title: Control strain in the presence of ATc at 1 minute after rifampicin treatment replicate 1


title: Control, HTP0527B

status: Public on Mar 20 2023

type: SRA

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

country: USA

institute: University of Colorado Anschutz Medical Campus

description: globin-depleted, poly(A)+ RNA from whole blood

library_source: transcriptomic

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

molecule: polyA RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a GlobinClear kit, NEBNext® Poly(A) mRNA Magnetic Isolation Module, and NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by Novogene Co., Ltd.

tag: tissue

value: whole blood

tag: karyotype

value: Control

tag: Sex

value: Male

tag: age

tag: sample source

value: A

tag: library type

value: strand-specific


title: Control strain in the presence of ATc at 0 minutes after rifampicin treatment replicate 2

city: Worcester

first: Scarlet

last: Shell

state: MA

address: 60 Prescott Street

department: Biology & Biotechnology

institute: Worcester Polytechnic Institute

data_processing:
For mRNA degradation profiling, reads were aligned to the reference genome using BWA-MEM v0.7.17 with default parameters.
For mRNA degradation profiling, the alignments were processed for each strand using SAMtools v1.10.
For mRNA degradation profiling, raw coverage of each coordinate was calculated using BEDTools v2.29.1.
For mRNA degradation profiling, the coverage for each gene was calculated as the summation of the coverage of its coordinates using custom Python script.
For mRNA degradation profiling, the raw coverage were nomalized by the library size, relative qPCR expression levels and gene length using custom Python script.
For RNaseE cleavage site analysis, reads were filtered using Trimmomatic v0.39 with the parameters "SLIDINGWINDOW:4:20 MINLEN:25".
For RNaseE cleavage site analysis, the filtered reads aligned to tRNA and rRNA were removed using Bowtie2 v2.4.5 with the parameter "--very-sensitive".
For RNaseE cleavage site analysis, the remaining reads were aligned to genome using Bowtie2 v2.4.5 with the parameter "--very-sensitive".
For RNaseE cleavage site analysis, the alignments were filtered using SAMtools v1.16.1 with the parameter "-q 10 -F 260".
For RNaseE cleavage site analysis, raw strand specific coverage of each coordinate was calculated using SAMtools v1.16.1 and BEDTools v2.30.0.
For RNaseE cleavage site analysis, the single-nucleotide coverage for each gene was normalized by the summed coverage of that gene.
Assembly: NC_008596.1
Supplementary files format and content: mRNA_halfLife_normalized_log2_coverage.txt is a text file including log2 normalized gene coverage for all replicates of all time points and conditions.
Supplementary files format and content: RNaseE_cleavageSite_normalized_coverage.txt is a text file including normalized single-nucleotide coverage and log2 coverage ratio between rne knockdown and control for qualified nucleotide coordinates, along with the annotations for each coordinate.

molecule: total RNA

organism: Mycolicibacterium smegmatis

source_name: Mycolicibacterium smegmatis mc2155

growth_protocol: Strains were growth in 7H9 supplemented with ADC, glycerol, and Tween-80.

extract_protocol:
Pellets were resuspended in Trizol and lysed by bead-beating. RNA was extracted with a Zymo Direct-zol kit, treated with DNase, and purified with a Zymo Clean and Concentrate kit.
Libraries were constructed by the Broad Institute Microbial 'Omics Core using the protocol described in https://doi.org/10.1038/nmeth.3313
Ligation of 3' and 5' adapters to sheared RNA to construct paired-end Illumina RNAseq libraries with TruSeq-style adapters

treatment_protocol:
For hypoxia, cultures were diluted to OD 0.01, sealed in bottles with a 1:1 airspace:culture ratio, and incubated with shaking for 18 hours. Rifampicin was then injected by a syringe to a final concentration of 150 µg/mL and cultures were harvested by freezing in liquid nitrogen at the indicated timepoints.
For non-hypoxic samples, strains were grown to OD 0.8-0.9, with or without addition of ATc 8 hrs prior as indicated. Rifampicin was then added to a final concentration of 150 µg/mL and cultures were harvested by freezing in liquid nitrogen at the indicated timepoints.

tag: cell line

value: Mycolicibacterium smegmatis mc2155

tag: genotype

value: A hygromycin resistance gene was inserted upstream of, and divergent from, the rne promoter.

tag: treatment

value: Rifampicin

tag: time

value: 0 minute


title: T21, HTP0525A

value: Female


title: Control strain in the presence of ATc at 0 minutes after rifampicin treatment replicate 1


title: Japanese quail forebrain cells

city: Haifa

first: Michael

last: Andreyanov

state: Israel

address: Efron 1

department: Medicine

country: Israel

institute: Technion - Israel Institute of Technology

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Coturnix_japonica_2.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Coturnix japonica

source_name: Forebrain

extract_protocol:
Neuronal cultures were prepared from forebrains of nine-day quail embryos. In a laminar hood, shells from post-fertilized eggs were gently removed (by breaking the shell at its upper tip). Embryos were isolated from the yolk and placed in Dulbecco’s Modified Eagle Media/Nutrient Mixture F-12 (denoted dissociation medium). Tissues were then enzymatically and mechanically dissociated . Briefly, skin, skull and meninges were removed by scissors and tweezers, and forebrains were isolated and placed in a 15 ml conical tube containing dissociation media enriched with Papain (30 U/ml) and DNAse 1 (57 U/ml), and placed at 37 °C for 30 min. Following incubation, the solution was gently removed without disturbing the forebrains. Digested forebrains were washed three times with PBS and after the last wash, PBS was completely removed and replaced by 2 ml of plating medium consisting of neurobasal medium (Gibco, Cat. 21103049) supplemented with 2% B-27 (Gibco, Cat. 17504044), 1% Pen/Strep and 0.25% Glutamax (Gibco, Cat. 35050061). Then, tissue was manually dissociated by gentle trituration of solution with a fire polished glass pipette (x15), followed by a single trituration with a 1000 ml plastic tip (to ensure complete dissociation). This solution was then applied onto a 40 mm cell strainer (placed on a 50 ml conical tube and pre-washed by 1 ml plating medium). Additional plating medium was added to strainer after passing the entire solution, to elute remaining cells from strainer. The filtered solution, containing the dissociated cells, was transferred to sterile tissue-culture grade plastic plates (Corning, 60 mm, Cat. 430166) pre-coated with PDL, and these were placed for one hour in an incubator (37°C, 5% CO2). Following incubation, medium was removed and replaced by fresh plating medium (pre-warmed in the incubator). Plates were placed back in incubator and half the media was replaced every two days by fresh and pre-warmed plating medium. Cultures produced from nine-day old embryos, grown for a week DIV had their medium replaced with dissection-dissociation medium supplemented with 20 U/ml papain. The plate was incubated for 10 minutes in 37C, 5% CO2. Cells were then pipetted thoroughly and moved to 15 ml canonical tube for gentle centrifugation (5 minutes at 300 rcf). Supernatant was removed and replaced with 1 ml DMEM with 10% FBS. Cells were then filtered through a cell strainer (40 µm nylon filter, LifeGene). Cells were then centrifuged again, and medium replaced as before. Cells were counted using a hemocytometer. Survival assay was performed with trypan blue.
One RNA single cell library was prepared according to 10X manufacture protocol (Chromium Next GEM Single Cell 3’ Library & Gel Bead Kit v3.1, PN-1000268) using 20,000 input cells (force_10000 was used).

value: Forebrain

value: exctracted at 9 day old embryonic brain, grown in vitro for 7 days


title: Control, HTP0524B


title: Dorsal Root Ganglion, IAV, 4dpi, 4

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Reads aligned to MesAur1.0 genome assembly using Ensembl GTF file and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Assembly: Mesocricetus Auratus MesAur1.0
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)

organism: Mesocricetus auratus

source_name: Dorsal Root Ganglion

extract_protocol:
Trizol Phenol Chloroform
Poly A tail enrichment and preparation using True Strand RNA-seq Prep

value: Dorsal Root Ganglion

value: WT

value: Influenza (100,000 PFU) --- 4 dpi


title: Dorsal Root Ganglion, SARS-CoV-2, 4dpi, 3

value: SARS-CoV-2 (1000 PFU) --- 4 dpi


title: Dorsal Root Ganglion, IAV, 4dpi, 2


title: Dorsal Root Ganglion, IAV, 4dpi, 1


title: Control strain in the presence of ATc at 0 minutes after rifampicin treatment replicate 3


title: Dorsal Root Ganglion, IAV, 4dpi, 3


title: Control strain in the absence of ATc at 32 minutes after rifampicin treatment replicate 3

value: 32 minutes


title: Dorsal Root Ganglion, MOCK, 4dpi, 2

value: Mock (PBS-treated) --- 4 dpi


title: Dorsal Root Ganglion, SARS-CoV-2, 4dpi, 4


title: Dorsal Root Ganglion, MOCK, 4dpi, 1


title: Control, HTP0523B

value: whole blood

value: Control


title: T21, HTP0519A

value: Male

value: A


title: Control strain in the absence of ATc at 32 minutes after rifampicin treatment replicate 2

value: Mycolicibacterium smegmatis mc2155


title: Dorsal Root Ganglion, IAV, 1dpi, 4

value: Influenza (100,000 PFU) --- 1 dpi


title: Dorsal Root Ganglion, IAV, 1dpi, 3


title: Control strain in the absence of ATc at 32 minutes after rifampicin treatment replicate 1

value: A hygromycin resistance gene was inserted upstream of, and divergent from, the rne promoter.

value: Rifampicin


title: Dorsal Root Ganglion, IAV, 1dpi, 2


title: Dorsal Root Ganglion, SARS-CoV-2, 4dpi, 1


title: Dorsal Root Ganglion, MOCK, 4dpi, 4


title: Control strain in the presence of ATc at 1 minute after rifampicin treatment replicate 3

value: 1 minute


title: T21, HTP0517A

value: strand-specific


title: Dorsal Root Ganglion, MOCK, 4dpi, 3


title: Dorsal Root Ganglion, SARS-CoV-2, 4dpi, 2


title: Dorsal Root Ganglion, SARS-CoV-2, 1dpi, 3

value: SARS-CoV-2 (1000 PFU) --- 1 dpi


title: Dorsal Root Ganglion, SARS-CoV-2, 1dpi, 4

value: Dorsal Root Ganglion


title: Control strain in the absence of ATc at 8 minutes after rifampicin treatment replicate 3

value: 8 minutes


title: T21, HTP0510A

value: Female


title: Control strain in the absence of ATc at 8 minutes after rifampicin treatment replicate 2


title: T21, HTP0515A


title: Dorsal Root Ganglion, MOCK, 1dpi, 2

value: WT

value: Mock (PBS-treated) --- 1 dpi


title: Dorsal Root Ganglion, MOCK, 1dpi, 3


title: Dorsal Root Ganglion, MOCK, 1dpi, 4


title: Dorsal Root Ganglion, SARS-CoV-2, 1dpi, 1


title: Dorsal Root Ganglion, MOCK, 1dpi, 1


title: Control, HTP0508B2


title: Control strain in the absence of ATc at 8 minutes after rifampicin treatment replicate 1


title: D8plus3W, iSOX18, No DOX, CD56plus, rep1

city: Madison

first: Igor

middle: I.

