neuron replication cohort: PFC_20_PD3561


title: MMAR_0500_IP

city: Shanghai

first: Wenyue

last: Dong

address: Fenglin road 300

institute: CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

description: Chipped DNA

data_processing:
FastQC version v0.11.5, generate NGS quality control report;
Trimmomatic version 0.36, filter out the adaptor and low quality reads;
STAR version 2.5.3a, mapping the reads to the genome;
RSeQC version 2.6, evaluate mapped reads distribution, coverage uniformity, strand specificity, etc.;
MACS2 version 2.1.1, gives robust and high resolution ChIP-Seq peak predictions;
Genome_build: Reference sequence: GenBank GCA_000018345.1
Supplementary_files_format_and_content: bam/bigWig/bed files, sequencing reads aligned to the reference genome

organism: Mycobacterium marinum

source_name: Bacterial cells

growth_protocol: Cells were grown in 7H9 medium with 0.2% glycerol and 10% ADC to an OD600 of ~0.8.

extract_protocol:
Lysates were clarified from sonicated genomic DNA and the FdmR protein-DNA complexes were isolated with antibody.
The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog NO. ND607, Vazyme). The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: Cells were cross-linked with 1% formaldehyde for 15 min at room temperature followed by quenching with 125 mM glycine.

value: bacterial aliquots

tag: strain

value: M strain

tag: chip target

value: FdmR-DNA complexes

tag: chip antibody

value: Monoclonal ANTI-FLAG M2 antibody produced in mouse


title: 6_PFC_neuron replication cohort: PFC_7_CON3547


title: 6_PFC_neuron replication cohort: PFC_18_CON3361


title: 6_PFC_neuron replication cohort: PFC_17_CON3548


title: MMAR_0500_Input

description: Input DNA

value: none (input)


title: 6_PFC_neuron replication cohort: PFC_16_CON3362


title: 6_PFC_neuron replication cohort: PFC_15_PD3441


title: 6_PFC_neuron replication cohort: PFC_11_PD3461


title: 6_PFC_neuron replication cohort: PFC_12_CON3469


title: 6_PFC_neuron replication cohort: PFC_10_CON3453


title: MV33_D141N.IonXpressRNA_009

city: Kraków

first: Iwona

last: Nowak

address: Kalwaryjska 92/5

country: Poland

institute: Jagiellonian University

data_processing:
verification of the quality of the reads (FastQC software version 0.11.5 )
trimming of adapters of raw sequencing reads (Cutadapt version 2.08 )
reads alignment   (Bowtie version 1.2.3)
Read normalization and identification of differentially expressed miRNAs (DESeq2 version 1.24.0 )
Genome_build: miRBase
Supplementary_files_format_and_content: excel, list of differentially expressed miRNAs for wt vs c, d141n vs c and overall

source_name: MCPIP1 D141N overexpressing cells rep 3

growth_protocol: MV3 melanoma cells were cultured in RPMI 1640 medium (R8758, Sigma, Darmstadt, Germany) supplemented with 10% foetal bovine serum (10270, Gibco, Waltham, MA USA), 1% non-essential amino acids (M7145, Sigma, Darmstadt, Germany) and 50 μg/ml gentamycin (G1397, Sigma, Darmstadt, Germany) at 37°C in an atmosphere containing 5% CO2. Cells were routinely assessed for mycoplasma contamination. All tests were negative.

extract_protocol:
RNA was isolated using the miRVana™ miRNA Isolation Kit (AM1560, Thermo Fisher Scientific, Waltham, MA, USA).
Libraries were generated with an Ion Total RNA-Seq Kit v2 (4479789, Thermo Fisher Scientific, Waltham, MA, USA).
As the input material, 10 µg of total RNA per sample was used.

treatment_protocol: The day prior to transfection, cells were seeded at a density of 10 500 cells/cm2. To achieve transient overexpression of MCPIP1-wt and MCPIP1-D141N pcDNA3 plasmid vecor with the expression cassette for the respective MCPIP1 form was used. As the corresponding control transfection with empty vector was conducted. For transfection, 3 µg of DNA per well of a 6-well plate was used. The DNA was mixed with polyethyleneimine (PEI; 408727, Sigma, Darmstadt, Germany) at a ratio of 1:3 and diluted in OPTI-MEM (11058021, Gibco, Waltham, MA, USA). The cells were incubated with the DNA:PEI solutions for 6 hours. Twenty-four hours following transfection, the medium was changed to selection medium containing 900 µg/ml geneticin (G418, Lab Empire, Rzeszów, Poland). The selection medium was changed daily until the 4th day after transfection, when the cells were collected.

