title: Disomes – Mutant

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

institute: UNIL

data_processing:
Library strategy: Ribosome footprinting
Read adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were trimmed using cutadapt (v 2.5) with the following options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30. Reads where quality filtered using  fastx_toolkit (-Q33 -q 30 -p 90)
UMI were extrracted from each read with UMItools  “extract” with the following options: --extract-method string --bc-pattern NNNNNNNNCCCCC --3prime --filter-cell-barcode --error-correct-cell –log2stderr
reads were then mapped to rRNA and tRNA databases to remove contaminants using bowtie2 (-p 2 -L 15 -k 20 --trim5 2) and to SARS-CoV-2 genome
Barcode indexing and deduplication was performed with UMItools “group” (--method=directional --per-cell –read-length) and in-house scripts
Genome_build: Sars-CoV-2 genome assembly 92 , NC_045512.2
Supplementary_files_format_and_content: WIG files containing read coverage along the transcript

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Rabbit Reticulocyte lysate

extract_protocol:
50µl Rabit reticulocyte lysate were digested in 1 volume of MNase buffer (5 mM CaCl2, 100 mM NaCl, 20 mM Tris-HCl pH 7.5, 10 mM MgCl2, 5 mM DTT) with 750 U MNase (NEB) for 45 min at room temperature. The samples were further digested in 2 volumes of lysis buffer (150 mM NaCl, 20 mM Tris-HCl pH 7.4, 5 mM MgCl2, 5 mM DTT, 1% Triton X-100, 0.5% Sodium deoxycholate, complete EDTA-free protease (Roche) and 40 U/ml RNasin plus (Promega))  with 100 U RNase I (Ambion) for 45 min at room temperature. Digested samples were passed over size exclusion columns for ribosome purification prior to RNA extraction and library preparation.
Sequencing libraries were generated using custom-designed riboPOOL (SiTools) and protocol adapted from previously reported protocols (Arpat et al., 2020; PMID 32703885 and McGlincy and Ingolia, 2017; PMID 28579404).

treatment_protocol: SARS-CoV-2 was mutated as follows:  The mutation site is from base 13466 to 13468 where the triplet AAC has been mutated to TAA (a stop codon).

tag: strategy

value: In-vitro translation

tag: experiment performed in

value: Rabbit Reticulocyte cells

tag: genotype

value: SARS-CoV-2 Mutant

tag: molecule subtype

value: Disome footprints


title: 4 dpt mock R2

status: Public on May 17 2021

type: SRA

city: Zürich

first: Susanne

last: Dora

address: Universitätsstrasse 2

department: D-Biology, Institute for molecular plant biology

country: Switzerland

institute: ETH Zürich

library_source: transcriptomic

data_processing:
sequenced reads were trimmed for low-quality bases with Trimmomatic, version 0.36
sequencing adapters were removed with Flexbar, version 3.0.3
Reads were mapped against the Arabidopsis thaliana genome (TAIR10) with STAR version 2.6.1c
Reads were mapped against the Fusarium oxysporum 5176 genome (Fokkens et al., 2020, G3) with STAR version 2.6.1c
Uniquely mapped reads were counted by featureCounts, based on the R package Rsubread (version 1.32.1)
Genome_build: ASM1311235v1
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files include the raw counts of reads mapped uniquely against the reference genomes in .txt format.
Supplementary_files_format_and_content: Processed data files include the normalized counts per million for the samples and time points used afterwards to draw conclusions (counts were normalized using trimmed means of M-values (TMM) normalization in EdgeR version 3.24.3; Robinson and Oshlack, 2010)
Supplementary_files_format_and_content: Samples and time points taken into account to calculate differential gene expression in Fusarium oxysporum 5176 using the protocols described for EdgeR. Reads are normalized to counts per million using the TMM-method described by Robinson and Oshlack, 2010.
Supplementary_files_format_and_content: Samples and time points taken into account to calculate differential gene expression in Arabidopsis thaliana Col-0 using the protocols described for EdgeR. Reads are normalized to counts per million using the TMM-method described by Robinson and Oshlack, 2010.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Arabidopsis seeds were germinated at 24° C, long day conditions, on 2 mm foam plugs suspended on 200 ml  ½ MS + 1% sucrose media in 330ml pots at pH 5.7 adjusted by KOH. The media was exchanged 6 days after germination to ½ MS and seedlings were further grown.

extract_protocol:
For Fo5176 transcriptomics in the absence of a plant host, 107 microconidia/ml were germinated in ½ MS + 1% (w/v) sucrose overnight at 180rpm at 28°C in the dark. The germinated microconidia were harvested via two centrifugation steps at 4000 xg for 15 minutes at 10° C, washed twice with water, discarding supernatant in between washes.
3’mRNA-libraries were prepared using the 3’mRNA-Seq library Prep Kit (QuantSeq, Lexogen). The manual from the supplier was followed with the following modifications. At least 1 µg RNA was used as input. For first strand synthesis of cDNA the incubation time at step 4 was increased to 60 min. For library indexing and amplification 13-17 amplification cycles of the given PCR were used depending on the amount of input RNA. 17 µl of the purified library was transferred to a fresh tube. The finished libraries were stored at -20° C until quality control and pooling.

treatment_protocol: For hydroponic infections, the roots of 10-day-old seedlings were infected with 20µl of a solution containing 107 microconidia/ml Fo5176. All pots were incubated for 30 minutes at 100 rpm on a rotary shaker. The media of the infected plants was then replaced with fresh ½ MS media. The plants were further grown under the same conditions until the roots were harvested for RNA extraction or for imaging at 0, 1, 2, 3, 4, and 6 days post treatment. For Fo5176 transcriptomics in the absence of a plant host, 107 microconidia/ml were germinated in ½ MS + 1% (w/v) sucrose overnight at 180rpm at 28°C in the dark. The germinated microconidia were harvested via two centrifugation steps at 4000 xg for 15 minutes at 10° C, washed twice with water, discarding supernatant in between washes.

tag: ecotype

tag: tissue

value: whole root

tag: treatment

value: untreated

tag: days post treatment


title: Disomes – Wild type

molecule: total RNA

value: Wildtype


title: WT_5_RNA

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

country: USA

institute: FHCRC

description: Wild type sample , total RNA, replicate5

data_processing:
Library strategy: Ribo-Seq
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

organism: Homo sapiens

source_name: Normal prostate tissue

growth_protocol: Tissues were obtained as frozen chunks, and manually pulverized before lysis

extract_protocol:
Total RNA and ribosome-protected RNA were extracted following the protocol in the TruSeq Ribo Profile kit from Illumina
RNA libraries were prepared for sequencing following the protocol in the TruSeq Ribo Profile kit from Illumina

value: Normal prostate

tag: genotype/variation

value: wild type/ normal


title: 3 dpt inf R2

value: Fusarium oxysporum 5176


title: EC_DNA_AGM_cell34

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

country: China

institute: Peking University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.

molecule: genomic DNA

organism: Mus musculus

source_name: aorta-gonad-mesonephros (AGM)

extract_protocol:
Following CoTECH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Organs were digested with 0.06 Collagenase II + 0.08% Trypsin and 0.09% Collagenase II + 0.12% Trypsin  at 37 °C.

tag: cell type

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)

tag: strain

tag: antibody


title: 3 dpt mock R2


title: WT_4_RNA

description: Wild type sample , total RNA, replicate4


title: 2 dpt inf R2


title: 6 dpt inf R2


title: EC_DNA_AGM_cell38


title: shLuc N4

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

data_processing:
Reads were aligned to the genome using STAR v2.5.3a
Gene abundances were estimated using RSEM v1.3.0 with parameters "--star --forward-prob 0 --paired-end"
Genome_build: mm10/GRCm38, GENCODE M24 annotation
Supplementary_files_format_and_content: The processed data file for each sample is the gene-level abundance output of RSEM and is a tab-delimited text file

organism: Mus musculus domesticus

source_name: shLuc-infected GFP+ erythroid progenitor cells (CD71intTer119-) and proerythroblasts (CD71int/+Ter119-)

growth_protocol: Cultured for 2 days in erythroid expansion media

extract_protocol:
GFP+ erythroid precursors (CD71intTer119-) and proerythroblasts (CD71int/+Ter119-) were purified by cell sorting. RNA was extracted using Trizol reagent.
SMARTer Stranded Total RNA-Seq Kit v2 - Pico (#634411)

treatment_protocol: Fetal livers were dissociated, lineage depleted and infected with retroviral vectors containg shRNAs.

tag: id of strain

tag: age

tag: age id

value: liver

tag: tissue id

value: erythroid progenitor cell; proerythroblast

tag: cell type id

tag: shRNA target

value: Luc


title: WT_3_RNA

description: Wild type sample , total RNA, replicate3


title: EC_DNA_AGM_cell32


title: EC_DNA_AGM_cell33


title: 2 dpt mock R2


title: WT_2_RP

description: Wild type sample, Ribosome bound RNA, replicate2

data_processing:
Library strategy: Ribo-Seq
Library strategy: Ribo-Seq
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.


title: WT_2_RNA

description: Wild type sample , total RNA, replicate2


title: Monosome – Mutant

tag: strategy

tag: experiment performed in

value: Ribosome footprints


title: EC_DNA_AGM_cell31


title: 1 dpt inf R2


title: WT_1_RNA

description: Wild type sample , total RNA, replicate1


title: EC_DNA_AGM_cell30


title: 1 dpt mock R2


title: shLuc N1


title: shLuc N2


title: EC_DNA_AGM_cell29


title: Monosome – Wild Type

tag: genotype

tag: molecule subtype


title: Pn-liver-rep3

city: Cambridge

first: Sudhakaran

last: Prabakaran

address: Downing Site, CB2 3EH, UK

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

data_processing:
HISAT2 2.1.0 for the alignment of reads to their respective genomes.
The aligned reads were assembled using Stringtie and their respective reference genome. The assembled transcriptomes for each biological replicate were merged using Stringtie merge utility to produce one transcriptome per tissue per species.
The assembled transcriptomes were filtered to remove unexpressed and duplicated transcripts. Ballgown's v2.10.0 k-mean clustering was used to reduce the number of highly similar transcripts. The transcripts were clustered within each locus and transcripts within each cluster were merged by taking union of the exon-coordinates of the individual transcripts. The minimum number of clusters was used at each locus such that at least 90% of the within-locus variation was retained.
Genome_build: ASM185804v2, PunNye1.0
Supplementary_files_format_and_content: ctab files generated by Stringtie are tab seprated files that include FPKM estimates

organism: Pundamilia nyererei

source_name: Pn-liver

growth_protocol: Tank-reared, P. nyererei (generation 1; Lake Victoria) and O. niloticus (generation ~93; Manzala, Egypt)

extract_protocol:
Total RNA was isolated using TRIzol (ThermoFisher) and then treated with DNase (TURBO DNase, ThermoFisher) to remove any DNA contamination.
Quality and quantity of total RNA extracts were determined using NanoDrop spectrophotometer (ThermoFisher), Qubit (ThermoFisher) and BioAnalyser (Agilent). Following ribosomal RNA depletion (RiboZero, Illumina), stranded rRNA-depleted RNA libraries (Illumina) were prepped and sequenced (paired-end 75bp-long reads) on HiSeq2500 V4 (Illumina). On average, 11.82±0.42Mio paired-end reads were generated.

treatment_protocol: 5-10mg of fresh liver tissue were snap-frozen upon dissection and were homogenized and used for RNA extraction.

