title: amanitinPROseq_amanitin_Rep2

data_processing:
Library strategy: PRO-seq
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
PRO-seq read counts were normalized according to the genomic coverage of mapped Drosophila reads using bedtools (version 2.29.2) and samtools (version 1.7).For PRO-seq data analysis of α-amanitin-treated samples, the read counts were normalized according to million rRNA reads to evaluate effect of α-amanitin on Pol II-dependent PRO-seq signals. rRNA reads were defined as reads mapped to chrUn_GL000220v1: 105424 -118780 and counted using bedtools.
Genome_build: GRCH38 and Drosophila melanogaster genome build5.41 from NCBI
Supplementary_files_format_and_content: BigWig files include normalized count data obtained from methods shown above.

extract_protocol:
For PRO-seq, 25 million wild type or mutant HEK293T cells were mixed with 2.5 million Drosophila S2 cells (10:1 ratio), permeabilized, and incubated with biotin-labeled NTPs. Biotinylated RNA was hydrolyzed with NaOH, and biotin containing RNA fragments were enriched by affinity purification using streptavidin-coated magnetic beads. A 3′ sequencing adaptor was ligated to the biotinylated RNA, the 5′ cap was removed, 5′ OH was generated by base hydrolysis and converted to 5′ phosphate by treatment with T4 polynucleotide kinase, a 5′ sequencing adaptor was ligated to RNA. RNA was purified to enrich for biotinylated fragments with adaptor at both ends and reverse transcribed. Detailed methods are in PRO-Seq, Mahat et al Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086.Detailed methods are in PRO-Seq, Mahat et al Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086.
Ribo-depleted RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina) following manufacturer's instructions. Libraries were checked for quality and quantity using Bioanalyzer. Equimolar concentrations of libraries were pooled, requantified and sequenced as 100 bp paired-end reads on the Illumina HiSeq 3000 instrument. Libraries for ChIP-seq and antibody-based in situ biotinylation-seq were prepared using TruSeq ChIP Library Prep Kit (Illumina) and IDT for illumina-TruSeq RNA UD Index (Illumina). Library purification and size selection were performed using Agencourt AMPure XP system. Libraries were checked for quality and quantity using Bioanalyzer. Equimolar concentrations of libraries were pooled, and sequenced as paired-end reads on the Illumina Novaseq 6000 platform (ChIP-seq) or Hiseq 2500 platform (antibody-based in situ biotinylation-seq). PRO-seq libraries were generated essentially as described in Mahat et al., 2016 (Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086). Primers RPI1, RPI2, RPI3 and RPI4 were used to barcode cDNAs from 293T-WT_Rep1 (Wild type, replicate 1), 293T-WT_Rep2 (Wild type, replicate 2), 293T-EAF1mut_Rep1 (Mutant EAF1, replicate 1), and 293T-EAF1mut_Rep2 (Mutant EAF1, replicate 2), respectively. PRO-seq libralies were pooled and sequenced as paired-end reads on the Illumina Novaseq 6000 platform. 4C-seq libraries werec generated essentially as described in Krijger et al., 2020 (Methods, 170: 17-32; doi: 10.1016/j.ymeth.2019.07.014). 4C-seq libralies were pooled and sequenced on Illumina Hiseq 2500 platform.

value: WT

tag: spike-in organism

value: Drosophila melanogaster

value: PRO-Seq, Mahat et al Nat Protoc, 11:1455-76;  doi:10.1038/nprot.2016.086

value: nascent RNA


title: Adt_FLX_Str_Tel_4

status: Public on Apr 26 2022

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
pool of 5 dissected telencephalon
Adt_FLX_Str_Tel_4_S39

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with CutAdapt, then aligned with STAR v 2.5 with parameter --clip5pNbases 10 and --quantMode TranscriptomeSAM GeneCounts.
Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups.
Genome_build: GRCz11v92
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample.

molecule: total RNA

organism: Danio rerio

extract_protocol:
Qiagene miliamp total RNA extraction- column based
Illumina TruSeq Stranded mRNA libraries were built following the manufacturer’s protocol using 250ng of starting material.

treatment_protocol: Exposing to Fluoxetine (54ug/L) as treatment or Ethanol (0.0053%) as vehicle from 0 to 6 days post fertilization in larvae

tag: genotype/variation

value: SR4G transgenic

tag: stress status

value: Str

tag: drug status

value: FLX

tag: tissue

value: telencephalon


title: Adt_FLX_Str_Tel_2

description:
pool of 5 dissected telencephalon
Adt_FLX_Str_Tel_2_S20


title: CCND2OEExos OE1

city: Hangzhou

first: meng

last: zhao

state: Zhejiang

address: 501 Buliding 1, 18 Shilongshan Road, Cloud Town, Xihu District, Hangzhou, P.R. China

department: Life Science school

country: China

institute: Westlake Universituy

data_processing:
Raw sequencing reads (40 nts) were obtained using Illumina’s Sequencing Control Studio software  version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's  Real-Time Analysis version 1.8.70 (RTA v1.8.70).
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in  hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species  precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived  miRNA candidates.
After the raw sequence reads, or sequenced sequences (sequ seqs) were extracted from image data, a series of digital filters (LC Sciences) were employed to remove various un-mappable sequencing reads. In this step, the “impurity” sequences due to sample preparation, sequencing chemistry and processes, and the optical digital resolution of the sequencer detector were removed. Those remaining sequ seqs (filtered sequ seqs with lengths between 15 and 32 bases) were grouped by families (unique seqs), and stored in the file [Sample]_mappableReads.fq, and were used to map with the reference database files.
Normalization of sequence counts in each sample (or data set) is achieved by dividing the counts by a library size parameter of the corresponding sample. The library size parameter is a median value of the ratio between the counts a specific sample and a pseudo-reference sample. A count number in the pseudo-reference sample is the count geometric mean across all samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: Summary of known and predicted miRNA in this study.

organism: Homo sapiens

source_name: exosomes from CCND2OECMs

growth_protocol: hiPSCs were seeded in a 6-well plate that had been coated with Matrigel (Corning), and cultured in mTeSR1 (STEMCELL Technologies) with daily medium changes to 80-90% confluency. For differentiation, the medium was replaced with RPMI 1640 medium supplemented with 2% B27 minus insulin (RB-medium; ThermoFisher Scientific) and 10 μM GSK-3β inhibitor CHIR99021 (CHIR, STEMCELL Technologies) when the cells reached 80-90% confluence (Day 0); 24 hrs later, the medium was replaced with CHIR-free RB-medium for another 48 hrs until day 3, followed by replacing with an RB-medium containing 10 μM of the Wnt inhibitor IWR1 (STEMCELL Technologies) for 48 hrs, until day 5. The medium was then replaced with IWR1-free RB-medium for 48 hrs until day 7. Furthermore, the medium was replaced with RPMI/B27 medium (containing insulin) (ThermoFisher Scientific). Spontaneously and rhythmically beating CMs, usually appearing around day 7 after initiation of the differentiation protocol (Day 0), were purified via a selection on a modified glucose-free RPMI medium (Thermo Fisher Scientific) supplemented with 4 mM lactate (Sigma) and B27 for at least 5 days. Exosomes from hiPSC-CMs were isolated from the cell culture media using a Total Exosome Isolation Kit (ThermoFisher Scientific).

extract_protocol:
Total RNA was extracted with TRIzol™ Reagent (Fisher Scientific) from exosomes for small RNA sequencing.
A small RNA library was generated from the samples using the Illumina Truseq™ Small  RNA Preparation kit according to Illumina’s TruSeq™ Small RNA Sample Preparation Guide.

treatment_protocol: CCND2 was overexpressed in the hiPSC with the lentivirus method. Firstly, the lenti-α-MHC/CCND2 plasmid was generated. Briefly, a pair of oligonucleotides (forward: 5'AGAGCCACCGGTATGGAGCTGCTGTGCCACGAGGT 3', reverse: 5'CTGCAGGCGCGCCGAATTTTTTTTTTAAGTTT CACCCT 3’; Invitrogen) were used to amplify the CCND2 insert from a plasmid (Addgene # 8958) by PCR. The amplified product was digested with AscI and AgeI endonucleases, and separated by a 2% agarose gel for purification. The purified product was subcloned into a lentivirus-α-MHC (myosin heavy chain) vector (Addgene # 21230). The inserted sequence was confirmed by Sanger sequencing. The lentivirus-α-MHC/CCND2 plasmid and the MISSION lentivirus packaging mixture (Sigma-Aldrich) were co-transfected into HEK293 cells with Lipofectamine 2000 (Invitrogen). Forty-eight hours later, the virus-containing supernatant was collected, concentrated (Clontech), filtered with a 0.45-μm low protein binding membrane (Millipore), and immediately transfected into hiPSCs. Forty-eight hours after transfection, G418 (400 μg/mL) was added for 7 days, and then the cells were allowed to grow in a standard culture medium until the colonies reached the size suitable for selection and expansion. CCND2 overexpression was verified by PCR and western blot.

tag: cell type

tag: hipsc source

value: human cardiac fibroblast

tag: treatment

value: CCND2 overexpression in hiPSC-CMs


title: Adt_FLX_Str_Tel_1

description:
pool of 5 dissected telencephalon
Adt_FLX_Str_Tel_1_S15


title: batch3_H3K36me3_ZMYND1_KO2

first: Dong

last: Fang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

library_source: genomic

data_processing:
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered RNA-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of RNA-seq

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated dishes in DMEM supplemented with 15% fetal bovine serum (FBS), 1% antibiotic solution (penicillin/streptomycin), 1% glutamax, 1% MEM nonessential amino acids, 1% sodium pyruvate, 0.1 mM-mercaptoethanol and 1000 U/ml recombinant leukemia inhibitory factor (LIF). All cells were grown at 37 °C and 5% CO2.

extract_protocol:
Lysates are clarified from sonicated nuclei and histone-DNA complexes are isolated with antibody for ChIP-seq.  RNA is harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) is used with 1 ug of total RNA for libraries of RNA-seq. GRO-seq library is constructed by pull-down of BrU labelled nascent RNA which is then subjected to strand specifice library construction. CUT&Tag libraries are constructed from nuclei extraction and antibody binding, transposome tagmentation.
ChIP-seq, RNA-seq libraries were prepared for sequencing using standard Illumina protocols. CUT&Tag libraries are prepared from directely PCR. GRO-seq library is prepared by strand-specific library construction.

tag: strain

tag: chip antibody

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

tag: age

tag: genotype

value: ZMYND1 KO


title: amanitinPROseq_amanitin_Rep1

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

growth_protocol: Cells were cultured in 1X DMEM (Nacalai tesque) supplemented with 10% fetal bovine serum and 1X penicillin/streptomycin (Nacalai tesque) in a CO2 incubator (5% CO2) at 37°C.

