title: OPBG/006 ET [2019-06-05-EPIICAL-04]


title: Tumor methylation_CAM20.0098

status: Public on Jul 14 2021

type: genomic

city: Toronto

first: Yasin

last: Mamatjan

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

hyb_protocol: Samples were fragmented, amplified and hybridized to the Illumina Infinium MethylationEPIC BeadChip as per standard Illumina protocols.

scan_protocol: standard protocol

data_processing:
Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.
The 'Matrix processed.txt' contains Normalized Beta using preprocessNoob.
The 'Matrix signal intensities.txt' contains Unmethylated and methylated signal intensities.

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: fresh-frozen human meningioma

label_protocol: 250-500 ng of converted DNA was used as input, and labelled as per standard Illumina protocols.

growth_protocol: not applicable

extract_protocol: Genomic DNA was extracted from fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles

treatment_protocol: During sample processing, genomic DNA from each specimen was processed.

tag: tissue

value: fresh-frozen human meningioma

tag: molecule subtype

value: bisulfite-treated DNA


title: OPBG/003 ET [2019-06-05-EPIICAL-03]

type: SRA

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

country: USA

institute: Case Western Reserve University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrices in CSV format containing raw as well as TMM normalized Log2(n+3) CPM summarized reads

molecule: total RNA

growth_protocol: in vivo

extract_protocol:
RNA was extracted from 1 million PBMC using RNeasy Plus Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using the Roche Kapa RNA hyper kit.

tag: donorid

tag: arttreatment

value: ET

tag: age at art start (months)

tag: cell type

value: PBMC


title: Tumor methylation_CAM20.0097


title: RNA-seq allograft biopsy DSA- #7

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
Alignment using HISAT2 2.1.0 build of Ensembl GRCh38 89 version of primary assembly with default paired-end unstranded parameters and converting to sorted bam files using Samtools 1.9
Counts were generated using HT-Seq 0.11.2 using Ensembl GRCh38 89 version as GTF file and using unstranded strandedness, gene_id GFF attribute, union mode, and exon feature type as parameters
edgeR in Rstudio using R version 4.0 including CPM values for each sample
Genome_build: HISAT2 GRCh38 DNA primary assembly fasta version 89
Supplementary_files_format_and_content: Raw Counts text files in tab-delimited format of each sample combining R1 and R2 generated by Htseq, each file containing a matrix count of all samples of specific cell type

source_name: kidney allograft tissue

growth_protocol: no growth, directly ex vivo

extract_protocol:
Total RNA was extracted from allograft biopsy samples. RNA was isolated using RNeasy FFPE Kit (Qiagen)
cDNA synthesis and amplification were performed with Reverse, SMARTer® Stranded Total RNA-Seq Kit v2 (Takara). Libraries were sequenced on an Illumina, Ion torrent, Solid using 75-bp paired-end reads.

treatment_protocol: no treatment, directly ex vivo

value: kidney allograft tissue

tag: patients

value: adult kidney transplant recipients

tag: group

value: STABLE


title: Tumor methylation_CAM20.0103


title: Tumor methylation_CAM20.0094


title: Tumor methylation_CAM20.0092


title: TotalUV-10hrs-5 [T_UV_10_5]

city: Guildford

first: Nicolas

last: Locker

state: Surrey

address: Stag Hill

department: FHMS

country: United Kingdom

institute: University of Surrey

data_processing:
Reads were mapped to the mouse genome (GRCm38 reference genome, Hisat2 pre-built index files downloaded from ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grch38_tran.tar.gz) using Hisat2 [v 2.0.5] and to the Murine Norovirus genome MNV1-CW1 (DQ285629) coding sequences (ORF1: ABB90153.1, ORF2: ABB90154.1, ORF3: ABB90155.1) using  Bowtie2 [v 2.2.5].
The function ‘featureCounts’ from the R Bioconductor package ‘Rsubread’ [v 1.16.1] was used to assign mapped sequencing reads to genome features. Genomic features of the host were defined by the tool’s in-built gene annotations for the mouse genome (NCBI RefSeq gene annotations Build 38.1). Host genomic features were annotated using the R package ‘org.Mm.eg.db’ [v 3.7.0], Ensembl (accessed September 2017 via the R package ‘biomaRt’ [v 2.38.0]) and GenBank (accessed September 2017 via the R package ‘Annotate’. The feature count matrix consisted of the set of Host and MNV feature count and genes annotated as rRNA, miRNA, snoRNA, snoRNA or scaRNA were filtered out of the feature count matrix.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV tables of raw counts where rows correspond to genes and columns correspond to samples.

organism: Mus musculus

growth_protocol: RAW264.7 cells were harvested and split at 1:3 every 2 days, cultivated on TC-treated plates and maintained in Dulbecco's modified Eagle's medium (DMEM), 4,5g/L D-glucose, NaPyruvate, L-Glutamine supplemented with 10% foetal calf serum (FCS), 100U of penicillin/ml, 100μg of streptomycin/ml and 10mM HEPES (all reagents from Invitrogen) at 37°C in a 5% CO2 environment.

extract_protocol:
RAW264.7 cells infected with UVi(MNV) or MNV at MOI 10 for 6 and 10h were treated with 100µg/mL of cycloheximide for 3min at 37°C to lock the translating ribosomes onto the transcripts before being placed on ice, washed twice with cold PBS(-) containing 100µg/ml CHX and lysed on plate with 1mL of cold lysis buffer (15mM Tris-HCl, pH 7.5, 300mM NaCl, 15mM MgCl2, 100µg/mL CHX, 1% (v/v) Triton X-100, 200u RNasin for 5min. The post-nuclei supernatants were aliquoted in 2 tubes for Total and Polysomal RNA isolation. 500µl of each lysate were loaded onto 10mL 10-60% discontinuous sucrose gradients (15mM Tris, pH 7.5, 300 mM NaCl, 15mM MgCl2, 100µg/mL CHX, 1mg/mL Heparin) and spun at 38krpm for 2h at 4°C using the SW41Ti rotor. Gradients were fractionated using the fraction collector FoxyR1 in 10 fractions of 1mL. Total lysates and gradient fractions were denatured in 1.5mL of 7M GnHCl, ethanol-precipitated and resuspended in 30µL of RNAse free water. The fractions containing the polyribosomes were identified by their composition in 40 and 60S ribosomal RNA on 2% agarose gel, pulled together, further purified by two rounds of LiCl precipitation and resuspended into 30µL of RNAse free water. Obtained RNA were quality controlled using the Agilent Bioanalyser and quantified on Nanodrop.
1µg of RNA per sample were sent to the Oxford Genomics Centre (Welcome Trust Centre for Human Genetics, Oxford, UK) which generated the cDNA libraries by enrichment in polyA-tailed messenger RNA and performed the RNA sequencing on Illumina HiSeq4000 machine, 75bp PairEnds protocol with multiplexing of the samples.

treatment_protocol: 10^7 RAW264.7 cells were incubated for 1hr with MNV or UV-irradiated MNV at MOI 10 in growth medium. The inocula were then replace with growth medium and the viral cycle allowed to progress to either 6 or 10hours.

tag: cell line

value: leukemic monocyte-macrophage

tag: treatment

value: UV-inactivated MNV

tag: time of lysis in hpi

value: cytoplasmic RNA


title: Tumor methylation_CAM20.0096


title: Tumor methylation_CAM20.0095


title: Tumor methylation_CAM20.0091


title: TotalUV-6hrs-5 [T_UV_6_5]


title: OPBG/002 LT [2019-06-05-EPIICAL-02]

value: LT


title: TotalMNV-10hrs-4 [T_MNV_10_4]

value: MNV


title: TotalMNV-6hrs-4 [T_MNV_6_4]


title: TotalUV-6hrs-4 [T_UV_6_4]


title: TotalUV-10hrs-4 [T_UV_10_4]


title: Tumor methylation_CAM20.0093


title: Tumor methylation_CAM20.0090


title: Tumor methylation_CAM20.0089


title: Tumor methylation_CAM20.0100


title: OPBG/001 ET [2019-06-05-EPIICAL-01]


title: RNA-seq allograft biopsy DSA- #4


title: Tumor methylation_CAM20.0088


title: Tumor methylation_CAM20.0087


title: RNA-seq allograft biopsy DSA- #5


title: TotalMNV-10hrs-3 [T_MNV_10_3]


title: RNA-seq allograft biopsy DSA- #6


title: TotalMNV-6hrs-3 [T_MNV_6_3]


title: Tumor methylation_CAM20.0085


title: Tumor methylation_CAM20.0084


title: Tumor methylation_CAM20.0083


title: RNA-seq allograft biopsy DSA- #3


title: Tumor methylation_CAM20.0082


title: Tumor methylation_CAM20.0078


title: RNA-seq allograft biopsy DSA- #1


title: Tumor methylation_CAM20.0079


title: TotalUV-6hrs-3 [T_UV_6_3]


title: Tumor methylation_CAM20.0080


title: TotalUV-10hrs-3 [T_UV_10_3]


title: PolysomalMNV-6hrs-5 [P_MNV_6_5]

value: polysomal RNA


title: PolysomalMNV-10hrs-5 [P_MNV_10_5]


title: RNA-seq allograft biopsy DSA- #2


title: Tumor methylation_CAM20.0076


title: RNA-seq allograft biopsy DSA+ABMR- #2

value: DSA


title: Tumor methylation_CAM20.0081


title: PolysomalUV-10hrs-5 [P_UV_10_5]


title: Tumor methylation_CAM20.0074


title: Tumor methylation_CAM20.0073


title: RNA-seq allograft biopsy DSA+ABMR+ #11

value: ABMR


title: Tumor methylation_CAM20.0071


title: PolysomalUV-6hrs-5 [P_UV_6_5]


title: Tumor methylation_CAM20.0070


title: Tumor methylation_CAM20.0077


title: RNA-seq allograft biopsy DSA+ABMR+ #12


title: PolysomalMNV-10hrs-4 [P_MNV_10_4]


title: RNA-seq allograft biopsy DSA+ABMR- #1


title: Tumor methylation_CAM20.0075


title: Tumor methylation_CAM20.0069


title: RNA-seq allograft biopsy DSA+ABMR+ #9


title: PolysomalMNV-6hrs-4 [P_MNV_6_4]


title: Tumor methylation_CAM20.0067


title: RNA-seq allograft biopsy DSA+ABMR+ #10


title: Tumor methylation_CAM20.0068


title: Tumor methylation_CAM20.0066


title: Tumor methylation_CAM20.0065


title: RNA-seq allograft biopsy DSA+ABMR+ #7


title: Tumor methylation_CAM20.0064


title: RNA-seq allograft biopsy DSA+ABMR+ #8


title: Tumor methylation_CAM20.0063


title: Tumor methylation_CAM20.0060


title: Tumor methylation_CAM20.0061


title: PolysomalUV-10hrs-4 [P_UV_10_4]


title: PolysomalUV-6hrs-4 [P_UV_6_4]


title: PolysomalMNV-10hrs-3 [P_MNV_10_3]


title: RNA-seq allograft biopsy DSA+ABMR+ #6


title: PolysomalMNV-6hrs-3 [P_MNV_6_3]


title: Tumor methylation_CAM20.0059


title: RNA-seq allograft biopsy DSA+ABMR+ #5


title: Tumor methylation_CAM20.0057


title: Tumor methylation_CAM20.0058


title: PolysomalUV-10hrs-3 [P_UV_10_3]


title: RNA-seq allograft biopsy DSA+ABMR+ #4


title: Tumor methylation_CAM20.0055


title: PolysomalUV-6hrs-3 [P_UV_6_3]


title: Tumor methylation_CAM20.0056


title: Tumor methylation_CAM20.0054


title: RNA-seq allograft biopsy DSA+ABMR+ #3


title: Tumor methylation_CAM20.0062


title: Tumor methylation_CAM20.0052


title: TotalMNV-10hrs-5 [T_MNV_10_5]


title: RNA-seq allograft biopsy DSA+ABMR+ #2


title: Tumor methylation_CAM20.0053


title: RNA-seq allograft biopsy DSA+ABMR+ #1


title: Tumor methylation_CAM20.0051


title: Tumor methylation_CAM20.0048


title: KI_1719_Cb

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: Whole cerebellar tissue with single dose tamoxifen from control mouse #4

data_processing:
Aligned to moouse genome (mm10) using STAR spliced read aligner
Count reads using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation and differential expression analysis using Bioconductor packages
FPKM values
Genome_build: mm10

extract_protocol:
Total RNA was extracted using RNeazy kit (Qiagen) accordance with the prescribed protocol provided with the kit.
Libraries prepared using the Illumina TruSeq Stranded RNA (100 ng) + RiboZero Gold Library Prep Kit  and sequenced on an Illumina HiSeq4000 sequencer using strand-specific

treatment_protocol: Tamoxifen was freshly prepared at a concentration of 25 mg/ml in corn oil and dissolved at 37 °C with continuous agitation. To induce gene expression, tamoxifen was administered intraperitoneally at 75 mg/kg body weight for one day, using a 1 ml syringe and a 25 G 5/8-inch needle.