tag: generation

tag: location

value: Lake Victoria

tag: Sex

value: male

tag: tissue


title: shExosc10 N4

source_name: shExosc10-infected GFP+ erythroid progenitor cells (CD71intTer119-) and proerythroblasts (CD71int/+Ter119-)

tag: cell type


title: Pn-liver-rep2


title: shExosc10 N3

tag: strain


title: Pn-liver-rep1


title: 0 dpt mock R2

tag: ecotype

tag: treatment

tag: days post treatment


title: 0 dpt inf R2


title: shLuc N3

tag: id of strain

tag: age

tag: age id


title: EC_DNA_AGM_cell27

tag: antibody


title: 6 dpt inf R1


title: shExosc10 N2

tag: tissue id

tag: cell type id

tag: shRNA target


title: Edema rep5

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs). Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 1.2.2, with default parameters, was used for alignment on the reference genome (Mycobacterium ulcerans Agy99, CP000325.1, from NCBI)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g ID -s 1).
Count data were analyzed using R version 3.3.1 and the Bioconductor package DESeq2 version 1.12.3. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed without applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure  and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: Mycobacterium ulcerans Agy99, CP000325.1, from NCBI
Supplementary_files_format_and_content: Count matrix from DESeq2

organism:
Mycobacterium ulcerans
Mus musculus

source_name: Mice infected tail skins

extract_protocol:
RNA was extracted from infected tail skin at the edema stage (30 days post-infection) and at the healing stage (60-75 days post-infection), by the differential lysis method, as previously described (Robbe-Saule M and al., An Optimized Method for Extracting Bacterial RNA from Mouse Skin Tissue Colonized by Mycobacterium ulcerans. Front Microbiol. 2017;8:512).
Ribosomal RNA was first removed from the total RNA using the RiboZero Epidemiology Illumina kit and the libraries were prepared with the TruSeq Stranded Total RNA LT Sample Prep kit (Illumina), according to manufacturer’s protocol respectively. The quality of all libraries was checked with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 1.0 fluorometer (Invitrogen). Clusters were generated for the resulting libraries, with Illumina HiSeq SR Cluster Kit v4 reagents. Sequencing was performed with the Illumina HiSeq 2500 system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven indexing cycles, to obtain 65-bp single-end reads. Sequencing data were processed with Illumina Pipeline software (Casava version 1.9).

tag: strain (mice)

value: FVB/N

tag: strain (bacteria)

value: Mycobacterium ulcerans strain 01G897

value: Mice infected tail skins

tag: infection stage

value: Edema stage


title: EC_DNA_AGM_cell26


title: 6 dpt mock R1

value: whole root

value: untreated


title: Edema rep4


title: shExosc10 N1


title: shDis3 N4

source_name: shDis3-infected GFP+ erythroid progenitor cells (CD71intTer119-) and proerythroblasts (CD71int/+Ter119-)


title: EC_DNA_AGM_cell25


title: 4 dpt inf R1


title: Healed rep3

value: Healing stage


title: Healed rep2


title: EC_DNA_AGM_cell24


title: 4 dpt mock R1


title: EC_DNA_AGM_cell23


title: 3 dpt inf R1


title: EC_DNA_AGM_cell28


title: shDis3 N2


title: Healed rep1


title: 3 dpt mock R1


title: shDis3 N1


title: Edema rep3


title: EC_DNA_AGM_cell22


title: EC_DNA_AGM_cell21


title: 0.6mM As (III) treated rep 2

city: Chandigarh

first: Prabhu

middle: B

last: Patil

state: Chandigarh

address: Sector 39 A

country: India

institute: CSIR Institute of Microbial Technology Chandigarh

description: Cells treated with 0.6mM arsenate As (III)

data_processing:
Basecalling,demultiplication and adaptor treaming was performed by Illumina HiSeq control software
Quality of raw reads was assessed by using FastQC tool
Clean reads that passed the quality filter were mapped to the reference genome (X. oryzae pv. oryzae IXO1088 accession number CP040687) using EDGE pro (version-1.3.1).
Differential gene expression analysis of treated samples with respect to control was performed using DESeq program.
Genome_build: NZ_CP040687
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Xanthomonas oryzae pv. oryzae

source_name: bacteria

growth_protocol: Strains were grown in nutrient broth media at 28̊ C at 180 rpm to an OD600 of 1.0. One percent of the aliquot was added to the fresh media and grown-up to OD600=0.4; then cultures were treated with different concentrations of arsenate (0.5mM and 1mM) or arsenite (0.6mM) for 30 minutes.

extract_protocol:
The cells were harvested by centrifugation at 6,000g for 5min for RNA isolation and then lysed using Trizol reagent. Total RNA was isolated using Direct-zol RNA MiniPrep kit (Zymo Research Corporation, Orange, CA, USA)
The rRNA was removed using ‘si-tools Pan-prokaryote ribopool probes,’ and further library preparation was done using TruSeq Stranded RNA library prep kit. Prepared libraries were sequenced using Illumina HiSeq x10 platform, and 150-bp paired-end reads were generated.

treatment_protocol: Cells were grown-up to OD600=0.4; then cultures were treated with different concentrations of arsenate (0.5mM and 1mM) or arsenite (0.6mM) for 30 minutes. Culture without treatment was used as control. The cells were harvested by centrifugation at 6,000g for 5min for RNA isolation.

tag: phase

value: exponential phase

value: treated [0.6mM As (III)]


title: EC_DNA_AGM_cell20

value: endothelial cells

tag: tissue


title: 2 dpt mock R1


title: EC_DNA_AGM_cell19

tag: cell type

value: aorta-gonad-mesonephros (AGM)


title: 0.6mM As (III) treated rep 1

tag: strain


title: 1 dpt inf R1

tag: ecotype

value: Fusarium oxysporum 5176


title: Edema rep1


title: in vitro Fo R2

organism: Fusarium oxysporum

source_name: Microconidia

value: Fo 5176 microconidia

tag: treatment

value: in vitro


title: 1mM As (V) treated rep 2

description: Cells treated with 1mM arsenate As (V)

value: treated [1mM As (V)]


title: shDis3 N3

value: liver

value: erythroid progenitor cell; proerythroblast


title: EC_DNA_AGM_cell18


title: 1mM As (V) treated rep 1

description: Cells treated with 1mM arsenate As (V)


title: in vitro Fo R1

tag: days post treatment


title: EC_DNA_AGM_cell17


title: 0.5mM As (V) treated rep 2

description: Cells treated with 0.5mM arsenate As (V)

value: treated [0.5mM As (V)]


title: 1 dpt mock R1


title: 0.5mM As (V) treated rep 1


title: Fat body-HSD-5#

city: Hangzhou

first: Danping

last: Chen

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang Univerisity

data_processing:
raw reads were mapped on dm3 genome by TopHat using the default settings. We counted the uniquely mapped reads in the exon regions of genes and calculate the RPKM values of the genes based on these reads.
Genome_build: Drosophila melanogaster genome (r3)
Supplementary_files_format_and_content: RPKM was used to quantify gene expression for each sample

organism: Drosophila melanogaster

source_name: Fat body-HSD

growth_protocol: Flies were cultured in normal food or high sugar diet for 5d.

extract_protocol:
The total RNA was harvested using the RNeasy Mini kit, subjected to poly(A) mRNA isolation, cDNA synthesization, library preparation (NEBNext Ultra RNA Library Prep Kit for Illumina, NEB, NEB)
RNA libraries were prepared for sequencing using standard NEB protocols.

treatment_protocol: The brains and fat body were harvest directly.

value: Oregon-R

tag: genotype/variation

value: WT

value: high sugar diet

value: Fat body


title: 2 dpt inf R1

value: whole root


title: 0 dpt inf R1


title: EC_DNA_AGM_cell15


title: Edema rep2

value: FVB/N

value: Mycobacterium ulcerans strain 01G897

value: Mice infected tail skins

value: Edema stage


title: Fat body-HSD-3#

tag: age


title: control rep 2

description: Control cells without  treatment

value: exponential phase

value: untreated


title: EC_DNA_AGM_cell16

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: control rep 1

description: Control cells without treatment


title: Fat body-HSD-2#


title: EC_DNA_AGM_cell13


title: EC_DNA_AGM_cell14


title: HeLa METTL5-KO clone 7

city: New Haven

first: Sigrid

last: Nachtergaele

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

data_processing:
Base calling was performed with Illumina bcl2fastq software.
Quality of sequenced reads was assessed with FastQC v0.11.5.
Adapter trimming and quality filtering was performed with Cutadapt.
For RNA-seq analysis, R1 files were aligned to the human genome hg19 using hisat2 v2.1.0, and resulting bam files were ssorted with samtools version 1.7.
DESeq2 and R v4.0.3 were used to analyze bam files and measure differential expression between wild type and METTL5-KO HeLa cells.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes gene name, baseMean, log2FoldChange, log2FoldChange standard error (SE), stat (Wald statistic), pvalue, and padj.

source_name: HeLa METTL5-KO clone 7 cells

growth_protocol: Replicates of wild type and METTL5-KO HeLa cells were grown to confluency prior to lysis in Trizol.

extract_protocol:
RNA was extracted using Trizol followed by choloroform extraction and isopropanol precipitation.
Sequencing libraries were prepared using RT-1306 as described in Zhou et al Nature Methods 2019 (PMID 31548705).

tag: cell line

value: HeLa

tag: genotype


title: Fat body-HSD-1#


title: EC_DNA_AGM_cell12

tag: antibody


title: Fat body-ND-5#

source_name: Fat body-ND

value: normal food diet


title: HeLa METTL5-KO clone 1

source_name: HeLa METTL5-KO clone 1 cells


title: 0 dpt mock R1


title: EC_DNA_AGM_cell11


title: Fat body-HSD-4#


title: HeLa WT replicate 3

source_name: Wild type HeLa cells


title: EC_DNA_AGM_cell10


title: HeLa WT replicate 2


title: Fat body-ND-4#


title: Fat body-ND-3#


title: EC_DNA_AGM_cell8


title: EC_DNA_AGM_cell7


title: EC_DNA_AGM_cell9


title: HeLa WT replicate 1


title: Fat body-ND-2#


title: Brain-HSD-5#

source_name: Brain-HSD

value: Brain


title: peritoneal macrophages from Fra-1ΔMxCre mice  (2)

type: RNA

city: Erlangen

first: Aline

last: Bozec

address: Ulmenweg 18

country: Germany

institute: Universitätsklinikum Erlangen, Department of Internal Medicine 3 – Rheumatology and Immunology

description: thioglycollate elicited peritoneal macrophages

hyb_protocol: following fragmentation, 600ng of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 8x60K Agilent Mouse Gene Expression_v2 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.6.6)

scan_protocol: Microarrays were scanned using Agilent G2565C Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.7.1 (Agilent Technologies Germany). Data extraction using protocol GE1_1105_Oct12

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.5 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in all replicates in at least one conditions were selected by filtering and subjected to an One-Way-ANOVA test (p-value </= 0.05) corrected by Bejamini-Hochberg-FDR). Entities differentially expressed mean an at least 2-fold change in expression level in all c-JunΔMx compared to wild-type macrophages were further analysed.