tag: cell type

value: MV3 melanoma cells

tag: genotype/variation

value: transfection with empty pcDNA.3 plasmid containing mutated MCPIP1 expression cassette


title: MV34_D141N.IonXpressRNA_012

source_name: MCPIP1 D141N overexpressing cells rep 4


title: MV31_D141N.IonXpressRNA_003

source_name: MCPIP1 D141N overexpressing cells rep 1


title: MV32_D141N.IonXpressRNA_006

source_name: MCPIP1 D141N overexpressing cells rep 2


title: 6_PFC_neuron replication cohort: PFC_1_CON3455


title: 6_PFC_neuron replication cohort: PFC_19_PD3360


title: 5_OFB: ROB_A25_Con3454

source_name: OFB

extract_protocol:
Genomic DNA was extracted using standard phenol-chloroform extraction methods from olfactory bulb tissue of PD patients and controls.
DNA methylation fine-mapping was performed using the bisulfite padlock probe technique. Bisulfite conversion of gDNA and purification was done using the EZ DNA Methylation-Lightning Kit (Zymo Research) and quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). For each sample, the bisulfite-converted DNA (200 ng) was hybridized to the padlock probes (1.5 ng) at 55ºC for 20 h. Target regions flanked by the hybridized padlock probes were extended using PfuTurbo Cx (Agilent Technologies) and circularization was completed using Ampligase (Epicentre). The non-targeted, non-circularized DNA was digested using exonuclease (Exonuclease I and III; New England Biolabs). The target circularized DNA was amplified using a common linker sequence within the padlock probe. Libraries were then PCR amplified, pooled in equimolar amounts, and purified by QIAquick Gel Extraction kit (Qiagen). Libraries were quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems). Next-generation sequencing of the libraries was performed on an Illumina HiSeq 2500 machine

value: olfactory bulb

value: Yes


title: MV31_wt.IonXpressRNA_002

source_name: MCPIP1 wild-type overexpressing cells rep 1

value: transfection with empty pcDNA.3 plasmid containing wild type MCPIP1 expression cassette


title: MV33_wt.IonXpressRNA_008

source_name: MCPIP1 wild-type overexpressing cells rep 3


title: MV34_wt.IonXpressRNA_011

source_name: MCPIP1 wild-type overexpressing cells rep 4


title: 5_OFB: ROB_A12_Con3446


title: MV32_wt.IonXpressRNA_005

source_name: MCPIP1 wild-type overexpressing cells rep 2


title: 5_OFB: OB_A9_Con3548


title: 6_PFC_neuron replication cohort: PFC_13_CON3452

value: prefrontal cortex neurons


title: MV32_C.IonXpressRNA_004

source_name: Control cells rep 2

value: transfection with empty pcDNA.3 plasmid


title: MV33_C.IonXpressRNA_007

source_name: Control cells rep 3


title: MV34_C.IonXpressRNA_010

source_name: Control cells rep 4


title: 5_OFB: OB_A7_Con3460

value: M


title: 5_OFB: OB_A5_Con3557

value: No


title: 5_OFB: OB_A8_Con3469

value: CTRL


title: 5_OFB: OB_A6_PD3525

value: PD


title: 2130T3_Liver tumor_Trp53-/-

city: Ulm

first: André

last: Lechel

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine I

institute: University hospital Ulm

hyb_protocol: Labeled DNA Samples were hybridized for 24 hours at 67°C and 20 rpm rotation speed according to manufacturer´s protocol (Agilent Technologies, Santa Clara, CA, USA).

scan_protocol: Microarray slides were scanned using a G2565CA microarray scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: The scanned images were analyzed with the Feature Extraction Software 12.0.0 (Agilent).

source_name: liver tumor

label_protocol: 1µg of the isolated genomic DNA was digested and labeled by random primer with Cyanine 5-UTP (liver tumor) or Cyanine 3-UTP (reference: liver) using the Agilent Genomic DNA Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer´s protocol.

growth_protocol: The animals were maintained in a specific pathogen-free environment with food and water ad libitum. Mice were housed in individually ventilated cages with a 12 hour day/night cycle.

extract_protocol: Genomic DNA was isolated from liver and liver tumor tissue according to standard phenol-chloroform extraction protocol.