last: Slukvin

address: 1220 Capitol Court

institute: University of Wisconsin

data_processing:
RNA-seq fragments were aligned by STAR (version 2.5.2b) to the human genome (hg38) with GENCODE basic gene annotations (version 38)
Gene expression levels were quantified by RSEM (version 1.3.0)
Genome_build: hg38
Supplementary_files_format_and_content: TSV: RSEM quantification results at the gene level

source_name: Natural killer cells generated from iSOX18 H1 hESCs

extract_protocol:
RNA was harvested using RNeasy micro kit (Qaigen), and used with 100 ng total RNA for preparing sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: cell type

value: Natural killer cells

tag: cell surface markers

value: Day 8 plus 3 weeks CD56+

value: no DOX

value: no SOX18 induction

tag: Stage

value: Day 8 plus 3 weeks


title: D8plus3W, iSOX18, No DOX, CD56plus, rep2


title: Dorsal Root Ganglion, IAV, 1dpi, 1

value: Influenza (100,000 PFU) --- 1 dpi


title: D8plus3W, iSOX18, DOX, CD56plus, rep2

value: DOX

value: SOX18 overexpression


title: T21, HTP0516A

value: whole blood

value: Male

value: A


title: D8, iSOX18, No DOX, CD43plusCD235aplusCD41aplusCD45neg, rep2

source_name: Day 8 differntiated iSOX18 H1 HSCs

value: Hematopoietic progenitors

value: Day 8


title: Control strain in the absence of ATc at 16 minutes after rifampicin treatment replicate 3

value: Mycolicibacterium smegmatis mc2155

value: A hygromycin resistance gene was inserted upstream of, and divergent from, the rne promoter.

value: Rifampicin

value: 16 minutes


title: Control strain in the absence of ATc at 4 minutes after rifampicin treatment replicate 3

value: 4 minutes


title: Dorsal Root Ganglion, SARS-CoV-2, 1dpi, 2

value: Dorsal Root Ganglion

value: WT

value: SARS-CoV-2 (1000 PFU) --- 1 dpi


title: D8, iSOX18, No DOX, CD43plusCD235aplusCD41aplusCD45neg, rep1

value: male

value: no DOX

value: no SOX18 induction


title: Control strain in the absence of ATc at 16 minutes after rifampicin treatment replicate 1


title: Control, HTP0506B

value: Control

value: strand-specific


title: T21, HTP0512A

value: whole blood

value: Male


title: D8, iSOX18, No DOX, CD43plusCD235anegCD41anegCD45neg, rep2

value: Hematopoietic progenitors


title: Control strain in the absence of ATc at 4 minutes after rifampicin treatment replicate 2


title: D8plus3W, iSOX18, DOX, CD56plus, rep1

value: Natural killer cells

value: Day 8 plus 3 weeks CD56+

value: DOX

value: SOX18 overexpression

value: Day 8 plus 3 weeks


title: Control strain in the absence of ATc at 16 minutes after rifampicin treatment replicate 2

value: Mycolicibacterium smegmatis mc2155

value: A hygromycin resistance gene was inserted upstream of, and divergent from, the rne promoter.

value: Rifampicin

value: 16 minutes


title: T21, HTP0507A

value: A


title: D8, iSOX18, No DOX, CD43plusCD235anegCD41anegCD45neg, rep1

value: male

value: no DOX

value: Day 8


title: Control strain in the absence of ATc at 4 minutes after rifampicin treatment replicate 1

value: 4 minutes


title: T21, HTP0501A

value: whole blood

value: strand-specific


title: D8, iSOX18, DOX, CD43plusCD235aplusCD41aplusCD45neg, rep1

value: Hematopoietic progenitors


title: Control, HTP0498B

value: Control

value: Male


title: D8, iSOX18, DOX, CD43plusCD235anegCD41anegCD45neg, rep2

value: DOX


title: D8, iSOX18, DOX, CD43plusCD235aplusCD41aplusCD45neg, rep2

value: SOX18 overexpression


title: D8, iSOX18, DOX, CD43plusCD235anegCD41anegCD45neg, rep1


title: D4, iSOX18, No DOX, CD144plusKDRplusDLL4negCXCR4neg, rep2

source_name: Day 4 differentiated iSOX18 H1 hESCs

value: Day 4 Hemogenic endothelium

value: Day 4 CD144+KDR+DLL4-CXCR4-

value: no SOX18 induction

value: Day 4


title: D4, iSOX18, No DOX, CD144plusKDRplusDLL4negCXCR4neg, rep1


title: D4, iSOX18, Dox, CD144plusKDRplusDLL4negCXCR4plus, rep2

value: Day 4 CD144+KDR+DLL4-CXCR4+


title: Control, HTP0502B

value: A


title: D4, iSOX18, Dox, CD144plusKDRplusDLL4negCXCR4neg, rep2

value: male


title: D4, iSOX18, Dox, CD144plusKDRplusDLL4negCXCR4plus, rep1


title: D4, iSOX18, Dox, CD144plusKDRplusDLL4negCXCR4neg, rep1


title: ND608, Lonza, D3, Rep2

city: Philadelphia

first: Shelley

middle: L.

last: Berger

state: PA

address: 3400 Civic Center Blvd

department: Penn Epigenetics Institute

institute: University of Pennsylvania

data_processing:
FASTQ files were aligned using STAR 2.7.1a using hg38 Gencode reference genome
Read counts of genes were quantified by STAR using --quantMode GeneCounts parameter.
Normalized read counts were generated using DESeq2. And batch corrected reads are further generated by limma.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read count and normalized batch corrected read count values for each sample

source_name: PBMC

extract_protocol:
Thermo TRIzol Reagent manual for RNA seperation; ZYMO RNA Clean & Concentrator™-5   RNA Clean-up protocol
Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L); NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760L) Instruction Manual

value: PBMC

value: T cell

tag: donor

value: female

value: Lonza

tag: replicate


title: ND608, Lonza, D3, Rep1


title: Control strain in the absence of ATc at 2 minutes after rifampicin treatment replicate 3

value: Mycolicibacterium smegmatis mc2155

value: A hygromycin resistance gene was inserted upstream of, and divergent from, the rne promoter.

value: Rifampicin

value: 2 minutes


title: 2102EP MPHv2 SAMv2, cisplatin

city: Bonn

first: Kai

last: Funke

state: NRW

address: Venusberg-Campus 1

department: Pathology, Developmental Pathology

country: Germany

institute: University Hospital Bonn

description: PCR with sgRNA encoding region specific primers was performed on the genomic DNA. The product was used for sequencing.

library_source: genomic

data_processing:
Bioinformatic analysis was carried out as described by Joung et al. 2017 (doi:10.1038/nprot.2017.016)  applying the count_spacers.py algorithm in Python 2.7/Biopython
Assembly: Guide spacer sequences are provided by Joung et al. 2017 (doi:10.1038/nprot.2017.016)
Supplementary files format and content: comma-separated text files include guide spacer sequences/ candidate gene name and corresponding read counts
Library strategy: DNA-Seq

molecule: genomic DNA

growth_protocol: 2102EP and JAR cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin (pen/strep) and 200 mM L-glutamine (L-glu). All cells were kept at 37 °C and 7.5 % CO2.

extract_protocol:
Genomic DNA was isolated using the Quick DNA Midi Prep Plus Kit (Zymo Research, Irvine, CA, USA)
Library construction was performed according to Joung et al. 2017 (doi:10.1038/nprot.2017.016). In brief, sgRNA encoding DNA regions were amplified with specific Illumina adapter/bar code labeled primers using NEBNext® High-Fidelity 2X PCR Master Mix (New England Biolabs GmbH, Frankfurt am Main, Germany). DNA sequencing was performed by the Core Facility Next Generation Sequencing (University of Bonn, Germany).

treatment_protocol: For the genome-scale activation screen stable JARMPHv2 and 2102EPMPHv2 cell lines expressing MS2-p65-HSF1 were transduced with the lentiSAMv2 library. The overexpression cell populations were treated with cisplatin, surviving cells were recovered in cell culture medium.

value: Embryonal Carcinoma

value: Cisplatin 2.5 µM day 1 to 14


title: JAR MPHv2 SAMv2, cisplatin

source_name: JAR

value: JAR

value: Choriocarcinoma

value: Cisplatin 10 µM day 1 to 2 and 5 µM day 3 to 9


title: Control strain in the absence of ATc at 1 minute after rifampicin treatment replicate 1

value: 1 minute


title: Control strain in the absence of ATc at 2 minutes after rifampicin treatment replicate 1


title: Control strain in the absence of ATc at 0 minutes after rifampicin treatment replicate 3

value: 0 minute


title: Control strain in the absence of ATc at 1 minute after rifampicin treatment replicate 3


title: Control, HTP0495B

value: whole blood

value: Control

value: Female

value: A

value: strand-specific


title: Control strain in the absence of ATc at 1 minute after rifampicin treatment replicate 2


title: T21, HTP0491A

value: Male


title: Control, HTP0492B


title: Control, HTP0493B


title: T21, HTP0494A


title: Control strain in the absence of ATc at 2 minutes after rifampicin treatment replicate 2

value: Mycolicibacterium smegmatis mc2155


title: Control strain in the absence of ATc at 0 minutes after rifampicin treatment replicate 1

value: A hygromycin resistance gene was inserted upstream of, and divergent from, the rne promoter.


title: ND608, PAGE, 6h, Rep2

value: PBMC

value: T cell

value: female

value: PAGE


title: ND608, Lonza, 6h, Rep1

value: Lonza


title: Control, HTP0497B


title: ND608, PAGE, D3, Rep2


title: ND608, PAGE, D3, Rep1


title: ND608, PAGE, 6h, Rep1


title: T21, HTP0487A

value: B


title: ND608, Mock, D3, Rep2

value: Mock


title: ND608, Lonza, 6h, Rep2


title: T21, HTP0485A


title: ND608, Mock, D3, Rep1


title: Control strain in the absence of ATc at 0 minutes after rifampicin treatment replicate 2

value: Rifampicin


title: T21, HTP0488A


title: ND608, Mock, 6h, Rep2


title: T21, HTP0484A

value: C


title: ND518, Lonza, D3, Rep1


title: C2C12_IAA_cyto_RNA_rep1

city: Hong Kong

first: QIANG

last: SUN

address: Ngan Shing Street

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: cytoplamic RNA

data_processing:
Adaptor sequence trimming, quality filtering (i.e. quality<38 and length<70) and duplication removal were first conducted.
Remaining reads were aligned to the mouse genome mm9 using STAR software with default parameters.
Cufflinks was then used to derive the fragments per kilobase per million (FPKM) values.
Genes were identified as differentially expressed genes (DEGs) if the change of expression level is greater than 2 folds and the p-value is less than 0.01 between two stages/conditions.
Alternative splicing events were then detected by rMATS with default parameters. A cutoff of absolute value of “IncLevelDifference” <0.1 was used to define differentially splicing events (DSE) in YTHDC1 iKO vs. Ctrl.
Assembly: mm9
Supplementary files format and content: *.fpkm_tracking: Tab-delimited files from Cufflinks containing FPKM values.

organism: Mus musculus

source_name: C2C12 cell

growth_protocol: C2C12 and mAID-YTHDC1 C2C12 cells  were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep. FACS sorted ASCs were cultured in F10+20%FBS+1%Pen/Strep+b-FGF. All cells were grown in 5% CO2 37°C incubator.

extract_protocol:
For total RNA-seq, 1ml Trizol(Invitogen) were added to cells and RNA were extracted according to manufacturer's protocol. For subcelluar RNA-seq, cells were treated with buffer A (HEPES-KOH 50 mM pH 7.5, 10 mM KCl, 350 mM sucrose, 1 mM EDTA, 1 mM DTT, 0.1% Triton X-100) for 5 min on ice and then homogenized with a T 10 basic ULTRA-TURRAX® homogenizer at 4th gear for 1min. The nuclei were harvested by brief centrifugation (2000g, 5 min), while the supernatant was collected as the cytoplasmic fraction. Nuclei pelltet were resuspended with same volume buffer A. Then 1ml Trizol were added to both nuclear and cytoplasmic fraction and subjected for RNA extracion. All RNA were subjected to polyA selection (Ambion, 61006) before library preparation.
RNA libraries were prepared with about 1μg RNA according to the manufacturer's protocol (NEB UltraII RNA library kit for illumina). The libraries were sequenced in 2 × 150 nt manner on HiSeq X ten (Illumina).