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 50ng total RNA (One-Color Microarray-based gene expression analysis v.6.65)

growth_protocol: The mice were bred and maintained on a 129/C57Bl6 background. Littermate mice were used as wild-type controls. All experiments were performed with male or female mice at the age of 8 weeks. Animals were housed in standardized conditions following the guidelines of the German Animal Welfare Act. Animals were kept in a standard diet and water ad libitum and kept with a 12 hour day/night cycle. All experiments with animals are authorized by the local ethics committee.

extract_protocol: RNeasy Mini Kit, Cat no 74104, Qiagen

tag: background

value: Fra-1lox/lox MxCre-/+

value: peritoneal macrophages


title: peritoneal macrophages from wild-type mice  (8)

value: wild-type Fra-1lox/lox


title: peritoneal macrophages from wild-type mice  (4)


title: Fat body-ND-1#

value: Oregon-R

value: WT


title: peritoneal macrophages from Fra-2ΔLysMCre mice  (3)

value: Fra-2lox/lox LysMCre-/+


title: Brain-HSD-4#

value: high sugar diet


title: peritoneal macrophages from Fra-2ΔLysMCre mice  (16)


title: peritoneal macrophages from Fra-1ΔMxCre mice  (10)


title: peritoneal macrophages from wild-type mice  (14)

value: wild-type Fra-2lox/lox


title: EC_DNA_AGM_cell5


title: peritoneal macrophages from wild-type mice  (5)


title: MiaPaCa2_NTC_Control

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

data_processing:
https://github.com/ENCODE-DCC/chip-seq-pipeline
Map reads with BWA-0.7.12
Post-alignment filtering steps were carried out using samtools-1.355 with MAPQ threshold of 30
Duplicate removal was performed using picard-tools-1.88
Peak enrichment were computed using phantompeakqualtools  implementing the SPP algorithm
Replicate consistency and peak ranking determined by irreproducible discovery rate (IDR) using the IDR-2.0.2 tool
Genome_build: hg38
Supplementary_files_format_and_content: TAR of BED of the IDR peaks for each replicate compared to the matching non-antibody control

source_name: MiaPaCa2 cells

growth_protocol: DMEM basal media (Gibco) supplemented with high glucose  GlutaMax (Gibco)  and penicillin/streptomycin

extract_protocol:
ChIP-seq protocol  Myers Lab: https://www.encodeproject.org/documents/73c95206-fc02-41ea-93e0-a929a6939aaf/
ChIP-seq protocol  Myers Lab; used antibodies: Santa Cruz Biotechnologies sc-81598 HDAC1(10E2) and Invitrogen HDAC1 Polyclonal Antibody PA1-860

treatment_protocol: MiaPaCa2 containg lentiMPHv2 plasmid were co-transfected with psPAX2  pMD2G  and lentiSAMv2 lentiviral plasmids containing NTC1  NTC2  or HDAC1 using Lipofecatming 2000 Transfection Reagent (ThermoFisher)

value: No antibody control with scrambled non-targeting sgRNA

tag: replicate #

tag: chip antibody


title: MiaPaCa2_e7_Control

value: No antibody control with HDAC1 activation sgRNA


title: alveolosphere in patient 8 with mock infection

city: Shinjuku-ku

first: Toshiki

last: Ebisudani

state: Tokyo

address: Shinanomachi 35

department: Organoid medicine

country: Japan

institute: Keio University

data_processing:
Adaptors were removed from raw fastq files with cutadapt (version 1.18).
Reads were aligned to hg38 using STAR (version 2.6.1b) and gene expression levels were estimated using RSEM (version 1.3.3).
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: Alveolosphere

growth_protocol: Human alveolospheres and airway organoids were cultured from single cells for 7–14 days in the identical culture medium containing Afamin-Wnt-3A, R-spondin-1, EGF, Noggin and A83-01.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN) for alveolosphere and airway organoid and the Direct-zol RNA MicroPrep Kit (Zymo Research) for SARS-CoV-2 and mock-infected alveolosphere according to the manufacturer's instructions.
Sequence library was prepared with TruSeq RNA Library Prep Kit v2 (Illumina).

value: Alveolosphere

tag: infection

value: mock


title: alveolosphere in patient 8 with SARS-CoV-2 infection


title: MiaPaCa2_e7_Santa Cruz, rep2

value: HDAC1 activation sgRNA

value: Santa Cruz Biotechnologies sc-81598 HDAC1(10E2)


title: alveolosphere in patient 5 with mock infection


title: 06-134M5_CRPC_LN

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome using STAR.v2.7.3a.
Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_processed_data.txt: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: CRPC lymph node (LN) metastasis

extract_protocol:
Total RNA was isolated from CRPC metastases frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) with RNA STAT-60 (Tel-Test). Using an H&E stained slide for each metastatic site for orientation, one millimeter core punches of tumor were obtained, or where appropriate multiple sections enriched for tumor were cut using a Leica CM3050S cryostat. Total RNA was isolated from cell line samples using the RNeasy Mini Kit (Qiagen, cat#74134) with DNase digestion.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

tag: gender

value: male

value: prostate cancer

tag: tumor site

value: lymph node (LN)

tag: patient

tag: molecular phenotype


title: MiaPaCa2_e7_Santa Cruz, rep1


title: Brain-HSD-2#

tag: strain

tag: tissue

value: Brain


title: EC_DNA_AGM_cell4

source_name: aorta-gonad-mesonephros (AGM)

tag: cell type

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: Brain-HSD-3#

value: Oregon-R

tag: treatment


title: airway organoid in patient 11

source_name: Airway organoid

value: Airway organoid


title: EC_DNA_AGM_cell3


title: airway organoid in patient 10


title: Brain-HSD-1#

tag: genotype/variation

value: WT


title: EC_DNA_AGM_cell2


title: Brain-ND-5#

source_name: Brain-ND

tag: age

value: normal food diet


title: EC_DNA_AGM_cell6


title: MiaPaCa2_NTC_Santa Cruz, rep2

tag: cell line

value: Scrambled non-targeting sgRNA


title: alveolosphere in patient 5 with SARS-CoV-2 infection


title: MiaPaCa2_NTC_Santa Cruz, rep1


title: MiaPaCa2_e7_Invitrogen, rep2

value: Invitrogen HDAC1 Polyclonal Antibody PA1-860


title: Brain-ND-3#


title: EC_DNA_AGM_cell1


title: Brain-ND-2#


title: IL-4-negative Lung

city: Denver

first: Richard

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

institute: National Jewish Health

description:
10x_rawData.txt
10x_scaledData.txt

data_processing:
Raw FASTQ files were demultiplixed, mapped, and quantified using CellRanger (verison 2.1.0, )
All post-quantification quality control and analysis was performed using the Seurat analysis suite. For each cell, we quantified four library/sequencing quality metrics: the number of genes for which at least one read was mapped, the total number of UMIs, the % of total UMIs which mapped to mitochondrial genes, and % of total UMIs which mapped to ribosomal genes.  All cells which had between 500 and 4500 unique expressed genes, between 1000 and 30000 UMIs, less than 5% mitochondrial UMIs, and greater than 20% ribosomal UMIs were used for downstream analysis. Expression values Ei,j for gene i in cell j were calculated by dividing UMI count values for gene i by the sum of the UMI counts in cell j, to normalize for differences in coverage, and then multiplying by 10,000 to create TPM-like values, and finally calculating log2(TPM+1) values.
Genome_build: mm10
Supplementary_files_format_and_content: Text files containing gene counts and metatadata describing the sample time for each cell

source_name: CD4 T cell from lung

extract_protocol:
CD4+ T cells were sorted into single cell suspensions and sample RNA was isolated using the Quick-RNA Microprep kit (Zymo Research) according to the manufacturer’s protocol.
Single cell RNA sequencing was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10x Genomics) according to the manufacturer’s protocol using the Chromium Controller. Single cell libraries were sequenced on an Illumina Novaseq 6000.

value: Lung

value: N. brasiliensis infection

tag: day post infecton

value: Day 9


title: IL-4-positive Lung

description:
10x_rawData.txt
10x_scaledData.txt


title: Brain-ND-4#


title: IL4-negative lymph node

description:
10x_rawData.txt
10x_scaledData.txt

source_name: CD4 T dells from mediastinal lymph node

value: Mediastinal lymph node


title: alveolosphere in patient 3

value: Alveolosphere


title: MiaPaCa2_NTC_Invitrogen, rep1


title: IL4-positive lymph node

description:
10x_rawData.txt
10x_scaledData.txt


title: MiaPaCa2_e7_Invitrogen, rep1

value: HDAC1 activation sgRNA


title: MiaPaCa2_NTC_Invitrogen, rep2


title: alveolosphere in patient 1


title: Dark.Day14.R2

status: Public on May 16 2021

city: Medellin

first: Adriana

middle: Gallego

last: Rua

state: Antioquia

address: Carrera 53 No. 61-30

department: Antioquia

country: Colombia

institute: Universidad de Antioquia

data_processing:
Illumina HiSeq 2500 software used to base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Theobroma cacao V2 whole genome using hisat2.
To count reads at gene level in the stranded mode and assigning sequence reads to genomic features we used the program "feature counts" according to Liao Y1, Smyth GK, Shi W. 2014, Bioinformatics. To quantifying abundances of transcripts from RNA-Seq data, we used kallisto programm with parameters  -b 100 --single -l 180 -s 20 -t 5  --rf-stranded
To quantifying differential expression, we used DESEq2 package according to Love MI, Huber W, Anders S (2014), Genome Biology
Genome_build: Theobroma_cacaoV2
Supplementary_files_format_and_content: Tab-delimited text files include row counts for each Sample

organism: Theobroma cacao

source_name: plant cell suspensions

growth_protocol: Mature, eight-month-old cacao pods of the Trinitario ecotype (coded as BIOA) were collected in the commercial crops of Compañía Nacional de Chocolates, during the 2016 harvest in the region of San Vicente de Chucurí- Santander, Colombia (06° 53' 00"N; 73° 24' 50" W). Cacao cell suspensions were induced following Gallego et al.48. The cultures were maintained at 23 ± 2°C under cool-white fluorescent lamps (12 µmol m−2. s −1) for 16 hours light at 100 rpm. After 12 days, cell suspensions were filtered using a 300 µm mesh and an inoculum (4g/L dry weight) was used for establishing cultures. These were sub-cultured every 7 days under dark conditions in order to prepare the suspensions for light treatments (see below). Media composition was prepared according to Gallego et al

extract_protocol:
Four replicates were sampled at each time point (d0, d1, d7, d8 and d14) from the W-B and D treatments for total of 36 samples. Total RNA was extracted from each cell suspension taking 0.1mL approximately of pellet volume using combined protocols of PureLink Plant RNA Reagent (Ref: 12322012, Thermo Fisher Scientific) and RNeasy Plus Universal Mini Kit (Cat No. 73404, QIAGEN) following the manufacturer’s protocol. RNA concentrations and quality were measured using an Agilent 2100 bioanalyzer. The construction of the cDNA libraries and RNAseq were performed by the Genomics Core Facility at Penn State University (University Park, USA). cDNA libraries were prepared with a TruSeq stranded mRNA library prep Kit (cat# RS-122-2101, Illumina, San Diego, CA, USA). The libraries were sequenced on a HiSeq™ 2500 (Illumina) using single-end runs of 100 nt.
Library construction was done following the TruSeq® Stranded mRNA Sample Preparation Guide by Illumina available in https://support.illumina.com/downloads/truseq_stranded_mrna_sample_preparation_guide_15031047.html

treatment_protocol: Cell suspension cultures were exposed to two light treatments during a time course of 14 days using light-emitting diode (LED) lights. In the first treatment, we evaluated a sequential exposure to white LED followed by exposure to blue LED 7 days each (W-B). In the second treatment, cells were kept in the dark for 14 days (D). In both treatments, the day 0 was considered as the reference point for flavonoid production and fresh media was added on day 7. White and blue LED arrays were designed to give an intensity of 60 µmol m-2s-1 under a photoperiod of 16 hours light and 8 hours dark. Erlenmeyer flasks of 100 mL containing 30 mL of cells were sampled at days 0, 1, 7, 8 and 14 during the time course. Four replicates were collected for each time point and treatment (W-B and D).