tag: condition

value: KI

value: Cerebellum

tag: strain

value: CalExflox mouse


title: KI_1714_Cb

description: Whole cerebellar tissue with single dose tamoxifen from control mouse #3


title: RNA-seq TLM cells DSA+ ABMR+ #3

data_processing:
Alignment using HISAT2 2.1.0 build of Ensembl GRCh38 89 version of primary assembly with default paired-end unstranded parameters and converting to sorted bam files using Samtools 1.9
Counts were generated using HT-Seq 0.11.2 using Ensembl GRCh38 89 version as GTF file and using unstranded strandedness, gene_id GFF attribute, union mode, and exon feature type as parameters
edgeR in Rstudio using R version 3.5.1 including CPM values for each sample
Genome_build: HISAT2 GRCh38 DNA primary assembly fasta version 89
Supplementary_files_format_and_content: Raw Counts text files in tab-delimited format of each sample combining R1 and R2 generated by Htseq, each file containing a matrix count of all samples of specific cell type

source_name: blood TLM B cells

extract_protocol:
Total RNA was extracted from blood RM, AM and TLM memory B cell subsets that were FACS-sorted directly into lysis buffer (Trizol). RNA was isolated using miRNeasy Mini Kit (Qiagen).
cDNA synthesis and amplification were performed with a SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara). Libraries were sequenced on an Illumina NextSeq 500 using 75-bp paired-end reads.

value: blood TLM B cells


title: RNA-seq TLM cells DSA+ ABMR+ #2


title: Tumor methylation_CAM20.0047

value: fresh-frozen human meningioma

value: bisulfite-treated DNA


title: Tumor methylation_CAM20.0045


title: KI_1708_Cb

description: Whole cerebellar tissue with single dose tamoxifen from control mouse #2


title: RNA-seq TLM cells DSA+ ABMR+ #1


title: RNA-seq TLM cells DSA+ ABMR- #3


title: TotalMNV-6hrs-5 [T_MNV_6_5]


title: KI_1613_Cb

description: Whole cerebellar tissue with single dose tamoxifen from control mouse #1


title: Tumor methylation_CAM20.0043


title: Tumor methylation_CAM20.0044


title: Tumor methylation_CAM20.0042


title: Db_1763_Cb

description: Whole cerebellar tissue with single dose tamoxifen from bigenic mouse #4

value: Db

value: Bigenic mouse


title: RNA-seq TLM cells DSA+ ABMR- #2

value: adult kidney transplant recipients


title: Tumor methylation_CAM20.0038


title: Tumor methylation_CAM20.0039


title: Tumor methylation_CAM20.0050


title: Db_1710_Cb

description: Whole cerebellar tissue with single dose tamoxifen from bigenic mouse #3


title: Tumor methylation_CAM20.0037


title: Db_1665_Cb

description: Whole cerebellar tissue with single dose tamoxifen from bigenic mouse #2


title: Tumor methylation_CAM20.0049


title: Tumor methylation_CAM20.0041


title: Tumor methylation_CAM20.0040


title: Tumor methylation_CAM20.0046


title: RNA-seq TLM cells DSA- #3


title: RNA-seq TLM cells DSA- #2


title: Tumor methylation_CAM20.0035


title: Tumor methylation_CAM20.0033


title: RNA-seq TLM cells DSA+ ABMR- #1


title: RNA-seq TLM cells DSA- #1


title: Tumor methylation_CAM20.0031


title: Tumor methylation_CAM20.0030


title: Tumor methylation_CAM20.0029


title: Tumor methylation_CAM20.0028


title: RNA-seq AM cells DSA+ ABMR+ #3

source_name: blood AM B cells

value: blood AM B cells


title: RNA-seq AM cells DSA+ ABMR+ #2


title: Tumor methylation_CAM20.0036


title: Δ0368 Δ0595 rep1

city: Shanghai

first: Xiujuan

last: Zhou

address: 800 Dongchuan RD

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence to get clean reads. Mapping was based on a minimal length of 50 bp with an allowance of up to two mismatches, and >90% of the each read length had to map to the reference sequence for it to be considered a mapped read.
The gene expression levels were measured in reads per kilobase of transcript per million mapped reads (RPKM).
The differentially expressed genes (DEGs) were identified using the DEGseq package (Wang et al,2010) with the false discovery rate < 0.05 and at least two-fold changes.
Genome_build: S. Choleraesuis SC-B67 (NC_006905.1)
Supplementary_files_format_and_content: .txt file includes GeneID, gene names, Normalized RPKM value, log2FoldChange

organism: Salmonella enterica subsp. enterica serovar Choleraesuis str. ATCC 10708

source_name: Shanghai Entry-Exit Inspection and Quarantine Bureau of China.

growth_protocol: For all experiments, a single colony from the overnight cultures was inoculated into LB broth and grown at 37°C for 16 h with agitation at 180 rpm. The overnight cultures were diluted 1:100 in fresh LB broth and incubated at 37°C for 8 h (late exponential phase) with agitation at 180 rpm. Approximately 109 CFU/ml of each strain was pelleted at 5,000 rpm, 4°C for 10 min. The cell pellets were used for total RNA extraction.

extract_protocol:
Total RNA extraction using an RNeasy Micro Kit (QIAGEN, GmBH, Germany). RNA integrity was assessed using a 2100 Bio-analyzer (Agilent, Foster City, CA). Total RNA was further purified by the RNase-Free DNase Set (QIAGEN, GmBH, Germany) after quantification. Total RNA samples were stored at -80°C until further use.
The mRNA was used to prepare individually bar-coded (indexed) RNA-Seq libraries with a TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA). Library QC and quantitation were performed on all individual libraries using the Qubit assay (Thermo Fisher Scientific, Waltham, MA) and the Agilent 2100 Bioanalyzer.

tag: genotype


title: Δ0368 Δ0595 rep2


title: Tumor methylation_CAM20.0027


title: Tumor methylation_CAM20.0023


title: Tumor methylation_CAM20.0025


title: Δ0595 rep2


title: RNA-seq AM cells DSA+ ABMR+ #1


title: Db_1612_Cb

description: Whole cerebellar tissue with single dose tamoxifen from bigenic mouse #1


title: RNA-seq AM cells DSA+ ABMR- #3


title: Tumor methylation_CAM20.0021


title: Δ0595 rep3


title: Tumor methylation_CAM20.0034


title: Δ0368 Δ0595 rep3


title: Tumor methylation_CAM20.0018


title: RNA-seq AM cells DSA+ ABMR- #2


title: Tumor methylation_CAM20.0017


title: Δ0595 rep1


title: Δ0368 rep3


title: RNA-seq AM cells DSA+ ABMR- #1


title: Tumor methylation_CAM20.0016


title: Tumor methylation_CAM20.0015


title: Tumor methylation_CAM20.0014


title: RNA-seq AM cells DSA- #3


title: Δ0368 rep2


title: Δ0368 rep1


title: Tumor methylation_CAM20.0013


title: RNA-seq AM cells DSA- #2


title: Tumor methylation_CAM20.0011


title: WT rep3

value: wild type


title: Tumor methylation_CAM20.0020


title: Tumor methylation_CAM20.0010


title: Tumor methylation_CAM20.0022


title: Tumor methylation_CAM20.0009


title: RNA-seq RM cells DSA+ ABMR+ #3

source_name: blood RM B cells

value: blood RM B cells


title: Tumor methylation_CAM20.0008


title: RNA-seq RM cells DSA+ ABMR+ #1


title: Tumor methylation_CAM20.0005


title: WT rep1


title: Tumor methylation_CAM20.0006


title: WT rep2


title: RNA-seq RM cells DSA+ ABMR+ #2


title: Tumor methylation_CAM20.0007


title: Tumor methylation_CAM20.0004


title: RNA-seq RM cells DSA+ ABMR- #3


title: Tumor methylation_CAM20.0003


title: Tumor methylation_CAM20.0012


title: Tumor methylation_CAM20.0002


title: Tumor methylation_CAM20.0001


title: RNA-seq RM cells DSA+ ABMR- #2


title: P19_retina_OIR+AFLx3_rep3

type: RNA

city: Cambridge

first: Jesus Eduardo

last: Rojo Arias

address: Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

description:
SAMPLE 12
Retina of P19 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13, 15 and 17 replicate 3

hyb_protocol: 5.5 ug of biotinylated and fragmented single-stranded cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Whole Transcriptome Arrays according to the GeneChip® WT PLUS Reagent Kit User Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The scanned images were processed with the Transcriptome Analysis Console (TAC) Software (Affymetrix) using default parameters to obtain background subtracted and summarized probe sets.
The data were analyzed with the Agilent GeneSpring GX software version 13.0 using Affymetrix default analysis settings and GC-RMA. No baseline transformation was done.

label: biotin

source_name: Retina, oxygen-induced retinopathy mouse treated with 25 mg per kg body weight AFL on P13, P15 and P17

label_protocol: Biotinylated cDNA samples were prepared according to the GeneChip WT PLUS Reagent Kit (902280) protocol from 250 ng total RNA.

growth_protocol: Mice were housed in standard conditions. OIR mice were subjected to 75% oxygen from postnatal day 6 to postnatal day 11. OIR+AFLx2 mice were treated with Aflibercept at 25 mg per kg body weight on postnatal day 13 and 15. OIR+AFLx3 mice were treated with Aflibercept at 25 mg per kg body weight on postnatal day 13, 15 and 17.

extract_protocol: Total RNA was isolated from whole retinas as follows. Mice were sacrificed on P19 by an overdose of ketamine and xylazine. Eyes were immediately removed from their orbits and retinal cups were promptly dissected in PBS at 37°C. After dissection, both retinas of a single normoxic, OIR, OIR+AFLx2 or OIR+AFLx3 mouse were pooled together and warm PBS was replaced by 750 µl TRIzol (Thermo Fisher Scientific, MA, USA). Next, retinal tissues were disrupted by 10 rounds of aspiration/ejection through 18G and 23G needles and incubated at RT for 5 min. Thereafter, 150 µl chloroform (Merck, Darmstadt, Germany) were added, samples were vortexed at maximum speed for 15 seconds, incubated at RT for 15 min, and centrifuged at 12 000 g for 20 min at 4°C. After centrifugation, the aqueous phase was collected, 1.5 µl RNA-grade glycogen (Thermo Fisher Scientific, MA, USA) and 375 µl isopropanol (Merck, Darmstadt, Germany) were added. Samples were subsequently vortexed 15 seconds at maximum speed and centrifuged at 12000 g for 20 min at 4°C. The supernatant was discarded, and pellets were washed twice in 1 ml 75% ethanol in molecular biology-grade water, air-dried for 10-20 min and re-suspended in 20 µl RNAse-free water.