tag: cell line

tag: protocol/antibody

tag: sequenced molecule


title: CCND2WTExos WT2

source_name: exosomes from CCND2WTCMs

value: wild type hiPSC-derived cardiomyocytes

value: untreated


title: batch3_H3K36me3_ZMYND21_KO2

value: ZMYND21 KO


title: amanitinPROseq_NT_Rep2


title: amanitinPROseq_NT_Rep1


title: Adt_FLX_Bsal_Tel_6

description:
pool of 5 dissected telencephalon
Adt_FLX_Bsal_Tel_6_S43

value: Bsal


title: CCND2WTExos WT1


title: Adt_FLX_Str_Tel_3

description:
pool of 5 dissected telencephalon
Adt_FLX_Str_Tel_3_S23


title: 4Cseq_293T-WT_HIST2H2AB-bait_Rep2_R1

data_processing:
Library strategy: 4C-seq
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
For 4C-seq, pipe4C was used with the default setting for the data analysis. R1 files of paired-end read files were used for 4C-seq data analysis.
Supplementary_files_format_and_content: BigWig files include normalized count data

extract_protocol:
For 4C-seq, HEK293T cells cultured in 10 cm dish were fixed with 4% formaldehyde for 10 min at room temperature. Cross-linked HEK293T cells were lysed, and the lysate was subjected to first restriction enzyme digestion using NlaIII (R0125S; NEB) followed by in situ ligation reaction using T4 DNA ligase (10799009001; Roche Diagnostics, Tokyo). After reverse-cross-linking, the ligated DNA templates were purified using P-beads (NucleoMag® NGS Clean-up and Size Select, 744970.5, Takara Bio Inc). Then, 2nd round of restriction enzyme digestion using DpnII (R0543S; NEB) and ligation was performed for trimming and circularization of template DNA. Resulting 4C-templates were purified by P-beads and subjected to sequencing library preparation.
4C-seq libraries werec generated essentially as described in Krijger et al., 2020 (Methods, 170: 17-32; doi: 10.1016/j.ymeth.2019.07.014). 4C-seq libralies were pooled and sequenced on Illumina Hiseq 2500 platform.

value: wildtype

tag: spike-in source

value: 4C-template DNA


title: Adt_FLX_Bsal_Tel_5

description:
pool of 5 dissected telencephalon
Adt_FLX_Bsal_Tel_5_S36


title: batch2_H3K36me3_ZMYND17_KO2

value: ZMYND17 KO


title: batch2_H3K36me3_SUV420h1_KO2#1

value: SUV420h1 KO


title: MED26mutPROseq_MED26mut_Rep1

value: Drosophila melanogaster

value: PRO-Seq, Mahat et al Nat Protoc, 11:1455-76;  doi:10.1038/nprot.2016.086

value: nascent RNA


title: Adt_FLX_Bsal_Tel_4

description:
pool of 5 dissected telencephalon
Adt_FLX_Bsal_Tel_4_S30

value: SR4G transgenic

value: FLX


title: CCND2_WT_Exos

value: human cardiac fibroblast


title: CCND2_OE_Exos

value: CCND2 overexpression in hiPSC-CMs


title: MED26mutPROseq_MED26mut_Rep2


title: MED26mutPROseq_WT_Rep2

value: WT


title: batch2_H3K36me3_PRDM1_KO2#1

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: PRDM1 KO


title: Adt_FLX_Bsal_Tel_2

description:
pool of 5 dissected telencephalon
Adt_FLX_Bsal_Tel_2_S12

value: telencephalon


title: batch2_H3K36me3_SETD5_KO2

value: SETD5 KO


title: batch3_H3K36me3_NSD3_KO2

value: NSD3 KO


title: Adt_FLX_Bsal_Tel_3

description:
pool of 5 dissected telencephalon
Adt_FLX_Bsal_Tel_3_S19

value: Bsal


title: batch1_H3K36me3_ZMYND9_KO2

value: ZMYND9 KO


title: MED26mutPROseq_WT_Rep1


title: Adt_Ctl_Str_Tel_6

description:
pool of 5 dissected telencephalon
Adt_Ctl_Str_Tel_6_S31

value: Str

value: Ctl


title: Adt_FLX_Bsal_Tel_1

description:
pool of 5 dissected telencephalon
Adt_FLX_Bsal_Tel_1_S6


title: Adt_Ctl_Str_Tel_5

description:
pool of 5 dissected telencephalon
Adt_Ctl_Str_Tel_5_S35


title: batch1_H3K36me3_SETD4_KO2

value: SETD4 KO


title: batch1_H3K36me3_KMT2A_KO2

value: KMT2A KO


title: ATAC_SK212n4

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

country: USA

institute: University of Iowa

data_processing:
Paired-end FastQ files were downloaded from the sequencing facility’s website and processed through FastQC  (Galaxy Version 0.72+galaxy1) for quality control
Reads were trimmed to remove adaptor sequences using Trim Galore (Galaxy Version 0.6.3)
Bowtie2 (Galaxy Version 2.3.4.3+ galaxy 0) was used to map the reads against the hg19 genome assembly. The --very-sensitive-local parameter was applied. Any reads not considered the primary alignment or without mapped mate were excluded by using samtools (version 1.3.1).
For generation of BogWig files the deepTools package (version 3.3.0) was used. With the help of the ‘bamCompare’ command the controls IgG and were subtracted from the CUT&RUN tracks. The resulting BigWig files were normalised using the RPKM option. Other options applied were ‘--binSize 50’  and ‘--centerReads’ for highest possible resolution and sharper signals.
Genome_build: Hg19
Supplementary_files_format_and_content: BigWig files representing anti-TFAP2A, anti-MITF, anti-H3K27Ac, anti-H3K4Me3 and anti-H3K27Me3 Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing and ATAC-Sequening SkMel28 WT and TFAP2A;TFAP2C mutant cells lines

growth_protocol: SK-MEL-28 cell lines were cultured in RPMI media contaning 10% FBS and 1% PS. Cells were maintained in log-phase growth (approximately 80% confluent) and media changed every 24 hour.

extract_protocol:
We performed anti-TFAP2A, anti-MITF, anti-H3K27Ac, anti-H3K4Me3 and anti-H3K27Me3 Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing and ATAC-Sequening in wild-type and TFAP2A; TFAP2C double mutant SK-MEL-28 cell lines essentially as described (Skene and Henikoff 2017).
CUT&RUN libraries were prepared using the KAPA Hyper Prep Kit (Roche). Quality control post-library amplification was conducted using the 2100 Bioanalyzer for fragment analysis. Libraries were pooled to equimolar concentrations and sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 instrument.
ATAC-seq was performed according to (Buenrostro et al., 2015; Liu et al., 2020) with minor alterations. Briefly, 70,000 TFAP2-KO cells (clone 2.12 and clone 4.3, four replicates each) and WT cells (four replicates) were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40: Sigma). Transposition was performed directly on nuclei using 25 µl tagmentation reaction mix (Tagment DNA Buffer #15027866, Tagment DNA Enzyme #15027865 from Illumina Tagment DNA kit #20034210). Tagged DNA was subjected to PCR amplification and library indexing, using the NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs #M0451S) with Nextera DNA CD Indexes (Illumina #20015882), according to the following program: 72 ̊C for 5 minutes; 98 ̊C for 30 seconds; 12 cycles of 98 ̊C for 10 seconds, 63 ̊C for 30 seconds, and 72 ̊C for 1 minute. The PCR product was purified with 1.8 times the volume of Ampure XP beads (Beckman Coulter #A63881). Library quality was assessed using a BioAnalyzer 2100 High Sensitivity DNA Chip (Agilent Technologies). All DNA libraries that exhibited a nucleosome pattern were pooled and processed for 150bp paired-end sequencing.
RNA-seq was performed on four replicate RNA-seq experiments were performed on TFAP2-KO cells (clone 2.12 and clone 4.3) and WT cells. Total RNA was extracted by direct cell lysis using the RNeasy Plus Mini Kit with QiaShredder (Qiagen #47134). RNA samples with an RNA integrity number (RIN) above nine were used for library generation and 150 bp paired-end sequencing on the Illumina HiSeq2500 platform (Novogene, Sacramento, CA). FASTQ sequence files were processed using FastQC (Babraham Bioinformatics) for quality control, and reads were trimmed using Trim Galore Version 0.6.3 (Developed by Felix Krueger at the Babraham Institute) and subsequently aligned to human genome assembly hg19 (GRCh37) using STAR. The output of the --quantMode GeneCounts function of STAR was used for the calculation of differential transcript expression using DESeq2 [1].The rlog function was used to generate log2-transformed normalized counts. Adjusted p-value < 0.05 was used as the threshold for statistically significant differences.

tag: type

value: Melanoma cell line

tag: mutation

value: SkMel28 TFAP2a;TFAP2c mutant cell line


title: ATAC_SK212n3


title: ATAC_SK212n2


title: ATAC_SK212n1


title: Adt_Ctl_Str_Tel_4

description:
pool of 5 dissected telencephalon
Adt_Ctl_Str_Tel_4_S26

tag: genotype/variation

value: SR4G transgenic


title: Pt-112

type: RNA

city: Kumamoto

first: Takashi

last: Takeshita

address: 4 Chome-1-60 Higashimachi, Higashi Ward

institute: Kumamoto City Hospital

scan_protocol: The procedure was performed using the GeneChip ™ Hybridization, Wash and Stain Kit by Thermo Fisher Scientific.  The GeneChip Scanner 3000 Dx by Thermo Fisher Scientific was used as the scanner.

data_processing: This data was normalized by .R/Bioconductor on May 29, 2020

label: biotin

source_name: Formalin-Fixed Paraffin-Embedded (FFPE) tissue

label_protocol: The extracted RNA was synthesized into cDNA using the Ovation FFPE WTA Systems (Affymetrix, Santa Clara, CA, USA) and the Encore Biotin Module (Affymetrix) kits according to the manufacturer’s instructions.

extract_protocol: FFPE tissues were stored until the study was performed and four sections of 10 µm thickness of FFPE specimens were obtained for RNA extraction. RNA extraction was performed using the RNeasy FFPE Kit according to the manufacturer’s protocol (Qiagen, Hilden, Germany)).

tag: menopausal state

value: Post

value: breast cancer


title: Pt-109

hyb_protocol: The procedure was performed using the GeneChip ™ Hybridization, Wash and Stain Kit by Thermo Fisher Scientific.