value: Dark


title: White.Day14.R4

value: White


title: Brain-ND-1#

value: Brain


title: alveolosphere in patient 2


title: White.Day14.R2


title: Dark.Day14.R3


title: White.Day14.R1


title: White.Day14.R3


title: Dark.Day14.R4


title: alveolosphere in patient 4


title: Dark.Day8.R4


title: Dark.Day14.R1


title: Dark.Day8.R3


title: Dark.Day8.R2


title: Dark.Day8.R1


title: White.Day8.R4


title: White.Day8.R3


title: White.Day8.R2


title: White.Day7.R2


title: White.Day7.R3


title: White.Day8.R1


title: Dark.Day7.R4


title: Dark.Day7.R3


title: White.Day7.R4


title: White.Day7.R1


title: Dark.Day1.R3


title: Dark.Day1.R1


title: White.Day1.R4


title: White.Day1.R3


title: Dark.Day1.R2


title: White.Day1.R2


title: White.Day1.R1


title: Dark.Day0.R3


title: Dark.Day0.R2


title: Dark.Day7.R1


title: Dark.Day0.R1


title: Dark.Day1.R4


title: Dark.Day7.R2


title: hBMEC cells infected by M.tb 0 d.p.i sample 1

city: Wuhan

first: Xiaojian

last: Cao

state: Hubei

address: No.1095 Jiefang Avenue

department: Department of Rehabilination Medicne

institute: Tongji Hospital

data_processing:
Alignment was conducted with Hisat2
Alignment result was sorted and formated with Samtools
Sorted alignemnt result was counted via Htseq
Differential analysis and the generating of normalized count matrix was performed by DEseq2
Genome_build: Human:GRCh38/ Mouse:GRCm38
Supplementary_files_format_and_content: A matrix merged by individual list from each samples showing the expession level of each gene

source_name: Cultured cells

extract_protocol:
Standard Trizol-based method
Libraries were prepared with the Vazyme stranded mRNA library preparation kit, briefly, mRNA was purified with poly(A) beads, than fraggmented into 100-150bp , fraggmented mRNA were reverse-trascripted, and was conducted 2nd strand synthesis. Dounle stranded cDNA was end-repaired, d(A) tailed and was subjected for the adapter ligation, than an amplification was performed which make the final library

value: hBMEC

value: brain microvascular endothelial cell

tag: time

value: 0 days post-infection


title: hBMEC cells uninfected sample 1

value: Untreated

value: N/A days post-infection


title: hBMEC cells infected by M.tb 0 d.p.i sample 2


title: A549 cells uninfected sample 2

value: epithelial cell


title: hBMEC cells uninfected sample 2


title: THP1 cells infected by M.tb 0 d.p.i sample 1

value: Macrophage


title: THP1 cells uninfected sample 1


title: THP1 cells uninfected sample 2


title: THP1 cells infected by M.tb 3 d.p.i sample 1

value: 3 days post-infection


title: THP1 cells infected by M.tb 0 d.p.i sample 2


title: hBMEC cells infected by M.tb 3 d.p.i sample 2


title: A549 cells uninfected sample 1


title: hBMEC cells infected by M.tb 3 d.p.i sample 1


title: A549 cells infected by M.tb 3 d.p.i sample 2


title: Dark.Day0.R4


title: THP1 cells infected by M.tb 3 d.p.i sample 2


title: A549 cells infected by M.tb 3 d.p.i sample 1


title: A549 cells infected by M.tb 0 d.p.i sample 1


title: A549 cells infected by M.tb 0 d.p.i sample 2


title: blood_sepsis_cd8_patient21

city: Houston

first: Carl

last: Allen

state: Texas

address: 1102 Bates Street, Suite 750

institute: Texas Children's Hospital

hyb_protocol: Fragmented and biotinylated cDNA was hybridized to GeneChip™ Human Transcriptome Array 2.0 according to the manufacturer’s procedures.

scan_protocol: Chips were scanned using the Affymetric Gene Chip Scanner 3000

data_processing: Raw data from all samples were normalized using the SST-RMA algorithm implemented in the Affymetrix Expression Console

label: biotin

label_protocol: Amplified cDNA was fragmented and abeled with the FL-ovation cDNA Biotin module V2.

extract_protocol: Total RNA was purified from sorted subpopulations from peripheral blood and lesion specimens according to the Arcturus PicoPure RNA Isolation Kit protocol. RNA quality was verified using the Pico Chip and all samples have RIN>6. cDNA amplification was performed using the Ovation Pico WTA V2 System according to the manufacturer’s protocol.

tag: disease

value: sepsis


title: blood_sepsis_cd8_patient23


title: blood_sepsis_cd8_patient20


title: blood_sepsis_cd68_patient18


title: blood_hlh_cd8_patient10

value: Hemophagocytic lymphohistiocytosis


title: blood_hlh_cd8_patient11


title: blood_sepsis_cd8_patient17


title: blood_sepsis_cd8_patient19


title: blood_sepsis_cd8_patient18


title: blood_sepsis_cd8_patient22


title: blood_sepsis_cd68_patient15


title: blood_sepsis_cd68_patient21


title: blood_hlh_cd8_patient13


title: blood_sepsis_cd68_patient20


title: blood_sepsis_cd8_patient16


title: blood_hlh_cd68_patient9


title: blood_sepsis_cd8_patient14


title: blood_sepsis_cd68_patient19


title: blood_sepsis_cd8_patient15


title: blood_sepsis_cd68_patient17


title: blood_hlh_cd68_patient11


title: blood_sepsis_cd68_patient16


title: ADCC resistant C35

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

hyb_protocol: Labeled cRNA was directly hybridized to the Illumina HumanHT-12 Expression BeadChip and washed per manufacturer's protocol.

scan_protocol: BeadChips were scanned using the Illumina iScan per manufacturer's protocol.

data_processing: log2 variance stabilization and quantile normalization using the R/Bioconductor package lumi.

source_name: A431 cell line

label_protocol: Biotin-labeled cRNA was generated from 100 ng of isolated RNA using a labeling kit per manufacturer's protocol.

extract_protocol: RNA was isolated using the PureLink RNA Mini Kit (Ambion) and assessed for quality by Bioanalyzer (Agilent) for RIN>6 using manufacturer's protocol.

tag: adcc sensitive / resistant

value: ADCC resistant


title: Raw264.7 cells uninfected sample 2


title: Raw264.7 cells uninfected sample 1


title: blood_sepsis_cd68_patient14


title: ADCC resistant C34


title: blood_hlh_cd8_patient9


title: bEnd.3 cells uninfected sample 2


title: ADCC resistant C33


title: ADCC sensitive C34

value: ADCC sensitive


title: blood_hlh_cd8_patient8


title: ADCC sensitive C33


title: blood_hlh_cd68_patient10


title: ADCC sensitive C32


title: blood_hlh_cd8_patient7


title: blood_hlh_cd68_patient12


title: blood_hlh_cd68_patient8


title: Raw264.7 cells infected by M.tb 3 d.p.i sample 1


title: blood_hlh_cd8_patient5


title: ADCC sensitive C35


title: Raw264.7 cells infected by M.tb 0 d.p.i sample 2


title: blood_hlh_cd68_patient7


title: ADCC resistant C31


title: ADCC resistant C32


title: bEnd.3 cells uninfected sample 1


title: bEnd.3 cells infected by M.tb 3 d.p.i sample 2


title: bEnd.3 cells infected by M.tb 3 d.p.i sample 1


title: Raw264.7 cells infected by M.tb 3 d.p.i sample 2


title: blood_hlh_cd68_patient5


title: blood_hlh_cd68_patient4


title: Long_4

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
FASTQs generated using bcl2fastq
Kallisto (v0.46.2) was used to pseudoalign samples to the GRCh38 human transcriptome without bootstraps.
Transcript-level counts and abundance data were imported into R using the TxImport package and TMM normalized using the package EdgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file containing raw Kallisto gene count from individual samples

source_name: SARS-CoV-2 reactive CD4+ T cell

extract_protocol:
RNA isolated from RLT+ buffer using a RNeasy Micro spin column according to the manufacuter's protocol
cDNA was generated using a SMART-Seq HT Kit (TaKaRa, 634455), and the final Illumina-compatible DNA sequencing libraries prepared using an Illumina Nextera XT DNA Library Preparation kit

treatment_protocol: Cryopreserved PBMC samples were thawed and resuspended in complete cell culture media at a concentration of 5 × 106 cell/mL and stimulated with 0.5 μg/mL of a SARS-CoV-2 Spike protein peptide pool  for 18 h at 37 °C. Spike-reactive CD4+ T cells were identified by expression of the activation markers CD134 and CD69 and isolated by flow cytometric sorting using BD FACSAria II instrument. Cells were sorted directly into 350ul RLT+ buffer supplemented with 1% 2-ME

value: CD4+ T cell

tag: symptom duration

value: Greater than 18 days

tag: antigen reactivity

value: SARS-CoV-2 Spike


title: ADCC sensitive C31


title: blood_hlh_cd68_patient6


title: Long_3


title: Raw264.7 cells infected by M.tb 0 d.p.i sample 1

tag: infection


title: blood_hlh_cd68_patient3


title: Long_5


title: RFe003_DPD190 WT 3

city: Stanford

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

data_processing:
Library strategy: LAM-HTGTS
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

source_name: CD34+ HSPCs

growth_protocol: CD34+ HSPCs were isolated as previously described (Dever et al., Nature 2016).  CD34+ HSPCs were cultured at 37 °C, 5% CO2 and 5% O2 in StemSpan SFEM II (StemCell Technologies) supplemented with SCF (100 ng ml−1), TPO (100 ng ml−1), Flt3 ligand (100 ng ml−1), IL-6 (100 ng ml−1), and StemRegenin1 (0.75 mM).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step omitted, using HBB locus primers and Illumina Miseq sequencing

treatment_protocol: CD34+ cells were resuspended in P3 buffer (Lonza, Basel, Switzerland) with complexed Cas9:HBB RNPs and subsequently, electroporated using the Lonza 4D Nucleofector (program DZ-100).

value: CD34+ HSPCs

tag: sample

value: wild type Cas9 genome-wide repair


title: RFe003_DPD190 HiFi 3

value: high fidelity Cas9 genome-wide repair


title: bEnd.3 cells infected by M.tb 0 d.p.i sample 2

value: brain microvascular endothelial cell


title: Short_5

value: Less than 8 days


title: ADCC sensitive C30


title: Short_4


title: blood_hlh_cd8_patient6


title: ADCC resistant C30


title: Long_1


title: Long_2


title: blood_hlh_cd8_patient3


title: blood_hlh_cd68_patient2


title: blood_hlh_cd68_patient1


title: Short_2


title: bEnd.3 cells infected by M.tb 0 d.p.i sample 1

value: 0 days post-infection


title: RFe003_DPD190 HiFi 1


title: RFe003_DPD190 WT 2


title: RFe003_DPD190 HiFi 2


title: Short_3


title: blood_hlh_cd8_patient1


title: blood_hlh_cd8_patient2


title: Short_1


title: RFe003_DPD190 WT 1


title: blood_hlh_cd8_patient4


title: MeSA exposed plant2

status: Public on May 15 2021

city: Moncada

first: Alberto

last: Urbaneja

state: Valencia

address: Carretera CV-315  Km 10,7

country: Spain

institute: Instituto Valenciano de Investigaciones Agrarias

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Trimmomatic 0.32. Adapter sequences and bases with base quality lower than 3 from the ends were removed. Using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Reads with length shorter than 36bp are dropped to produce trimmed data.
Read quality was checked for each sample using FastQC v0.11.5. Reads over score of 20 (99% accuracy) are accepted as good quality
Reads were mapped using HISAT2 version 2.0.5, Bowtie2 2.2.6
Known genes and transcripts are assembled with StringTie version 1.3.3b based on reference genome model . The abundance of gene/transcript is calculated in the read count and normalized  value as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and as TPM (Transcripts Per Kilobase Million) for a sample.
Genome_build: SL2.50_GCF_000188115.3
Supplementary_files_format_and_content: tab-delimited text files include coverage,RPKM and TPM values for each gene in a sample; gtf files include  coverage, RPKM and TPM values per gene, transcripts and exons

organism: Solanum lycopersicum

source_name: Apical part of tomato plant

growth_protocol: Moneymaker seeds were sown in soil. Two weeks after germination seedlings were individually transplanted into pots (8 × 8 × 8 cm). Plants were maintained undisturbed at 25 ± 2 ºC, with constant relative humidity of 65% ± 5% and a photoperiod of 14:10 h (light: dark). Pesticide-free tomato plants were used for the experiments at four weeks of age (approximately 20 cm high).