treatment_protocol: Aflibercept was administered to OIR mice intra-peritoneally at 25 mg per kg body weight on postnatal days 13 and 15 (OIR+AFLx2) or on postnatal days 13, 15 and 17 (OIR+AFLx3).

value: Retina

tag: developmental stage

value: Postnatal day 19


title: CF-rGO-2

city: xi'an

first: Dengfeng

last: Gao

address: NO.157 Xiwu Rd,Xi'an City

institute: The Second Affiliated Hospital, Xi’an Jiaotong University

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Oﬀ-Line Base Caller software, v1.8)
Sequence quality was examined using the FastQC software.
The trimmed reads (trimmed 5’, 3’-adaptor bases using cut-adapt) were aligned to reference genome using Hisat2 software.
The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown.
The diﬀerentially expressed genes and transcripts were fltered using R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown, then use CPAT
Genome_build: RNO6
Supplementary_files_format_and_content: FPKM

organism: Rattus norvegicus

source_name: CFs-rGO

growth_protocol: Primary CFs were isolated from 2- to 3-day-old neonatal rats by using enzyme digestion and cultured (typically 2-3 × 10^6 cells) with DMEM/F-12 culture medium containing 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from above samples by using Trizol reagent (Invitrogen)
KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing library.

treatment_protocol: CFs cells exposed to rGO for 24h

value: Sprague-Dawley

value: heart

tag: age

value: post-natal day 3

value: cardiofibroblasts (CFs)

value: reduced graphene oxide (rGO) for 24hrs


title: CF-rGO-1


title: RNA-seq RM cells DSA+ ABMR- #1


title: P19_retina_OIR+AFLx3_rep2

description:
SAMPLE 11
Retina of P19 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13, 15 and 17 replicate 2


title: CF-3

source_name: CFs

value: control


title: P19_retina_OIR+AFLx3_rep1

description:
SAMPLE 10
Retina of P19 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13, 15 and 17 replicate 1


title: RNA-seq AM cells DSA- #1


title: CF-2


title: P19_retina_OIR+AFLx2_rep3

description:
SAMPLE 9
Retina of P19 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13 and 15 replicate 3

source_name: Retina, oxygen-induced retinopathy mouse treated with 25 mg per kg body weight AFL on P13 and P15


title: P19_retina_OIR+AFLx2_rep2

description:
SAMPLE 8
Retina of P19 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13 and 15 replicate 2


title: RNA-seq RM cells DSA- #3


title: P19_retina_OIR+AFLx2_rep1

description:
SAMPLE 7
Retina of P19 mouse subjected to the OIR protocol and treated with 25 mg per kg body weight Aflibercept on postnatal days 13 and 15 replicate 1


title: RNA-seq RM cells DSA- #2


title: CF-1


title: P19_retina_OIR_rep3

description:
SAMPLE 6
Retina of P19 mouse subjected to the OIR protocol replicate 3

source_name: Retina, oxygen-induced retinopathy mouse


title: P19_retina_OIR_rep2

description:
SAMPLE 5
Retina of P19 mouse subjected to the OIR protocol replicate 2


title: P19_retina_OIR_rep1

description:
SAMPLE 4
Retina of P19 mouse subjected to the OIR protocol replicate 1


title: RNA-seq RM cells DSA- #1


title: P19_retina_normoxia_rep3

description:
SAMPLE 3
Retina of P19 normoxic mouse replicate 3

source_name: Retina, normoxic mouse


title: P19_retina_normoxia_rep1

description:
SAMPLE 1
Retina of P19 normoxic mouse replicate 1


title: P19_retina_normoxia_rep2

description:
SAMPLE 2
Retina of P19 normoxic mouse replicate 2


title: time_9_replicate_3

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Genome_build: ASM970v1 available from  https://www.ebi.ac.uk/ena/browser/view/GCA_000009705.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: liquid culture

growth_protocol: Nostoc sp. PCC 7120 cultures were grown at 30ºC under continuous illumination (75 µE m-2 s-1) in BG11 medium ( Rippka, R. 1988  Methods Enzymol, 167, 3-27. ) supplemented with 10 mM NaHCO3. 1% (w/v) and bubbled with a mixture of CO2 and air (1% v/v).

extract_protocol:
RNA was extracted by the hot phenol method as described in Luque et al. 2002  Mol Microbiol, 46, 1157-1167.
250 ng of total RNA from each culture were used to prepare libraries compatible with Illumina sequencing. Libraries were prepared using the Zymo-Seq RiboFree™ Total RNA Library Kit (Zymo, Cat. No. R3000) following the instructions of the manufacturer.

treatment_protocol: Chloramphenicol 40 µg ml-1 was added to cultures at the beginning of the experiment

value: Nostoc sp. PCC 7120

tag: time point (h)


title: time_0_replicate_3


title: 038B_S40 RNA-seq

first: Miles

last: Mee

address: 661 University Ave Suite 510

institute: Ontario Institute for Cancer Research

data_processing:
Reads aligned to CanFam3.1 reference genome with Hisat2  2.1.0
Gene annotation and expression with StringTie 1.3.3
Raw read counts calculated using prepDE .py from Ballgown R package
FPKM values calculated using the Ballgown R package
Genome_build: CanFam3.1 reference genome
Supplementary_files_format_and_content: Tab-delimited text files include either raw read count or FPKM values for

organism: Canis lupus familiaris

source_name: Lymphoma

extract_protocol:
Qiagen Rneasy
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: lymphoma tumour

tag: immunophenotype

value: T-Cell

tag: time of sampling

value: 6 weeks into treatment


title: LN229-SurvGFPNES-treated_b [13b_S20]

city: Mainz

first: Christian

last: Schwarzenbach

address: Obere Zahlbacher Str. 67

department: Institute of Toxicology

country: Germany

institute: University medical center Mainz

data_processing:
Basecalls were performed using Cufflinks Assembly & DE (BaseSpace Workflow) version 2.1.0
Alignments were performed using STAR (version STAR_2.5.0b)
Count quantification was performed using Cufflinks (version 2.2.1)
Filtering was performed for genes with at least 10 counts in 4 samples
Normalisation was performed with the EdgeR functions calcNormFactors and estimateDisp
Statistical analysis was performed with the EdgeR functions glmQLFit, makeContrasts and glmQLFTest
Genome_build: UCSChg19
Supplementary_files_format_and_content: differential gene expression data, including CPM, FC, P-value, FDR
Supplementary_files_format_and_content: .txt file of filtered counts

growth_protocol: DMEM + 10% FBS + 0.75 mg/ml G418 (as selection marker), in T25 flasks, routinely passaged 2 times a week

extract_protocol:
RNA-isolation kit, (Machery-Nagel, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Temozolomide was dissolved to a 35 mM stock solution in dimethyl sulfoxide (DMSO) and stored in aliquots at -80°C; cells were exposed to 50 µM TMZ final for 48h.

value: Glioblastoma multiforme

tag: plasmid

tag: nes status

value: mutated; (T>G) and (T>C) in each codon leads to the substitution of leucine by alanine at positions 96 (L96A) and 98 (L98A)

tag: survivin localisation

value: predominantly nuclear


title: time_24_replicate_3


title: time_3_replicate_3


title: 037B_S38 RNA-seq

value: B-Cell


title: time_24_replicate_2


title: LN229-SurvGFPNES-treated_a [13a_S19]

tag: cell type


title: LN229-SurvGFPNES-untreated_b [12b_S18]


title: 035B_S34 RNA-seq

value: Unknown


title: 036B_S36 RNA-seq


title: LN229-SurvGFPNES-untreated_a [12a_S17]


title: 034B_S32 RNA-seq


title: time_9_replicate_2


title: 033B_S30 RNA-seq


title: LN229-SurvGFP-treated_b [11b_S16]

value: functional (WT)

value: predominantly cytoplasmic


title: time_3_replicate_2


title: 032B_S28 RNA-seq


title: 030B_S26 RNA-seq


title: 029B_S24 RNA-seq


title: LN229-SurvGFP-treated_a [11a_S15]


title: 028B_S22 RNA-seq


title: LN229-SurvGFP-untreated_b [10b_S14]


title: time_0_replicate_2


title: 027B_S20 RNA-seq


title: time_24_replicate_1


title: 026B_S18 RNA-seq


title: 025B_S16 RNA-seq


title: time_9_replicate_1


title: 003B_S4 RNA-seq


title: time_3_replicate_1


title: 024B_S14 RNA-seq


title: time_0_replicate_1


title: 037A_S37 RNA-seq

value: Prior to treatment


title: 034A_S31 RNA-seq


title: 036A_S35 RNA-seq


title: 035A_S33 RNA-seq


title: 031A_S27 RNA-seq


title: 030A_S25 RNA-seq


title: 029A_S23 RNA-seq


title: 028A_S21 RNA-seq


title: 026A_S17 RNA-seq


title: 027A_S19 RNA-seq


title: 025A_S15 RNA-seq


title: Tyro3_KO2

city: Houston

first: Zhou

last: Jiang

state: Texas

address: 6565 MD Anderson Blvd

department: Molecular and Cellular Oncology

institute: MD Anderson Cancer Center

description:
Tyro3 knocked out resistant cells
KO_2

data_processing:
raw data was transformed to raw reads by CASAVA and stored in FASTQ files
adaptor sequences were trimmed and low quality reads containg >10% N were removed
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FPKM (fragments per kilobase of transcript sequence per million basepairs) were calculated
For the samples with biological replicates, differential expression analysis between two groups was performed using DESeq2 R package.
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: A xlsx file of gene expression level (FPKM value and read counts) of all samples.

source_name: triple negative breast cancer cell line

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (SH3024301, Cytiva HyClone) with 10% fetal bovine serum (FBS; 10437028, Gibco).

extract_protocol:
Flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: phenotype

value: anti-PD1 resistant cells

value: Tyro3 KO


title: LN229-SurvGFP-untreated_a [10a_S13]

tag: cell line


title: 4T1_R2

description:
anti-PD1 resistant cells
R3_2


title: 024A_S13 RNA-seq


title: HCT116 - shTGM2-1 -d

city: Frankfurt am Main

first: Michael

last: Rieger

address: Theodor-Stern-Kai 7

institute: Universitätsklinikum Frankfurt/DKFZ

data_processing:
The resulting FASTQ files were aligned to the hg38 draft of the human genome and counts per gene were estimated using STAR (v. 2.7.7)
Counts per gene were normalized and knock-down gene expression compared to controls using DESeq2 (v. 1.30.0) in R (3.4.4)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with the normalized per gene counts as reads per million (RPM) output from DESeq2 (v. 1.30.0)

source_name: Human colon adenocarcinoma

growth_protocol: Cells were cultured according ATCC recomandations in McCoys growth medium in a75 cm² flask

extract_protocol:
RNA isolation was performed using RNAeasy isolation kit (Quiagen) according to the manufacturer’s instructions. The quality and concentration of libraries were determined by an Agilent 2100 Bioanalyzer and RiboGreen fluorescence on Qubit (Invitrogen).
Library preparation was performed at the MPI for Heart and Lung Research (Bad Nauheim) according to protocol
The library was prepared using ClonTech’s SMARTer Stranded Total RNA Sample Prep Kit and sequenced on an Illumina HiSeq 2000 (San Diego, CA, USA) system using a 100-bp paired-end approach.