treatment_protocol: To induce YTHDC1 degradation,C2C12 mAID-YTHDC1 cell line were treated with 1 μM 5-Ph-IAA(IAA) for 8 hours. As control, the same C2C12 mAID-YTHDC1 cell line were treated with DMSO(Ctrl/WT).

value: YTHDC1 degradation


title: ND518, PAGE, D3, Rep1


title: ND518, Lonza, 6h, Rep1


title: C2C12_WT_nuc_RNA_rep1

description: nuclear RNA

value: WT


title: ND518, PAGE, D3, Rep2


title: C2C12_IAA_nuc_RNA_rep1

description: nuclear RNA


title: ND518, PAGE, 6h, Rep2


title: ND608, Mock, 6h, Rep1


title: C2C12_WT_cyto_RNA_rep1

description: cytoplamic RNA


title: ND518, PAGE, 6h, Rep1


title: ND518, Lonza, D3, Rep2


title: ND518, Lonza, 6h, Rep2


title: ASC48_iKO_nuc_RNA_rep2

description: nuclear RNA

value: ASC

value: YTHDC1 iKO


title: ND518, Mock, D3, Rep2


title: ASC48_iKO_cyto_RNA_rep2

description: cytoplamic RNA


title: ASC48_iKO_cyto_RNA_rep1

description: cytoplamic RNA


title: T21, HTP0480A

value: whole blood

value: Female

value: strand-specific


title: T21, HTP0482A

value: Male


title: ND518, Mock, 6h, Rep2

value: PBMC


title: T21, HTP0479A


title: ASC48_WT_nuc_RNA_rep2

description: nuclear RNA


title: T21, HTP0478A


title: ND518, Mock, D3, Rep1

value: T cell


title: T21, HTP0476A


title: ND518, Mock, 6h, Rep1

value: female


title: T21, HTP0475A


title: ASC48_iKO_nuc_RNA_rep1

description: nuclear RNA


title: Brain, control of the water avoidance stress, biol rep 3

city: Daejeon

first: Seyun

last: Kim

address: Daehak-ro 291

country: South Korea

institute: KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Read count extraction using bedtools.
Assembly: mm10 (UCSC)
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Brain

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: The 1 h water avoidance stress (WAS) procedure consisted in placing each mouse on a small platform (3 cm width × 5 cm length × 4 cm height) in the middle of a small plastic basin (40 cm length × 40 cm width × 60 cm height) filled with warm water (22 °C) at the height level of the platform. Control group mice were placed on the same platform but in a waterless container for 1 h.

value: Brain

tag: strain

value: male

tag: treatment time

value: 1 h

value: control of the water avoidance stress (waterless)


title: ASC48_WT_nuc_RNA_rep1

description: nuclear RNA


title: Brain, control of the water avoidance stress, biol rep 1

tag: tissue


title: Brain, control of the water avoidance stress, biol rep 2

tag: Sex


title: Brain, water avoidance stress, 1hour, biol rep 3

value: water avoidance stress


title: T21, HTP0473A

tag: karyotype

tag: age

value: C


title: ASC48_WT_cyto_RNA_rep2

description: cytoplamic RNA


title: T21, HTP0469A

tag: sample source

tag: library type


title: C2C12_IAA_total_RNA_rep2

description: Total RNA

tag: cell line

value: YTHDC1 degradation


title: T21, HTP0477A


title: T21, HTP0471A


title: C2C12_IAA_total_RNA_rep1

description: Total RNA

tag: treatment


title: Brain, water avoidance stress, 1hour, biol rep 1


title: D3TAM960

city: Pamplona

first: Juan

middle: Jose

last: Lasarte

state: Navarra

address: Avda Pio XII, 55

department: Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación Médica Aplicada

data_processing:
RNA-seq reads are trimmed using Trim Galore v0.4.4 using default parameters to remove the Nextera adapter sequence.
Mapping is performed using STAR (2.6) against the mouse NCBIM37 genome, guided by gene models from Ensembl annotation release 68
Quantification and generation of gene expression matrices were performed with the function featureCounts, implemented in the R package Rsubread
Aligned fragments are imported into RStudio and before statistical analysis, the function filterbyExpr, implemented in the R package edgeR was used to determine genes with enough counts for further analyse
Differential gene expression analysis is performed using the DESeq2 algorithm within R and RStudio

source_name: Highly purified CD4 + T cells from  Rosa26-CreERT2 +/- Sin3AF/F mice cultured for 6 days with  IL7 and for 3 aditional days in the presence of Th17 polarizing conditions and  in the presence of Tamoxifen (Sin3A deficient)

extract_protocol:
Purified CD4+ T cells were resuspended in 100 μL of Lysis/Binding Buffer (Ambion), vortexed and stored at -80°C until further processing.
llumina strand specific mRNA Roughly 100ng of high quality total RNA (RIN >8) was used for the transcriptomic interrogation of control and SIN3A deleted CD4 T cells using Illumina’s Stranded mRNA Prep ligation according to the manufacturer’s instructions. Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules in the total RNA. The purified mRNA was fragmented and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. A second strand cDNA synthesis step removed the RNA template while incorporating dUTP in place of dTTP in order to preserve strand specificity. Next, double-stranded cDNA was A-tailed, then ligated to Illumina anchors bearing T-overhangs. PCR-amplification of the library allowed the barcoding of the samples with 10bp dual indexes and the completion of Illumina sequences for cluster generation. Libraries were quantified with Qubit dsDNA HS Assay Kit and their profile was examined using Agilent’s HS D1000 ScreenTape Assay. Sequencing was carried out in an Illumina NextSeq2000 using paired end, dual-index sequencing (Rd1: 59 cycles; i7: 10 cycles; i5: 10 cycles, Rd2 59 cycles) at a depth of 30 million reads per sample.

treatment_protocol: CD4 + T cells  were cultured  in the presence of IL7  in the presence/absence of Tamoxifen to silence Sin3A. When indicated, cells were cultured for 3 aditional days in Th17 polarizing coditions

value: CD4 + T cells

tag: sin3a status

value: deficient

value: C57BL/6 J Rosa26-CreERT2 +/- Sin3AF/F  mice

value: Two months


title: Brain, water avoidance stress, 1hour, biol rep 2


title: D3TAM959

tag: gender

value: Female


title: ASC48_WT_cyto_RNA_rep1

description: cytoplamic RNA

value: ASC

value: WT


title: T21, HTP0467A

value: whole blood

value: strand-specific


title: Control, HTP0466B

value: Control


title: D3TAM957

tag: cell type

value: Male


title: Mouse Liver tumor, Nrf2 KO, AcH3K27, rep1

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

description: Mouse Liver tumor_AcH3K27_EMDMillipore

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
reads were mapped with Bowtie2 and analyzed by MACS2 for the peak calling
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Liver tumor

growth_protocol: Male Nrf2 wild type or knockout mice were were treated with hepatic carcinogen diethylnitrosamine (DEN) (25 mg/kg body weight) via intraperitoneal injection at 14-day-old to initiate tumor formation. At the 36 weeks post-DNE treatment, mice were sacrificed for liver tumor collection.

extract_protocol:
Liver tumor tissues were crosslinked with 1% formaldehyde, sonicated, and immunoprecipitated with AcH3K27 antibody.
10 ng ChIP pulldown DNA was prepared for the library using TruSeq ChIP Sample Preparation kit (Illumina). Libraries were amplified using 18 cycles on the thermocycler, followed by size selection at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter.

value: male

value: Liver tumor

tag: genotype

value: Knockout Nrf2-/-

tag: chip antibody


title: Mouse Liver tumor, Nrf2 WT, AcH3K27, rep2

description: Mouse Liver tumor_AcH3K27_EMDMillipore

value: wild type Nrf2+/+


title: BASALTAM960

source_name: Highly purified CD4 + T cells from  Rosa26-CreERT2 +/- Sin3AF/F mice cultured for 6 days with  IL7  in the presence of Tamoxifen (Sin3A deficient)


title: D3TAM955


title: C2C12_WT_total_RNA_rep2

description: Total RNA


title: T21, HTP0465A

value: C


title: C2C12_WT_total_RNA_rep1

description: Total RNA


title: Mouse Liver tumor, Nrf2 KO, AcH3K27, rep2

description: Mouse Liver tumor_AcH3K27_EMDMillipore


title: Mouse Liver tumor, Nrf2 WT, AcH3K27, rep1

description: Mouse Liver tumor_AcH3K27_EMDMillipore


title: ASC48_iKO_total_RNA_rep2

description: Total RNA

value: YTHDC1 iKO


title: T21, HTP0464A


title: BASALTAM959

value: CD4 + T cells


title: T21, HTP0468A2

value: D


title: ASC48_iKO_total_RNA_rep1

description: Total RNA


title: BASALTAM957

value: deficient

value: C57BL/6 J Rosa26-CreERT2 +/- Sin3AF/F  mice


title: D3960

source_name: Highly purified CD4 + T cells from Rosa26-CreERT2 +/- Sin3AF/F mice cultured for 6 days with  IL7 and for 3 aditional days in the presence of Th17 polarizing conditions in the absence of Tamoxifen (Sin3A suficient)

value: sufficient

value: Two months


title: BASALTAM955


title: ASC48_WT_total_RNA_rep2

description: Total RNA

value: ASC

value: WT


title: D3957


title: T21, HTP0463A

value: whole blood

value: Female

value: strand-specific


title: D3959


title: T21, HTP0461A


title: BASAL960

source_name: Highly purified CD4 + T cells from  Rosa26-CreERT2 +/- Sin3AF/F mice cultured for 6 days with  IL7  in the absence of Tamoxifen (Sin3A suficient)

value: Male


title: T21, HTP0462A


title: BASAL959


title: ASC48_WT_total_RNA_rep1

description: Total RNA


title: ASC24_iKO_total_RNA_rep1

description: Total RNA


title: T21, HTP0460A


title: BASAL957


title: O GSH-low RNA-Seq replicate 2

city: Palo Alto

first: Jamie

middle: O.

last: Brett

state: CA

address: 3801 Miranda Avenue, Building 100, Room E4-216

department: Neurology and Neurological Sciences

institute: Stanford University

description:
Olo2
PolyA-selected RNA
processed data file: GSH_MuSC_RNASeq.txt

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore) (quality cutoff 20, adapter stringency 1, final length filter 50). Trimmed reads were mapped to mm10 (Ensembl release 89, no patches) using transcript annotations from Ensembl with STAR (Dobin et al. 2013). Exonic reads that mapped uniquely were summarized over genes with the featureCounts module of the Subread package (Liao et al. 2014).
Genes lacking an Entrez ID were filtered out. To exclude spurious reads, only genes with at least 0.5 RPKM in at least 2 samples were included. Raw count data were then normalized using edgeR with the TMM method (Robinson et al. 2010).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GSH_MuSC_RNASeq.txt: Tab-delimited text file containing normalized FPKMs for each gene.

source_name: Skeletal muscle stem cells

extract_protocol:
FACS-isolated MuSCs were snap-frozen before RNA extraction.
RNA was reverse-transcribed using oligo(dT) priming. The cDNA was then sheared and subjected to end repair, multiplexed adapter ligation, and library amplification. Libraries underwent single-end 150-bp sequencing at the Stanford Genome Sequencing Service Center with a NextSeq 500 in high-output mode to a depth of 68-98 million reads.