value: Pre


title: Pt-111


title: batch12_H3K36me3_MMSET_KO2

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: MMSET KO


title: batch11_H3K36me3_WT

value: WT


title: ATAC_SK_43n4


title: Adt_Ctl_Str_Tel_1

description:
pool of 5 dissected telencephalon
Adt_Ctl_Str_Tel_1_S2

tag: stress status

tag: drug status

value: telencephalon


title: Adt_Ctl_Str_Tel_2

description:
pool of 5 dissected telencephalon
Adt_Ctl_Str_Tel_2_S11

tag: tissue


title: Pt-110


title: ATAC_SK_43n3


title: ATAC_SK_43n2


title: Pt-108


title: ATAC_SK_43n1


title: Adt_Ctl_Bsal_Tel_6

description:
pool of 5 dissected telencephalon
Adt_Ctl_Bsal_Tel_6_S40


title: batch10_H3K36me3_SMYD5_KO2

tag: cell type

value: SMYD5 KO


title: batch10_H3K36me3_ZMYND1_KO2

tag: treatment

value: ZMYND1 KO


title: ATAC_SK_WTn4

value: SkMel28 cell line


title: batch10_H3K36me3_SETD2_KO2#2

tag: strain

value: SETD2 KO


title: batch12_H3K36me3_SETD2_KO2#1

tag: chip antibody


title: Pt-107


title: Pt-106


title: Pt-105


title: batch11_H3K36me3_SUV420h1_KO2#2

tag: age

value: SUV420h1 KO


title: Pt-103


title: Pt-104


title: ATAC_SK_WTn1


title: batch9_H3K36me3_ZMYND12_KO1

tag: genotype

value: ZMYND12 KO


title: Adt_Ctl_Bsal_Tel_3

description:
pool of 5 dissected telencephalon
Adt_Ctl_Bsal_Tel_3_S16

value: Bsal

value: Ctl


title: batch10_H3K36me3_NSD3_KO2

value: NSD3 KO


title: Adt_Ctl_Bsal_Tel_5

description:
pool of 5 dissected telencephalon
Adt_Ctl_Bsal_Tel_5_S41

value: SR4G transgenic


title: Adt_Ctl_Bsal_Tel_4

description:
pool of 5 dissected telencephalon
Adt_Ctl_Bsal_Tel_4_S45


title: batch9_H3K36me3_WT


title: ATAC_SK_WTn2

value: Melanoma cell line


title: MITF_mutant_IgG_CnR_rep2

data_processing:
Library strategy: CUT&RUN
Paired-end FastQ files were downloaded from the sequencing facility’s website and processed through FastQC  (Galaxy Version 0.72+galaxy1) for quality control
Reads were trimmed to remove adaptor sequences using Trim Galore (Galaxy Version 0.6.3)
Bowtie2 (Galaxy Version 2.3.4.3+ galaxy 0) was used to map the reads against the hg19 genome assembly. The --very-sensitive-local parameter was applied. Any reads not considered the primary alignment or without mapped mate were excluded by using samtools (version 1.3.1).
For generation of BogWig files the deepTools package (version 3.3.0) was used. With the help of the ‘bamCompare’ command the controls IgG and were subtracted from the CUT&RUN tracks. The resulting BigWig files were normalised using the RPKM option. Other options applied were ‘--binSize 50’  and ‘--centerReads’ for highest possible resolution and sharper signals.
Genome_build: Hg19
Supplementary_files_format_and_content: BigWig files representing anti-TFAP2A, anti-MITF, anti-H3K27Ac, anti-H3K4Me3 and anti-H3K27Me3 Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing and ATAC-Sequening SkMel28 WT and TFAP2A;TFAP2C mutant cells lines

value: SkMel28 MITF mutant cell line


title: MITF_mutant_IgG_CnR_rep1


title: ATAC_SK_WTn3


title: batch9_H3K36me3_SETDB2_KO1

value: SETDB2 KO


title: Adt_Ctl_Bsal_Tel_2

description:
pool of 5 dissected telencephalon
Adt_Ctl_Bsal_Tel_2_S17


title: Adt_Ctl_Bsal_Tel_1

description:
pool of 5 dissected telencephalon
Adt_Ctl_Bsal_Tel_1_S21


title: Adt_FLX_Str_Hyp_5

description:
pool of 5 dissected hypothalamus
Adt_FLX_Str_Hyp_5_S25

value: Str

value: FLX

value: hypothalamus


title: Adt_FLX_Str_Hyp_4

description:
pool of 5 dissected hypothalamus
Adt_FLX_Str_Hyp_4_S32


title: Adt_FLX_Str_Hyp_6

description:
pool of 5 dissected hypothalamus
Adt_FLX_Str_Hyp_6_S37


title: batch8_H3K36me3_ZMYND1_KO1

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)


title: batch9_H3K36me3_SETD2_KO1#1


title: Adt_FLX_Str_Hyp_3

description:
pool of 5 dissected hypothalamus
Adt_FLX_Str_Hyp_3_S13


title: TFAP2a;TFAP2c mutant_clone2_IgG_CnR_rep1

value: SkMel28 TFAP2a;TFAP2c mutant cell line


title: TFAP2a;TFAP2c mutant_clone2_IgG_CnR_rep2


title: Adt_FLX_Str_Hyp_1

description:
pool of 5 dissected hypothalamus
Adt_FLX_Str_Hyp_1_S8


title: batch7_H3K36me3_ZMYND19_KO1#2

value: ZMYND19 KO


title: batch8_H3K36me3_SETD2_KO1#2


title: batch8_H3K36me3_WT

value: WT


title: Adt_FLX_Str_Hyp_2

description:
pool of 5 dissected hypothalamus
Adt_FLX_Str_Hyp_2_S1


title: TFAP2a;TFAP2c mutant_clone1_IgG_CnR_rep1


title: WT_IgG_CnR_rep2

value: SkMel28 cell line


title: batch7_H3K36me3_ZMYND17_KO1

value: ZMYND17 KO


title: Adt_FLX_Bsal_Hyp_6

description:
pool of 5 dissected hypothalamus
Adt_FLX_Bsal_Hyp_6_S48


title: TFAP2a;TFAP2c mutant_clone1_IgG_CnR_rep2


title: WT_IgG_CnR_rep1


title: AC_null_clone2_MITF_CnR_rep2


title: batch7_H3K36me3_WT


title: batch7_H3K36me3_ZMYND11_KO1#2

value: ZMYND11 KO


title: Pt-102

value: Pre

value: breast cancer


title: Adt_FLX_Bsal_Hyp_3

description:
pool of 5 dissected hypothalamus
Adt_FLX_Bsal_Hyp_3_S24

value: Bsal


title: Pt-101

value: Post


title: Pt-098


title: Pt-100


title: Adt_FLX_Bsal_Hyp_2

description:
pool of 5 dissected hypothalamus
Adt_FLX_Bsal_Hyp_2_S18

value: SR4G transgenic


title: AC_null_clone1_MITF_CnR_rep2

value: Melanoma cell line


title: AC_null_clone1_MITF_CnR_rep1


title: Adt_FLX_Bsal_Hyp_4

description:
pool of 5 dissected hypothalamus
Adt_FLX_Bsal_Hyp_4_S28


title: batch7_H3K36me3_SETMAR_KO1#2

value: SETMAR KO


title: batch7_H3K36me3_SMYD5_KO1#2

value: SMYD5 KO


title: Pt-097


title: Pt-095


title: Pt-094


title: batch7_H3K36me3_PRDM9_KO1#2

value: PRDM9 KO


title: Adt_FLX_Bsal_Hyp_5

description:
pool of 5 dissected hypothalamus
Adt_FLX_Bsal_Hyp_5_S42

value: FLX

value: hypothalamus


title: Pt-096


title: Pt-099


title: AC_null_clone2_MITF_CnR_rep1

value: SkMel28 TFAP2a;TFAP2c mutant cell line


title: Pt-093


title: Adt_FLX_Bsal_Hyp_1

description:
pool of 5 dissected hypothalamus
Adt_FLX_Bsal_Hyp_1_S4


title: WT_MITF_CnR_rep2


title: Pt-090


title: batch7_H3K36me3_PRDM13_KO1

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: PRDM13 KO


title: Adt_Ctl_Str_Hyp_6

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Str_Hyp_6_S38

value: Str

value: Ctl


title: Pt-091


title: Adt_Ctl_Str_Hyp_5

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Str_Hyp_5_S46


title: WT_MITF_CnR_rep1

value: SkMel28 cell line


title: batch7_H3K36me3_KMT2D_KO1#3

value: KMT2D KO


title: MITF_mutant_TFAP2a_CnR_rep2

value: SkMel28 MITF mutant cell line


title: Pt-092

value: breast cancer


title: MITF_mutant_TFAP2a_CnR_rep1


title: Adt_Ctl_Str_Hyp_4

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Str_Hyp_4_S33


title: batch6_H3K36me3_WT

value: WT


title: batch6_H3K36me3_SETD8_KO1#2

value: SETD8 KO


title: Adt_Ctl_Str_Hyp_3

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Str_Hyp_3_S14

value: SR4G transgenic


title: batch6_H3K36me3_SETD8_KO1#1


title: Adt_Ctl_Str_Hyp_2

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Str_Hyp_2_S22


title: AC_null_clone2_TFAP2a_CnR_rep2

value: Melanoma cell line


title: Pt-089

value: Post


title: Pt-088


title: Pt-086


title: batch6_H3K36me3_KMT2E_KO1

value: KMT2E KO


title: AC_null_clone2_TFAP2a_CnR_rep1


title: Pt-084


title: AC_null_clone1_TFAP2a_CnR_rep2


title: batch6_H3K36me3_Brd4_KO1

value: Brd4 KO


title: Adt_Ctl_Str_Hyp_1

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Str_Hyp_1_S9

value: hypothalamus


title: Pt-087


title: Pt-085


title: AC_null_clone1_TFAP2a_CnR_rep1

value: SkMel28 TFAP2a;TFAP2c mutant cell line


title: Adt_Ctl_Bsal_Hyp_5

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Bsal_Hyp_5_S27

value: Bsal


title: Adt_Ctl_Bsal_Hyp_6

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Bsal_Hyp_6_S29


title: batch5_H3K36me3_WT

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)


title: Pt-082


title: Adt_Ctl_Bsal_Hyp_4

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Bsal_Hyp_4_S34


title: WT_TFAP2a_CnR_rep1


title: Pt-081


title: WT_TFAP2a_CnR_rep2


title: batch5_H3K36me3_SETD1A_KO1#2

value: SETD1A KO


title: Adt_Ctl_Bsal_Hyp_3

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Bsal_Hyp_3_S5

value: Ctl


title: Pt-083


title: Adt_Ctl_Str_Tel_3

description:
pool of 5 dissected telencephalon
Adt_Ctl_Str_Tel_3_S7

value: Str

value: telencephalon


title: Pt-080

value: Pre


title: batch5_H3K36me3_SETD1A_KO1#1


title: batch5_H3K36me3_SETD6_KO1

value: SETD6 KO


title: Pt-078

value: breast cancer


title: batch5_H3K36me3_PRDM14_KO1

value: PRDM14 KO


title: Adt_Ctl_Bsal_Hyp_2

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Bsal_Hyp_2_S3

value: SR4G transgenic


title: Adt_Ctl_Bsal_Hyp_1

description:
pool of 5 dissected hypothalamus
Adt_Ctl_Bsal_Hyp_1_S10


title: batch5_H3K36me3_G9a_KO1

value: G9a KO


title: Control Population 19 (NextSeq 500)

city: Detroit

first: Grace

middle: Michelle

last: Swanson

state: MI

address: 275 E. Hancock, C.S. Mott Center room 271

institute: Wayne State University

description: Control Population 19

data_processing:
Sequences were aligned to the human genome using HISAT2.
BAM files were visualized on the UCSC genome browser for transcript intactness.
BAM files were processed using the transcript integrity index algorithm.
Intact transcripts from manual and computational analysis were compared for similarity.
Interquartile range was used to define a cut-off for intact transcripts and sample RNA quality.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains the transcript integrity index value for the merged data of the 22 transcripts used to define transcript integrity.

source_name: sperm

extract_protocol:
RNA was extracted as previously described in the publications Goodrich R et al. 2007; Goodrich RJ et al. 2013; Mao et al. 2013; Jodar et al. 2015 using a PureSperm gradient.
Libraries were constructed as previously described in the publications Goodrich R et al. 2007; Goodrich RJ et al. 2013; Mao et al. 2013; Jodar et al. 2015.