value: human colon epithelial cells

tag: shRNA


title: 003A_S3 RNA-seq


title: HCT116 - shTGM2-1 -c


title: 038A_S39 RNA-seq


title: 4T1_R1

description:
anti-PD1 resistant cells
R3_1


title: HCT116 - shTGM2-1 -b


title: 033A_S29 RNA-seq


title: Tyro3_OE1

description:
Tyro3 overexpressed parental cells
Tyro3OE_1

value: Parental cells

value: Tyro3 OE


title: HCT116 - shTGM2-1 -a


title: HCT116 - shSCRML-b

value: shSCRML


title: Male_2

city: Colchester

first: Antonio

last: Marco

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

data_processing:
Reads were mapped to the D. Pseudoobscura assembly 104 with HISAT2, and reads for microRNAs were counted with featureCounts.
Genome_build: D. Pseudoobscura assembly 104
Supplementary_files_format_and_content: featureCounts

organism: Drosophila pseudoobscura

source_name: Male sample 2

growth_protocol: All flies were kept at 18ºC on cornmeal based media, with 12 hours light/dark cycles. Adult males and females were collected at age 7 days.

extract_protocol:
We extracted total RNA form samples using TRIzol (Life Technologies) as recommended by the manufacturer. RNA was dissolved in RNase-free wate
For small RNA sequencing we used the TruSeq Small RNA Sample Preparation Kit (Illumina) to generate the cDNA library and we selected constructs of sizes 145 to 160 bp in a 6% PAGE gel, and precipitated in ethanol

tag: Sex

value: Male


title: Female_1

source_name: Female sample 1

value: Female


title: Male_1

source_name: Male sample 1


title: HCT116 - shSCRML-a


title: 4T1_P1

description:
Parental cell line
P_1

value: control


title: Female_2

source_name: Female sample 2


title: 4T1_P2

description:
Parental cell line
P_2


title: Tyro3_KO1

description:
Tyro3 knocked out resistant cells
KO_1


title: CF-rGO-3

value: Sprague-Dawley

value: heart

value: post-natal day 3

value: cardiofibroblasts (CFs)

tag: treatment

value: reduced graphene oxide (rGO) for 24hrs


title: HCT116 - shSCRML-d


title: s_testis_Mov10l1_KO_9dpp_So820-M10_r2.SE

status: Public on Jul 13 2021

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Raw RNA-seq reads were mapped to golden hamster (mesAur1) and the newest golden hamster (PRJDB10770) genomes using STAR 2.7.3a with following parameters:  STAR --readFilesIn $ {FILE}.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 5000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --sjdbScore 2  For analysis of expression of protein coding genes, reads were mapped with maximum of 20 multimapping alignments allowed.
Reads mapped to mesAur1 were counted over exon features annotated by Ensembl (release 99) using featureCounts v2.0.0:  featureCounts -a $ {FILE}.gtf -o $ {FILE}.counts.txt $ {FILE}.bam -T 12 -F GTF -M -O –fraction  For the paired-end libraries -p flag was added. For the stranded libraries, -s 2 flag was added.
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: MesAur1.0
Supplementary_files_format_and_content: ensembl.99.MesAur1.0.Piwil3_Tex101.from_RefSeq.raw_counts.testis.txt: counts of reads over exon coordinats from Ensembl Release 99 .gtf file with added Piwil3 and Tex101 annotated by RefSeq, samples are in columns, genes in rows
Supplementary_files_format_and_content: Coverage genome browser tracks files: bigWig format generated in a non-stranded mode, not normalized for library size

molecule: polyA RNA

organism: Mesocricetus auratus

source_name: whole testis_Mov10l1 KO

extract_protocol:
Total RNA was extracted from adult, 21dpp, 13dpp, 9dpp and 0dpp hamster testes using Sigma-Aldrich miR Premier micro RNA isolation kit according to the manufacturer´s protocol. Ribosomal RNA (rRNA) was depleted from RNA used for transcriptome analysis using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Epicentre) according to the manufacturer´s protocol. rRNA depletion was confirmed by 2100 Bioanalyzer (Agilent Technologies).
RNA-seq libraries were generated using NEBNext Ultra II directional RNA library Prep kit for Illumina (BioLabs, #E7765S) according to the manufacturer´s protocol. RNA-seq libraries from adult, 21dpp and 13dpp testes were sequenced by 150 nt pair-end reading. RNA-seq libraries from 9dpp and 0dpp testes were sequenced by 75 nt single-end reading using the Illumina NextSeq500/550 platform.

treatment_protocol: Production of knock-out hamsters was carried out using an in vivo electroporation CRISPR/Cas9 system. Pairs of sgRNAs were designed to cleave Mov10l1 genomic sequence in intron 19 (sequence of DNA targets: 5´- gggtatcacatgacttgggg – 3´; 5´- ggtgttgggatcatagtgggg – 3´) and intron 20 (sequence of DNA targets: 5´-tctccactcttccatgtgggg - 3´; 5´- taccattacatttgtcagggg - 3´) in order to delete exon 20. Five animals were born of which one did not exhibit any deletion, two appeared homozygous for the deletion and were not used for breeding, and one male and one female showed modification of one allele. The male was fertile but did not transmit the allele (# of progeny = 13; 8 males + 5 females) while the female (#4) transmitted the allele into progeny (# of progeny = 10; 3 males + 4 females carried the mutant allele) when bred to a wild type animal. Subsequent breeding of heterozygotes for two generations with wild type outbred animals was performed in order to minimize possible off-targeting and inbreeding effects when heterozygotes were mated to produce homozygotes.

value: Mov10l1 KO

value: whole testis


title: Tyro3_OE2

description:
Tyro3 overexpressed parental cells
Tyro3OE_2


title: HCT116 - shSCRML-c


title: s_testis_Mov10l1_KO_0dpp_So843-M5_r2.SE

data_processing:
Raw RNA-seq reads were mapped to golden hamster (mesAur1) and the newest golden hamster (PRJDB10770) genomes using STAR 2.7.3a with following parameters:  STAR --readFilesIn $ {FILE}.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 5000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --sjdbScore 2  For analysis of expression of protein coding genes, reads were mapped with maximum of 20 multimapping alignments allowed.
Reads mapped to mesAur1 were counted over exon features annotated by Ensembl (release 99) using featureCounts v2.0.0:  featureCounts -a $ {FILE}.gtf -o $ {FILE}.counts.txt $ {FILE}.bam -T 12 -F GTF -M -O –fraction  For the paired-end libraries -p flag was added. For the stranded libraries, -s 2 flag was added.
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: MesAur1.0
Supplementary_files_format_and_content: ensembl.99.MesAur1.0.Piwil3_Tex101.from_RefSeq.raw_counts.testis.txt:  - tab delimited table with counts of reads over exon coordinats from Ensembl Release 99 .gtf file with added Piwil3 and Tex101 annotated by RefSeq  - samples are in columns, genes in rows  Coverage genome browser tracks files:  - bigWig format  - generated in a non-stranded mode  - not normalized for library size


title: s_testis_Mov10l1_WT_0dpp_So817-M4_r2.SE

source_name: whole testis_WT

value: WT


title: s_testis_Mov10l1_KO_9dpp_So820-M10_r1.SE


title: s_testis_Mov10l1_WT_0dpp_So807-M3_r1.SE


title: s_GV_Mov10l1_WT_So834_12xoo_r1.SE

data_processing:
Small RNA-seq reads were trimmed using bbduk.sh version 38.87 (https://jgi.doe.gov/data-and-tools/bbtools/):  bbduk.sh -Xmx20G threads=6 in=$ {FILE}.fastq.gz out=$ {FILE}.atrim.fastq.gz literal= TGGAATTCTCGGGTGCCAAGG stats=$ {FILE}.atrim.stats overwrite=t ktrim=r k=21 rcomp=f mink=10 hdist=1 minoverlap=8
Libraries were then deduplicated from PCR duplicates. First, using custom scripts (availible at github.com/fhorvat) both UMI sequences from read (4 random nucleotides from each end of trimmed read) were added to the read header. UMI sequences were then removed from read sequence using Cutadapt version 2.10:   cutadapt -u 4 -o ${FILE}.trim_1.fastq -j 6 ${FILE}.umi.fastq  cutadapt -m 18 -u  -4 -o ${FILE}.trim_2.fastq -j 6 ${FILE}.trim_1.fastq  Trimmed reads were then mapped to the new golden hamster (PRJDB10770) genome using STAR 2.7.3a:   STAR --readFilesIn $ {FILE}.dedup.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 1 --outFilterMismatchNoverReadLmax 1 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 5000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outFilterMultimapScoreRange 0 --alignIntronMax 1 --alignSJDBoverhangMin 999999999999  UMI tools version 1.1.1. were then used on mapped .bam files in order to deduplicate them:  umi_tools dedup --method=directional --multimapping-detection-method=NH -I ${FILE}.trim_1.fastq --output-stats=${FILE}.dedup_stats --log=${FILE}.dedup_log.txt -S ${FILE}.dedup.bam.   Last, reads .fastq files were generated from deduplicated mapped reads .bam files using samtools version 1.10:   samtools fastq -@ 12 ${FILE}.dedup.bam > ${FILE}.dedup.fastq
Trimmed and deduplicated reads were mapped to the mesAur1 genome with following parameters:  STAR --readFilesIn $ {FILE}.dedup.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 1 --outFilterMismatchNoverReadLmax 1 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMultimapNmax 99999 --outFilterMultimapScoreRange 0 --alignIntronMax 1 --alignSJDBoverhangMin 999999999999
Genome browser coverage tracks in bigWig format were produced from bam files (size filtere to include only 18-32 nucleotide long reads) using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.18to32nt.bam -bg -split -g chrNameLength.txt > ${FILE}.18to32nt.bedGraph  wigToBigWig ${FILE}.18to32nt.bedGraph chrNameLength.txt ${FILE}.18to32nt.bw
Genome_build: MesAur1.0
Supplementary_files_format_and_content: coverage genome browser tracks files:  - bigWig format  - generated in a non-stranded mode  - not normalized for library size

source_name: GV oocyte

extract_protocol:
For small RNA-seq analysis of oocytes, at least 5 oocytes per animal were collected and incubated at 75°C for 3 min to release small RNAs.
Small RNAs libraries were prepared using the NextFlex Small RNA-seq v3 kit (Amplicon) according to the manufacturer´s protocol with 3´ adapter ligation overnight at 16 °C, 25 cycles used for PCR amplification and gel purification used for size selection. For gel purification, libraries were separated on a 2,5% agarose gel using (1x) lithium borate (LB) buffer and visualized with ethidium bromide. The 140-170 bp fraction was cut off the gel and DNA was isolated using the MinElute Gel Extraction Kit (Qiagen). Final libraries were sequenced by 75 nt single-end reading using the Illumina NextSeq500/550 platform.