extract_protocol:
The apical part of the tomato plant samples were immediately ground in liquid nitrogen. Portions of the ground samples were used for RNA extraction. Total RNA was extracted using a Plant RNA Kit (Omega Bio-Tek Inc., Doraville, GA, USA) and was treated with RNase-free DNase (Promega Corporation, Madison, Wisconsin, USA) to eliminate genomic DNA contamination.
The library was constructe using TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: To carry out these exposures cards of 2 x 2 cm filter paper (volatile emitter) were impregnated each with 10 µl of each corresponding volatile at a concentration of 1:10,000 or in the case of the control 1:10,000 methanol:water.Two impregnated cards with the corresponding volatile were placed in the bottom part of a 30 × 30 × 30 cm plastic cage (BugDorm-1 insect tents) together with an intact tomato. Plants and volatiles were kept undisturbed for 24 hours in isolated climatic chambers to avoid any volatile interference and maintained at at 25 ± 2ºC, 65 ± 10% RH and a 14:10 h (L:D) photoperiod.

value: Apical part of tomato plant

tag: cultivar

value: Moneymaker

value: four weeks of age

value: MeSA exposed plant


title: MeSA exposed plant3


title: (Z)-3-HP exposed plant4

value: (Z)-3-HP exposed plant


title: (Z)-3-HP exposed plant3


title: MeSA exposed plant1


title: Control4

value: Control


title: (Z)-3-HP exposed plant1


title: Control2


title: Control1


title: (Z)-3-HP exposed plant2


title: Control3


title: PC_single_DOX_G401

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
HiSeq Control Software 2.2.58, RTA 1.18.64, bcl2fastq-1.8.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.1.0 with the --local parameter set for soft-trimming
Data were filtered using the following specifications: samtools view -F 268
PCR duplicates were removed using samtool's rmdup
Peaks were called using MACS2 version 2.2.7.1 with the -f BAMPE parameter set for paired read data
Differentially bound regions were identified with MACS2 bdgdiff
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using bamCompare, subtracting Input from ChIP, with binsize of 1 and RPKM normalisation

source_name: Kidney

growth_protocol: All cells have been tested negative for mycoplasma contamination. G401 and BT16 cells were cultured in DMEM with 10% FBS  at 37°C with 5% CO2.

extract_protocol:
Standard one-step crosslinking was performed when targeting histone post-translational modifications (H3K4me3, H3K27ac, H3K4me1 and H3K27me3) for ChIP-sequencing. G401 and BT16 HA-SMARCB1 cells were cultured in T75 flasks (Corning) and treated with 0.01 ng/uL doxycycline or DMSO (mock-treatment) for 72 hours. The cell monolayer or homogenised kidney tissue was washed twice with pre-warmed PBS. Cells were incubated at room temperature in 1% formaldehyde (FA) solution (Millipore Sigma) for 10 minutes before adding 0.125 M glycine (Millipore Sigma) to quench the crosslinking reaction. Two-step crosslinking [67] was performed to target SWI/SNF subunits; BAF170, BAF155, BRG, SS18, ARID1A, BRD9, BAF180, ARID2, BRG7 and HA-SMARCB1 for ChIP-sequencing. 2 mM disuccinimidyl glutarate (DSG; ThermoFisher scientific) was added to cells for 30 minutes at room temperature. Excess DSG was removed by washing twice in PBS and cells were crosslinked with FA solution for 10 minutes as described above. Crosslinked cells were washed twice in PBS and lysed in 5 mL SDS lysis buffer (100 mM NaCl, 50 mM Tris-Cl, 5 mM EDTA, 0.02% NaN3, and 1% SDS) containing protease inhibitors (1 μg/mL leupeptin, 1 μg/mL aprotenin, 10 μM PMSF; Millipore Sigma). Cells were snap-frozen in liquid nitrogen and stored at -80oC for later use.
ChIP-DNA was quantified using the Qubit® 2.0 Fluorometer (Thermo Fisher Scientific). ChIP-libraries were prepared from 10 ng DNA using the NEBNext®Ultra-library preparation kit for Illumina (New England BioLabs) with Dual indexing NEBNext® Multiplex Oligos (Dual Index Primers Set 1) following manufactures protocol. DNA libraries were purified and size selected (200 – 500 base pairs) by two rounds of AMPure bead purification. Library fragment length was validated using the High Sensitivity (HS) ScreenTape for 2200 TapeStation (Agilent). ChIP library-amplification was validated by qPCR at a set of known positive and negative control genes.

treatment_protocol: The G401 and BT16 cell line were stably transfected with doxycycline-inducible HA-tagged-SMARCB1 following a previously published protocol by Kenny et al. 2018 (PMID: 29243812) with minor modifications. SMARCB1 was amplified from normal kidney tissue and cloned with HA-tag into a doxycycline/tetracycline-inducible pLVX Tight Puro lentiviral (Clontech) expression system. Cells were transfected with viral packaging vector Pax2, envelope vector MD2G, and pLVX Tight Puro containing HA-SMARCB1 using Lipofectamine 2000 (Invitrogen). The optimum dose of doxycycline to induce HA-SMARCB1 expression was determined as 0.1 ng/ μL. SMARCB1 protein expression was verified by western blot analysis prior to each experiment.

tag: chip antibody

value: DOX


title: SS18_DOX_BT16

source_name: Brain


title: SS18_MOCK_BT16

value: MOCK


title: PC_single_MOCK_G401


title: SS18_DOX_G401


title: SMARCB1_HA-TAG_DOX_BT16


title: PC_Single_MOCK_BT16


title: SS18_MOCK_G401


title: wild type 0mM Zn 2

city: Saint Louis

first: Ciro

last: Cubillas Ramirez

state: Missouri

address: 4577 McKinley, Campus Box 8103, 3607 Cancer Research Building

department: Developmental Biology

institute: Washington University in St Louis, School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Fastq files were aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl WBcel235.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

organism: Caenorhabditis elegans

source_name: whole animal RNA extraction

growth_protocol: Mixed-stage populations of the wild type and hizr-1 strains were collected by washing and then cultured 16-18h at 20oC on NAMM dishes seeded with 10X concentrated E. coli OP50 and supplemented with 0mM and 200 mM zinc sulfate ZnSO4. For this purpose, 80 NGM plates seeded with 1X E. coli OP were used. A half of the plates containing 3 C. elegans wild type L4 stage hermaphrodites were grown for 4 days at 20oC, the other 40 plates contained 3 C. elegans hizr-1 L4 stage hermaphrodites and were grown in parallel. After these 4 days, the mixed-stage populations were collected by washing them with M9 buffer and then cultured on the same number of NAMM plates seeded with 10X E. coli OP50 supplemented with either 0mM ZnSO4 (40 plates) or with 200mM ZnSO4 (40 plates) as follows: one group of 20 wild type NGM plates were transferred into NAMM supplemented with 200mM ZnSO4 while the other 20 wild type NGM plates were transferred into NAMM without supplemented ZnSO4. This same procedure was followed with the hizr-1 loss-of-function mutant allele, am286. The animals were grown for 16-18h at 20oC and then collected by washing with M9; animals from 10 plates were pooled into one biological sample, so duplicated samples for wild type and hizr-1 mutant coming from the NAMM 0mM and NAMM 200mM supplemented ZnSO4 were used to extract RNA

extract_protocol:
Trizol extraction, in-column DNAase treatment followed by Rneasy column purification
Ribo-Zero v1

treatment_protocol: Noble Agar Minimal Medium plates supplemented with or without 200mM zinc sulfate

tag: strain

tag: genotype

value: wild tpe

value: non-supplemented


title: wild type 0mM Zn 1


title: wild type 200mM Zn 2

value: 200 uM Zn


title: SMARCB1_HA_TAG_DOX_G401


title: PNT1A_HDB_1e-6M_rep3

city: Montreal

first: Claudia

last: Lalancette

state: QC

address: 3655 Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

description:
Gene expression after 48hr incubation with HDB 1e-6M
HDB_MID3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K microarrays (G4851A) 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), dried briefly and put in Agilent Ozone-Barrier Slide holder.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid 028004_D_F_20120411) to obtain background subtracted and Processed Signal intensities.

source_name: PNT1A_48hr_1e-6M HDB

label_protocol: 25 ng of total RNA was used for labeling, according to Agilent's One color Low Input Quick Amp labeling kit protocol.

growth_protocol: PNT1A cells were grown at 37°C, 5% CO2 in RPMI 1640 supplemented with 0.025 M glucose, 2mM glutamine, 10mM Hepes, 1mM sodium pyruvate and 0.018 M sodium bicarbonate, 10% head inactivated fetal bovine serum (FBS), 100 IU/mL of penicillin and 100 ug/mL of streptomycin

extract_protocol: RNA was prepared using the RNEasy Plus Mini Kit, according to the manufacturer's protocol. RNA quality and quantification was obtained using the Bioanalyzer 2000 and the Nano 6000 RNA kit. Protein and other contaminants were assessed using the NanoDrop 2000.

treatment_protocol: PNT1A cells were treated with 1e-06 M (mid) or 1e-08 M (low) of plasticizers, or 0.4% DMSO (vehicle) for 48h at 37°C and 5% CO2

tag: tissue

value: prostate

tag: Stage

value: non cancerous

tag: cell type

value: prostate cell line

tag: treated with

value: 1e-6M HDB


title: PNT1A_HDB_1e-8M_rep4

description:
Gene expression after 48hr incubation with HDB 1e-8M
HDB_LOW_4

source_name: PNT1A_48hr_1e-8M HDB

tag: cell line

value: 1e-8M HDB


title: PC_Duel_MOCK_G401

tag: treatment


title: hizr-1 0mM Zn 1

value: N2 derivative

value: hizr-1 loss-of-function mutant


title: PC_Duel_MOCK_BT16


title: hizr-1 0mM Zn 2


title: K4me3_MOCK_G401


title: hizr-1 200mM Zn 2


title: PNT1A_HDB_1e-8M_rep2

description:
Gene expression after 48hr incubation with HDB 1e-8M
HDB_LOW_2


title: hizr-1 200mM Zn 1


title: PNT1A_HDB_1e-6M_rep4

description:
Gene expression after 48hr incubation with HDB 1e-6M
HDB_MID_4


title: PNT1A_HDB_1e-8M_rep3

description:
Gene expression after 48hr incubation with HDB 1e-8M
HDB_LOW_3


title: PNT1A_BDB_1e-8M_rep3

description:
Gene expression after 48hr incubation with BDB 1e-8M
BDB_LOW_3

source_name: PNT1A_48hr_1e-8M BDB

value: 1e-8M BDB


title: PNT1A_HDB_1e-6M_rep1

description:
Gene expression after 48hr incubation with HDB 1e-6M
HDB_MID_1


title: PNT1A_HDB_1e-6M_rep2

description:
Gene expression after 48hr incubation with HDB 1e-6M
HDB_MID_2


title: PC_Duel_DOX_G401


title: PNT1A_BDB_1e-8M_rep4

description:
Gene expression after 48hr incubation with BDB 1e-8M
BDB_LOW_4


title: PC_Duel_DOX_BT16


title: K4me3_DOX_G401


title: K4me3_DOX_BT16


title: K4me3_MOCK_BT16


title: STB_031

city: Southampton

first: Michaela

last: Reichmann

address: Tremona Road

institute: University of Southampton

data_processing:
Basecalling was performed with Ion Torrent Suite 5.0.5
After quality control for adapter contamination by FastQC software, fastq files were mapped to the  human genome transcriptome (Homo_sapiens.GRCh38.cdna) using kallisto software (version 0.44.0).
Reads were imported by tximport (version 1.10.1, R), and annotated to gene level with ensembldb program (version 2.6.8, R)
Inter-sample normalisation with TMM normalisation using edgeR (version 3.24.3, R).
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lymph node