value: sperm


title: batch4_H3K36me3_ZMYND13_KO1

value: ZMYND13 KO


title: batch4_H3K36me3_WT

value: WT


title: Pt-077

value: Post


title: Control Population 18 (NextSeq 500)

description: Control Population 18


title: Pt-079


title: Control Population 16 (NextSeq 500)

description: Control Population 16


title: batch4_H3K36me3_PRDM13_KO1

value: PRDM13 KO


title: batch4_H3K36me3_PRDM15_KO1

value: PRDM15 KO


title: Control Population 17 (NextSeq 500)

description: Control Population 17


title: batch4_H3K36me3_PHF8_KO1

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: PHF8 KO


title: Control Population 15 (NextSeq 500)

description: Control Population 15


title: batch4_H3K36me3_PRDM11_KO1

value: PRDM11 KO


title: Pt-075


title: Control Population 20 (NextSeq 500)

description: Control Population 20


title: Pt-076


title: Pt-072


title: Pt-074


title: Pt-073


title: Pt-071


title: Control Population 14 (NextSeq 500)

description: Control Population 14


title: Control Population 13 (NextSeq 500)

description: Control Population 13


title: Pt-070


title: batch4_H3K36me3_KMT2D_KO1#2

value: KMT2D KO


title: Control Population 12 (NextSeq 500)

description: Control Population 12


title: batch3_H3K36me3_ZMYND20_KO1

value: ZMYND20 KO


title: Pt-068

value: Pre


title: Control Population 11 (NextSeq 500)

description: Control Population 11


title: batch4_H3K36me3_KMT2D_KO1#1


title: batch3_H3K36me3_WT


title: Control Population 9 (NextSeq 500)

description: Control Population 9


title: batch2_H3K36me3_ZMYND8_KO1

value: ZMYND8 KO


title: Control Population 10 (NextSeq 500)

description: Control Population 10


title: Pt-069

value: breast cancer


title: Control Population 8 (NextSeq 500)

description: Control Population 8


title: Pt-067


title: batch2_H3K36me3_ZMYND1_KO1

value: ZMYND1 KO


title: Pt-066


title: Control Population 7 (NextSeq 500)

description: Control Population 7


title: batch2_H3K36me3_ZMYND19_KO1#1

value: ZMYND19 KO


title: batch2_H3K36me3_ZMYND16_KO1

value: ZMYND16 KO


title: Pt-063


title: Pt-064


title: Control Population 6 (NextSeq 500)

description: Control Population 6

value: sperm


title: Control Population 5 (NextSeq 500)

description: Control Population 5


title: batch2_H3K36me3_ZMYND11_KO1#1

value: ZMYND11 KO


title: Pt-062


title: batch2_H3K36me3_SMYD5_KO1#1

value: SMYD5 KO


title: batch2_H3K36me3_WT

value: WT


title: Control Population 2 (NextSeq 500)

description: Control Population 2


title: Control Population 3 (NextSeq 500)

description: Control Population 3


title: Control Population 1 (NextSeq 500)

description: Control Population 1


title: Pt-065

value: Post


title: batch1_H3K36me3_WT


title: Pt-061


title: Pt-060


title: batch1_H3K36me3_SMYD2_KO1

value: SMYD2 KO


title: Trappc1WT-GMP-4

city: Beijing

first: Zhaoqi

last: Zhang

state: Beijing

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

institute: University of Chinese Academy of Sciences

data_processing:
Using Hisat String-Tie to mapped and analyszed data
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files includereads counts values for each Sample

source_name: Bone Marrow

extract_protocol:
Cells were stained with fluorescein conjugated antibodies  in PBS containing 0.1% BSA and 0.1% NaN3 at 4 ℃ for 30 minutes in dark. The stained samples were then sorted by MoFlo Astrios EQ Cell Sorter (Beckman Coulter)，CMPs (Lin-Sca1-CD117+CD16/32lowCD34+)，GMPsCMPs (Lin-Sca1-CD117+CD16/32highCD34+)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Bone Marrow

value: GMP


title: batch2_H3K36me3_ZMYND10_KO1

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: ZMYND10 KO


title: Trappc1WT-GMP-3


title: Pt-056


title: batch1_H3K36me3_SETMAR_KO1#1

value: SETMAR KO


title: batch1_H3K36me3_SETD7_KO1

value: SETD7 KO


title: batch1_H3K36me3_SMYD1_KO1

value: SMYD1 KO


title: Trappc1WT-GMP-2


title: Pt-054

value: Pre

value: breast cancer


title: Pt-055


title: Trappc1WT-GMP-1


title: Pt-059


title: batch1_H3K36me3_SETD3_KO1

value: SETD3 KO


title: Trappc1WT-CMP-4

value: CMP


title: Pt-058


title: Control Population 4 (NextSeq 500)

description: Control Population 4

value: sperm


title: Trappc1WT-CMP-3


title: Pt-057


title: Pt-052


title: Pt-050


title: Pt-053


title: batch1_H3K36me3_PRDM9_KO1#1

value: PRDM9 KO


title: Pt-051


title: Trappc1WT-CMP-2


title: batch1_H3K36me3_KMT2C_KO1

value: KMT2C KO


title: batch1_H3K36me3_ASH1L_KO1

value: ASH1L KO


title: Trappc1KO-GMP-4


title: Trappc1WT-CMP-1


title: batch12_H3K36me3_TOP1_KO1

value: TOP1 KO


title: batch12_H3K36me3_WT

value: WT


title: Pt-048


title: Pt-049


title: batch12_H3K36me3_MMSET_KO1

value: MMSET KO


title: batch12_H3K36me3_NSD3_KO1

value: NSD3 KO


title: batch10_H3K36me3_WT

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)


title: Trappc1KO-CMP-4

value: Bone Marrow


title: Trappc1KO-CMP-3


title: Pt-046


title: Pt-044


title: KPNYN_PRRX1_DOX2

city: West Lafayette

first: Nathaniel

middle: Wesley

last: Mabe

state: Indiana

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
Illumina Novaseq 6000
Samples were trimmed of low-quality base pairs and adapters with trimmomatic package and processed for quality control with FastQC software.
Processed reads were mapped to the GRCh37/hg19 human genome with STAR aligner and passed through featureCounts software to generate gene level reads.
Differential gene expression analysis was determined with DESeq2 software.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix-file containing normalized counts

source_name: KP-N-YN

extract_protocol:
RNAeasy Mini Kit (Qiagen)
Samples were submitted to Novogene corporation for library preparation and sequencing. Sequencing depth varied between 35-50 million for each sample, 150 base pair, paired-end reads on the Novaseq platform.

treatment_protocol: Kelly;tetON-PRRX1 or KP-N-YN;tetON-PRRX1 cells were treate with 0.5 mg / mL doxycycline or vehicle for 21 days

tag: lineage

value: Neuroblastoma

value: Doxycycline


title: Pt-043

value: Post


title: batch10_H3K36me3_SETD1B_KO1

value: SETD1B KO


title: H3K36me3_THZ1_rep2


title: Trappc1KO-CMP-1


title: Pt-047

value: Pre

value: breast cancer


title: Trappc1KO-CMP-2

value: CMP


title: H3K36me3_THZ1_rep1


title: Pt-041


title: Trappc1KO-GMP-3

value: GMP


title: NSCs P7C3-A20-2

city: beijing

first: hong

last: yao

state: beijing

address: shuangqing road 30

department: school of pharmacy

institute: Tsinghua

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Neural stem cells

extract_protocol:
Neural stem cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We used 2-day-old C57BL/6J mice from the THU-LARC. The hippocampus from each hemisphere was micro-dissected and dissociated with enzymatic digestion with 0.25% trypsin-EDTA for 10 min at 37   C. NSCs were grown in NSCs culture Medium. For promoting differentiation, the culture medium was switched to a drop-out medium without bFGF or EGF. NSCs treated with 3   M NAT (a new small molecule compound) or 3   M P7C3-A20 were subjected to RNA-seq analysis for differential expression of genes compared with vehicle (DMSO) control in drop-out medium (n = 3 biological replicates).

value: Brain

value: 2 days old

value: wild type


title: NSCs P7C3-A20-3


title: KPNYN_PRRX1_Veh2

value: Vehicle


title: KPNYN_PRRX1_DOX1


title: Trappc1KO-GMP-1


title: KPNYN_PRRX1_Veh1


title: NSCs P7C3-A20-1


title: SKNBE2_PRRX1_DOX2

source_name: Kelly


title: H3K36me3_High_Salt_rep1

value: WT


title: H3K36me3_Flavopiridol_rep2

value: Flavopiridol


title: NSCs NAT-3

value: 3 uM NAT


title: Pt-042


title: SKNBE2_PRRX1_DOX1


title: Pt-040


title: Pt-039


title: Pt-045


title: NSCs NAT-2


title: Pt-038


title: H3K36me3_High_Salt_rep2

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)


title: H3K36me3_Flavopiridol_rep1


title: SKNBE2_PRRX1_Veh2


title: NSCs NAT-1


title: Pt-037


title: Pt-036


title: SKNBE2_PRRX1_Veh1


title: Pt-035


title: Pol2_rep2

value: Mouse monoclonal anti-RNA polymerase II (Millipore, Cat. #05-623)


title: Pol2_rep1


title: Pt-034


title: Kelly_High_3

data_processing: Samples were trimmed of low-quality base pairs and adapters with trimmomatic package and processed for quality control with FastQC software. Processed reads were mapped to the GRCh38/hg38 human genome with STAR aligner and passed through featureCounts software to generate gene level reads. Differential gene expression analysis was determined with DESeq2 software. Volcano plots were generated in R (v.4.0.3) with ggplot2 software and heatmaps were generated with pheatmap package. Significance cut-offs were log2-fold change ≥ 1 and q-value ≤ 0.05.

treatment_protocol: Parental Kelly cells were stained with GD2-APC antibody, then FACS-sorted into GD2-low (GD2_L) and GD2-high (GD2_H) populations

value: Neuroblastoma


title: Pol2_THZ1_rep1


title: Pt-033


title: Kelly_High_1


title: NSCs DMSO-2

value: DMSO


title: Kelly_High_2


title: Pol2_High_Salt_rep1


title: Kelly_High_4


title: Kelly_low_4


title: Liver_Recovery_rep2 [miRNA]

city: Chengdu

first: Yang

last: Tai

state: Sichuan

address: NO. 37, Xiang Xue Guo

institute: West China Hospital, Sichuan University

data_processing:
Raw data were firstly processed through custom perl and python scripts, and were then filtered by Q20, Q30 and GC contents.
The acquired clean data were mapped to the mouse reference genome (mm10) and aligned against miRbase (Release 22.1) by Bowtie (v1.3.0) to identify mature miRNAs.
For each sample, the miRNA expression profiles were normalized by transcript per million (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with miRNA TPM for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from liver samples using TRIzol reagent (Thermo Fisher Scientific, USA).
Small RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver

value: 8-week thioacetamide i.p., spontaneous recovery for additional 8 weeks


title: Pol2_Flavopiridol_rep2


title: Liver_Recovery_rep1 [miRNA]


title: Pt-032

value: Post


title: Kelly_low_3


title: Pol2_THZ1_rep2


title: Kelly_low_2


title: Pt-030

value: Pre

value: breast cancer


title: Pol2_Flavopiridol_rep1


title: Liver_TAA_rep3 [miRNA]

value: 8-week thioacetamide i.p.