treatment_protocol: non treated mice

tag: genotype

tag: gender

value: male

value: liver tumor

source_name: spleen

value: spleen


title: 1601T1_Liver tumor_Trp53-/-


title: MV31_C.IonXpressRNA_001

source_name: Control cells rep 1


title: 2103T1_Liver tumor_Trp53-/-


title: 1698T1_Liver tumor_Trp53-/-


title: 5_OFB: OB_A4_Con3512

tag: Sex

value: F


title: 5_OFB: ROB_A4_Con3512


title: 5_OFB: OB_A29_PD3508


title: 5_OFB: OB_A3_Con3363


title: 5_OFB: OB_A28_PD3531


title: 5_OFB: OB_A27_Con3453


title: P19_shPerk

first: Zhang

last: Yin

address: Xin Gang West 135

institute: Sun Yat-sen University

description: Small RNA Seq

data_processing:
The raw data (raw reads) from Illumina HiseqTM 2500 sequencing were filtered by removing the joints at both ends of the reads and removing the fragment length <17nt.
Clean reads were compared with the reference genome to obtain the distribution map of whole-genome reads.
Clean reads were classified and annotated for ncRNA classification, and miRNA expression clustering was calculated for the identified miRNA. miRNA differential expression was analyzed between samples.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.miRNA.txt: miRNA profile and fold change.

source_name: P19, shPerk

extract_protocol:
Total RNA was extracted from C2C12 cells or P19 cells with TRIzol reagent according to the manufacturer’s instruction.
The total RNA or purified SRNA fragments of the samples were extracted and connected to the 3-terminal and 5-terminal joints first and then reverse-transcribed into cDNA. PCR amplification was carried out and then the gel was cut to recover the target fragment library. Computer sequencing was performed on the library that passed the quality inspection.

tag: cell line

tag: treatment

value: shPerk


title: C2C12_shPerk_D3

description: Small RNA Seq

source_name: C2C12, shPerk, D3

tag: time point


title: C2C12_ATF4

description: Small RNA Seq

source_name: C2C12, ATF4

value: ATF4 overexpression


title: C2C12_vector

description: Small RNA Seq

source_name: C2C12, vector

value: vector


title: C2C12_shPerk_D0

description: Small RNA Seq

source_name: C2C12, shPerk, D0


title: 5_OFB: OB_A24_Con3511

tag: tissue

tag: subject id


title: 5_OFB: OB_A25_Con3454

tag: replicate

tag: group


title: 5_OFB: OB_A23_Con3455

tag: pmi


title: C2C12_shNC_D0

description: Small RNA Seq

source_name: C2C12, shNC, D0

value: shNC


title: 5_OFB: OB_A22_PD3440

source_name: OFB

value: olfactory bulb

tag: age


title: 5_OFB: OB_A21_Con3547


title: 5_OFB: OB_A13_PD3441


title: 5_OFB: OB_A12_Con3446

value: Yes


title: 5_OFB: OB_A15_PD3554


title: RTOC_spDCs_2

city: Braunschweig

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Tophat2 (V1.20) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq)
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization. Cook distance cutoff filter disabled
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: CSV format with raw read counts per gene; htseqcounts*.rpkm files: CSV format with RPKM normalized read counts per gene;  DESeq2_genes_diffexp*.xls: XLS files with differentially expressed genes

growth_protocol: RTOCs were generated from single-cell suspensions of thymi isolated from E14.5 to E16.5 fetuses of Foxp3hCD2 reporter mice (BALB/c background) and 0.15x106 sorted sp‑DCs or t‑DCs were added to the 0.65x106 cells from the fetal thymi before pelleting.

extract_protocol: Sp‑DCs and t‑DCs were isolated from 4-8 weeks old CD45.1xBALB/c mice by fluorescence-activated cell sorting. T‑DCs were sorted as CD49b-F4/80-CD90.2-CD45.1+CD11chi cells and sp‑DCs were sorted as CD49b-F4/80-CD3-CD19-CD45.1+CD11chi. Total RNA was isolated using the RNeasy® Mini Kit (Qiagen).

tag: strain

value: DCs

tag: isolation method

value: re-isolated from d2 RTOC


title: ex_vivo_spDCs_1

value: ex vivo isolated


title: ex_vivo_spDCs_2


title: ex_vivo_tDCs_3

source_name: thymus


title: RTOC_spDCs_3


title: ex_vivo_spDCs_3


title: 5_OFB: OB_A11_PD3461

value: M


title: RTOC_spDCs_1


title: ex_vivo_tDCs_1


title: 5_OFB: OB_A1_Con3551

value: No


title: 5_OFB: OB_A10_Con3452

value: CTRL


title: P19_shNC

description: Small RNA Seq

source_name: P19, shNC


title: C2C12_shNC_D3

description: Small RNA Seq

source_name: C2C12, shNC, D3


title: RTOC_tDCs_2


title: RTOC_tDCs_1