value: GV oocyte

tag: molecule subtype

value: small RNA


title: s_testis_Mov10l1_KO_0dpp_So843-M4_r1.SE

tag: genotype


title: s_GV_Mov10l1_WT_So846_8xoo_r1.SE


title: s_testis_Mov10l1_WT_9dpp_So802-M3_r2.SE


title: s_testis_Mov10l1_WT_9dpp_So802-M1_r1.SE


title: s_testis_Mov10l_KO_21dpp_F58-M2_r2.reseq [small RNA-seq]

data_processing:
Small RNA-seq reads were trimmed in two rounds using bbduk.sh version 38.87 (https://jgi.doe.gov/data-and-tools/bbtools/). First, NEXTflex adapter were trimmed from right end:  bbduk.sh -Xmx20G threads=6 in=$ {FILE}.fastq.gz out=$ {FILE}.atrim.fastq.gz literal= TGGAATTCTCGGGTGCCAAGG stats=$ {FILE}.atrim.stats overwrite=t ktrim=r k=21 rcomp=f mink=10 hdist=1 minoverlap=8  Next, 4 random bases from both sides of reads were trimmed:  bbduk.sh -Xmx20G threads=6 in=$ {FILE}.atrim.fastq.gz out=$ {FILE}.trimmed.fastq.gz stats=$ {FILE}.ftrim.stats overwrite=t forcetrimright2=4 forcetrimleft=4 minlength=18
Trimmed reads were mapped to the genomes with following parameters:  STAR --readFilesIn $ {FILE}.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 1 --outFilterMismatchNoverReadLmax 1 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 5000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outFilterMultimapScoreRange 0 --alignIntronMax 1 --alignSJDBoverhangMin 999999999999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: MesAur1.0
Supplementary_files_format_and_content: coverage genome browser tracks files: bigWig format generated in a non-stranded mode, not normalized for library size

extract_protocol:
Total RNA was extracted from adult, 21dpp, 13dpp and 9dpp hamster testes using Sigma-Aldrich miR Premier micro RNA isolation kit according to the manufacturer´s protocol. Ribosomal RNA (rRNA) was depleted from RNA used for transcriptome analysis using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Epicentre) according to the manufacturer´s protocol. rRNA depletion was confirmed by 2100 Bioanalyzer (Agilent Technologies). For small RNA-seq analysis of testes, total RNA isolated from testes as described above was used for NextFlex Small RNA-seq v3 kit (Amplicon).
Libraries were prepared according to the manufacturer´s protocol with 3´ adapter ligation overnight at 16 °C, 15 cycles used for PCR amplification and NextFlex beads used for size selection. RNA-seq libraries were sequenced by 75 nt single-end reading using the Illumina NextSeq500/550 or 100 nt single-end reading using NovaSeq6000 platform.


title: s_testis_Mov10l1_WT_9dpp_So820-M12_r3.SE


title: s_testis_Mov10l_KO_13dpp_F64-M3_r2.reseq [small RNA-seq]


title: s_testis_Mov10l_KO_13dpp_F60-M3_r1.reseq [small RNA-seq]


title: s_testis_Mov10l_WT_13dpp_F64-M2_r2.reseq [small RNA-seq]


title: s_testis_Mov10l_KO_21dpp_F43-M5_r1.reseq [small RNA-seq]


title: s_testis_Mov10l_WT_13dpp_F60-M2_r1.reseq [small RNA-seq]


title: s_GV_Mov10l1_KO_So869_5xoo_r1.SE


title: s_testis_Mov10l1_KO_9dpp_So820-M10_r1.SE [small RNA-seq]


title: s_testis_Mov10l1_WT_9dpp_So802-M1_r1.SE [small RNA-seq]


title: s_testis_Mov10l1_KO_9dpp_So820-M10_r2.SE [small RNA-seq]


title: H4-BA

city: hebei

first: xitian

last: Hu

address: No.9 Fangbei Road, Shijiazhuang

institute: Shijiazhuang People'sHospital

description: heart failure (HF)

data_processing:
seqenced reads were inmmed for adptor sequnce and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data(reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene/transcript COUNT expression matrix

source_name: heart

extract_protocol:
HiSeq LncRNA-Seq
RNA libraries were prepared for sequencing using standard illumina protacal

value: blood

tag: state

value: disease


title: H3-BA

description: heart failure (HF)

tag: age


title: C5-BA

description: myocardial fibrosis (MF)


title: C4-BA

description: myocardial fibrosis (MF)


title: A2-BA

description: acute myocardial infarction (AMI)


title: A3-BA

description: acute myocardial infarction (AMI)


title: A1-BA

description: acute myocardial infarction (AMI)


title: t24h11

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

library_source: genomic

data_processing:
Base calling with Illumina Software
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore
The effect of trimming and overall quality distribution was determined using FastQC
Alignment was performed using Bismark
Read totals were called using Bismark Methylation Extractor
Genome_build: custom  genome based on GRCh38p13 by adding the consensus rDNA repeat sequences, GenBank U13369.1, as a separate chromosome and masking sequences highly similar to the rDNA sequence within the rest of the reference genome.
Supplementary_files_format_and_content: Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome

source_name: vastus lateralis

extract_protocol:
DNA isolation from human biopsy samples (≤5 mg) using the QIAamp DNA micro kit (Qiagen), muscle samples or myonuclear pellets were re-suspended in “buffer ATL” supplemented with proteinase K overnight at 56°C. DNA binding to the column was conducted using 1 µg of carrier RNA (only for myonuclear samples), and washes and centrifugations were carried out according to the manufacturer’s instructions. DNA was eluted in 20 µl of molecular grade H2O and was stored at   -80°C until the time of analysis.
“Classic” RRBS library preparation was performed by digesting 5 ng of genomic DNA with 30 units of MspI enzyme (New England BioLabs), and fragments were ligated to pre-annealed adapters containing 5’-methyl-cyotosine. Adapter-ligated fragments ≥50 bp were recovered using the DNA Clean & Concentrator Kit (Zymo Research, D4003) and bisulfite-treated using the EZ DNA Methylation-Lightning Kit (Zymo Research, D5030). Preparative-scale PCR was performed, and the products were purified again using the Clean and Concentrator kit.

treatment_protocol: Resistance exercise intervention consisted of the two lower limb exercises; leg press (Nordic Gym AB, Bollnäs, Sweden) and knee extension (Nordic Gym AB). After a short warm-up on submaximal loads, the subjects performed 4 sets per exercise at 7RM load with 2 min rest between sets and 5 min between exercises. Subjects were instructed to eat a standard dinner (plate model) the evening before the experiment and in the evening on the day of the experiment. Skeletal muscle biopsies were collected before the intervention and at 30 min and 24h post exercise. Muscle biopsies were obtained from the vastus lateralis muscle percutaneously after injection of local anesthetic (carbocain 10 mg/ml), by using the Bergström biopsy needle with a diameter of 5 mm (Stille AB, Torshälla, Sweden). Skeletal muscle tissue was blotted for excess blood, cleaned of non-skeletal muscle tissue and snap-frozen in liquid nitrogen. All samples were stored at -80 C until further analysis.

value: Skeletal Muscle

tag: conditions

value: Exercise

tag: time point


title: pre11

tag: tissue

value: Pre


title: s_testis_Mov10l1_WT_9dpp_So802-M3_r2.SE [small RNA-seq]


title: C1-BA

description: myocardial fibrosis (MF)


title: t30m11


title: s_testis_Mov10l1_WT_9dpp_So820-M12_r3.SE [small RNA-seq]


title: t30m10

value: Sedentary


title: H5-BA

description: heart failure (HF)


title: pre10


title: t24h9


title: t24h10


title: t30m9


title: pre9


title: t24h8


title: pre7


title: t24h6


title: t30m8


title: t24h7


title: t30m6


title: t24h5


title: pre6


title: pre5


title: t30m5


title: t24h4


title: t30m4


title: t30m7


title: t24h3


title: t30m3


title: pre8


title: pre4


title: pre3


title: t30m2


title: t30m1


title: pre2


title: pre1


title: t24h1


title: t24h2


title: merged_Samples (gene expression library; D20-5085_S2)

first: Caleb

middle: R

last: Perez

email: crperez@mit.edu, mbirnb@mit.edu

state: MA

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

data_processing:
Demultiplexed fastq files (D20-5085 as gene expression library, D20-5084 as HTO library) were generated using the MIT BMC/BCC 1.8 pipeline (details available here https://openwetware.org/wiki/BioMicroCenter:Software#BMC-BCC_Pipeline)
Feature-barcode matrices were generated from demultiplexed fastq files using the 10X Genomics CellRanger count pipeline (v4.0.0). Separate cell-gene matrices and cell-HTO matrices were generated.
Genome_build: GRCh38
Supplementary_files_format_and_content: A single feature-barcode matrix is presented in market exchange (MEX) format, containing cells from all four samples and their associated HTO counts (to assign sample identity), as well as their associated gene counts.

source_name: Peripheral blood mononuclear cells

growth_protocol: CD4+ and CD8+ primary human T cells were separately isolated from healthy donor PBMCs and activated with anti-CD3/CD28 Dynabeads in medium supplemented with IL-2 (100 U/mL). With the exception of the untransduced/unstimulated sample, each respective CAR variant was introduced by lentiviral transduction 24h post-activation. After 3 days, Dynabeads were removed, and CAR+ cells were sorted by FACS and rested for 3 additional days before challenging with NALM6 cells.

extract_protocol:
Live CAR T cells were enriched using a Dead Cell Removal (Annexin V) kit (Stem Cell Technologies), then stained separately with a unique TotalSeq-B cell hashing antibody (BioLegend). Labeled cells from all four samples were then pooled and single cells were encapsulated in a single channel of a 10X Chromium Single Cell 3' v3.1 chip.
Gene expression libraries were prepared according to the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) User Guide (CG000317 Rev B). Hashtag oligo libraries were prepared according to the CITE-seq cell hashing protocol (version: 2019-02-13; available here https://citeseq.files.wordpress.com/2019/02/cell_hashing_protocol_190213.pdf).

treatment_protocol: CD4+ and CD8+ CAR T cells were pooled at a 1:1 ratio, then challenged with NALM6 cancer cells at a 1:10 E:T ratio. NALM6 challenges were repeated twice more (Days 0, 3, and 5). 48h after the third NALM6 challenge, CAR T cells were sampled for scRNA-seq. Untransduced/unstimulated controls were not challenged with NALM6 cells.

value: Primary human T cells

tag: hto antibody

value: TotalSeq-B 0252 anti-human Hashtag 2 (BioLegend, Cat. 394633)

value: TotalSeq-B 0253 anti-human Hashtag 2 (BioLegend, Cat. 394635)

value: TotalSeq-B 0254 anti-human Hashtag 2 (BioLegend, Cat. 394637)

value: TotalSeq-B 0255 anti-human Hashtag 2 (BioLegend, Cat. 394639)


title: merged_Samples (HTO library; D20-5084_S1)


title: vector control, replicate 1

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

data_processing:
The indexed libraries were pooled in equal molar ratio and sequenced on the Illumina NextSeq 500 system using 2x151bp paired-end sequencing.
Paired-end reads were directionally mapped to the genomic loci of lncRNA (GRCh38 /hg18) by TopHat2.
Cufflinks/Cuffdiff analysis was run to identify the dysregulated RNAs
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression file generated by cuffdiff analysis

source_name: A549 cells

extract_protocol:
Total RNA was isolated from A549 cells  by using Tri Reagents
Libraries were prepared with the Illumina TruSeq Stranded mRNA Library Preparation kit. Briefly, poly-adenylated mRNA were selected using oligo-dT beads and fragmented to 300-500bp. Each fragment undergoes cDNA synthesis using random hexamer. Indexed adapters were ligated to the resulting cDNA.