value: 23 months

value: Skeletal muscle stem cells

tag: glutathione status

value: low


title: O GSH-high RNA-Seq replicate 2

description:
Ohi2
PolyA-selected RNA
processed data file: GSH_MuSC_RNASeq.txt

value: High


title: O GSH-low RNA-Seq replicate 1

description:
Olo1
PolyA-selected RNA
processed data file: GSH_MuSC_RNASeq.txt


title: ASC24_WT_total_RNA_rep1

description: Total RNA


title: T21, HTP0459A

source_name: whole blood

value: C


title: BASAL955

value: CD4 + T cells


title: T21, HTP0458A


title: Control, HTP0457B

value: Control


title: Y GSH-all RNA-Seq replicate 2

description:
Yall2
PolyA-selected RNA
processed data file: GSH_MuSC_RNASeq.txt

value: 4 months


title: D3955

value: C57BL/6 J Rosa26-CreERT2 +/- Sin3AF/F  mice


title: O GSH-high RNA-Seq replicate 1

description:
Ohi1
PolyA-selected RNA
processed data file: GSH_MuSC_RNASeq.txt


title: T21, HTP0456A


title: Y GSH-all RNA-Seq replicate 1

description:
Yall1
PolyA-selected RNA
processed data file: GSH_MuSC_RNASeq.txt


title: C5 or rep4_AZA

city: Berlin

first: Markus

last: Morkel

address: Ihnestraße 63-73

institute: Max Planck Institute for molecular Genetics

description:
C5_or_4_AZA
processed data file: modifiers_rnaseq_counts.csv

data_processing:
Alignment of RNA-seq reads to the PWD(assembly)/B6(mm10) mixed reference using bwa.
PWD reads are mapped to their corresponding position in the mm10 reference genome.
Quantification of reads per gene with htseq-count
Genome_build: mm10/PWD assembly version 2b
Supplementary_files_format_and_content: modifiers_rnaseq_counts.csv: Comma-separated text file with RNA-seq read counts per gene.

source_name: organoid

extract_protocol:
Intestinal tissue as indicated was processed using the Qiagen Allprep RNA/DANN Kit according to manufacturer's instructions.
For RNA sequencing, 4 µg of total RNA were depleted for ribosomal RNA using the RiboMinus Eukaryote Kit for RNA-seq (Invitrogen) following the manufacturer’s instructions. The RiboMinus depleted RNA was then used for the generation of single-end RNA-seq libraries. cDNA libraries were size selected on a 2% agarose gel, fragments of 150-200 nt were excised (corresponding to insert sizes of 80-130 nt) and purified using the QiaQuick Gel extraction kit (Qiagen). Sequencing was performed on an Illumina Genome Analyser IIx.

value: CSS C57BL/6 chr5 PWD

value: APC min

value: organoid

value: 15-19 weeks


title: C5 or rep4_CON

description:
C5_or_4_CON
processed data file: modifiers_rnaseq_counts.csv

value: control


title: Control, HTP0455B

value: whole blood

value: Female


title: T21, HTP0454A

value: Male

value: strand-specific


title: T21, HTP0452A


title: T21, HTP0451A


title: NASH3

city: Nanjing

first: Kangpeng

last: Jin

state: Jiangsu Province

address: 321 Zhongshan Road

department: Department of Hepatobiliary Surgery

country: China

institute: The Affiliated Drum Tower Hospital of Nanjing 9 University Medical School

data_processing:
Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the mouse mm10 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: hg38
Supplementary_files_format_and_content: raw count and FPKM

source_name: liver tissue

extract_protocol:
RNAiso Plus Total RNA extraction reagent  (Cat#9109, TAKARA)
VAHTS Stranded mRNA-seq Library Prep Kit for Illumina®（Cat#NR602-02，Vazyme）

value: liver tissue

tag: with nash

value: Yes


title: NASH5


title: NASH4


title: atrial cardiac fibroblasts_2

type: RNA

city: Shinjuku, Tokyo

first: Shinako

last: Masuda

address: 8-1 Kawada-cho

department: Institute of Advanced Biomedical Engineering and Science

country: Japan

institute: Tokyo Women's Medical University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: atrial cardiac fibroblasts

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

growth_protocol: Normal human atrial cardiac fibroblasts, normal human ventricular cardiac fibroblasts, normal human dermal fibroblasts and bone marrow-derived mesenchymal stem cells were cultured in commercially available growth media (lonza): FGM-2 for normal human dermal fibroblasts, FGM-3 for normal human atrial cardiac fibroblasts and normal human ventricular cardiac fibroblasts, MSCGM for bone marrow-derived mesenchymal stem cells. These primary cells were used at passages 5-7. iPS cell-derived fibroblasts were prepared from 201B7 or 253G1 cell lines.

extract_protocol: Total RNA was extracted from cells using an RNeasy Plus Mini Kit (Qiagen, Hilden, Germany), according to manufacturer's instructions. RNA quantity and quality were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc.) and Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA), as recommended by the manufacturers.


title: T21, HTP0449A


title: Normal 3

value: No


title: NASH1


title: ventricular cardiac fibroblasts_3

source_name: ventricular cardiac fibroblasts


title: ventricular cardiac fibroblasts_1


title: B6 or rep2_CON

description:
B6_or_2_CON
processed data file: modifiers_rnaseq_counts.csv

tag: strain


title: B6 or rep1_CON

description:
B6_or_1_CON
processed data file: modifiers_rnaseq_counts.csv


title: B6 or rep2_AZA

description:
B6_or_2_AZA
processed data file: modifiers_rnaseq_counts.csv


title: atrial cardiac fibroblasts_1


title: C5 or rep3_AZA

description:
C5_or_3_AZA
processed data file: modifiers_rnaseq_counts.csv


title: C5 or rep3_CON

description:
C5_or_3_CON
processed data file: modifiers_rnaseq_counts.csv


title: B6 or rep1_AZA

description:
B6_or_1_AZA
processed data file: modifiers_rnaseq_counts.csv


title: T21, HTP0448A

description: globin-depleted, poly(A)+ RNA from whole blood

value: C


title: Normal 2


title: Normal 1


title: Normal 5


title: ventricular cardiac fibroblasts_2


title: T21, HTP0450A


title: bone marrow-derived mesenchymal stem cells_3


title: dermal fibroblasts_3

source_name: dermal fibroblasts


title: dermal fibroblasts_1


title: Normal 4


title: dermal fibroblasts_2


title: NASH2

description: NASH2 SYZ


title: T21, HTP0446A


title: T21, HTP0445A


title: Control, HTP0447B2

value: D


title: Control, HTP0444B2

value: Control


title: Wild type_Rep2

city: Chicago

first: Maria

middle: Paula

last: Zappia

state: IL

address: 900 S Ashland Ave

department: Biochemistry and Molecular Genetics

institute: University of Illinos at Chicago

description: ATACseq was performed using Actif Motif kit

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
Quality of read was checked using MultiQC v1.5
Illumina paired end raw FastQ file (2x150) were trimmed using cutadapt 2.3 with Python 3.6.10. Trimmed reads were aligned using Bowtie2 (2.4.1) against Drosophila melanogaster genome version BDGP6.32 (From Ensembl) and corresponding gene model is extracted from Ensembl version 105
Aligned BAM file were sorted and PCR duplicates were marked using picard
Peak calling was run using MACS2 v2.2.7.1
Assembly: BDGP6.32
Supplementary files format and content: bed file

organism: Drosophila melanogaster

source_name: wild type flies

growth_protocol: Flies were kept at 25 °C in vials containing standard cornmeal- agar medium.

extract_protocol:
At least 40 pharate animals per sample were staged. Thoracic muscles were collected and flight muscles were dissected. Nuclei were extracted by mincing tissue with douncer and lysis buffer as in (Buenrostro et al, Curr. Protoc. Mol. Biol, 2015) with some modification. A final concentration of TritonX-100 0.5% was used and nuclei suspension was mixed with percoll solution (9:1) to remove myofibrils from the nuclei suspension (Hahn and Covault Analytical Biochemistry, 1990). Nuclei were tagmented and tagmented chromatin was used to make libraries using ATAC-Seq kit (Active Motif, 53150) and these were sequenced.
ATAC-Seq kit from Active Motif (cat# 53150)
ATAC-Seq: Indexed primers based on Illumina’s Nextera adapters

treatment_protocol: no treatment

value: thoracic muscles enriched for flight muscles

tag: developmental stage

value: pharate animal (96h after pupa formation at 25 C)


title: Pgk12DeltaE2F_Rep2

source_name: Pgk mutant with E2F site mutated in regulatory region upstream Pgk gene

tag: tissue

value: w[1118];Pgk[Delta.E2F]; + line 12


title: Wild type_Rep1


title: T21, HTP0442A2

tag: Sex


title: MeDIP of C5 no, sample 16_2

description:
C5_no_MeDIP16_2
processed data file: modifiers_medipseq_counts_all.csv

data_processing:
Alignment of MeDIP-seq reads to the PWD(assembly)/B6(mm10) mixed reference using bwa.
PWD reads are mapped to their corresponding position in the mm10 reference genome.
Quantification of reads per window with qsea.
Genome_build: mm10/PWD assembly version 2b
Supplementary_files_format_and_content: modifiers_medipseq_counts_all.csv.gz: Comma-separated text file with the MeDIP counts per 250 base genomic window. Input samples have not been quantified.

source_name: normal intestinal mucosa

extract_protocol:
DNA was isolated using the Allprep DNA Mini Kit (Qiagen, Hilden, Germany), according to manufacturer´s protocols. Methyl-DNA enrichment was done according to Grimm C, Adjaye J (2012) Analysis of the methylome of human embryonic stem cells employing methylated DNA immunoprecipitation coupled to next-generation sequencing. Methods Mol Biol 873: 281–295.
Library construction was done according to Grimm C, Adjaye J (2012) Analysis of the methylome of human embryonic stem cells employing methylated DNA immunoprecipitation coupled to next-generation sequencing. Methods Mol Biol 873: 281–295. Sequencing was performed on an Illumina Genome Analyser IIx.

value: CSS C57BL/6 chr5 PWD

value: APC min

value: normal intestinal mucosa

tag: antibody


title: MeDIP of PWD wt, sample 11_1

description:
PWD_wt_MeDIP11_1
processed data file: modifiers_medipseq_counts_all.csv

value: PWD/Ph

value: wild type

tag: age

value: 15-19 weeks


title: MeDIP of PWD wt, sample 11_2

description:
PWD_wt_MeDIP11_2
processed data file: modifiers_medipseq_counts_all.csv


title: MeDIP of PWD wt, sample 16_9

description:
PWD_wt_MeDIP16_9
processed data file: modifiers_medipseq_counts_all.csv


title: MeDIP of C5 wt, sample 16_1

description:
C5_wt_MeDIP16_1
processed data file: modifiers_medipseq_counts_all.csv


title: T21, HTP0443A2

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a GlobinClear kit, NEBNext® Poly(A) mRNA Magnetic Isolation Module, and NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by Novogene Co., Ltd.