extract_protocol:
Samples were thawed on ice, and 200µl Chloroform added per 1ml of sample.  Samples were shaken for 15 seconds, incubated for 3 minutes at room temperature, then centrifuged at 12000g for 15 minutes at 4OC.   The upper aqueous layer was extracted.  Then manufacturer’s instructions were followed (RNeasy® Midi Kit, QIAGEN), adding 70% ethanol, shaking, and then samples added to RNeasy Midi columns, and washed with Buffer RW1 and Buffer RPE.  Total RNA was eluted with H20 and stored at -80°C.
Ion PITM Hi-QTM Chef Kit on Ion ChefTM instrument was used for library construction, assembling two chips from eight diluted samples at a time.  The Ion ProtonTM System was used as per manufacturer’s instructions to sequence RNA.  Total RNA of 15ng per sample was used to produce a mean average of 18 million single end ~100 base pair reads per sample

tag: condition

tag: location

value: Mediastinum

tag: gender

value: Female

value: z

tag: age


title: PNT1A_DMSOctl_rep4 [set3]

description:
Gene expression after 48hr incubation with 0.4% DMSO control
DMSO_4

source_name: PNT1A_48hr_0.4% DMSO

value: 0.4% DMSO


title: PNT1A_BDB_1e-8M_rep2

description:
Gene expression after 48hr incubation with BDB 1e-8M
BDB_LOW_2


title: PNT1A_BDB_1e-8M_rep1

description:
Gene expression after 48hr incubation with BDB 1e-8M
BDB_LOW_1


title: STB_029

value: Sarcoidosis


title: K4me1_MOCK_BT16

value: MOCK


title: STB_032


title: PNT1A_BDB_1e-6M_rep2

description:
Gene expression after 48hr incubation with BDB 1e-6M
BDB_MID_2

source_name: PNT1A_48hr_1e-6M BDB

value: 1e-6M BDB


title: PNT1A_BDB_1e-6M_rep4

description:
Gene expression after 48hr incubation with BDB 1e-6M
BDB_MID_4


title: PNT1A_HDB_1e-8M_rep1

description:
Gene expression after 48hr incubation with HDB 1e-8M
HDB_LOW_1


title: STB_030

value: TB


title: K4me1_MOCK_G401


title: PNT1A_DMSOctl_rep3 [set3]

description:
Gene expression after 48hr incubation with 0.4% DMSO control
DMSO_3


title: PNT1A_DMSOctl_rep2 [set3]

description:
Gene expression after 48hr incubation with 0.4% DMSO control
DMSO_2


title: PNT1A_BDB_1e-6M_rep3

description:
Gene expression after 48hr incubation with BDB 1e-6M
BDB_MID_3


title: PNT1A_DMSOctl_rep1 [set3]

description:
Gene expression after 48hr incubation with 0.4% DMSO control
DMSO_1


title: PNT1A_BDB_1e-6M_rep1

description:
Gene expression after 48hr incubation with BDB 1e-6M
BDB_MID_1


title: PNT1A_BDB_1e-4M_rep3

description:
Gene expression after 48hr incubation with BDB 1e-4M
BDB_high_3

source_name: PNT1A_48hr_1e-4M BDB

treatment_protocol: PNT1A cells were treated with 1e-4M (high) of plasticizers, or 1% DMSO (vehicle) for 48h at 37°C and 5% CO2

value: 1e-4M BDB for 48hrs


title: PNT1A_DOS_1e-4M_rep2

description:
Gene expression after 48hr incubation with DOS 1e-4M
DOS_high_2

source_name: PNT1A_48hr_1e-4M DOS

value: prostate

value: 1e-4M DOS for 48hrs


title: PNT1A_BDB_1e-4M_rep4

description:
Gene expression after 48hr incubation with BDB 1e-4M
BDB_high_4

value: non cancerous

value: prostate cell line


title: PNT1A_DOS_1e-4M_rep1

description:
Gene expression after 48hr incubation with DOS 1e-4M
DOS_high_1


title: PNT1A_DOS_1e-4M_rep4

description:
Gene expression after 48hr incubation with DOS 1e-4M
DOS_high_4


title: PNT1A_BDB_1e-4M_rep2

description:
Gene expression after 48hr incubation with BDB 1e-4M
BDB_high_2


title: PNT1A_DOS_1e-4M_rep3

description:
Gene expression after 48hr incubation with DOS 1e-4M
DOS_high_3


title: PC_single_DOX_BT16

value: DOX


title: K4me1_DOX_BT16


title: K27ac_MOCK_G401


title: STB_025

value: Neck

value: Male


title: STB_024

value: Control


title: K27ac_MOCK_BT16


title: STB_027

value: Mediastinum


title: STB_023

value: Female

value: y


title: PNT1A_MEHP_1e-4M_rep3

description:
Gene expression after 48hr incubation with MEHP 1e-4M
MEHP_high_3

source_name: PNT1A_48hr_1e-4M MEHP

value: 1e-4M MEHP for 48hrs


title: K27ac_DOX_G401


title: STB_022


title: K4me1_DOX_G401


title: K27ac_DOX_BT16


title: STB_026

value: Sarcoidosis

value: z


title: STB_021


title: CREST_SS18L_MOCK_G401

value: CREST

value: MOCK


title: PNT1A_MEHP_1e-4M_rep4

description:
Gene expression after 48hr incubation with MEHP 1e-4M
MEHP_high_4


title: PNT1A_BDB_1e-4M_rep1

description:
Gene expression after 48hr incubation with BDB 1e-4M
BDB_high_1

value: 1e-4M BDB for 48hrs


title: PNT1A_MEHP_1e-4M_rep2

description:
Gene expression after 48hr incubation with MEHP 1e-4M
MEHP_high_2

value: prostate


title: PNT1A_DMSOctl_rep4 [set2]

description:
Gene expression after 48hr incubation with 1% DMSO control
DMSO_4

source_name: PNT1A_48hr_1% DMSO

value: 1% DMSO for 48hrs


title: PNT1A_DMSOctl_rep3 [set2]

description:
Gene expression after 48hr incubation with 1% DMSO control
DMSO_3

value: non cancerous


title: CREST_MOCK_BT16


title: PNT1A_MEHP_1e-4M_rep1

description:
Gene expression after 48hr incubation with MEHP 1e-4M
MEHP_high_1

value: prostate cell line


title: STB_020


title: STB_018


title: CREST_SS18L_DOX_BT16

value: DOX


title: MeSA exposed plant4

value: Apical part of tomato plant

value: Moneymaker

value: four weeks of age

value: MeSA exposed plant


title: PNT1A_DMSOctl_rep1 [set2]

description:
Gene expression after 48hr incubation with 1% DMSO control
DMSO_1


title: STB_015

value: TB

value: Neck

value: Female


title: STB_017

value: Sarcoidosis

value: Mediastinum

value: y


title: PNT1A_DMSOctl_rep2 [set2]

description:
Gene expression after 48hr incubation with 1% DMSO control
DMSO_2


title: CREST_DOX_G401

value: CREST


title: PNT1A_MEHP_1e-8M_rep1

description:
Gene expression after 48hr incubation with MEHP 1e-8M
MEHP_low_1

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid 028004_D_F_20120411) to obtain background subtracted and Processed Signal intensities.
Please note that control probes were filtered out and only probes for which there was at least 4 samples with normalized signal of at least 10% higher to the background were included in the analysis.

source_name: PNT1A_48hr_1e-8M MEHP

tag: tissue origin

value: 1e-8M MEHP for 48hrs


title: PNT1A_MEHP_1e-8M_rep3

description:
Gene expression after 48hr incubation with MEHP 1e-8M
MEHP_low_3

value: prostate


title: PNT1A_MEHP_1e-6M_rep4

description:
Gene expression after 48hr incubation with MEHP 1e-6M
MEHP_mid_4

source_name: PNT1A_48hr_1e-6M MEHP

value: 1e-6M MEHP for 48hrs


title: PNT1A_MEHP_1e-6M_rep3

description:
Gene expression after 48hr incubation with MEHP 1e-6M
MEHP_mid_3

value: non cancerous


title: BRG1_mock_BT16

value: MOCK


title: PNT1A_MEHP_1e-8M_rep2

description:
Gene expression after 48hr incubation with MEHP 1e-8M
MEHP_low_2

value: prostate cell line


title: PNT1A_MEHP_1e-6M_rep1

description:
Gene expression after 48hr incubation with MEHP 1e-6M
MEHP_mid_1


title: PNT1A_MEHP_1e-6M_rep2

description:
Gene expression after 48hr incubation with MEHP 1e-6M
MEHP_mid_2


title: STB_014


title: BRG1_MOCK_G401


title: PNT1A_DOS_1e-8M_rep3

description:
Gene expression after 48hr incubation with DOS 1e-8M
DOS_low_3

source_name: PNT1A_48hr_1e-8M DOS

value: 1e-8M DOS for 48hrs


title: STB_013

value: Control

value: Male

value: x


title: PNT1A_DOS_1e-8M_rep4

description:
Gene expression after 48hr incubation with DOS 1e-8M
DOS_low_4


title: BRG1_dox_BT16

value: DOX


title: PNT1A_DOS_1e-6M_rep4

description:
Gene expression after 48hr incubation with DOS 1e-6M
DOS_mid_4

source_name: PNT1A_48hr_1e-6M DOS

value: 1e-6M DOS for 48hrs


title: STB_012

value: TB


title: PNT1A_DOS_1e-8M_rep1

description:
Gene expression after 48hr incubation with DOS 1e-8M
DOS_low_1


title: BRD9_MOCK_G401

source_name: Kidney


title: BRG1_DOX_G401


title: PNT1A_DOS_1e-6M_rep2

description:
Gene expression after 48hr incubation with DOS 1e-6M
DOS_mid_2


title: PNT1A_DOS_1e-6M_rep3

description:
Gene expression after 48hr incubation with DOS 1e-6M
DOS_mid_3


title: PNT1A_DOM_1e-8M_rep4

description:
Gene expression after 48hr incubation with DOM 1e-8M
DOM_low_4

source_name: PNT1A_48hr_1e-8M DOM

value: 1e-8M DOM for 48hrs


title: BRD9_MOCK_BT16

source_name: Brain


title: STB_008

value: Mediastinum

value: Female


title: STB_007

value: Sarcoidosis


title: PNT1A_DOS_1e-8M_rep2

description:
Gene expression after 48hr incubation with DOS 1e-8M
DOS_low_2


title: PNT1A_DOS_1e-6M_rep1

description:
Gene expression after 48hr incubation with DOS 1e-6M
DOS_mid_1


title: STB_011


title: BRD9_DOX_G401


title: wild type 200mM Zn 1

source_name: whole animal RNA extraction

value: wild tpe

value: 200 uM Zn


title: BRD9_DOX_BT16


title: PNT1A_DOM_1e-8M_rep3

description:
Gene expression after 48hr incubation with DOM 1e-8M
DOM_low_3

value: prostate


title: PNT1A_DOM_1e-6M_rep3

description:
Gene expression after 48hr incubation with DOM 1e-6M
DOM_mid_3

source_name: PNT1A_48hr_1e-6M DOM

value: non cancerous

value: 1e-6M DOM for 48hrs


title: PNT1A_DOM_1e-8M_rep1

description:
Gene expression after 48hr incubation with DOM 1e-8M
DOM_low_1

value: prostate cell line


title: PNT1A_DOM_1e-6M_rep1

description:
Gene expression after 48hr incubation with DOM 1e-6M
DOM_mid_1


title: PNT1A_DOM_1e-8M_rep2

description:
Gene expression after 48hr incubation with DOM 1e-8M
DOM_low_2


title: PNT1A_DOM_1e-6M_rep2

description:
Gene expression after 48hr incubation with DOM 1e-6M
DOM_mid_2


title: STB_006


title: STB_005


title: PNT1A_DINCH_1e-8M_rep2

description:
Gene expression after 48hr incubation with DINCH 1e-8M
DINCH_low_2

source_name: PNT1A_48hr_1e-8M DINCH

value: 1e-8M DINCH for 48hrs


title: STB_001

source_name: Lymph node


title: BRD7_MOCK_G401

value: MOCK


title: BRD7_MOCK_BT16


title: BRD7_DOX_G401


title: TC1 V6.5-siNC-1 RNA-seq

city: Beijing

first: Min

last: Yang

address: No. 5, yiheyuan road, haidian district,

institute: Peking University

data_processing:
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the mm10 reference genome with default parameters. For 4sU-seq data, All reads were trimmed by Trimmomatic. The reads which were not aligned to the mm10 repeats or BK000964.3 (rRNA) sequence were used to mapped to the mm10 reference genome with the same commands in PolyA(+) RNA-seq analysis. The ATAC-seq data were processed using ATAC-seq pipeline from Kundaje lab, including trimming, alignment, filtration and quality control.
The expression count matrix was obtained by FeatureCounts.
Data were normalized by total mapped reads of each library (CPM: count per million).
Genome_build: mm10