value: Lung

value: epithelial cell

value: male

value: vector control

tag: infected with

value: PR/8 at a MOI of 0.01


title: vector control, replicate 2


title: lnc-PINK1-2:5-overexpression, replicate 3


title: lnc-PINK1-2:5-overexpression, replicate 2


title: lnc-PINK1-2:5-overexpression, replicate 1


title: vector control, replicate 3


title: Differentiation screen CD138+ rep2

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

data_processing:
Library strategy: CRISPR screen
The start of the iCRISPR scaffold sequence (GTTTAAGAGCTAT) within each read was identified, and the 19 bases immediately preceding this sequence extracted.
The resulting 19 base reads were mapped using Bowtie to a custom genome comprising the sgRNA library sequences, without allowing mismatches.
The number of reads mapped to each sgRNA was quantified using Seqmonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: CLIPper_peaks_m6A_eCLIP_1/2.bed: BED file for each replicate containing locations of all m6A clusters identified by CLIPper. The 'name' column (4) contains -log10(p value), and the 'score' column (5) contains the log2-fold enrichment relative to the corresponding input sample.
Supplementary_files_format_and_content: Pureclip_xl_sites_m6A_eCLIP_1/2.bed: BED file for each replicate containing locations of all m6A crosslink sites identified by PureCLIP. The 'name' column (4) contains score calculated by the PureCLIP algorithm, and the 'score' column (5) contains the fold enrichment at the read start coordinate relative to the corresponding input sample.
Supplementary_files_format_and_content: sgRNA_library_counts.txt: tab-delimited text file containing counts for each guide RNA across all samples. Names of guide RNAs comprise the target gene and sequence.

source_name: Naïve B cells cultured in iGB conditions

extract_protocol: Genomic DNA was isolated as previously described (doi:10.1016/j.cell.2015.02.038)

treatment_protocol: In vitro induced germinal centre B cell cultures (iGB) involve a 3T3 feeder layer expressing mouse CD40L and human BAFF (40LB cells). The 40LB feeder cell line was maintained in supplemented Roswell Park Memorial Institute 1640 (RPMI-1640) media with 10% FBS and 1x GlutaMAX™ (Gibco: 35050061). Irradiated (~120Gγ) 40LB cells were seeded at 80x10^3 cells per well in a 12-well plate in supplemented RPMI-1640 media. The next day, naïve B cells were isolated with a B cell isolation kit (Miltenyi Biotec: 130-090-862) and 30x10^3 were cultured on the irradiated 40LB cells with IL-4 in supplemented RPMI-1640 media (final: 10% FBS, 1x GlutaMAX™, 50µM 2-mercaptoethanol Thermo Scientific™: 31350-010, 100 units/ml penicillin, and 100μg/ml streptomycin Thermo Scientific™: 15140, 10ng/ml mIL-4 PeproTech 214-14). After three days, B cells were transduced with the mouse sgRNA library at an MOI of 0.1 in the presence of 4ng/ml polybrene (Sigma-Aldrich®: H9268), by spinfection at 1000g for 45 minutes at 32ºC. On day 4 transduced cells were positively selected by magnetic assisted cell sorting (MACS) via the cell surface antigen CD90.1 (Thy1.1) using microbeads (Miltenyi Biotec: 130-094-523); the manufacturer’s protocol was adjusted by using 4x less reagents and by maintaining cells at room temperature, and cells were reseeded on freshly irradiated 40LB cells with IL-21 in supplemented RPMI-1640 media (final: 10% FBS, 1x GlutaMAX™, 50µM 2-mercaptoethanol, 100 units/ml penicillin, and 100μg/ml streptomycin, 10ng/ml mIL-21 PeproTech 210-21). On day 8, viable singlet CD138- and CD138+ B cells were physically separated by fluorescence activated cell sorting, washed in PBS, and snap frozen on dry ice in a 15ml conical tube before storage at -80ºC for future analysis of terminal differentiation. In addition, on day4 and day8, bulk B cells, unselected for transduction or CD138 expression, were processed and stored in a comparable fashion for future analysis of proliferation/survival. Enough cells to ensure a representation of >1000x transduced cells per sgRNA in the library were maintained at all timepoints and in all populations.

tag: strain

value: Rosa26 Cas9+

value: Spleen

tag: screen

value: Differentiation

tag: days in culture

tag: flow cytometry marker

value: CD138 positive


title: Proliferation/survival screen day8

value: Proliferation/survival

value: Unsorted


title: Differentiation screen CD138+ rep1


title: Differentiation screen CD138- rep1

value: CD138 negative


title: sPIA Female 4

city: Minneapolis

first: Tate

last: Gisslen

state: MN

address: 2450 Riverside Avenue, East Building, MB630

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Tophat (v2.0.13) using the mouse (mm10 as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: mm10

source_name: hippocampus

extract_protocol:
Invitrogen RNAqueous total RNA isolation kit extration protocol followed. RNA was isolated from the hippocampus
RNA libraries were prepared for sequencing using Illumina Truseq protocols

treatment_protocol: Pups are randomized to different levels of anemia: moderate anemia at 25% (mPIA) severe anemia at 18% (sPIA) or non-bled controls (NBCs), which receive a needle prick to the back of the neck. Anemia is induced by phlebotomy of 5.25ul/g twice daily from facial vein starting in pups at postnatal day (P) 3 until goal is reached. Then pups are phlebotomized 3.5 ul/g daily until pups are killed on P14 and hippocampus is removed for RNA isolation.

tag: gender

value: female

tag: anemia level

value: severe (18%)


title: Proliferation/survival screen day4


title: Differentiation screen CD138- rep2


title: sPIA Male 4


title: sPIA Female 1


title: sPIA Female 3


title: sPIA Male 1


title: ccRCC tissue from patient PG-7

city: Milano

first: Chiara

last: Gargiuli

address: via Amadeo

department: Dept. of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

description: Gene expression data from FFPE specimens of ccRCC

hyb_protocol: Hybridization was performed according to manufacturer’s standard protocols.

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 scanner

data_processing:
Raw CEL files were imported in R and pre-processed using the robust multi-array average method implemented in the oligo Bioconductor package
Gene-level log2-normalized intensity

source_name: FFPE tissue of clear cell renal cell carcinoma

label_protocol: RNA was labeled and processed according to manufacturer’s recommended protocols.

extract_protocol: RNA was extracted using the QIAGEN miRNeasy FFPE mini kit

tag: patient

tag: Sex

value: M

tag: histology

value: ccRCC

tag: nephrectomy


title: Normal kidney tissue from patient PG-9

description: Gene expression data from FFPE specimens of normal renal tissue

source_name: FFPE normal renal tissue

value: F

value: Normal kidney


title: sPIA Female 2


title: Normal kidney tissue from patient PG-7


title: ccRCC tissue from patient PG-9


title: sPIA Male 2


title: Normal kidney tissue from patient PG-8


title: CDC tissue from patient PG-6

description: Gene expression data from FFPE specimens of CDC

source_name: FFPE tissue of collecting duct carcinoma

value: CDC


title: ccRCC tissue from patient PG-8


title: CDC tissue from patient PG-3


title: CDC tissue from patient PG-4


title: CDC tissue from patient PG-16


title: CDC tissue from patient PG-15


title: ccRCC tissue from patient PG-5


title: Normal kidney tissue from patient PG-3


title: CDC tissue from patient PG-2


title: ccRCC tissue from patient PG-14


title: mPIA Female 4

value: moderate (25%)


title: mPIA Female 3


title: sPIA Male 3

value: male


title: mPIA Female 1


title: mPIA Male 4


title: mPIA Male 2


title: mPIA Male 3


title: NBC Female 4

value: non-bled control


title: NBC Female 2


title: NBC Female 1


title: Kras*+Injury_shBrd4_ATAC_3

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description:
ATAC_T4_shBrd4_rep3_D15-5
T4_shBrd4_rep3_D15.5
PE-50

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences using trimgalore.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
Read count tables were created using featureCounts v1.6.0.
To create density files, the signal was normalised using the scalefactors from DESeq2 converted to BigWig using BEDTools.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: BigWig files containing read densities normalized using DESeq2.
Supplementary_files_format_and_content: Table of normalized counts over the union peak atlas.

source_name: sorted primary pancreatic epithelial cells

growth_protocol: 5-week-old KCsh (p48-Cre;RIK;LSLKrasG12D;CHC:TRE-GFP-shRNA) male mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) for 2 consecutive days, and FACS-sorted cells were analyzed 2 days thereafter. 6 days prior to the caerulein treatment, mice were placed on doxycycline diet to induce the expression of GFP-linked shRNA targeting Brd4 or Ren (control).

extract_protocol:
Lysis Buffer 10mM Tris·Cl, pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% (v/v) Igepal CA-630 (Buenrostro et al., 2015 protocol).
Buenrostro et al., 2015 protocol

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2- or GFP-positive, CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected in 2 % 1x PBS buffer containing 2% fetal bovine serum (FBS).

tag: experimental condition

tag: model

value: KC-shRNA GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: KrasG12D (Brd4-knockdown)

tag: treatment

value: Caerulein

tag: sample collection time point

value: Day 2 post-caerulein

value: pancreas

tag: sorting strategy

tag: age / stage (upon sample collection)

value: 5 - 6 weeks old

value: Male


title: Kras*+Injury_shBrd4_ATAC_2

description:
ATAC_T4_shBrd4_rep2_D15-4
T4_shBrd4_rep2_D15.4
PE-50

tag: tissue


title: NBC Male 2


title: NBC Male 3


title: Kras*+Injury_shRen_ATAC_3

description:
ATAC_T4_shRen_rep3_D16-4
T4_shRen_rep3_D16.4
PE-50

value: Kras*+Injury-shRen

value: KrasG12D (control)


title: Kras*+Injury_shRen_ATAC_2

description:
ATAC_T4_shRen_rep2_D15-3
T4_shRen_rep2_D15.3
PE-50


title: mPIA Male 1


title: Kras*_rIL-33_ATAC_2

description:
A8_DACE118
KrasG12D_rIL33_t0_rep2_A8
PE-50

growth_protocol: 5-6 weeks-old KC (p48-Cre;RIK;LSLKrasG12D) mice were injected intraperitoneally once daily doses with 1 ug of murine recombinant IL-33 (#580504, R&D Systems) or vehicle (PBS) for 5 consecutive days.

treatment_protocol: Pancretata were harvested and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2- or GFP-positive, CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected in 2 % 1x PBS buffer containing 2 % fetal bovine serum (FBS).