title: NSCs DMSO-1

value: Brain


title: Kelly_low_1


title: Liver_TAA_rep2 [miRNA]


title: Liver_Recovery_rep3 [miRNA]


title: Pol2_High_Salt_rep2


title: H3K36me3_WT_FixChIP_rep2

value: corsslinked


title: NSCs DMSO-3

value: 2 days old

value: wild type


title: Pt-031


title: H3K36me3_WT_FixChIP_rep1

value: WT


title: SKNAS_T4

source_name: SK-N-AS

treatment_protocol: SK-N-AS cells were treated for 14 days with vehicle (V) or 1 uM tazemetostat (T) in biological quadruplicate

value: Tazemetostat


title: H3K36me3_Setd2_KO_FixChip_rep2

value: Setd2 KO


title: Liver_NS_rep3 [miRNA]

value: 8-week normal saline i.p.


title: Pt-028


title: Liver_NS_rep2 [miRNA]


title: H3K36me3_Setd2_KO_FixChip_rep1

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)


title: SKNAS_T2

value: Neuroblastoma


title: SKNAS_T3


title: Pt-027


title: Pt-026


title: H3K36me3_WT_nativeChIP_rep2

value: native


title: Pt-025


title: Liver_TAA_rep1 [miRNA]

value: liver


title: Liver_NS_rep1 [miRNA]


title: Pt-029


title: SKNAS_T1


title: H3K36me3_WT_nativeChIP_rep1


title: Pt-024


title: SKNAS_C3

value: Vehicle


title: H3K36me3_Setd2_KO_native_ChIP_rep2


title: Rad21KO primary dissociated cortical neuron Rep3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
RNA-seq of ribosome associated mRNA from  dissociated cortical neurons at Day In Vitro (DIV10)
Rad21 KO Rep3

data_processing:
Library strategy: Ribo-Tag
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand” with gene annotation from Ensembl version 67
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm9
Supplementary_files_format_and_content: reads counts on genes

molecule: polyA RNA

source_name: Primary dissociated cortical neuron

growth_protocol: Mouse cortices were dissected and dissociated from individual E17.5-E18.5 mouse embryos as described in (Beaudoin et al., 2012) with minor modifications. Dissociated neurons were maintained in Neurobasal medium with B27 supplement (Invitrogen), 1 mM L-glutamine, and 100 U/mL penicillin/streptomycin for 10 days in vitro (DIV10). Cells were plated at a density of 0.8 × 106 cells per well on 6-well plates pre-coated overnight with 0.1 mg/ml poly-D-lysine (Millipore) and one third of the media in each well was replaced every 3 days. Cultures were treated with 5M Cytosine β-D-arabinofuranoside (Ara-C, Sigma) from day 2-4.

extract_protocol:
For polysome immunoprecipitation, homogenates from DIV10 dissociated cortical neurons from Rad21lox/lox;NexCre/+;RiboTag+ and Rad21+/+;NexCre/+;RiboTag+ were prepared as described in (Sanz et al., 2009) with minor modifications. RNA was extracted with QIAshredder and RNeasy mini kit (Qiagen).
RNA-seq libraries were prepared from 300 ng of total RNA (RIN>9.0) with TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina).

value: cortical neuron

tag: molecule subtype

value: Ribosome-associated mRNA


title: Rad21KO primary dissociated cortical neuron Rep2

description:
RNA-seq of ribosome associated mRNA from  dissociated cortical neurons at Day In Vitro (DIV10)
Rad21 KO Rep2


title: IgG_WT_rep2

value: Rabbit IgG


title: SKNAS_C4


title: H3K36me3_Setd2_KO_native_ChIP_rep1


title: SKNAS_C2


title: Rad21KO primary dissociated cortical neuron Rep1

description:
RNA-seq of ribosome associated mRNA from  dissociated cortical neurons at Day In Vitro (DIV10)
Rad21 KO Rep1


title: SKNAS_C1


title: Rad21WT primary dissociated cortical neuron Rep3

description:
RNA-seq of ribosome associated mRNA from  dissociated cortical neurons at Day In Vitro (DIV10)
WT Rep3


title: SKNAS_T4_ATACseq

data_processing:
ATAC-Seq data analysis was performed in alignment with the ENCODE Consortium standards (https://www.encodeproject.org/atac-seq/). Briefly, the paired-end reads were trimmed and filtered using Trimmomatic v0.39  and mapped to the hg38 reference genome using bowtie2 with the –local –very sensitive –X 2000 and MAPQ > 5 options. Bam files were deduplicated using Picard.  Only reads with MAPQ > 5 and mapping to chromosomes 1-22 and chrX were retained. Reads were shifted with 4 bp on the positive strand and -5 bp on the negative strand using AlignmentSieve available in deepTools v3.5.162. Replicate correlations were computed with the multiBamSummary and bamCorrelate tools available in deepTools and visualized as dendrograms and in PCA plots. Fragment size distributions were computed with the bamPEFragmentSize tool available in deepTools. Properly aligned reads for replicates were merged for each condition.
The merged reads for the four vehicle replicates were labeled “SKNAS_ATAC_CTRL” and similarly, the merged reads for the four tazemetostat treated replicates were labeled “SKNAS_ATAC_TAZE”. The mapped reads for individual and merged replicates were normalized in units of Reads Per Kilobase per Million (RPKM or rpm/bp) and coverage tracks for the RPKM signal were created as bigwig files for bins of size 20 base pairs by using the bamCoverage tool available in deepTools.
Peak calling  was performed for properly aligned and for the merged reads with MACS2, with the –nomodel, --extsize to fragment length and –q 0.01 options. Area under curve (AUC) binding signal for peaks was computed with the bwtool64.
The binding sites identified by MACS263 on merged reads were aggregated into consensus peaks per condition by requiring AUC binding signal > 1000 for each replicate. The consensus peaks for both conditions were merged into a high confidence union peak set. A peak by sample counts matrix was created by counting the reads overlapping each peak with the multiBamSummary tool available from deepTools. The counts matrix was used to perform differential peak analysis in DESeq2. Differential binding across conditions was assessed based on the significance cut-offs |Delta(log2(AUC+1))| ≥ 0.5 and adjP-value ≤ 0.10. Genome track files were created with the bamCoverage tool available in deepTools and visualized as heatmaps created with the computeMatrix tool available in deepTools,  and with the Integrative Genomic Viewer (IGV).

extract_protocol:
Briefly, 50,000 cells per replicate were pelleted and then resuspended and lysed in 50 uL ATAC resuspension buffer supplemented with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. After lysis, nuclei were pelleted and transposed using 2.5 uL Tn5 transposase in a 50 uL reaction.
Finally, the transposed DNA was purified using a commercial PCR cleanup kit and libraries were amplified and prepared for sequencing. Paired end sequencing (2x75) was performed on an Illumina NovaSeq.

treatment_protocol: 14 days treatment with tazemetostat or vehicle


title: H3K36me3_WT_rep2


title: IgG_WT_rep1


title: H3K36me3_WT_rep1


title: Pt-023

value: Post

value: breast cancer


title: H3K36me3_Setd2_KO_rep2


title: SKNAS_T3_ATACseq


title: SKNAS_T2_ATACseq


title: Pt-019


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 and 6h KCl Rep2

description: Rad21 KO KCl 6H Rep2

data_processing:
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand” with gene annotation from Ensembl version 67
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm9
Supplementary_files_format_and_content: reads counts on genes

extract_protocol:
Total RNA was obtained in parallel from dissociated cortical neurons at DIV10 without stimulation (baseline); after overnight treatment with TTX and D-AP5 (TTX); and after overnight treatment with TTX and D-AP5 and depolarization with KCl for 1h (KCl1h) or 6h (KCl6h). RNA was extracted with QIAshredder and RNeasy mini kit (Qiagen).
RNA-seq libraries were prepared from 600 ng of total RNA (RNA integrity number (RIN) >8.0) with TruSeq Stranded Total RNA Human/Mouse/Rat kit (Illumina).

treatment_protocol: For KCl depolarization experiments, neuronal cultures were pre-treated with 1μM tetrodotoxin (TTX, Tocris) and 100μM D-(-)-2-Amino-5-phosphonopentanoic acid (D-AP5, Tocris) overnight to reduce endogenous neuronal activity prior to stimulation. Neurons were membrane depolarized with 55 mM extracellular KCl by addition of prewarmed depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM HEPES pH7.5).

value: TTX/D-AP5 + KCl 6h


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 and 6h KCl Rep3

description: Rad21 KO KCl 6H Rep3


title: Rad21WT primary dissociated cortical neuron Rep1

description:
RNA-seq of ribosome associated mRNA from  dissociated cortical neurons at Day In Vitro (DIV10)
WT Rep1


title: Rad21WT primary dissociated cortical neuron Rep2

description:
RNA-seq of ribosome associated mRNA from  dissociated cortical neurons at Day In Vitro (DIV10)
WT Rep2


title: Pt-021


title: SKNAS_T1_ATACseq


title: Pt-017


title: Pt-018

value: Pre


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 and 6h KCl Rep1

description: Rad21 KO KCl 6H Rep1


title: H3K36me3_Setd2_KO_rep1


title: SKNAS_C4_ATACseq


title: SKNAS_C3_ATACseq


title: Pt-016


title: Liver_Recovery_rep2 [mRNA]

data_processing:
Raw data were firstly processed through custom perl and python scripts, and were then filtered by Q20, Q30 and GC contents.
The acquired clean data were mapped to the mouse reference genome (mm10) using HISAT2 (v2.2.1).
For each sample, read counts for each gene were obtained with featureCounts (v1.5.0-p3) and were standardized as fragments per kilobase million (FPKM).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: mRNA_gene.FPKM.txt: Matrix table with mRNA FPKM for each sample.

extract_protocol:
Total RNA was extracted from liver samples using TRIzol reagent (Thermo Fisher Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: 8-week thioacetamide i.p., spontaneous recovery for additional 8 weeks


title: Pt-022


title: Pt-014


title: Pt-015


title: SKNAS_C2_ATACseq


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep2

description: Rad21 KO KCl 1H Rep2

value: TTX/D-AP5 + KCl 1h


title: Liver_Recovery_rep1 [mRNA]


title: Liver_TAA_rep3 [mRNA]

value: 8-week thioacetamide i.p.