value: whole blood

tag: karyotype

value: Male

tag: sample source


title: MeDIP of C5 no, sample 12_4

description:
C5_no_MeDIP12_4
processed data file: modifiers_medipseq_counts_all.csv


title: T21, HTP0440A

tag: library type

value: strand-specific


title: MeDIP of C5 wt, sample 12_11

description:
C5_wt_MeDIP12_11
processed data file: modifiers_medipseq_counts_all.csv


title: MeDIP of C5 ad, sample 12_5

description:
C5_ad_MeDIP12_5
processed data file: modifiers_medipseq_counts_all.csv

source_name: intestinal adenoma

value: intestinal adenoma


title: MeDIP of C5 ad, sample 12_3

description:
C5_ad_MeDIP12_3
processed data file: modifiers_medipseq_counts_all.csv


title: bone marrow-derived mesenchymal stem cells_1


title: T21, HTP0439A2

value: A


title: bone marrow-derived mesenchymal stem cells_2


title: MC38-OVA untreated (g001)

city: Brussels

first: Benoit

last: Van den Eynde

state: Please Select

address: Avenue Hippocrate, 75 - Bte B1.74.10

country: Belgium

institute: de Duve Institute

data_processing:
Cells were processed with the CellRanger platform
Barcodes, features and count matrix for valid cells were imported and further processed with Scanpy and R/Bioconductor
We performed clustering with PhenoGraph
Cluster identities were assigned with known markers
Assembly: GRCm38.96
Supplementary files format and content: archived 10X counts directory (mtx counts and feature/sample csv files)

source_name: Tumour

extract_protocol:
Standard 10x Genomics protocol
The DNA libraries was paired end sequenced on an Illumina Novaseq S4, with a 2x150 bp Illumina kit.

value: 10 weeks

tag: treatment

value: untreated


title: T21, HTP0438A

city: Aurora

first: Matthew

last: Galbraith

institute: University of Colorado Anschutz Medical Campus

value: Female

value: C


title: MC38-OVA treated (g002)

value: clonidine


title: iPS cell-derived fibroblasts_3

source_name: iPS cell-derived fibroblasts


title: iPS cell-derived fibroblasts_2


title: iPS cell-derived fibroblasts_1


title: MeDIP of C5F1 wt, sample 16_7

description:
C5F1_wt_MeDIP16_7
processed data file: modifiers_medipseq_counts_all.csv

value: C57BL/6 x CSS C57BL/6 chr5 PWD F1


title: MeDIP of C5 ad, sample 16_3

description:
C5_ad_MeDIP16_3
processed data file: modifiers_medipseq_counts_all.csv

value: CSS C57BL/6 chr5 PWD


title: MeDIP of C5 no, sample 12_2

description:
C5_no_MeDIP12_2
processed data file: modifiers_medipseq_counts_all.csv

value: APC min


title: MeDIP of B6 ad, sample 10_2

description:
B6_ad_MeDIP10_2
processed data file: modifiers_medipseq_counts_all.csv


title: KO-Guanabenz_2

data_processing:
Samples were QC-tested and  trimmed with trim galore! 0.6.5 using default settings
Reads were mapped with Kallisto 0.46.0 and returned as pseudocounts
Pseudocounts were then mapped to gene-level with TxDB
Assembly: GRCm38.96
Supplementary files format and content: txt

growth_protocol: MC38 OVA tumor cells were implanted into wildtype or Adra2a KO mice

extract_protocol: Tumors were collected 7 days after treatment

treatment_protocol: Mice were treated with Clonidine, Guanabenz or PBS daily by i.p. Injection

value: Untreated


title: KO-Control_3


title: KO-Guanabenz_3


title: KO-Control_2


title: Arg1_Positive_Male_16S12

city: Stockholm

first: Vassilis

last: Stratoulias

address: Nobels Väg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

data_processing:
Basecalling and demultiplexing was performed using Illumina bcl2fastq v2.20.0 software.
Reads were aligned to Ensembl GRCm38/mm10 reference genome using STAR v2.6.1d
Gene counts were estimated using featureCounts v1.5.1.
Sample group comparisons were performed using R package DESeq2 v1.28.1
No filtering was performed prior to sample group comparisons, where the default DESeq2 independent filtering was applied
Assembly: GRCm38/mm10
Supplementary files format and content: Tab delimeted text file of counts generated by featureCounts.

source_name: Microglia

extract_protocol:
Tissue of interest was minced and cells of interest were extracted by mechanical dissosiation, Percoll gradient and FACS sorting.
Takara Smart seq V4 Clontech reagents (cDNA synth) and Illumina Nextera XT (library prep)

value: YARG

value: brain (BF/striatum)


title: T21, HTP0437A


title: Input of B6 ad, sample 2_1

value: 15-19 weeks


title: MeDIP of C5F1 wt, sample 12_12

description:
C5F1_wt_MeDIP12_12
processed data file: modifiers_medipseq_counts_all.csv

value: wild type

value: normal intestinal mucosa


title: Arg1_Positive_Male_12S11

value: Male


title: KO-Guanabenz_1


title: MeDIP of C5F1 wt, sample 12_10A

description:
C5F1_wt_MeDIP12_10A
processed data file: modifiers_medipseq_counts_all.csv


title: T21, HTP0436A

description: globin-depleted, poly(A)+ RNA from whole blood

value: whole blood

value: strand-specific


title: T21, HTP0434A


title: KO-Control_1

value: 10 weeks


title: Arg1_Positive_Male_11S10


title: KO-Clonidine_3

value: Clonidine


title: T21, HTP0431A2

value: Female

value: D


title: Arg1_Negative_Male_14S9


title: MeDIP of C5F1 no, sample 16_10

description:
C5F1_no_MeDIP16_10
processed data file: modifiers_medipseq_counts_all.csv


title: T21, HTP0435A2


title: MeDIP of C5F1 wt, sample 12_10

description:
C5F1_wt_MeDIP12_10
processed data file: modifiers_medipseq_counts_all.csv


title: KO-Clonidine_2


title: MeDIP of C5F1 no, sample 12_8

description:
C5F1_no_MeDIP12_8
processed data file: modifiers_medipseq_counts_all.csv


title: Arg1_Negative_Male_6S8


title: Control, HTP0429B

value: Control

value: C


title: Arg1_Positive_Female_8S5


title: Arg1_Negative_Male_5S7


title: Arg1_Positive_Female_15S6


title: T21, HTP0428A


title: WT-Guanabenz_1

value: Guanabenz


title: WT-Guanabenz_3


title: MeDIP of C5F1 ad, sample 12_9

description:
C5F1_ad_MeDIP12_9
processed data file: modifiers_medipseq_counts_all.csv

value: C57BL/6 x CSS C57BL/6 chr5 PWD F1

value: APC min

value: intestinal adenoma


title: T21, HTP0426A


title: MeDIP of C1_5F1 no, sample 5_1

description:
C1_5F1_no_MeDIP5_1
processed data file: modifiers_medipseq_counts_all.csv

value: C57BL/6 x CSS C57BL/6 chr1 and 5 PWD F1


title: WT-Guanabenz_2


title: MeDIP of C5F1 ad, sample 12_6

description:
C5F1_ad_MeDIP12_6
processed data file: modifiers_medipseq_counts_all.csv

value: 15-19 weeks


title: atrial cardiac fibroblasts_3


title: MeDIP of C5F1 no, sample 12_7

description:
C5F1_no_MeDIP12_7
processed data file: modifiers_medipseq_counts_all.csv


title: T21, HTP0425A


title: WT-Control_3

value: Untreated

value: wild type


title: Arg1_Positive_Female_7S4

value: YARG

value: brain (BF/striatum)


title: MeDIP of C1_5F1 no, sample 5_3

description:
C1_5F1_no_MeDIP5_3
processed data file: modifiers_medipseq_counts_all.csv

value: normal intestinal mucosa


title: Arg1_Negative_Female_13S3


title: T21, HTP0424A

value: whole blood

value: strand-specific


title: WT-Control_2

value: 10 weeks


title: MeDIP of C1_5F1 ad, sample 5_4

description:
C1_5F1_ad_MeDIP5_4
processed data file: modifiers_medipseq_counts_all.csv


title: Arg1_Negative_Female_2S2

value: Female


title: WT-Control_1


title: T21, HTP0423A

value: Male


title: T21, HTP0430A

value: C


title: MeDIP of B6xPWD wt, sample 16_4

description:
B6xPWD_wt_MeDIP16_4
processed data file: modifiers_medipseq_counts_all.csv

value: C57BL/6xPWD F1


title: KO-Clonidine_1

value: Clonidine


title: T21, HTP0421A


title: MeDIP of C1_5F1 ad, sample 5_2

description:
C1_5F1_ad_MeDIP5_2
processed data file: modifiers_medipseq_counts_all.csv

value: APC min


title: T21, HTP0419A


title: MeDIP of C5 wt, sample 12_1

description:
C5_wt_MeDIP12_1
processed data file: modifiers_medipseq_counts_all.csv

value: CSS C57BL/6 chr5 PWD


title: WT-Clonidine_3


title: ASC48_LACE_seq_bio2_tech2

data_processing:
The adapter sequences and poly(A) tails at the 3’ end of raw reads were removed using Cutadapt (v.1.15) with following parameters: -f fastq -m 18 -n 2 -a A{15} --quality-base=33
Clean reads were first aligned to mouse pre-rRNA using Bowtie software (v.1.2.3) with default parameters, and the remaining unmapped reads were then aligned to the mouse (mm9) reference genome with Bowtie parameters: --best --strata -v 2 -k 10.
Pearson’s correlation coefficient between LACE-seq replicates was performed using multiBamSummary module of deeptools
LACE-seq peaks are called by Piranha software (http://smithlabresearch.org/software/piranha/, v.1.2.1) in ASC cells. The parameters were as follows: -sort -p_threshold 0.001 -b 20 -d ZeroTruncatedNegativeBinomial.
Assembly: mm9
Supplementary files format and content: *.piranha.bed: Tab-delimited files from Piranha containing binding sites. *.bw: binary signal file generated by bedGraphToBigWig

growth_protocol: C2C12  were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep in 5% CO2 37°C incubator.

extract_protocol:
YTHDC1 antibody (Abcam, ab122340) was used to pull down specific protein-RNA complex from lysate.MNase was used to cut RNAs into YTHDC1-associated short fragments on beads. The 3’ ends of fragmented RNAs were then dephosphorylated and ligated with a 5’ pre-adenylated linker containing four randomized nucleotides. Biotinylated primer containing the T7 promoter was used for reverse transcription which stopped at crosslinking site (YTHDC1 binding site). cDNAs were poly(A) tailed and purified with streptavidin beads. Second-strand cDNAs were synthesized on beads with an adaptor containing oligo-(dT). After a pre-amplifying step by PCR, T7 RNA polymerase was used to amplify trace amounts of truncated cDNAs linearly.
Then the products were PCR converted into libraries for single end sequencing on Illumina platform (Nextseq 550)

treatment_protocol: Cells were washed with ice cold PBS and subjected to 400mJ UV treatment to crosslink proteins with their interacting RNAs. After crosslink, cells were pelleted and kept at -80°C before library preparation.

tag: cell line

value: ASC

value: WT

value: YTHDC1 antibody (Abcam, ab122340)


title: MeDIP of B6xPWD wt, sample 11_3

description:
B6xPWD_wt_MeDIP11_3
processed data file: modifiers_medipseq_counts_all.csv

value: wild type

value: 15-19 weeks


title: ASC48_LACE_seq_bio2_tech1


title: T21, HTP0415A


title: T21, HTP0414A


title: WT-Clonidine_1


title: WT-Clonidine_2


title: RAW264.7+LPS_rep2

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: mouse macrophage RAW264.7 lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Thermo Fisher) with high glucose and 10% fetal bovine serum (FBS; Gibco), and 1% penicillin/streptomycin.