value: KC + rIL-33

value: KC;RIK GEMM

value: Day 0 (last treatment day)

value: 5 weeks old


title: Kras*_rIL-33_ATAC_1

description:
A3_DACE117
KrasG12D_rIL33_t0_rep1_A3
PE-50


title: Kras*_PBS_ATAC_1

description:
A10_DACE115
KrasG12D_PBS_t0_rep1_A10
PE-50

value: KC + Vehicle

value: PBS


title: Kras*_rIL-33_ATAC_3

description:
B3_DACE116
KrasG12D_rIL33_t0_rep3_B3
PE-50


title: Kras*+Injury_shRen_ATAC_1

description:
ATAC_T4_shRen_rep1_D4-2
T4_shRen_rep1_D4.2
PE-50


title: Kras*+Injury_shBrd4_ATAC_1

description:
ATAC_T4_shBrd4_rep1_D4-1
T4_shBrd4_rep1_D4.1
PE-50


title: Kras*_PBS_ATAC_3

description:
A6_DACE060
KrasG12D_PBS_t0_rep3_A6
PE-50

value: 6 weeks old


title: Kras*_PBS_ATAC_2

description:
A4_DACE114
KrasG12D_PBS_t0_rep2_A4
PE-50


title: mPIA Female 2

value: female

value: moderate (25%)


title: BRD3_input_JQ1_r2

city: Daejeon

first: Seung-Kyoon

last: Kim

address: 99 Daehak-ro, Yuseong-gu,

department: Convergent Bioscience and Informatics

country: South Korea

institute: Chungnam National University

description:
CHIPSEQ
raw data file is identical to raw data for BRD2_input_JQ1_r2 and BRD4_input_JQ1_r1

data_processing:
The sequencing reads were mapped to the mm10 UCSC annotation using TOPHAT (Trapnell, et al., 2009) with the parameters (-a 8 -m 0 -I 500000 -p 8 -g 20 --library-type fr-firststrand --no-novel-indels  --segment-mismatches 2 for RNA-Seq.
For GRO-Seq, the raw fastq reads were trimmed using cutadapt with parameters -a AAAAAAAAAAAAAAAAAAAA -z -e 0.10 -f fastq -m 32 (Chae et al., 2015).
The CHIPSEQ FASTQ reads were aligned to UCSC's mm10 genome using Bowtie2 with default parameters (Langmead, et al., 2012). Reads with mapping quality less than 10 were removed using SAMtools (Li, et al., 2009) for ChIP-seq. To normalize the differences induced from sequencing depths, the mapped reads were “down sampled” to the lowest number of the uniquely mapped reads with duplicates followed by duplicate reads removal using our inhouse perl scripts. The downsampled, duplicates removed mapped reads were extended to the fragment estimate from MACS using inhouse perl and R scripts. Wig files followed by bigWig files were generated through perl scripts for visualization on UCSC using these extended reads. The coverage values in bigWig files were normalized to 10million.
RPKM calculations were done using the HOMER package by normalizing to 10 million reads
Tracks for visualization on UCSC browser are generated using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Strand specific bigWig files for visualizing expression levels on a genome browser.

source_name: Cortical neurons

growth_protocol: Primary cortical neurons from E16/18 mice were cultured in Neurobasal media with B-27 and Glutamax until DIV7

extract_protocol:
RNA was extracted using Trizol reagent for mRNA- or GRO-seq. Protein was crosslinked with DNA, cross-linked samples incubated with antibodies, and genomic DNA was purified for ChIP-seq.
mRNA-seq libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturer's instructions. GRO-seq libraries was prepared as previously described (C. G. Danko, Molecular cell 50, 212-222, 2013). ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set (NEB).

treatment_protocol: DIV7 Neurons neurons were made quiescent overnight in 1 μM tetrodotoxin (TTX). In the BDNF experiment, neurons were incubated with BDNF (10 ng/ml) for different length of time. For JQ1 experiment, TTX treated neurons were pre-treated with -/+ JQ1 (0.5 µM) for 5 min, then followed by treating with 55 mM KCl for different length of time. For C646 experiment, TTX treated neurons were pre-treated with C646 (20 µM) for 48 hr, then followed by treating with 55 mM KCl for 30 min.

tag: strain

tag: cell type

value: Cortical neurons

tag: developmental stage


title: BRD4_input_JQ1_r2

description:
CHIPSEQ
raw data file is identical to raw data for BRD2_input_JQ1_r2 and BRD3_input_JQ1_r1


title: BRD4_plus_JQ1_r2

description: CHIPSEQ


title: BRD4_minus_JQ1_r2

description: CHIPSEQ


title: NBC Female 3

tag: gender

tag: anemia level

value: non-bled control


title: NBC Male 4

value: male


title: BRD3_plus_JQ1_r2

description: CHIPSEQ


title: BRD2_input_JQ1_r2

description:
CHIPSEQ
raw data file is identical to raw data for BRD3_input_JQ1_r2 and BRD4_input_JQ1_r1


title: BRD2_minus_JQ1_r2

description: CHIPSEQ


title: BRD4_input_JQ1_r1

description:
CHIPSEQ
raw data file is identical to raw data for BRD2_input_JQ1_r1 and BRD3_input_JQ1_r1


title: BRD3_input_JQ1_r1

description:
CHIPSEQ
raw data file is identical to raw data for BRD2_input_JQ1_r1 and BRD4_input_JQ1_r1


title: BRD2_input_JQ1_r1

description:
CHIPSEQ
raw data file is identical to raw data for BRD3_input_JQ1_r1 and BRD4_input_JQ1_r1


title: BRD4_plus_JQ1_r1

description: CHIPSEQ


title: BRD3_minus_JQ1_r1

description: CHIPSEQ


title: BRD4_minus_JQ1_r1

description: CHIPSEQ


title: BRD2_plus_JQ1_r1

description: CHIPSEQ


title: mRNA_sh234_3hr-r2

description: RNASEQ

tag: knockdown


title: mRNA_sh234_un-r2

description: RNASEQ


title: mRNA_shScr_3hr-r2

description: RNASEQ

value: shScrambled Ctr


title: mRNA_shScr_1hr-r2

description: RNASEQ


title: mRNA_shScr_un-r2

description: RNASEQ


title: BRD2_minus_JQ1_r1

description: CHIPSEQ


title: mRNA_sh234_3hr-r1

description: RNASEQ


title: mRNA_sh234_1hr-r1

description: RNASEQ


title: mRNA_sh234_1hr-r2

description: RNASEQ


title: BRD3_plus_JQ1_r1

description: CHIPSEQ


title: BRD3_minus_JQ1_r2

description: CHIPSEQ


title: mRNA_shScr_1hr-r1

description: RNASEQ


title: mRNA_shScr_un-r1

description:
RNASEQ
raw data file for this sample is identical to mRNA_shScrCtr_un-r1


title: BRD2_plus_JQ1_r2

description: CHIPSEQ


title: mRNA_plus180-r2

description: RNASEQ


title: mRNA_plus0-r2

description: RNASEQ


title: mRNA_minus0-r2

description: RNASEQ


title: mRNA_sh234_un-r1

description: RNASEQ


title: mRNA_shScr_3hr-r1

description:
RNASEQ
raw data file for this sample is identical to mRNA_shScrCtr_3hr-r1


title: mRNA_minus180-r2

description: RNASEQ


title: mRNA_minus60-r2

description: RNASEQ


title: mRNA_plus60-r2

description: RNASEQ


title: mRNA_plus0-r1

description: RNASEQ


title: mRNA_minus180-r1

description: RNASEQ


title: mRNA_minus0-r1

description: RNASEQ


title: LB2, repeat 2

city: Dubna

first: Mikhail

last: Zarubin

address: Russia, Moscow region, Dubna, Juliot Curie, 20

country: Russia

institute: Joint Institute for Nuclear Research

data_processing:
Quality control of sequencing results performed in FastQC software.
Pre-filtering of readings by length and quality, as well as removal of adapter sequences, were performed using TrimGalore and Cutadapt.
The BDGP version 6 assembly (BDGP Release 6 + ISO1 MT / dm6, source UCSC) with masked repeating elements was used as a reference genome for Drosophila melanogaster.
Readings were mapped to the reference genome using HiSat2, taking into account splicing sites and exon boundaries according to the NCBI RefSeq annotation.
The quality assessment of the mapping results was carried out using the RSeQC package. Expression was calculated using the HTSeq package programs.

organism: Drosophila melanogaster

source_name: 3 day old fly

extract_protocol:
D. melanogaster organisms were removed and disolved in RNA-intact reagent,frozen on ice, then RNA was harvested using trizol reagent, on next step samples were prepared with Illumina RNA Sample Prep Kit. 1 ug of total RNA for the construction of sequencing libraries was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Low background radiation

value: 3rd day, adult fly

tag: line

value: Oregon


title: LB1, repeat 1


title: LB3, repeat 3


title: F3, repeat 2

value: Normal background radiation


title: mRNA_plus180-r1

description: RNASEQ


title: F1, repeat 1


title: CoKO Rep1

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

institute: UCL

data_processing:
Base Calling was done using RTA v(2.4.1.1)
Alignment was done using TopHat v(2.0.7)
Peak Calling was performed using Picard
The Bioconductor package DESeq2 was used to generate normalised estimates of transcript abundance
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file including RPKM values for each Sample.

source_name: CD69+CD4+CD8+ Adult thymocytes_CoKO

extract_protocol:
Thymocyte suspensions were prepared from adult (6 week old) Foxa1fl/flFoxa2fl/fl.CD4Cre-tg+ (Foxa1/2coKO) and Foxa1fl/flFoxa2fl/fl.Cre- (control) thymus.  Cells were stained with anti-CD69, anti-CD4 and anti-CD8 and facs sorted to purify CD69+CD4+CD8+ cells.  RNA was extracted from this CD69+CD4+CD8+ cells defined as DP.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: age

value: 6 weeks

tag: genotype/variation

value: Foxa1fl/flFoxa2fl/fl CD4Cre+

value: Adult thymus

value: CD69+CD4+CD8+ Adult thymocytes


title: CoKO Rep2


title: Control Rep1

source_name: CD69+CD4+CD8+ Adult thymocytes_control

value: Foxa1fl/flFoxa2fl/fl CD4Cre-


title: mRNA_plus60-r1

description: RNASEQ


title: mRNA_minus60-r1

description: RNASEQ


title: PV+ cSNAIL ATAC-seq E3_M1_PVpos

city: Pittsburgh

first: BaDoi

middle: Nguyen

last: Phan

address: 5000 Forbes Ave

department: Computational Biology

institute: Carnegie Mellon University

description:
dissected primary motor (M1) cortex
E3_M1_PVpos
processed data file:
Pfenning_PVpos_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

data_processing:
We processed raw FASTQ files of ATAC-seq experiments with the official ENCODE ATAC-seq pipeline (Landt et al., 2012) accessed by https://github.com/ENCODE-DCC/atac-seq-pipeline. We ran this pipeline using the mm10 genome assembly for mouse and the hg38 genome for human with the following settings: smooth_win = 150, multimapping = 0, idr_thresh = 0.1, cap_num_peak = 300,000, keep_irregular_chr_in_bfilt_peak = true. We grouped biological replicates when processing data to obtain individual de-duplicated, filtered bam files and reproducible (IDR) peaks for each condition. Unless otherwise stated, we used the optimal reproducible set of peaks for downstream analyses. We removed samples that had low periodicity indicated by ENCODE quality control metrics and reprocessed the remaining replicates with the pipeline.
We created a consensus set of non-overlapping IDR peaks from the ATAC-seq pipeline for cSNAIL ATAC-seq and Mo et al. INTACT samples (Tissue: Ctx, Cpu, and NAc ; Celltype: EXC, PV, SST, VIP, D1, D2). We extended the peak set 200bp up- and down-stream, count overlapping fragments with Rsubread v2.0.1 using the de-duplicated BAM files from the pipeline(Liao et al., 2014). This is the raw counts matrix including experiments published with this work and
We used Deeptools v3.5.0 to convert the deduplicated BAM files to normalized bigWig files (Ramírez et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: peak: optimal IDR peaks from ENCODE pipeline. bigWig = normalized bigWig files from BAM alignment. counts= featurecounts summarized rangedExperiment of consensus IDR peaks across celltypes/tissues