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 Rep3

description: Rad21 KO TTX Rep3


title: Pt-020


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep1

description: Rad21 KO KCl 1H Rep1


title: SKNAS_C1_ATACseq


title: Liver_Recovery_rep3 [mRNA]


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep3

description: Rad21 KO KCl 1H Rep3


title: Liver_TAA_rep2 [mRNA]


title: Liver_TAA_rep1 [mRNA]


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 Rep1

description: Rad21 KO TTX Rep1


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 Rep2

description: Rad21 KO TTX Rep2


title: primed-to-naïve day 8 [Pton8d_S40_L002]

city: Shanghai

first: Bi

last: Yan

address: Siping Road 1239

institute: Tongji university

data_processing:
10× Genomics single-cell data were pre-processed using the Cell Ranger pipeline (v.4.0.0) with default parameters.
Integration, Dimensionality reduction,clusering and visualization were done by Seurat (v.3.2.3)
Single-cell RNA-seq trajectory inference and branch analysis was done by Monocle2  (v.2.14.0)
Genome_build: hg38
Supplementary_files_format_and_content: tsv files of cell barcodes and features. mtx files of UMI matrix

source_name: primed-to-naïve day 8

growth_protocol: Cells were cultured in 5iLAF medium containing DMEM/F12: Neurobasal (1:1) (ThermoFisher), 1% N2 supplement (ThermoFisher), 2% B27 supplement (ThermoFisher), 0.5% KnockOut SR (ThermoFisher), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin (Millipore), 20 ng/ml human LIF (Milipore), 8 ng/ml bFGF (Peprotech), 50 mg/ml BSA (Sigma) and the following cytokines and small molecules: 1 mM PD0325901 (Selleck), 0.5 mM SB590885 (Selleck), 1 mM WH-4-023 (Selleck), 10 mM Y-27632 (Selleck), and 20 ng/ml Activin A (Peprotech)

extract_protocol:
Standard 10× genomics scRNA-seq protocol
10× genomics scRNA-seq: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics) , according to the manufacturer’s instructions. Briefly,  cells were washed with 0.04% BSA DPBS for three times and were resuscitated to a concentration of 700~1200 cells/ul (viability≥85%). Cells were captured in droplets at a targeted cell recovery of cells. After the reverse transcription step, emulsions were broken and Barcoded-cDNA was purified with Dynabeads, followed by PCR amplification. Amplified cDNA was then used for 3’gene expression library construction. For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads, and sequenced on an NovaSeq platform (Illumia) to generate 150 bp paired-end Reads.

treatment_protocol: For primed to naive state transition, 200,000~300,000 dissociated single cells of  pESCs were seeded on the irradiated feeder layer in conventional ESC medium supplemented with Y-27632 (Selleck, 10 mM). Medium was then switched to 5iLAF medium on the second day, and was changed every day. Intermediate cells were collected at different time points during primed-to-naïve transition.

tag: cell type source

value: H9 primed ESC

value: pluripotent stem cells


title: primed-to-naïve day 8 [Pton8d_S41_L002]


title: Rad21KO primary dissociated cortical neuron untreated Rep3

description: Rad21 KO Rep3

value: untreated


title: primed-to-naïve day 8 [Pton8d_S13_L003]


title: Liver_NS_rep3 [mRNA]

value: 8-week normal saline i.p.


title: Rad21KO primary dissociated cortical neuron untreated Rep2

description: Rad21 KO Rep2


title: primed-to-naïve day 8 [Pton8d_S42_L002]


title: primed-to-naïve day 8 [Pton8d_S39_L002]


title: Rad21KO primary dissociated cortical neuron untreated Rep1

description: Rad21 KO Rep1


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 and 6h KCl Rep2

description: WT KCl 6H Rep2


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 and 6h KCl Rep3

description: WT KCl 6H Rep3


title: Liver_NS_rep1 [mRNA]


title: Liver_NS_rep2 [mRNA]


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 and 6h KCl Rep1

description: WT KCl 6H Rep1


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep3

description: WT KCl 1H Rep3


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep2

description: WT KCl 1H Rep2


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep1

description: WT KCl 1H Rep1


title: primed-to-naïve day 8 [Pton8d_S11_L003]


title: primed-to-naïve day 8 [Pton8d_S12_L003]


title: primed-to-naïve day 6 [Pton6d_S9_L003]

source_name: primed-to-naïve day 6


title: primed-to-naïve day 8 [Pton8d_S10_L003]


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 Rep3

description: WT TTX Rep3


title: primed-to-naïve day 6 [Pton6d_S7_L003]


title: primed-to-naïve day 6 [Pton6d_S6_L003]


title: primed-to-naïve day 6 [Pton6d_S48_L004]


title: primed-to-naïve day 6 [Pton6d_S8_L003]


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 Rep2

description: WT TTX Rep2


title: Rad21WT primary dissociated cortical neuron treated with TTX/D-AP5 Rep1

description: WT TTX Rep1


title: Rad21WT primary dissociated cortical neuron untreated Rep2

description: WT Rep2


title: primed-to-naïve day 6 [Pton6d_S47_L004]


title: primed-to-naïve day 6 [Pton6d_S45_L004]


title: primed-to-naïve day 6 [Pton6d_S44_L003]


title: primed-to-naïve day 6 [Pton6d_S46_L004]


title: Rad21WT primary dissociated cortical neuron untreated Rep3

description: WT Rep3


title: Rad21WT primary dissociated cortical neuron untreated Rep1

description: WT Rep1


title: Pt-013


title: primed-to-naïve day 6 [Pton6d_S42_L003]


title: RAD21TEV depleted, untreated Rep3

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Trim_galore (v0.4.4) was applied for trimming adapter and low quality reads.
Trimmed reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand” with gene annotation from Ensembl version 67
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: Primary neuron

growth_protocol: Mouse cortices were dissected and dissociated from individual E14.5 mouse embryos as described in (Beaudoin et al., 2012) with minor modifications. Dissociated neurons were maintained in Neurobasal medium with B27 supplement (Invitrogen), 1 mM L-glutamine, and 100 U/mL penicillin/streptomycin for 11 days in vitro (DIV11). Cells were plated at a density of 2.5 × 10e05 cells per well on 24-well plates pre-coated overnight with 0.1 mg/ml poly-D-lysine (Millipore) and half of the media in each well was replaced every 3 days. Cells were transduced after 3 days in culture with lentivirus encoding NLS-TEV at a multiplicity of infection of 1. AraC was added 2 days later. Following ten days in culture cultures were treated with 500nM 4-OHT or EtOH for 24 hours. Cells were then either stimulated with BDNF (50ng/ml) for 30 or 120 minutes, where indicated, or left untreated.

extract_protocol:
RNA was purified using the PicoPure RNA isolation kit (ThermoFisher) following the manufacturer's instructions.
200ng of total RNA was used to prepare libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (polyA enrichment), following the manufacturer recommendations. Library quality and quantity were assessed on a Bionalayser and Qubit respectively. Libraries were sequenced on an Illumina Hiseq2500 (v4 chemistry) and at least 40million paired end 100bp reads per sample were generated per library.

treatment_protocol: On DIV10 500nM 4-hydroxy tamoxifen or ethanol (as indicated in each individual sample) was added to the cells for 24 hours. Cells were then treated with BDNF (50ng/ml) for 30 or 120 minutes, where indicated, or left untreated.

value: Primary neuron

value: 4-hydroxy tamoxifen

tag: time point (mins)


title: primed-to-naïve day 6 [Pton6d_S41_L003]


title: RAD21TEV depleted, untreated Rep4


title: primed-to-naïve day 6 [Pton6d_S43_L003]


title: RAD21TEV depleted, untreated Rep2


title: primed-to-naïve day 10 [Pton10d_S5_L003]

source_name: primed-to-naïve day 10


title: primed-to-naïve day 10 [Pton10d_S4_L003]


title: Pt-008


title: MHV and RV infected cells, biological rep2

city: Moscow

first: James

middle: Theodore

last: Van Leuven

state: ID

address: 709 S Deakin St

department: Center for Modeling Complex Interactions

institute: University of Idaho

hyb_protocol: Samples were hybridized to the Roche Nimblegen 12x135k MM9 Microarray (Design 100718_MM9_EXP).

scan_protocol: Scan protocol not provided.

data_processing: The data were processed with the 'oligo' and 'pdInfoBuilder' packages in R using Robust Multichip Average (rma) preprocessing methodology. This strategy allows background subtraction, quantile normalization and summarization (via median-polish).

source_name: simultaneous coinfection

label_protocol: Microarray analysis was done on RNA samples submitted to the Genomics Resources Core Laboratory at The Institute for Bioinformatics and Evolutionary Studies at the University of Idaho, Moscow, ID.

growth_protocol: PR8 (A/Puerto Rico/8/1934 (H1N1)), obtained from BEI Resources (NR-3169), was grown and titrated by plaque assay in MDCK (ATCC: CCL-34) cells. MHV, obtained from ATCC (VR-261), was grown and titrated by plaque assay in 17Cl.1 cells (Sturman and Takemoto, 1972) (provided by Dr. Kathryn Holmes, University of Colorado Denver School of Medicine). RV, obtained from ATCC (VR-1645), was grown and titrated by tissue culture infectious dose 50% (TCID50) assay in HeLa cells (ATCC: CCL-2). LA4 (ATCC: CCL-196), a murine lung epithelial cell line, was cultured in Ham's F12K medium (Mediatech, Manassas, VA).

extract_protocol: RNA was isolated from cell cultures using an RNeasy Plus kit (QIAGEN).

treatment_protocol: Our experimental approach was to infect LA4 cells with the three viruses at either t=0 h or t=12 h and harvest RNA for microarray analysis at t=24 h. Simultaneous infections occurred at t=12h. Controls were mock-inoculated at both time points. Preliminary experiments were done to establish a multiplicity of infection (MOI) for each virus that resulted in comparable numbers of cells positive for viral antigen at 24 h post-infection. Based on this, LA4 cells were inoculated with 3 TCID50/cell RV, 1 PFU/cell PR8, or 3 PFU/cell MHV. Triplicate wells of LA4 cells in 6-well plates were inoculated with each virus diluted in serum-free medium or were mock-inoculated with serum-free medium for 1 h at 37C. Viral inocula were removed and the cells were rinsed twice with serum-free medium. The cells were incubated in Ham's F12K medium with 2% FBS for 12 or 24 h, at which time RNA was isolated. For the 24 h samples, the media were removed and replaced with fresh media 12 h after inoculation.

tag: cell line

tag: virus 1 infection

value: MHV (VR-261 ATCC)

tag: virus 2 infection

value: RV (VR-1645 ATCC)


title: Pt-011

tag: menopausal state


title: RAD21TEV depleted, untreated Rep1


title: MHV then RV infected cells, biological rep2

source_name: sequential coinfection


title: non-heparanized blood, Ct-negative, control, rep1

city: New Delhi

first: Ankita

last: Ray

state: Delhi

address: Safdarjung hospital campus

country: India

institute: ICMR-National Institute of Pathology

description: miRNA expression

hyb_protocol: The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking solution (Agilent Technologies, Part Number: 5190-0456) and Hi-RPM Hybridization Buffer (Agilent Technologies, Part Number: 5190-0456) and incubated at 100oC for 5 minutes followed by snap chill on ice for 5 minutes. The samples were hybridized on the Human miRNA 8x60K Arrays. The hybridization was carried out at 55°C for 20 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes.

scan_protocol: The microarray slide was scanned on a G2600D scanner (Agilent Technologies). Data extraction from Images was done using Feature Extraction software v 11.5.1.1 of Agilent.

source_name: non-heparanized blood

label_protocol:
200ng of total RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) master mix
The dephosphorylated miRNA sample was denatured by adding Dimethyl Sulfoxide
and heating at 100 oC for 10 minutes and transferred to ice-water bath. The Ligation master mix (Agilent Technologies, Part Number: 5190-0456) containing Cyanine 3-pCp was added to the denatured miRNA sample and incubated at 16oC for 2 hours. The Cyanine 3-pCp labeled miRNA sample was dried completely in the vacuum concentrator (Eppendorf, Concentrator Plus, Catalog Number 5305000) at 45oC for 2 hour

extract_protocol: Total RNA was extracted using Trizol(Ambion). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn blood from recurrent spontaneous aborters and controls were collected. Serum was separated and stored for further use.