source_name: mESC

extract_protocol:
DNA and RNA extracted according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina). 4sU-seq libraries preparation using TruSeq Stranded Total RNA Sample Prep Kits (Illumina). ATAC-seq Library Preparation is according to insructions of Corces et al. Nature Methods 2017.

value: mESC cultured in serum/lif medium


title: TC1 V6.5-siNC-2 RNA-seq


title: BRD7_DOX_BT16


title: TC1 V6.5-siIsy1_S RNA-seq


title: BAF180_MOCK_G401


title: TC1 V6.5-siIsy1_1 RNA-seq


title: Social stress (SS)_Nptx2 KO_rep3

first: Meifang

last: Xiao

address: 725 N Wolfe Street, PCTB904

department: Neuroscience

institute: JHMI

description: Ribosome-associated RNA was extracted from PV-Cre k/+; RiboTag k/k mouse brain by RiboTag pulldown.

data_processing:
RNA-Seq reads were aligned to mouse genome GRCm38 using HISAT2.
Gene expression levels (FPKM) were obtained using StringTie.
FPKM values were log2-transformed after adding a pseudo-count of one. Then, genes with log2-transformed FPKM values less than 1 in all samples were filtered out and the retained data were further quantile-normalized across samples.
To identify genes that change between conditions (i.e., WT vs. KO and SS_WT vs. SS_KO), we applied differential gene analysis using limma.
Genome_build: mouse genome GRCm38
Supplementary_files_format_and_content: excel file includes log2 (FPKM+1) values for each Sample.

extract_protocol:
Immunoprecipitation and purification of ribosome-associated RNA was performed from PV-Cre k/+; RiboTag k/k mouse brains as described (Sanz et al., 2009).
libraries were prepared using Illumina TruSeq stranded mRNA library preparation kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Upon weaning, WT and Nptx2 KO mice were either group-housed or single-housed for at least 4 weeks before experiments.

tag: background strain

value: Nptx2 KO

value: social stress (single-housed)


title: PNT1A_DINCH_1e-8M_rep3

description:
Gene expression after 48hr incubation with DINCH 1e-8M
DINCH_low_3


title: PNT1A_DINCH_1e-8M_rep4

description:
Gene expression after 48hr incubation with DINCH 1e-8M
DINCH_low_4


title: PNT1A_DINCH_1e-8M_rep1

description:
Gene expression after 48hr incubation with DINCH 1e-8M
DINCH_low_1


title: PNT1A_DOM_1e-6M_rep4

description:
Gene expression after 48hr incubation with DOM 1e-6M
DOM_mid_4


title: PNT1A_DINCH_1e-6M_rep3

description:
Gene expression after 48hr incubation with DINCH 1e-6M
DINCH_mid_3

source_name: PNT1A_48hr_1e-6M DINCH

value: 1e-6M DINCH for 48hrs


title: PNT1A_DINCH_1e-6M_rep4

description:
Gene expression after 48hr incubation with DINCH 1e-6M
DINCH_mid_4


title: PNT1A_DINCH_1e-6M_rep1

description:
Gene expression after 48hr incubation with DINCH 1e-6M
DINCH_mid_1


title: PNT1A_DHS_1e-8M_rep4

description:
Gene expression after 48hr incubation with DHS 1e-8M
DHS_low_4

source_name: PNT1A_48hr_1e-8M DHS

value: 1e-8M DHS for 48hrs


title: PNT1A_DHS_1e-8M_rep3

description:
Gene expression after 48hr incubation with DHS 1e-8M
DHS_low_3


title: PNT1A_DHS_1e-8M_rep1

description:
Gene expression after 48hr incubation with DHS 1e-8M
DHS_low_1


title: BAF180_DOX_G401

value: DOX


title: Social stress (SS)_Nptx2 KO_rep2


title: PNT1A_DINCH_1e-6M_rep2

description:
Gene expression after 48hr incubation with DINCH 1e-6M
DINCH_mid_2


title: PNT1A_DHS_1e-6M_rep3

description:
Gene expression after 48hr incubation with DHS 1e-6M
DHS_mid_3

source_name: PNT1A_48hr_1e-6M DHS

value: 1e-6M DHS for 48hrs


title: PNT1A_DHS_1e-6M_rep4

description:
Gene expression after 48hr incubation with DHS 1e-6M
DHS_mid_4


title: PNT1A_DHS_1e-8M_rep2

description:
Gene expression after 48hr incubation with DHS 1e-8M
DHS_low_2


title: PNT1A_DHS_1e-6M_rep2

description:
Gene expression after 48hr incubation with DHS 1e-6M
DHS_mid_2


title: PNT1A_DMSOctl_rep2

description:
Gene expression after 48hr incubation with 0.4% DMSO control
DMSO_2

source_name: PNT1A_48hr_0.4% DMSO

value: 0.4% DMSO for 48hrs


title: BAF170_MOCK_G401


title: PBMCs-HC-Pair1

first: min

last: wei

address: No 8, Xishiku Street

institute: perking university First Hospital

description: blood collected 3 years after diagnosis of the IgAN patient

hyb_protocol: Affymetrix's standard protocol

scan_protocol: AGCC Standard Protocol / GCS 3000

data_processing: Data processing was carried out using TAC (v4.0.2) software. During quality control, the quality of starting sample, hybridization efficiency and the target labeling process were estimated. Samples with a pos vs neg AUC value less than 0.80 were filtered out. The raw expression signals were log transformed and normalized with SST-RMA method.

source_name: PBMCs

label_protocol: Labeling was performed using WT Terminal Labeling and Controls Kit according to manufacturer’s instruction

extract_protocol: Whole blood was collected in sterile vacutainer tubes containing the anticoagulant EDTA and PBMCs were isolated by means of density gradient centrifugation.RNA was extracted using RNeasy Mini Kit (Qiagen, Stockach, Germany)according to manufacturer’s instruction.Total RNA was quantified by the NanoDrop ND-2000 and RNA's integrity was assessed using Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

value: PBMCs

tag: patient diagnosis

value: healthy

value: male


title: PBMCs-IgAN-Pair1

value: IgA nephropathy


title: BAF180_DOX_BT16


title: Social stress (SS)_Nptx2 KO_rep1

description: Ribosome-associated RNA was extracted from PV-Cre k/+; RiboTag k/k mouse brain by RiboTag pulldown.


title: BAF180_MOCK_BT16


title: Nptx2 KO_rep3

value: untreated


title: PNT1A_DMSOctl_rep1

description:
Gene expression after 48hr incubation with 0.4% DMSO control
DMSO_1

value: prostate

value: non cancerous


title: PNT1A_DMSOctl_rep3

description:
Gene expression after 48hr incubation with 0.4% DMSO control
DMSO_3

value: prostate cell line


title: PBMCs-HC-Pair2

description: blood collected 16 years after diagnosis of the IgAN patient

value: female


title: PNT1A_DHS_1e-6M_rep1

description:
Gene expression after 48hr incubation with DHS 1e-6M
DHS_mid_1


title: PBMCs-IgAN-Pair2


title: Nptx2 KO_rep2


title: PNT1A_DMSOctl_rep4

description:
Gene expression after 48hr incubation with 0.4% DMSO control
DMSO_4


title: BAF170_DOX_G401


title: BAF170_MOCK_BT16

value: MOCK


title: Nptx2 KO_rep1

value: Nptx2 KO


title: Social stress (SS)_WT__rep3

value: wild-type

value: social stress (single-housed)


title: hPGCLC_A4_c71_WGBS

city: Charlestown

first: Mutsumi

last: Kobayashi

state: Massachusetts

address: Building 147, 13th street, Rm# 7103

institute: MGH, center for cancer reserch

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bismark.
CpG methylation count was extracted by bismark command, "bismark_methylation_extractor".
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated from bedgraph files produced by bismark

source_name: human PGCLC

growth_protocol: Human iPSCs were maintained in the mTeSR plus medium and converted to hPGCLCs. Freshly isolated hPGCLCs were cultured in the hPGCLC maintenance media. Human EGCs were converted from long-term cultured hPGCLCs using EG derivation madium.

extract_protocol:
Genomic DNA was isolated using QIAGEN AllPrep Mini or Micro kits.
WGBS library was prepared by Pico Methyl-Seq Library Prep Kit.

treatment_protocol: human PGCLCs were harvested at each time point.

tag: Sex

tag: cell id

value: long-term culture human PGCLC c71


title: hPGCLC_F2_c63_WGBS

value: long-term culture human PGCLC c63


title: hPGCLC_A5_rep2_c56_WGBS

value: long-term culture human PGCLC c56


title: Social stress (SS)_WT__rep2


title: BAF155_MOCK_G401

tag: chip antibody


title: BAF170_DOX_BT16

value: DOX


title: hPGCLC_A5_rep1_c56_WGBS


title: hPGCLC_A5_rep2_c84_WGBS

value: long-term culture human PGCLC c84


title: hPGCLC_A5_rep2_c0_WGBS

value: freshly isolated human PGCLC


title: hPGCLC_A5_rep1_c84_WGBS

value: male


title: WT_rep3

tag: genotype


title: Social stress (SS)_WT__rep1


title: hEGC_A4_WGBS

source_name: human EG

value: human EGC


title: hEGC_A5_rep2_WGBS


title: BAF155_MOCK_BT16


title: BAF155_DOX_G401


title: BAF155_DOX_BT16


title: hEGC_A5_rep1_WGBS


title: WT_rep2

value: untreated


title: hiPSC_F2_WGBS

source_name: human iPSC

value: human iPSC


title: ARID2_MOCK_G401


title: WT_rep1


title: hiPSC_A5_rep2_WGBS


title: ARID2_DOX_G401


title: neuronal_72hpf_Sample1

city: Charlottesville

first: Sarah

last: Kucenas

state: VA

address: 90 Galderd Dr, Rm 312

department: Biology

institute: University of Virginia

description: Dissociated cells

data_processing:
For data quality control, FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases.
After adapter clipping, we removed leading and trailing ambiguous or low quality bases (below Phred quality scores of 3).
Trimmomatic works with a user-defined window spanning the read from 5′ to 3′ and removes bases only at the 3′-end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20, the 3′-end is clipped.
The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: danRer10
Supplementary_files_format_and_content: normalized FPKM counts with annotations

organism: Danio rerio

source_name: Zebrafish embryo trunk

growth_protocol: Gt(foxd3:mCherry);Tg(sox10:mEGFP) (for Schwann cells), Tg(olig2:dsred);Tg(sox10:megfp) (for OPC), and Tg(nbt:dsred) (for neurons) zebrafish embryos were raised in egg water at 28.5C to 72 hpf

extract_protocol:
Qiagen rneasy micro
Smartseq v4 Ultra Low Input RNA Kit for Sequencing

treatment_protocol: 72 hpf embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium-free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS (D-PBS) and then transferred to microcentrifuge tubes along with 100ul D-PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C, 1ml 1x Trypsin with 5% EDTA solution was added, and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D-PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D-PBS+BSA. Three samples of cells (1750 ± 750) at each stage were used for RNA-sequencing.