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

treatment_protocol: Monoclonal cell line RAW 264.7 cell lines which steadily expressed DCLK1 shRNA or negative control shRNA were plated at 200,000 cells/well in six-well plates. Cells were challenged with 500 ng/mL LPS for 6 h.

value: macrophage

tag: knockdown

value: treated with LPS(500ng/ml) for 6 hours


title: T21, HTP0418A

value: whole blood


title: RAW264.7+LPS_rep3

tag: cell type


title: T21, HTP0420A

value: strand-specific


title: Input of B6xPWD wt, sample 11_6

tag: genotype

value: normal intestinal mucosa


title: ASC48_LACE_seq_bio1_tech2


title: T21, HTP0413A

value: Female


title: ASC48_LACE_seq_bio1_tech1


title: RAW264.7-shDCLK1+LPS_rep3


title: MeDIP of B6xPWD no, sample 18_1

description:
B6xPWD_no_MeDIP18_1
processed data file: modifiers_medipseq_counts_all.csv


title: T21, HTP0412A

value: Male


title: Arg1_Negative_Female_1S1

value: YARG

value: brain (BF/striatum)


title: C2C12_LACE_seq_bio1

source_name: C2C12 cell


title: C2C12_LACE_seq_bio2


title: MeDIP of C5F1 ad, sample 16_11

description:
C5F1_ad_MeDIP16_11
processed data file: modifiers_medipseq_counts_all.csv

value: C57BL/6 x CSS C57BL/6 chr5 PWD F1

value: intestinal adenoma


title: RAW264.7-shDCLK1+LPS_rep2


title: MeDIP of B6xPWD wt, sample 11_4

description:
B6xPWD_wt_MeDIP11_4
processed data file: modifiers_medipseq_counts_all.csv

value: C57BL/6xPWD F1


title: MeDIP of B6xPWD no, sample 16_5

description:
B6xPWD_no_MeDIP16_5
processed data file: modifiers_medipseq_counts_all.csv

value: APC min


title: T21, HTP0411A

description: globin-depleted, poly(A)+ RNA from whole blood

value: C


title: RAW264.7-shDCLK1+LPS_rep1


title: MeDIP of B6xPWD no, sample 11_6

description:
B6xPWD_no_MeDIP11_6
processed data file: modifiers_medipseq_counts_all.csv


title: DLPFC_Sample29

city: Irvine

first: Marquis

middle: P.

last: Vawter

address: 837 Health Sciences Rd

department: Psychiatry & Human Behavior

institute: University of California, Irvine

data_processing:
Trimming of TruSeq adapters using cutadapt v2.5 with settings -n 3 --trim-n -m 40
Pseudoalignment to transcriptome using Salmon v0.14.1 with settings: -l IU --gcBias --seqBias  --validateMappings –mimicBT2
Assembly: hg 38
Supplementary files format and content: Comma-delimited file with transcript-level estimated counts from Salmon
Supplementary files format and content: Comma-delimited file with transcript-level transcripts per million (TPM) values from Salmon

source_name: DLPFC

extract_protocol:
RNA was harvested using Trizol (ThermoFisher). 750 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA library following manufacturer's protocols.

value: DLPFC

tag: psychiatric diagnosis

value: Schizophrenia

tag: age (years)

tag: ethnicity

value: Caucasian

tag: pmi (hours)

tag: ph

tag: rin (cerebellum)

tag: toxicology (cerebellum)

value: fluoxetine,Norfluoxetine


title: RAW264.7+LPS_rep1

tag: strain

value: macrophage

value: treated with LPS(500ng/ml) for 6 hours


title: T21, HTP0410A

tag: tissue

value: whole blood

tag: Sex

tag: age

value: strand-specific


title: RAW264.7-shDCLK1_rep3

value: untreated


title: MeDIP of B6xPWD ad, sample 18_2

description:
B6xPWD_ad_MeDIP18_2
processed data file: modifiers_medipseq_counts_all.csv

value: 15-19 weeks

tag: antibody


title: DLPFC_Sample27

value: Male

value: Caffeine,Clozapine,Norclozapine


title: DLPFC_Sample26


title: T21, HTP0409A

tag: karyotype

value: Female

tag: sample source

tag: library type


title: T21, HTP0408A


title: RAW264.7-shDCLK1_rep1

tag: cell line

tag: cell type

tag: knockdown

tag: treatment


title: RAW264.7-shDCLK1_rep2


title: MeDIP of B6xPWD ad, sample 16_6

description:
B6xPWD_ad_MeDIP16_6
processed data file: modifiers_medipseq_counts_all.csv

tag: genotype

value: intestinal adenoma


title: DLPFC_Sample25

tag: psychiatric diagnosis

tag: age (years)

tag: ethnicity

value: Hispanic

tag: pmi (hours)


title: T21, HTP0407A


title: RAW264.7-control_rep3

tag: strain


title: Input of B6xPWD ad, sample 11_5

value: C57BL/6xPWD F1

value: APC min

tag: tissue


title: T21, HTP0406A

tag: Sex

value: C


title: DLPFC_Sample30

value: DLPFC

value: Control

tag: ph

tag: rin (cerebellum)

tag: toxicology (cerebellum)


title: RAW264.7-control_rep2


title: DLPFC_Sample24

value: Schizophrenia

value: Caucasian

value: Citalopram/Escitalopram


title: MeDIP of B6 wt, sample 4_5

description:
B6_wt_MeDIP4_5
processed data file: modifiers_medipseq_counts_all.csv

value: wild type

value: normal intestinal mucosa

tag: age

tag: antibody


title: T21, HTP0405A

value: whole blood

tag: karyotype

tag: sample source

tag: library type

value: strand-specific


title: DLPFC_Sample23

value: Male


title: DLPFC_Sample28


title: T21, HTP0404A


title: MeDIP of B6 wt, sample 16_8

description:
B6_wt_MeDIP16_8
processed data file: modifiers_medipseq_counts_all.csv

value: 15-19 weeks


title: MeDIP of B6xPWD ad, sample 11_5

description:
B6xPWD_ad_MeDIP11_5
processed data file: modifiers_medipseq_counts_all.csv


title: T21, HTP0403A


title: DLPFC_Sample21

value: Asian


title: T21, HTP0402A


title: GRTH Knock-in round spermatids miRNA (KI-RS-mirna-5b)

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
Raw sequence reads were processed using lcdb-wf (lcdb.github.io/lcdb-wf/) according to the following steps. Raw sequence reads were trimmed with cutadapt v3.4  to remove any adapters while performing light quality trimming with parameters ‘-a AACTGTAGGCACCATCAAT -q 20 –minimum-length = 15.’
Sequencing library quality was assessed with fastqc v0.11.9 with default parameters. The presence of common sequencing contaminants was evaluated with fastq_screen v0.14.0 with parameters ‘–subset 100000 –aligner bowtie2.’ Trimmed reads were mapped to the Mus musculus reference genome (Gencode m18) using Bowtie2 v2.4.2.
Multimapping reads were filtered using samtools v1.12 .
Uniquely aligned reads were then counted in annotated miRNAs with the featureCounts program of the subread package v2.0.1 using Mus musculus miRBase release 18 annotations.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes featureCounts raw counts.

source_name: testes

extract_protocol:
Round spermatids were isolated from the testes of WT, GRTH-KO, and GRTH-KI mice (75-85 days old). Small RNA ( > 200 bp) was extracted using Qiagen miRNeasy micro kit
Libraries prepared according to Qiagen small RNA-Seq kit

value: testes

tag: cell type

value: round spermatids

value: GRTH KI

tag: experimental batch


title: Pgk12DeltaE2F_Rep1

description: ATACseq was performed using Actif Motif kit

value: thoracic muscles enriched for flight muscles

tag: developmental stage

value: pharate animal (96h after pupa formation at 25 C)

tag: genotype

value: w[1118];Pgk[Delta.E2F]; + line 12


title: GRTH Knock-in round spermatids miRNA (KI-RS-mirna-6b)


title: DLPFC_Sample19

value: DLPFC

tag: psychiatric diagnosis

value: Female

tag: age (years)

tag: ethnicity

value: Other

value: Caffeine,Quetiapine


title: T21, HTP0401A

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

tag: tissue

value: C


title: Input of B6 wt, sample 1_6

tag: strain

value: wild type

value: normal intestinal mucosa


title: GRTH Knock-in round spermatids miRNA (KI-RS-mirna-3b)


title: DLPFC_Sample18

value: Schizophrenia

tag: Sex

value: African American

tag: pmi (hours)

tag: ph

value: Norhydroxyzine,Quetiapine,Hydroxyzine


title: MeDIP of B6 no, sample 9_4

description:
B6_no_MeDIP9_4
processed data file: modifiers_medipseq_counts_all.csv

value: APC min

tag: age

value: 15-19 weeks


title: GRTH Knock-in round spermatids miRNA (KI-RS-mirna-2b)

value: testes

value: round spermatids


title: DLPFC_Sample17

value: Control

value: Male

value: Caucasian

tag: rin (cerebellum)

tag: toxicology (cerebellum)

value: Caffeine


title: Input of B6 wt, sample 10_1

tag: antibody


title: T21, HTP0399A2

value: whole blood

tag: karyotype

tag: sample source

value: D

tag: library type

value: strand-specific


title: RAW264.7-control_rep1

tag: cell line

tag: cell type

value: macrophage

tag: knockdown

tag: treatment

value: untreated


title: MeDIP of B6 no, sample 9_2

description:
B6_no_MeDIP9_2
processed data file: modifiers_medipseq_counts_all.csv

tag: genotype

value: normal intestinal mucosa


title: DLPFC_Sample22

tag: tissue

value: DLPFC

tag: psychiatric diagnosis

value: Female

tag: age (years)

tag: ethnicity


title: GRTH Knock-in round spermatids miRNA (KI-RS-mirna-1b)

value: GRTH KI

tag: experimental batch


title: T21, HTP0398A

tag: Sex

tag: age

value: C


title: MeDIP of B6 wt, sample 10_1

description:
B6_wt_MeDIP10_1
processed data file: modifiers_medipseq_counts_all.csv

tag: strain

value: wild type

value: 15-19 weeks


title: DLPFC_Sample20

value: Schizophrenia

tag: pmi (hours)

tag: ph

tag: rin (cerebellum)

tag: toxicology (cerebellum)


title: GRTH Knock-in round spermatids miRNA (KI-RS-mirna-4b)

value: testes

value: round spermatids


title: MeDIP of B6 no, sample 4_3

description:
B6_no_MeDIP4_3
processed data file: modifiers_medipseq_counts_all.csv

value: APC min

tag: antibody


title: T21, HTP0397A

tag: karyotype

value: Male

tag: sample source

tag: library type


title: DLPFC_Sample16

value: Caucasian

value: Caffeine


title: GRTH Knock-out round spermatids miRNA (KO-RS-mirna-5a)

tag: cell type

tag: genotype

value: GRTH KO


title: GRTH Knock-out round spermatids miRNA (KO-RS-mirna-3a)

tag: tissue


title: T21, HTP0396A

value: whole blood

value: strand-specific


title: DLPFC_Sample14

tag: psychiatric diagnosis

value: Control

tag: age (years)


title: T21, HTP0400A


title: Input of B6 no, sample 4_3

value: normal intestinal mucosa


title: GRTH Knock-out round spermatids miRNA (KO-RS-mirna-4a)

tag: experimental batch


title: DLPFC_Sample13

value: DLPFC

tag: Sex

value: Female

tag: ethnicity


title: GRTH Knock-out round spermatids miRNA (KO-RS-mirna-2a)


title: MeDIP of B6 ad, sample 9_3A

description:
B6_ad_MeDIP9_3A
processed data file: modifiers_medipseq_counts_all.csv

tag: strain

value: intestinal adenoma

tag: age


title: Input of B6 no, sample X_X


title: T21, HTP0394A

value: C


title: DLPFC_Sample12

tag: pmi (hours)

tag: ph


title: GRTH Knock-out round spermatids miRNA (KO-RS-mirna-1a)