value: serum

tag: gender

value: female

tag: infection

value: Ct-negative

tag: history

value: control


title: Pt-005

value: Post

tag: tissue

value: breast cancer


title: Pt-007

value: Pre


title: Pt-010


title: MHV then RV infected cells, biological rep1


title: MHV then RV infected cells, biological rep3


title: Pt-012


title: Pt-009


title: Pt-006


title: MHV and RV infected cells, biological rep3


title: Pt-002


title: Pt-001


title: Pt-004


title: non-heparanized blood, Ct-negative, control, rep2

description: miRNA expression

data_processing: Data extraction from Images was done using Feature Extraction software v 11.5.1.1 of Agilent.


title: Pt-003


title: MHV and RV infected cells, biological rep1


title: non-heparanized blood, Ct-negative, spontaneous abortion, rep3

description: miRNA expression

value: recurrent spontaneous aborter (RSA)


title: RV then MHV infected cells, biological rep3


title: RAD21TEV depleted, +BDNF 30 minutes Rep4

tag: cell type

tag: treatment


title: primed-to-naïve day 10 [Pton10d_S3_L003]

tag: genotype/variation


title: RV then MHV infected cells, biological rep2


title: RV then MHV infected cells, biological rep1


title: RAD21TEV depleted, +BDNF 30 minutes Rep3


title: primed-to-naïve day 10 [Pton10d_S26_L002]


title: non-heparanized blood, Ct-negative, spontaneous abortion, rep1

description: miRNA expression

tag: age


title: non-heparanized blood, Ct-negative, spontaneous abortion, rep2

description: miRNA expression


title: RAD21TEV depleted, +BDNF 30 minutes Rep2

tag: genotype


title: primed-to-naïve day 10 [Pton10d_S25_L002]


title: RAD21TEV depleted, +BDNF 120 minutes Rep4


title: RAD21TEV depleted, +BDNF 30 minutes Rep1


title: primed-to-naïve day 10 [Pton10d_S24_L002]


title: primed-to-naïve day 10 [Pton10d_S23_L002]


title: GM_S_Fe

city: Qingdao

first: Xiangmei

last: Liu

state: Shandong Province

address: 72 Binhai Road

department: State Key laboratory of Microbial Technology

institute: Shandong University

data_processing:
RTA 2.7.3 was used for basecalling and bcl2fastq2-v2.16 was used for file conversion
Remove reads with adaptors, remove reads in which unknown bases are more than 10%, remove low-quality reads (the percentage of low quality bases is over 20% in a read), then map to A. ferrooxidans ATCC 23270 reference genome using SOAPaligner/SOAP2.
Expression levels of genes were determined based on the value of RPKM, which is the abbreviation of reads per kilobase per million mapped reads.
Genome_build: A. ferrooxidans ATCC 23270
Supplementary_files_format_and_content: txt files include RPKM values for all genes that have a difference express

organism: Acidithiobacillus ferrooxidans ATCC 23270

source_name: Δcyc2 mutant strain grown on switched energy source from S0 to Fe(II)

growth_protocol: The cells of A. ferrooxidans ATCC 23270 wild type and the Δcyc2 mutant were prepared in two ways. One was unvaried Fe(II) energy substrate by using the inoculum cultivated from 9K-Fe(II) medium and the other was altered Fe(II) energy substrate by employing the inoculum cultured from 9K-S0 medium.

extract_protocol:
Cells were harvested after the ferric precipitates produced or sulfur powder remained was intercepted by qualitative filter papers. Total RNA was then extracted with TRIzolTM reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: delta cyc2


title: GM_Fe_Fe

source_name: Δcyc2 mutant strain grown on Fe(II)


title: RAD21TEV depleted, +BDNF 120 minutes Rep3


title: W_S_Fe

source_name: Wild type strain grown on switched energy source from S0 to Fe(II)

value: wildtype


title: primed-to-naïve day 10 [Pton10d_S2_L003]

value: H9 primed ESC

value: pluripotent stem cells


title: non-heparanized blood, Ct-postive, spontaneous abortion, rep3

description: miRNA expression

value: Ct-postive


title: non-heparanized blood, Ct-postive, spontaneous abortion, rep2

description: miRNA expression


title: PROseq_siNELFE_Rep1

data_processing:
Library strategy: PRO-seq
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
For PRO-seq, raw datas of sequence were trimmed using Trim Galore (v 0.64_dev).
PRO-seq reads were mapped to human genome GRCh38 and Drosophila melanogaster genome build5.41 using the Bowtie2 alignment tool (version 2.3.5.1) with the default settings.
PRO-seq read counts were normalized according to the genomic coverage of mapped Drosophila reads using bedtools (version:2.29.2) and samtools (version:1.7).
For PRO-seq, pileup tracks of the last base pair of the reads were generated using bedtools (version:2.29.2)
Genome_build: GRCH38 and Drosophila melanogaster genome build5.41 from NCBI
Supplementary_files_format_and_content: BigWig files include normalized count data obtained from methods shown above.

extract_protocol:
For PRO-seq, 25 million wild type or mutant HEK293T cells were mixed with 2.5 million Drosophila S2 cells (10:1 ratio), permeabilized, and incubated with biotin-labeled NTPs. Biotinylated RNA was hydrolyzed with NaOH, and biotin containing RNA fragments were enriched by affinity purification using streptavidin-coated magnetic beads. A 3′ sequencing adaptor was ligated to the biotinylated RNA, the 5′ cap was removed, 5′ OH was generated by base hydrolysis and converted to 5′ phosphate by treatment with T4 polynucleotide kinase, a 5′ sequencing adaptor was ligated to RNA. RNA was purified to enrich for biotinylated fragments with adaptor at both ends and reverse transcribed. Detailed methods are in PRO-Seq, Mahat et al Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086.Detailed methods are in PRO-Seq, Mahat et al Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086.
Ribo-depleted RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina) following manufacturer's instructions. Libraries were checked for quality and quantity using Bioanalyzer. Equimolar concentrations of libraries were pooled, requantified and sequenced as 100 bp paired-end reads on the Illumina HiSeq 3000 instrument. Libraries for ChIP-seq and antibody-based in situ biotinylation-seq were prepared using TruSeq ChIP Library Prep Kit (Illumina) and IDT for illumina-TruSeq RNA UD Index (Illumina). Library purification and size selection were performed using Agencourt AMPure XP system. Libraries were checked for quality and quantity using Bioanalyzer. Equimolar concentrations of libraries were pooled, and sequenced as paired-end reads on the Illumina Novaseq 6000 platform (ChIP-seq) or Hiseq 2500 platform (antibody-based in situ biotinylation-seq). PRO-seq libraries were generated essentially as described in Mahat et al., 2016 (Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086). Primers RPI1, RPI2, RPI3 and RPI4 were used to barcode cDNAs from 293T-WT_Rep1 (Wild type, replicate 1), 293T-WT_Rep2 (Wild type, replicate 2), 293T-EAF1mut_Rep1 (Mutant EAF1, replicate 1), and 293T-EAF1mut_Rep2 (Mutant EAF1, replicate 2), respectively. PRO-seq libralies were pooled and sequenced as paired-end reads on the Illumina Novaseq 6000 platform. 4C-seq libraries werec generated essentially as described in Krijger et al., 2020 (Methods, 170: 17-32; doi: 10.1016/j.ymeth.2019.07.014). 4C-seq libralies were pooled and sequenced on Illumina Hiseq 2500 platform.

value: siNELFE

tag: spike-in source

value: Drosophila melanogaster

tag: protocol/antibody

value: PRO-Seq, Mahat et al Nat Protoc, 11:1455-76;  doi:10.1038/nprot.2016.086

tag: sequenced molecule

value: nascent RNA


title: RAD21TEV depleted, +BDNF 120 minutes Rep2

value: Primary neuron

value: 4-hydroxy tamoxifen

tag: time point (mins)


title: RAD21TEV control, untreated Rep4

value: ethanol


title: W_Fe_Fe

source_name: Wild type strain grown on Fe(II)


title: RAD21TEV control, untreated Rep3


title: PROseq_siCBP80_Rep2

tag: cell line


title: PROseq_siCBP80_Rep1


title: PROseq_siNELFE_Rep2


title: RAD21TEV depleted, +BDNF 120 minutes Rep1


title: Kidney 27min sc

city: Hannover

first: Svenja

last: Gaedcke

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

data_processing:
10x Genomics CellRanger pipeline (v3.0.2)  with default parameters, except expected cells (10,000)
demultiplex data with mkfastq resulting in fastq-files and 10x specific metadata
align read data to reference (10x Genomics Mus musculus reference 3.0.0, mm10) using STAR
for sc: build pre-mRNA reference with CellRanger as described by 10x Genomics
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: left kidney

extract_protocol:
Kindey samples were processed into single cells and single nucleus and were barcoded using 10x Chromium platform.  Barcoded RNA was extracted using  Chromium Single Cell 3ʹ Reagent Kits v3 User Guide
RNA libraries were prepared for sequencing using standard Illumina protocols. All Samples were sequenced twice.

value: kidney

tag: ir injury

tag: sample type

value: sc

tag: strain

value: 12 weeks

value: male


title: Kidney 27min sn

value: sn

tag: gender


title: Kidney 17min sc


title: non-heparanized blood, Ct-postive, spontaneous abortion, rep1

description: miRNA expression

value: serum

value: female

tag: infection

value: recurrent spontaneous aborter (RSA)


title: RAD21TEV control, untreated Rep1


title: Kidney 17min sn


title: PROseq_control_Rep2

value: control


title: Kidney ctrl sn


title: PROseq_control_Rep1


title: ChIPseq_293T-WT_ELL_IP_Rep2_R1

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
For ChIP-seq, adapter sequences were trimmed using Trim Galore (v 0.64_dev).
ChIP-seq reads were mapped to human genome GRCH38 using the Bowtie2 alignment tool (version 2.3.5.1) with default settings.
The mapped ChIP-seq reads were subjected to count per million (CPM) normalization, then used for downstream analysis. IP/input or IP-input enrichment per gene was calculated with R (v. 4.0.2) and its package rtracklayer (version:1.48.0) using Ensemble GRCH38.92 gene annotation model.
Genome_build: GRCH38

extract_protocol:
For ELL ChIP-seq, cross-link of the cells was performed using 1% formaldehyde for 7 min. The cross-linked chromatin was sonicated to generate fragments of 150-500 bp prior to immunoprecipitation. Immunoprecipitation of protein-DNA complex was performed using anti-ELL antibody (14468; Cell Signaling Technology) and Dynabeads M280 Sheep Anti-Rabbit IgG (11203D; Invitrogen). The immunoprecipitated DNA was purified using the QIAquick PCR purification kit (28106; Qiagen).
Libraries for ChIP-seq and antibody-based in situ biotinylation-seq were prepared using TruSeq ChIP Library Prep Kit (Illumina) and IDT for illumina-TruSeq RNA UD Index (Illumina). Library purification and size selection were performed using Agencourt AMPure XP system. Libraries were checked for quality and quantity using Bioanalyzer. Equimolar concentrations of libraries were pooled, and sequenced as paired-end reads on the Illumina Novaseq 6000 platform (ChIP-seq) or Hiseq 2500 platform (antibody-based in situ biotinylation-seq). PRO-seq libraries were generated essentially as described in Mahat et al., 2016 (Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086). Primers RPI1, RPI2, RPI3 and RPI4 were used to barcode cDNAs from 293T-WT_Rep1 (Wild type, replicate 1), 293T-WT_Rep2 (Wild type, replicate 2), 293T-EAF1mut_Rep1 (Mutant EAF1, replicate 1), and 293T-EAF1mut_Rep2 (Mutant EAF1, replicate 2), respectively.