tag: strain

value: AB* Tg(nbt:dsred)

value: 72 hours post fertilization

tag: tissue

value: trunk


title: ARID2_MOCK_BT16

value: MOCK


title: neuronal_72hpf_Sample2

description: Dissociated cells


title: mRNA_#8 (Th17 cells + biglycan) [79_8]

city: North Chicago

first: Joseph

middle: M

last: Reynolds

state: IL

address: 3333 Green Bay Road

department: Microbiology and Immunology

institute: Rosalind Franklin University of Medicine and Science

data_processing:
Total RNA was rRNA-depleted, fragmented, converted to cDNA, adapter-ligated with unique indices and PCR amplified. The final libraries were quantified and sequenced using paired-end 75bp chemistry on NextSeq 500 (Illumina). RNA-seq reads were aligned to UCSC mm9 with Bowtie2 and reads were counted with HTseq count (Dobin et al., 2013, Anders and Huber, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: HTseq count

source_name: Th17 cells + biglycan

extract_protocol:
mRNA was purified using a Qiagen Kit
Illumina stranded mRNA kit

treatment_protocol: Naïve CD4+ T cells were were isolated from the spleens and lymph nodes of mice. These cells were stimulated with antibodies against CD3e and CD28. Th17 cells were polarized with TGFb and IL6 in the absence or presence of Pam3CSK4 or biglycan. After 3 days of differentiation, mRNA was harvest for RNA sequencing

value: Polarized with TGFb/IL-6/biglycan 3 days

value: Spleen and Lymph node

tag: cell type

value: Naive CD4+ T cells


title: hEGC_F2_WGBS

value: female


title: hiPSC_A5_rep1_WGBS


title: mRNA_#7 (Th17 cells + biglycan) [79_7]


title: ARID2_DOX_BT16


title: neuronal_72hpf_Sample3

description: Dissociated cells


title: mRNA_#4 (Th17 cells + PAM3CSK4) [79_6]

source_name: Th17 cells + PAM3CSK4

value: Polarized with TGFb/IL-6/PAM3CSK4 3 days


title: OPC_72hpf_Sample3

description: Dissociated cells

value: AB* Tg(olig2:dsred);Tg(sox10:megfp)


title: hPGCLC_A5_rep1_c0_WGBS


title: mRNA_#2 (Th17 cells) [79_4]

source_name: Th17 cells

value: Polarized with TGFb/IL-6 3 days


title: ARID1A_DOX_G401

source_name: Kidney

value: DOX


title: OPC_72hpf_Sample2

description: Dissociated cells


title: Bo-ao-3

city: Guangzhou

first: Li

last: Zhang

state: Guangdong

address: No. 19, Nonglinxia Road

institute: The First Affiliated Hospital of Guangdong Pharmaceutical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts, TPM for every gene and every sample

source_name: treated with olmesartan

growth_protocol: Human aorta VMSCs were cultured in Dulbecco’s modified Eagle’s medium containing 10% FBS  at 37°C in a 5% CO2 atmosphere. Medium was renewed every 2 to 3 days.

extract_protocol:
RNA was harvested using Trizol reagent. miRNeasy Mini Kit (Cat # 217004， Qiagen) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: VMSCs of third to fifth generation cells were used as unaging cells (Bo-1, -2, -3), and cells treated with 50 nM Olmesartan was set as treated cells (Bo-ao-1, -2, -3).

value: vascular smooth muscle cells (VSMCs)

tag: tissue source

value: blood vessel

tag: treatment/sample group

value: treated with olmesartan


title: Bo-ao-2


title: hiPSC_A4_WGBS

value: male


title: RNAseq_MDAMB231_ANTILUC_rep3

city: Mobile

first: Justin

last: Roberts

address: 5851 USA Drive North, MSB 3370

department: Pharmacology

institute: University of South Alabama

description: polyA-RNA

data_processing:
For meCLIP samples, the reads were analyzed using the Snakemake workflow that is described in the protocol (PMID:33376190).
For the RNAseq samples, the reads were first inspected for appropriate quality using FastQC (v. 0.11.7).
The indexed Illumina adapters were then removed using Cutadapt (v. 2.4) and then briefly analyzed visually once more with FastQC to ensure all adapters are successfully removed.
Gene expression was quantified using Salmon (1.4.0) and then analyzed using DEseq2 (3.12) to generate lists of differentially expressed genes.
Genome_build: hg19 (meCLIP) / hg38 (RNAseq)
Supplementary_files_format_and_content: BED files were generated using the meCLIP workflow and consist of identified m6A sites for each sample.
Supplementary_files_format_and_content: quant.sf files were generated using Salmon and consist of quantification estimates (TPM) for each transcript.

source_name: breast cancer cell

extract_protocol: KAPA® RNA HyperPrep™ Kit.

tag: cell line

tag: genotype/variation

value: overexpressing lncRNA ANTILUC


title: OPC_72hpf_Sample1

description: Dissociated cells


title: Bo-2

source_name: passage 10 to 15 as aging group

value: Senescent


title: mRNA_#1 (Th17 cells) [79_3]

tag: treatment


title: SC_72hpf_Sample3

description: Dissociated cells

value: AB* Gt(foxd3:mCherry);Tg(sox10:mEGFP)

value: 72 hours post fertilization


title: Bo-ao-1


title: Naïve_#2 (Naïve CD4+ T cells) [79_2]

source_name: Naïve CD4+ T cells


title: ARID1A_MOCK_G401

value: MOCK


title: RNAseq_MDAMB231_ANTILUC_rep2

description: polyA-RNA


title: RNAseq_MDAMB231_ANTILUC_rep1

description: polyA-RNA


title: Zhengchang-3

source_name: unaging cells

value: Normal; unaging cells


title: Naïve_#1 (Naïve CD4+ T cells) [79_1]

value: Spleen and Lymph node


title: SC_72hpf_Sample2

description: Dissociated cells

value: trunk


title: SC_72hpf_Sample1

description: Dissociated cells


title: mRNA_#3 (Th17 cells + PAM3CSK4) [79_5]

value: Naive CD4+ T cells


title: Wildtype

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
Cell Ranger ATAC
Cell Ranger produces a count matrix consisting of the counts of fragment ends within each peak region for each barcode. The matrix is then filtered to consist of only cell barcodes, and dimensional reduction is performed via  LSA on the filtered peak-barcode matrix consisting of cut site counts for cell barcodes.
Genome_build: mm10
Supplementary_files_format_and_content: filtered_peak_bc_matrix

source_name: Inguinal Adipose Tissue

extract_protocol:
Adipose tissue is digested and enriched for the mature fraction. Adipocytes are then processed for nuclei isolation.
10X genomics scATAC-seq library construction protocol

value: Cold acclimated followed by 1wk 6C

value: Wildtype


title: Zhengchang-2


title: RNAseq_MDAMB231_HOTAIR_A783U_rep3

state: AL

description: polyA-RNA

value: overexpressing lncRNA HOTAIR_A783U


title: UCP1-KO


title: Bo-3


title: hPGCLC_F2_c63

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR. The STAR genome reference was constructed for 75 nt, and run parameters included --sjdbOverhang 74.
Reads mapped on genes were counted using Bioconductor package 'Rsubread," and the counts were subjected to normalization and differentially expressged gene detection using Bioconductor package 'edgeR.'
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Normalized counts by EdgeR for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Three thousand cells were subjected to direct lysis for cDNA synthesis using Smart-Seq v4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using Nextera XT DNA Library Prep Kit

value: female

value: long-term culture human PGCLC c63


title: TC1-EGFP ATAC-TBLC

state: Beijing

source_name: mESC

value: mESC cultured in SLP medium


title: RNAseq_MDAMB231_HOTAIR_rep3

description: polyA-RNA

value: overexpressing lncRNA HOTAIR


title: Zhengchang-1

value: vascular smooth muscle cells (VSMCs)

value: blood vessel


title: hPGCLC_A4_c71

value: male

value: long-term culture human PGCLC c71


title: RNAseq_MDAMB231_HOTAIR_A783U_rep1

description: polyA-RNA


title: Ribo-TBLC

data_processing:
Library strategy: Ribo-Seq
For single-cell RNA seq, cellranger was used for the pre-processing and Seurat was used for the downstream analysis. Bismark was used for WGBS analysis. The company, Lc-bio Technologies, constructed the Ribo-seq libraries and performed the preliminary bioinformatics.
Genome_build: mm10
Supplementary_files_format_and_content: count, bismark.coverage

extract_protocol:
DNA and RNA extracted according to the manufacturer’s instructions.
Libraries of WGBS-seq, single-cell seq and ribo-seq constructed according to the manufacturer's instructions.


title: meCLIP_MDAMB231_ANTILUC_INPUT

description: cDNA

data_processing:
Library strategy: MeCLIP
For meCLIP samples, the reads were analyzed using the Snakemake workflow that is described in the protocol (PMID:33376190).
For the RNAseq samples, the reads were first inspected for appropriate quality using FastQC (v. 0.11.7).
The indexed Illumina adapters were then removed using Cutadapt (v. 2.4) and then briefly analyzed visually once more with FastQC to ensure all adapters are successfully removed.
Gene expression was quantified using Salmon (1.4.0) and then analyzed using DEseq2 (3.12) to generate lists of differentially expressed genes.
Genome_build: hg19 (meCLIP) / hg38 (RNAseq)
Supplementary_files_format_and_content: BED files were generated using the meCLIP workflow and consist of identified m6A sites for each sample.
Supplementary_files_format_and_content: quant.sf files were generated using Salmon and consist of quantification estimates (TPM) for each transcript.

value: overexpressing antisense luciferase control


title: RNAseq_MDAMB231_HOTAIR_rep2

description: polyA-RNA


title: Ribo-PSC

value: mESC cultured in serum/lif medium


title: meCLIP_MDAMB231_ANTILUC_IP

description: cDNA


title: hPGCLC_A5_rep2_c84

value: long-term culture human PGCLC c84


title: hPGCLC_A5_rep1_c84


title: Bo-1

value: Senescent


title: WGBS-TBLC

data_processing:
For single-cell RNA seq, cellranger was used for the pre-processing and Seurat was used for the downstream analysis. Bismark was used for WGBS analysis. The company, Lc-bio Technologies, constructed the Ribo-seq libraries and performed the preliminary bioinformatics.
Genome_build: mm10
Supplementary_files_format_and_content: count, bismark.coverage


title: RNAseq_MDAMB231_HOTAIR_rep1

description: polyA-RNA


title: RNAseq_MDAMB231_HOTAIR_A783U_rep2

description: polyA-RNA


title: TC1-EGFP ATAC-PSC


title: hPGCLC_A5_rep2_c56

value: long-term culture human PGCLC c56


title: meCLIP_MDAMB231_HOTAIR_A783U_rep2_INPUT

description: cDNA


title: WGBS-PSC


title: hPGCLC_A5_rep1_c56


title: meCLIP_MDAMB231_HOTAIR_A783U_rep2_IP

description: cDNA