source_name: cortex

extract_protocol:
We performed bulk and cSNAIL ATAC-seq from cortex (CTX) and dorsal striatum/nucleus accumbens C57Bl/6J mice  as described in Buenrostro et al., 2015(Buenrostro et al., 2015) with the following minor differences in buffers and reagents. We euthanized mice with isoflurane, rapidly decapitated to extract the brain, and sectioned it in ice-cold oxygenated aCSF (119mM NaCl, 2.5 mM KCl, 1mM NaH2PO4(monobasic), 26.2mM NaHCO3, 11mM glucose) at 200-micron sections on a vibratome (Leica VT1200). We further micro-dissected sections for cortex and dorsal striatum on a stereo microscope and transferred dissected regions into chilled lysis buffer (Buenrostro et al., 2015). We dounce homogenized the dissected brains in 5mL of lysis buffer with the loose pestle (pestle A) in a 15mL glass dounce homogenizer (Pyrex #7722-15). We washed nuclei lysate off the pestle with 5mL of lysis buffer and filtered the nuclei through a 70-micron cell strainer into a 50mL conical tube. We washed the dounce homogenizer again with 10mL of BL buffer and transferred the lysate through the 70-micron filter (Foxx 1170C02). We pelleted the 20 mL of nuclei lysate at 2,000 x g for 10 minutes in a refrigerated centrifuge at 4°C. We discarded the supernatant and resuspended the nuclei in 100-300 microliters of water to approximate a concentration of 1-2 million nuclei/ mL. We filtered the nuclei suspension through a 40-micron cell strainer. We stained a sample of nuclei with DAPI (Invitrogen #D1206) and counted the sample to measure 50k nuclei per ATAC-seq transposition reaction. On the day of the ATAC-seq experiments, we dissected brain regions from fresh tissue and extracted nuclei in the same manner as described for bulk tissue experiments. Then, we sorted the nuclei suspension into Sun1GFP+ (Cre+) and Sun1GFP- (Cre-) fractions using affinity purification with Protein G Dynabeads (Thermo Fisher, cat. 10004D). A pre-clearing incubation with beads and nuclei for 10-15 minutes removes effects from non-specific binding events. Next, we incubated the remaining free nuclei with anti-GFP antibody (Invitrogen, #G10362) for 30 minutes to bind Sun1GFP. Finally, we added new beads to the solution to conjugate with the antibody and incubated the reaction for an additional 20 minutes. The pre-clear step and all incubations took place in wash buffer (0.25M Sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine with KOH to pH 7.8, and 0.4% IGEPAL) at 4°C with end-to-end rotation. After the binding process, we separated bead-bound nuclei on a magnet, washed three times with wash buffer, and filtered through a 20µM filter to ensure purity. We resuspended nuclei in nuclease-free water for input into the ATAC-seq tagmentation reaction. We performed nuclei quantification and tagmentation in the same manner described for bulk tissue ATAC-seq above. We list in the table below the number of animals, the genotypes, and which regions collected for ATAC-seq experiments in this study. N=2 Pvalb-cre samples from CPU/NAc region had received a sham surgery with saline injection into the external globus pallidus 5 days before they were sacrificed (Lawler et al, 2020 in press J. Neuro.) N=2 Drd1-cre samples from both CPU and NAc regions had received headcap surgeries 3 weeks before they were sacrificed. Both Pvalb-cre and Drd1-cre were overall healthy at time of sacrifice.
The remaining steps follow the Buenrostro et al., 2015(Buenrostro et al., 2015) protocol for tagmentation and library amplification.
We shallowly sequenced barcoded ATAC-seq libraries at 1-5 million reads per sample on an Illumina MiSeq and processed individual samples through the ENCODE pipeline for initial quality control. We used these QC measures (clear periodicity, library complexity, and minimal bottlenecking) to filter out low-quality samples and re-pooled a balanced library for paired-end deep sequencing on an Illumina NextSeq to target 30 million uniquely mapped fragments per sample after mitochondrial DNA and PCR duplicate removal. These raw sequencing files entered processing through the ENCODE ATAC-seq pipeline as above by merging technical replicates and grouping biological replicates by brain region for each pipeline run.

treatment_protocol: For cSNAIL, cell type-specific ATAC-seq, we used the following treatment protocol on C57 mice. The cSNAIL genome (pAAV-Ef1a-DIO-Sun1-Gfp-WPRE-pA) contains loxP sites to invert the Sun1-Gfp fusion gene and integrate into the nuclear membrane of cells expressing the Cre gene, allowing these cell populations to be profiled for various genomic assays (Lawler et al, 2020 in press J. Neuro).  We packaged the cSNAIL genome with AAV variant PHP.eB (pUCmini-iCAP-PHP.eB) in AAVpro(R) 293T cells (Takara, cat #632273). Viviana Gradinaru provided us with the pUCmini-iCAP-PHP.eB (http://n2t.net/addgene:103005; RRID: Addgene 103005)(Chan et al., 2017). We precipitated viral particles with polyethylene glycol, isolated with ultracentrifugation on an iodixanol density gradient, and purified in PBS with centrifugation washes and 0.2µM syringe filtration. We injected each mouse with 4.0 x 1011vg into the retro-orbital cavity under isoflurane anesthesia. We allowed the virus to incubate in the animal for 3-4 weeks to reach peak expression. We closely monitored the health of the animals throughout the length of the virus incubation and did not note any concerns.

tag: animal

tag: assay

value: cSNAIL ATAC-seq

tag: surgery

value: retro-orbital AAV injection

tag: virus

tag: genotype

value: Pvalb-cre

tag: project

value: PV+


title: PV+ cSNAIL ATAC-seq E4_M1_PVpos

description:
dissected primary motor (M1) cortex
E4_M1_PVpos
processed data file:
Pfenning_PVpos_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: PV+ cSNAIL ATAC-seq E2_M1_PVpos

description:
dissected primary motor (M1) cortex
E2_M1_PVpos
processed data file:
Pfenning_PVpos_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Bulk ATAC-seq, mouse, 082917B_STR2_S4

description:
("B" = 7 weeks old)
082917B_STR2_S4
processed data file:
Pfenning_bulk_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

source_name: Striatum

value: ATAC-seq

value: C57BL/6J wild-type

value: Bulk ATAC-seq, mouse

value: Bulk


title: Bulk ATAC-seq, mouse, 090417B_CTX2_S6

description:
("B" = 7 weeks old)
090417B_CTX2_S6
processed data file:
Pfenning_bulk_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

source_name: Cortex


title: Bulk ATAC-seq, mouse, 082917B_STR1_S3

description:
("B" = 7 weeks old)
082917B_STR1_S3
processed data file:
Pfenning_bulk_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Control Rep2

tag: tissue


title: Bulk ATAC-seq, mouse, 090417B_STR1_S7

description:
("B" = 7 weeks old)
090417B_STR1_S7
processed data file:
Pfenning_bulk_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Bulk ATAC-seq, mouse, 082917B_CTX1_S1

description:
("B" = 7 weeks old)
082917B_CTX1_S1
processed data file:
Pfenning_bulk_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Bulk ATAC-seq, mouse, 082417C_STR2_S7

description:
("C" = 12 weeks old) technical replicate of 1
082417C_STR2_S7
processed data file:
Pfenning_bulk_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Bulk ATAC-seq, mouse, 082417C_CTX2_S5

description:
("C" = 12 weeks old), technical replicate of 1
082417C_CTX2_S5
processed data file:
Pfenning_bulk_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Bulk ATAC-seq, mouse, 082317C_CTX_S1

description:
("C" = 12 weeks old)
082317C_CTX_S1
processed data file:
Pfenning_bulk_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Bulk ATAC-seq, mouse, 082317C_STR_S2

description:
("C" = 12 weeks old)
082317C_STR_S2
processed data file:
Pfenning_bulk_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Bulk ATAC-seq, mouse, 082417C_CTX1_S4

description:
("C" = 12 weeks old)
082417C_CTX1_S4
processed data file:
Pfenning_bulk_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Bulk ATAC-seq, mouse, 082417C_STR1_S6

description:
("C" = 12 weeks old)
082417C_STR1_S6
processed data file:
Pfenning_bulk_Cpu.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS


title: Organoid_50mM_Alcohol_2

city: Milwaukee

first: Thiago

last: Arzua

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College f Wisconsin

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5μl 10 × Blocking Agent and 1μlof 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Cerebral organoid, ethanol (50 mM, 6 hours)

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μgcRNA) were measured by NanoDrop ND-1000.

growth_protocol: The protocol we used for the generation of cerebral organoids was developed by Lancaster et al 2013

extract_protocol: Total RNA was extracted with the QIAzol lysis reagent kit (Qiagen Inc., Valencia, CA).Before performing the microarray assay, RNA underwent quality control analysis of RNA integrity, quantity, and purity, in addition to the detection of genomic DNA contamination and the efficacy of probe labeling

treatment_protocol: 2-month old cerebral organoids were exposed to 50 mM of ethanol for 6 hours by mixing ethanol (Sigma-Aldrich) into 15 mL of culture medium and adding it to the cell culture plate.

value: 2-month old iPSC-derived cerebral organoid

tag: agent

value: ethanol


title: Bulk ATAC-seq, mouse, 082917B_CTX2_S2

description:
("B" = 7 weeks old)
082917B_CTX2_S2
processed data file:
Pfenning_bulk_Ctx.narrowPeak.gz
cSNAIL_featureCounts_RangeSummarizedExperiment_n31_20200827.RDS

tag: cell type


title: D12_plate 5A_E10.5_liver

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

institute: King's College London

description:
BSSE-QGF-65044
processed data file: E8.5-E14.5_AllCells_genes.csv

data_processing:
Libraries were sequenced SR75 on an Illumina NextSeq 500 system (75 cycles High Output v2.5 kit).
Reads were uniquely aligned to mouse reference genome (GRCm38) using STAR (v.2.5.3.a).
Comparison of expression level between samples had been conducted with cufflinks.cuffdiff (2.2.1).
The gene expression matrices were generated employing GeneCounts as quantification type in STAR.
The gtf and fasta formatted annotations for mouse were retrieved from GENCODE project (released version v26, primary assembly).
Scater Package was used for filtering. All samples with at least 2000 genes and 500000 counts (visualised in log10 scale) were retained. These thresholds were calculated based on the average of library size and number of expressed genes in each library. We also applied a gene filtering step (transcript > 2 in at least 2 cells). Scran package was used for data normalization. For data visualization, we used t-SNE plot with a perplexity value of 20% of the total number of cells. Clustering of the cells was computed using SC3 package. Pseudo-time reconstruction was performed using Tscan package.
Genome_build: UCSC mm 10 (GRCm38)
Supplementary_files_format_and_content: E8.5-E14.5_AllCells_genes.csv: Comma-separated text file including a table of genes (rows) x cells (columns) showing logcounts (normalized counts) per single cell. Processed data file includes only samples that passed the QC check.

source_name: Liver Bud

extract_protocol:
GFP+ ventral foregut (E8.5), pancreatic (E10.5, E14.5), and hepatic progenitors (E10.5) were dissected from Tg(Prox1-EGFP) transgenic mice and dissociated into single-cell suspensions. GFP+ cells were FACS sorted at 4°C using an Aria II or Aria III flow cytometer (BD) into 96-well plates containing cell lysis buffer. Plates containing FACS-sorted cells were then frozen and kept at -80°C until shipment to ETH Genomic Facility for library preparation and sequencing.
Libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina) protocols.

value: Liver

tag: developmental stage


title: Organoid_0mM_Control_3

source_name: Cerebral organoid, control (6 hours)

value: normal media


title: F12_plate 5A_E10.5_liver

description:
BSSE-QGF-65046
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C12_plate 5A_E10.5_liver

description:
BSSE-QGF-65043
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Organoid_0mM_Control_4


title: Organoid_0mM_Control_1


title: B12_plate 5A_E10.5_liver

description:
BSSE-QGF-65042
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Organoid_50mM_Alcohol_3


title: Organoid_50mM_Alcohol_4


title: H11_plate 5A_E10.5_liver

description:
BSSE-QGF-65040
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F11_plate 5A_E10.5_liver

description:
BSSE-QGF-65038
processed data file: E8.5-E14.5_AllCells_genes.csv