title: MeDIP of B6 ad, sample 4_2

description:
B6_ad_MeDIP4_2
processed data file: modifiers_medipseq_counts_all.csv

value: 15-19 weeks


title: T21, HTP0393A


title: DLPFC_Sample11

tag: rin (cerebellum)

tag: toxicology (cerebellum)


title: MeDIP of B6 ad, sample 4_1

description:
B6_ad_MeDIP4_1
processed data file: modifiers_medipseq_counts_all.csv

tag: antibody


title: T21, HTP0392A

tag: karyotype

tag: sample source


title: DLPFC_Sample10


title: DLPFC_Sample15


title: Wild-type round spermatids miRNA (WT-RS-mirna-6b)

tag: cell type

value: WT


title: MeDIP of B6 wt, sample 4_4

description:
B6_wt_MeDIP4_4
processed data file: modifiers_medipseq_counts_all.csv

tag: genotype

value: wild type


title: Wild-type round spermatids miRNA (WT-RS-mirna-5b)

tag: tissue

value: testes

value: round spermatids


title: PWD wt rep3

description:
PWD_wt_3
processed data file: modifiers_rnaseq_counts.csv

value: PWD/Ph


title: Wild-type round spermatids miRNA (WT-RS-mirna-4b)


title: DLPFC_Sample9

tag: psychiatric diagnosis

value: Male

value: African American


title: MeDIP of B6 ad, sample 2_1

description:
B6_ad_MeDIP2_1
processed data file: modifiers_medipseq_counts_all.csv

value: APC min


title: T21, HTP0390A

description: globin-depleted, poly(A)+ RNA from whole blood

value: whole blood

tag: library type


title: T21, HTP0391A

value: strand-specific


title: T21, HTP0395A


title: T21, HTP0389A


title: DLPFC_Sample7

value: Schizophrenia

tag: age (years)


title: PWD wt rep2

description:
PWD_wt_2
processed data file: modifiers_rnaseq_counts.csv

value: normal intestinal mucosa


title: DLPFC_Sample8

value: DLPFC

value: Control

tag: Sex


title: PWD wt rep1

description:
PWD_wt_1
processed data file: modifiers_rnaseq_counts.csv


title: Wild-type round spermatids miRNA (WT-RS-mirna-1b)

tag: experimental batch


title: Wild-type round spermatids miRNA (WT-RS-mirna-2b)


title: T21, HTP0388A

value: Female


title: DLPFC_Sample6

tag: ethnicity

value: Caucasian

value: Caffeine


title: T21, HTP0387A

tag: age

value: C


title: DLPFC_Sample5

tag: pmi (hours)


title: Wild-type round spermatids miRNA (WT-RS-mirna-5a)

value: WT


title: C5 wt rep2

description:
C5_wt_2
processed data file: modifiers_rnaseq_counts.csv

tag: strain

value: CSS C57BL/6 chr5 PWD

value: wild type

value: 15-19 weeks


title: T21, HTP0385A

value: Male


title: Wild-type round spermatids miRNA (WT-RS-mirna-4a)

value: testes

value: round spermatids


title: C5 wt rep1

description:
C5_wt_1
processed data file: modifiers_rnaseq_counts.csv


title: T21, HTP0386A

value: whole blood


title: C5 no rep3

description:
C5_no_3
processed data file: modifiers_rnaseq_counts.csv

value: APC min


title: DLPFC_Sample4

value: Schizophrenia

tag: ph

tag: rin (cerebellum)

value: Benztropine


title: Wild-type round spermatids miRNA (WT-RS-mirna-3a)


title: Wild-type round spermatids miRNA (WT-RS-mirna-2a)


title: T21, HTP0384A

value: strand-specific


title: Wild-type round spermatids miRNA (WT-RS-mirna-3b)


title: DLPFC_Sample1

value: DLPFC

value: Control

tag: toxicology (cerebellum)

value: Theophylline


title: DLPFC_Sample2

value: Caucasian

value: Caffeine,Diphenhydramine,Norfluoxetine


title: Wild-type round spermatids miRNA (WT-RS-mirna-1a)

value: WT


title: C5 no rep2

description:
C5_no_2
processed data file: modifiers_rnaseq_counts.csv

value: CSS C57BL/6 chr5 PWD

value: normal intestinal mucosa


title: T21, HTP0382A

tag: karyotype

value: C


title: GRTH Knock-out round spermatids mRNA (KO_6)

data_processing:
Raw sequence reads were processed using lcdb-wf (lcdb.github.io/lcdb-wf/) according to the following steps. Raw sequence reads were trimmed with cutadapt v3.4  to remove any adapters while performing light quality trimming with parameters ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 –minimum-length = 25.’
Sequencing library quality was assessed with fastqc v0.11.9 with default parameters. The presence of common sequencing contaminants was evaluated with fastq_screen v0.14.0 with parameters ‘–subset 100000 –aligner bowtie2.’ Trimmed reads were mapped to the Mus musculus reference genome (Gencode m18) using STAR v2.7.8a.
Multimapping reads were filtered using samtools v1.12 .
Uniquely aligned reads were then counted in genes with the featureCounts program of the subread package v2.0.1 using Mus musculus reference (Gencode m18) annotations .
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes featureCounts raw counts.

extract_protocol:
Round spermatids were isolated from the testes of WT, GRTH-KO, and GRTH-KI mice (75-85 days old). Total RNA was extracted using Qiagen RNAeasy Plus micro kit
Libraries prepared according to Takara Pico-RNA-Seq kit without polyA selection step

value: GRTH KO


title: C5 no rep1

description:
C5_no_1
processed data file: modifiers_rnaseq_counts.csv

value: 15-19 weeks


title: C5 ad rep3

description:
C5_ad_3
processed data file: modifiers_rnaseq_counts.csv

value: intestinal adenoma


title: T21, HTP0381A

value: whole blood

value: Male

tag: sample source


title: T21, HTP0380A


title: GRTH Knock-out round spermatids mRNA (KO_5)

value: testes

tag: cell type

value: round spermatids


title: treated 60h 64 ng rep3

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to the human reference genome (GRCh38)
Salmon quantification was performed on reads longer than 20nt after trimming. Next, DESeq2 was used for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: For the xlsx file gene expression level was estimated using RSEM v1.2.15

source_name: EpiOral 3D tissue

growth_protocol: The EpiOral 3D tissue is cultured in cell culture inserts with microporous membranes bottoms, coated with collagen having a pore size of 0.4um. Growth media was placed beneath the culture inserts and the tissue was nourished by media permeating through the microporous membrane.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
KAPA Stranded mRNA-Seq, which includes poly(a) selection

treatment_protocol: The 3D tissues were treated with 32 and 64 ng/ml of everolimus mixed with the growth media for 40 or 60 hours.

value: EpiOral 3D tissue

tag: conc everolimus (ng/ml)

tag: hours of treatment


title: treated 60h 64 ng rep1

tag: tissue


title: DLPFC_Sample3

value: DLPFC

tag: psychiatric diagnosis

value: Schizophrenia

value: Other

value: Acetaminophen,Clozapine,Norclozapine


title: T21, HTP0379A

source_name: whole blood

value: Female

tag: library type

value: strand-specific


title: GRTH Knock-out round spermatids mRNA (KO_4)

tag: genotype


title: C5 ad rep2

description:
C5_ad_2
processed data file: modifiers_rnaseq_counts.csv

value: CSS C57BL/6 chr5 PWD

value: APC min


title: C5 wt rep3

description:
C5_wt_3
processed data file: modifiers_rnaseq_counts.csv

value: wild type

value: normal intestinal mucosa


title: treated 60h 64 ng rep2


title: T21, HTP0378A

tag: Sex

value: C


title: treated 60h 32 ng rep2


title: C5 ad rep1

description:
C5_ad_1
processed data file: modifiers_rnaseq_counts.csv

value: intestinal adenoma

value: 15-19 weeks


title: treated 60h 32 ng rep3


title: GRTH Knock-out round spermatids mRNA (KO_3)

value: GRTH KO


title: C5F1 wt rep3

description:
C5F1_wt_3
processed data file: modifiers_rnaseq_counts.csv

value: C57BL/6 x CSS C57BL/6 chr5 PWD F1


title: Control, HTP0376B

value: whole blood

value: Control


title: GRTH Knock-out round spermatids mRNA (KO_2)

value: testes

value: round spermatids


title: C5F1 wt rep2

description:
C5F1_wt_2
processed data file: modifiers_rnaseq_counts.csv


title: T21, HTP0375A


title: T21, HTP0374A

value: Male


title: control 60h 0 ng rep3

value: EpiOral 3D tissue


title: GRTH Knock-out round spermatids mRNA (KO_1)


title: GRTH Knock-in round spermatids mRNA (KI_6)

value: GRTH KI


title: C5F1 wt rep1

description:
C5F1_wt_1
processed data file: modifiers_rnaseq_counts.csv


title: C5F1 no rep3

description:
C5F1_no_3
processed data file: modifiers_rnaseq_counts.csv


title: T21, HTP0373A

value: A

value: strand-specific


title: control 60h 0 ng rep2


title: T21, HTP0370A


title: control 60h 0 ng rep1


title: C5F1 no rep2

description:
C5F1_no_2
processed data file: modifiers_rnaseq_counts.csv

value: APC min


title: T21, HTP0368A

description: globin-depleted, poly(A)+ RNA from whole blood


title: GRTH Knock-in round spermatids mRNA (KI_4)


title: C5F1 no rep1

description:
C5F1_no_1
processed data file: modifiers_rnaseq_counts.csv


title: GRTH Knock-in round spermatids mRNA (KI_3)


title: T21, HTP0367A


title: C5F1 ad rep3

description:
C5F1_ad_3
processed data file: modifiers_rnaseq_counts.csv


title: treated 40h 64 ng rep3


title: treated 40h 64 ng rep1


title: treated 40h 64 ng rep2


title: T21, HTP0364A


title: C5F1 ad rep2

description:
C5F1_ad_2
processed data file: modifiers_rnaseq_counts.csv


title: treated 60h 32 ng rep1


title: C5F1 ad rep1

description:
C5F1_ad_1
processed data file: modifiers_rnaseq_counts.csv


title: GRTH Knock-in round spermatids mRNA (KI_2)


title: control 40h 0 ng rep2


title: control 40h 0 ng rep3


title: B6xPWD wt rep3

description:
B6xPWD_wt_3
processed data file: modifiers_rnaseq_counts.csv

value: C57BL/6xPWD F1

value: wild type


title: Control, HTP0361B2


title: T21, HTP0357A


title: GRTH Knock-in round spermatids mRNA (KI_1)


title: Wild-type round spermatids mRNA (WT_5)

value: WT


title: Wild-type round spermatids mRNA (WT_6)


title: B6xPWD wt rep2

description:
B6xPWD_wt_2
processed data file: modifiers_rnaseq_counts.csv

value: normal intestinal mucosa


title: T21, HTP0354A


title: Wild-type round spermatids mRNA (WT_4)


title: GRTH Knock-in round spermatids mRNA (KI_5)


title: B6xPWD wt rep1

description:
B6xPWD_wt_1
processed data file: modifiers_rnaseq_counts.csv

value: 15-19 weeks


title: Wild-type round spermatids mRNA (WT_3)


title: Control, HTP0352B


title: B6xPWD no rep3

description:
B6xPWD_no_3
processed data file: modifiers_rnaseq_counts.csv


title: control 40h 0 ng rep1


title: control 24h 0 ng rep1


title: Wild-type round spermatids mRNA (WT_2)


title: Wild-type round spermatids mRNA (WT_1)