value: wildtype

value: ChIP/anti-ELL D7N6U , Cell Signaling cat 14468S

value: genomic DNA IP


title: RAD21TEV control, +BDNF 30 minutes Rep1


title: Fezf2Control_Upper_rep2

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: single cell

data_processing:
For scRNA-seq, sequencing and basecalling were performed with NextSeq 500 instrument (Illumina). For snRNA-seq, sequencing and basecalling were performed with NovaSeq instrument (Illumina).
Cellranger mkfastq (10x Genomics v2.1.0) was used to demultiplex bcl files to fastq files using standard parameters
Cellranger count (10x Genomics v2.1.0) was used to produce an aligned single cell feature count matrix, using mm10 genome as a reference.
Seurat (v3.1.1) pipeline including SCTransform was used to normalize and scale the single cell data. Default parameters were used. The following parameters were used for regression: percent.mt, nCount_RNA, and replicate.
PCA and t-SNE were used to for dimensionality reduction and visualization of single cells data.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts
Supplementary_files_format_and_content: tab-delimited file with the metadata for each sample in the matrix

source_name: P14 Fezf2Control S1 cortex Layers 1-4

growth_protocol: Standard mouse housing conditions

extract_protocol:
Samples were maintained at 4C. S1 cortex was micro-dissected, homogenized and sorted for all nuclei in nuclei solubilization buffer. For scRNA-seq, S1 cortex layers were micro-dissected, homogenized in PBS with DNAse and RNAse-inhibitor, followed by FACS in BSA-containing PBS.
Libraries were produced using 10x genomics technology.

treatment_protocol: Fezf2 WT and KO mice were equally housed and treated. Genotypes were obtained through standard breeding.

value: S1 cortex


title: RAD21TEV control, +BDNF 30 minutes Rep3


title: ChIPseq_293T-WT_ELL_IP_Rep1_R1


title: ChIPseq_293T-WT_ELL_Input_R1

value: Input for ELL ChIP

value: genomic DNA Input


title: Fezf2Control_Middle_rep2

description: single cell

source_name: P14 Fezf2Control S1 cortex Layer 5


title: RAD21TEV control, +BDNF 120 minutes Rep4

value: Primary neuron


title: Kidney ctrl sc


title: RAD21TEV control, +BDNF 120 minutes Rep2

value: ethanol


title: PROseq_293T-WT_Rep2_R1

data_processing:
Library strategy: PRO-seq
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
For PRO-seq, raw datas of sequence were trimmed using Trim Galore (v 0.64_dev).
PRO-seq reads were mapped to human genome GRCh38 and Drosophila melanogaster genome build5.41 using the Bowtie2 alignment tool (version 2.3.5.1) with the default settings.
PRO-seq read counts were normalized according to the genomic coverage of mapped Drosophila reads using bedtools (version:2.29.2) and samtools (version:1.7).
For PRO-seq, pileup tracks of the last base paired of the reads were generated using bedtools (version:2.29.2)
Genome_build: GRCH38 and Drosophila melanogaster genome build5.41 from NCBI
Supplementary_files_format_and_content: BigWig files include normalized count data

extract_protocol:
For PRO-seq, 25 million wild type or mutant HEK293T cells were mixed with 2.5 million Drosophila S2 cells (10:1 ratio), permeabilized, and incubated with biotin-labeled NTPs. Biotinylated RNA was hydrolyzed with NaOH, and biotin containing RNA fragments were enriched by affinity purification using streptavidin-coated magnetic beads. A 3′ sequencing adaptor was ligated to the biotinylated RNA, the 5′ cap was removed, 5′ OH was generated by base hydrolysis and converted to 5′ phosphate by treatment with T4 polynucleotide kinase, a 5′ sequencing adaptor was ligated to RNA. RNA was purified to enrich for biotinylated fragments with adaptor at both ends and reverse transcribed. Detailed methods are in PRO-Seq, Mahat et al Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086.Detailed methods are in PRO-Seq, Mahat et al Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086.
PRO-seq libraries were generated essentially as described in Mahat et al., 2016 (Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086). Primers RPI1, RPI2, RPI3 and RPI4 were used to barcode cDNAs from 293T-WT_Rep1 (Wild type, replicate 1), 293T-WT_Rep2 (Wild type, replicate 2), 293T-EAF1mut_Rep1 (Mutant EAF1, replicate 1), and 293T-EAF1mut_Rep2 (Mutant EAF1, replicate 2), respectively. PRO-seq libralies were pooled and sequenced as paired-end reads on the Illumina Novaseq 6000 platform.

value: Drosophila melanogaster

value: PRO-Seq, Mahat et al Nat Protoc, 11:1455-76;  doi:10.1038/nprot.2016.086

value: nascent RNA


title: Fezf2KO_rep2

description:
single nuclei
snRNA_Fezf2WTKO_raw_counts.dge.txt
snRNA_Fezf2WTKO_metadata.txt

molecule: nuclear RNA

source_name: P14 Fezf2KO S1 cortex


title: Fezf2Control_Lower_rep2

description: single cell

source_name: P14 Fezf2Control S1 cortex Layer 6


title: Fezf2WT_rep1

source_name: P14 Fezf2WT S1 cortex


title: PROseq_293T-EAF1mut_Rep1_R1

source_name: HEK293T EAF1-mutant


title: Fezf2WT_rep2


title: RAD21TEV control, untreated Rep2


title: PROseq_293T-WT_Rep1_R1


title: Fezf2KO_Lower_rep2

description: single cell

source_name: P14 Fezf2KO S1 cortex Layer 6


title: RAD21TEV control, +BDNF 120 minutes Rep3

source_name: Primary neuron


title: Fezf2KO_rep1


title: RAD21TEV control, +BDNF 120 minutes Rep1


title: Control sample 3

status: Public on Apr 25 2022

city: Kolkata

first: Suparno

last: Chakrabarti

state: West Bengal

address: PGH Shah Road

department: Cellular Therapy and Immunology

institute: Manashi Chakrabarti Foundation

data_processing:
FAST5 files were base-called with CPU based Guppy basecaller to generate fastq files.
Demultiplexing of the pooled samples and adapter removal was carried out using inbuilt algorithm of Minknow.
A comprehensive report of the sequencing was generated by NanoComp tool
Sample reads were subjected to a minimum phred quality score of 9 and reads with lower quality were filtered out using NanoFilt tool.
Differential Gene Expression analysis (DGE) was done using “pipeline-transcriptome-de” pipeline from Oxford nanopore technology
Genome_build: GRCh38
Supplementary_files_format_and_content: Differentially Expressed Genes with log2 Fold Change and associated p-value

source_name: Peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated from whole blood samples by density gradient centrifugations using HiSep™ LSM 1077 media (Himedia, Mumbai, India). 5 x 106 PBMCs were used for RNA isolation using the Trizol method and followed by DNase treatment for RNA purification. Purified RNA was quantified using a Qubit 4.0 fluorometer. Take 5μg of total RNA used for the polyA RNA selection using NEB NEXT oligo d(T)25 beads (NEB, MA, USA). PolyA RNA was quantified and integrity assessed using Qubit 4.0 fluorometer (Invitrogen, Waltham, Massachusetts, United States) according to manufacturer instructions.
Libraries were prepared according to Oxford nanopore technologies protocol accompanying the Direct cDNA Native Barcoding Sequencing kit (SQK-DCS109 with EXP-NBD104, Oxford, UK). 100ng of polyA RNA was used for the library preparation. Using H minus Reverse Transcriptase (Invitrogen, Waltham, Massachusetts, United States), complementary DNA (cDNA) was synthesised, followed by RNA degradation and second-strand synthesis of cDNA. Double-stranded cDNA was used for the end preparation, followed by native barcoding and adaptor ligation (all steps were followed, according to the manufacturer’s instructions). Ligated cDNA was loaded on the flow cell (R9.4.1) in MinION and were sequenced specifying 72 hours protocol. MinKNOW (v21.06.10, Microsoft Windows OS based) was used to generate FAST5 files.

treatment_protocol: 0.1 ml Mw (Sepsivac, Cadila Pharmaceuticals, India) administration intradermally in each arm on day 1 of the study

value: mononuclear cells


title: Control sample 2


title: Control sample 1


title: Control sample 4


title: RAD21TEV control, +BDNF 30 minutes Rep2


title: Mw treated sample 4

value: treated


title: Mw treated sample 3


title: PROseq_293T-EAF1mut_Rep2_R1


title: Fezf2KO_Upper_rep2

description: single cell

source_name: P14 Fezf2KO S1 cortex Layers 1-4


title: Mw treated sample 2


title: Fezf2KO_Middle_rep2

description: single cell

source_name: P14 Fezf2KO S1 cortex Layer 5


title: Mw treated sample 1


title: HAT4g-3

city: Daejeon

first: Kwang-Soo

last: Shin

department: Life Science

country: South Korea

institute: Daejeon 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(using fastx_trimmer), then mapped to Aspergillus fumigatus whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: Aspergillus fumigatus
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Aspergillus fumigatus

source_name: Asexual spore and mycelium

growth_protocol: Incubate 1-2 day in liquid media

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

treatment_protocol: Freeze-dry

value: 4g10910 deletion mutant

tag: sample

value: conidia and mycelium


title: WT_dev.replicate.3

city: Bern

first: Michael

last: Raissig

address: Altenbergrain 12

department: Institute of Plant Sciences

country: Switzerland

institute: University of Bern

data_processing:
Read quality was assessed with FastQC
mapped against the Bd21-3v1.0 genome using bowtie2
Mapped reads were counted using summarised overlap and differentially expressed genes were analysed using DeSeq2 in R
Assembly: Bd21-3v1.0
Supplementary files format and content: DeSEQ2 analysis file comparing WT and bdmute containing all output statistics
Supplementary files format and content: Raw count files of the three replicates per 2 individuals

organism: Brachypodium distachyon

source_name: developing leaf tissue

growth_protocol: grown on ½ MS plates at 20ºC with ~100 µmol photons m-2 s-1 light for 7 days

extract_protocol:
Total RNA was isolated using Qiagen’s RNeasy Plant Mini kit with on-column DNAse digestion according to the manufacturer's instructions
Kapa mRNA HyperPrep (Roche)

tag: tissue

value: developing leaf tissue

value: Bd21-3 (wild type)


title: WT_dev.replicate.1


title: sid_dev.replicate.3


title: HAT4g-2


title: WT_dev.replicate.2


title: HAT3g-1

value: 3g09610 deletion mutant


title: sid_dev.replicate.1


title: HAT5g-3

value: 5g06140 deletion mutant


title: sid_dev.replicate.2


title: HAT3g-3


title: HAT3g-2


title: HAT4g-1


title: HAT5g-2


title: HDM5g-3

value: 5g03430 deletion mutant


title: WT rep3

value: Wild type


title: HAT5g-1


title: HDM5g-1


title: WT rep2


title: HDM5g-2


title: HDM1g-2

value: 1g12332 deletion mutant


title: HDM1g-1