title: Control, HTP0349B

value: Female


title: B6xPWD no rep2

description:
B6xPWD_no_2
processed data file: modifiers_rnaseq_counts.csv


title: Patient Sample 4 VIP152

city: Columbus

first: Steven

last: Sher

state: OH

department: Division of Hematology, Department of Internal Medicine

institute: The Ohio State University

data_processing:
Base Calling
Sequence Alignment
Coverage Profiling
Profile Aggregation
Model Fitting
Transition Detection
deseq2
Assembly: hg38

source_name: CD5+_CD19+ Leukemic Cells

growth_protocol: 5% CO2 37 Degrees; 10% FBS in RPMI1640

extract_protocol:
Cells obtained from patients on an IRB approved protocol were separated using Ficoll and Rosette Separation for B-cell selection. 500 cells were treated for 2 hours and sorted for live cells co-expressing CD5 & CD19. Cells were lysed using SmartSeq lysis buffer
Libraries were prepared according to the TaKaRa SMARTseq Protocol

treatment_protocol: 2hr treatment with 1µM VIP152 or DMSO

tag: disease state

value: Chronic lymphocytic leukemia (CLL)

value: Peripheral Blood

value: Leukemic B-lymphocytes

tag: treatment


title: Patient Sample 4 Vehicle

value: DMSO


title: B6xPWD no rep1

description:
B6xPWD_no_1
processed data file: modifiers_rnaseq_counts.csv

tag: age


title: B6xPWD ad rep3

description:
B6xPWD_ad_3
processed data file: modifiers_rnaseq_counts.csv

tag: strain

value: intestinal adenoma


title: T21, HTP0348A

value: whole blood


title: Patient Sample 3 VIP152


title: Control, HTP0347B

value: Control


title: B6xPWD ad rep2

description:
B6xPWD_ad_2
processed data file: modifiers_rnaseq_counts.csv


title: Patient Sample 3 Vehicle


title: Control, HTP0355B

value: Male


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 5 (adult mesenteric lymph nodes)

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts, normalized fragments-per-kilobase-per-million-mapped (FPKM), or normalized transcripts-per-million-mapped (TPM).

source_name: mesenteric lymph node

extract_protocol:
Total RNA from tissue samples was extracted using TRIzol reagent (Invitrogen) following the manufacture’s protocol. RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Tecan/Nugen Universal Plus mRNA Kit. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the University of Colorado Cancer Center Genomics Shared Resource.

value: mesenteric lymph node

tag: age in_weeks


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 6 (adult mesenteric lymph nodes)


title: control 24h 0 ng rep2

value: EpiOral 3D tissue


title: B6xPWD ad rep1

description:
B6xPWD_ad_1
processed data file: modifiers_rnaseq_counts.csv

data_processing:
Alignment of RNA-seq reads to the PWD(assembly)/B6(mm10) mixed reference using bwa.
PWD reads are mapped to their corresponding position in the mm10 reference genome.
Quantification of reads per gene with htseq-count
Genome_build: mm10/PWD assembly version 2b
Supplementary_files_format_and_content: modifiers_rnaseq_counts.csv: Comma-separated text file with RNA-seq read counts per gene.

extract_protocol:
Intestinal tissue as indicated was processed using the Qiagen Allprep RNA/DANN Kit according to manufacturer's instructions.
For RNA sequencing, 4 µg of total RNA were depleted for ribosomal RNA using the RiboMinus Eukaryote Kit for RNA-seq (Invitrogen) following the manufacturer’s instructions. The RiboMinus depleted RNA was then used for the generation of single-end RNA-seq libraries. cDNA libraries were size selected on a 2% agarose gel, fragments of 150-200 nt were excised (corresponding to insert sizes of 80-130 nt) and purified using the QiaQuick Gel extraction kit (Qiagen). Sequencing was performed on an Illumina Genome Analyser IIx.

value: APC min


title: Control, HTP0346B

value: A

value: strand-specific


title: B6 wt rep3

description:
B6_wt_3
processed data file: modifiers_rnaseq_counts.csv

value: wild type


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 2 (adult mesenteric lymph nodes)


title: T21, HTP0345A


title: T21, HTP0351A


title: Patient Sample 2 Vehicle


title: Control, HTP0343B


title: B6 wt rep2

description:
B6_wt_2
processed data file: modifiers_rnaseq_counts.csv

value: normal intestinal mucosa


title: Patient Sample 1 VIP152


title: B6 wt rep1

description:
B6_wt_1
processed data file: modifiers_rnaseq_counts.csv

value: 15-19 weeks


title: Patient Sample 1 Vehicle


title: B6 no rep3

description:
B6_no_3
processed data file: modifiers_rnaseq_counts.csv


title: T21, HTP0342A

description: globin-depleted, poly(A)+ RNA from whole blood

value: Female


title: Dp16; sample 6 (adult mesenteric lymph nodes)

description: Dp16; sample 6


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 4 (adult mesenteric lymph nodes)


title: Dp16; sample 4 (adult mesenteric lymph nodes)

description: Dp16; sample 4


title: B6 no rep2

description:
B6_no_2
processed data file: modifiers_rnaseq_counts.csv


title: T21, HTP0340A


title: B6 no rep1

description:
B6_no_1
processed data file: modifiers_rnaseq_counts.csv


title: Dp16; sample 5 (adult mesenteric lymph nodes)

description: Dp16; sample 5


title: 36 hpf Zebrafish VDA scRNA_seq

city: Shanghai

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
For scRNA-seq  and scATAC-seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters, using the GRCz11 reference genome.
For STRT-seq, raw reads were first de-multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells, then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously, UMI sequences in reads 2 were integrated into reads 1. The template switching oligo (TSO) sequence, polyA sequence and the low-quality reads (N > 10%) in reads 1 were subsequently removed by Python scripts and Trimmomatic (version 0.36). Next, the clean reads were aligned to the zebrafish genome (GRCz11 from Ensembl) using HISAT2 (version 2.1.0) with known gene annotation. Only protein-coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded.
For cut&tag, reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. After merging replicates, MACS2 was used for the peak calling.
Assembly: GRCz11

organism: Danio rerio

source_name: Zebrafish VDA

extract_protocol:
For 10x Genomics-based scRNA-seq and scATAC-seq in zebrafish, 40,000 mCherry+ GFP- cells, 40,000 mCherry+ GFP+ cells and 30,000 mCherry- GFP+ cells were sorted from Tg (kdrl:mCherry/runx1:enGFP) at 36 hpf. For STRT-seq in zebrafish, single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry- hematopoietic cells were sorted from the trunk region of Tg (spi2: Gal4;UAS:GFP/ kdrl:mCherry) at 36 hpf. For scRNA-seq of spi2 morphants at 36 hpf in zebrafish, ECs (kdrl+runx1-), HECs (kdrl+runx1+) and hematopoietic cells (kdrl-runx1+) were sorted. For bulk CUT&TAG in zebrafish, fli1a-flag-spi2-EGFP+ cells were sorted from the trunk region of Tg (fli1a-flag-spi2-GFP) embryos at 36 hpf.
For 10x Genomics-based scRNA-seq and scATAC-seq in zebrafish, we loaded ~20,000 cells for further 10x Genomics-based scRNA-seq and ~90,000 cells for further 10x Genomics-based scATAC-seq. For scRNA-seq, libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For ATAC-seq, nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit, and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired-end reads. For 10x Genomics-based scRNA-seq in mice, libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For STRT-seq in zebrafish, the end-repair and dA-tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. After the adaptor ligation step, the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For bulk CUT&TAG, libraries were prepared according to Hyperactive In-Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired-end reads.

value: Zebrafish VDA 36hpf

tag: cells

value: VDA-derived kdrl+runx1-, kdrl+runx1+, and kdrl-runx1+ cells

tag: Stage

value: 36 hours post fertilization


title: T21, HTP0341A

tag: karyotype


title: Dp16; sample 3 (adult mesenteric lymph nodes)

description: Dp16; sample 3


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 3 (adult mesenteric lymph nodes)


title: cmt2/cmt3 progeny of high CO2

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Adapters were trimmed from paired-end raw reads using Fastp (Chen et. al., PMID: 30423086). The reads were mapped to the genome and DNA methylation was called for each cytosine using methylpy (Schultz et. al., PMID: 26030523). The output of this tool - allC file is provided as a processed fle.
Assembly: TAIR10
Supplementary files format and content: Output of methylpy tool - allC files are provided as processed data files. “allC” stands for all cytosine (C). Each row corresponds to one cytosine in the genome. The columns are as described in the tool’s github page (https://github.com/yupenghe/methylpy)

organism: Arabidopsis thaliana

source_name: leaves from 25 day old plants

growth_protocol: All plants were grown at 22℃ under 16-hour day conditions in a growth chamber. 25 days after planting, whole leaves were collected and stored at -80℃.

extract_protocol:
Genomic DNA was isolated from frozen leaf tissue using the Qiagen DNAEasy prep kit. Quality was assessed by gel electrophoresis.
NEBNext Enzymatic Methyl-seq kit was used at the Genomics Technology Core at University of Missouri to construct the EM-Seq libraries.
Multiplexed libraries were sequenced on Illumina NovaSeq with paired-end 150 bp strategy.

treatment_protocol: Control plants were grown at ambient CO2 levels (which ranged between 450-500 ppm CO2) and the experimental plants were grown at high CO2 (set to 1,000 ppm). The progeny of high CO2 plants were grown at ambient CO2 levels.

tag: ecotype

value: Columbia

value: leaves from 25 day old plants

value: high CO2


title: T21, HTP0339A

value: whole blood

tag: sample source


title: B6 ad rep3

description:
B6_ad_3
processed data file: modifiers_rnaseq_counts.csv

value: intestinal adenoma


title: Control, HTP0338B

value: Control

value: Male


title: Patient Sample 2 VIP152

value: Chronic lymphocytic leukemia (CLL)

value: Peripheral Blood

tag: cell type

value: Leukemic B-lymphocytes


title: cmt2/cmt3 high CO2


title: 36 hpf Zebrafish VDA scRNA_seq (spi2 morphant)

description: Zebrafish.36 hpf.scRNA_seq


title: B6 ad rep2

description:
B6_ad_2
processed data file: modifiers_rnaseq_counts.csv

value: APC min


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 1 (adult mesenteric lymph nodes)

value: mesenteric lymph node


title: Dp16; sample 2 (adult mesenteric lymph nodes)

description: Dp16; sample 2


title: cmt2/cmt3 ambient CO2

value: ambient CO2


title: Dp16; sample 1 (adult mesenteric lymph nodes)

description: Dp16; sample 1


title: T21, HTP0337A

value: A

value: strand-specific


title: B6 ad rep1

description:
B6_ad_1
processed data file: modifiers_rnaseq_counts.csv

value: 15-19 weeks


title: T21, HTP0336A

value: Female


title: pol IV progeny of high CO2

value: Columbia

value: pol IV


title: Wild-type; sample 5 (adult mesenteric lymph nodes)

description: Wild-type; sample 5

value: wild-type C57/BL6


title: pol IV high CO2

value: leaves from 25 day old plants

value: high CO2


title: T21, HTP0335A2

value: whole blood


title: Wild-type; sample 4 (adult mesenteric lymph nodes)

description: Wild-type; sample 4


title: T21, HTP0334A2

value: Male


title: pol IV ambient CO2


title: Wild-type; sample 3 (adult mesenteric lymph nodes)

description: Wild-type; sample 3


title: T21, HTP0333A2


title: ddm1 high CO2


title: T21, HTP0332A


title: Wild-type; sample 1 (adult mesenteric lymph nodes)

description: Wild-type; sample 1


title: Wild-type; sample 2 (adult mesenteric lymph nodes)

description: Wild-type; sample 2


title: T21, HTP0331A


title: ddm1 ambient CO2