title: PEAC-seq target VEGFA ts2 site and MLH1dn overexpression mdnPET2.18R

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

description:
PEAC-seq target VEGFA ts2 site and MLH1dn overexpression
PEAC-seq target VEGFA ts2 site and MLH1dn overexpression

data_processing:
The PEAC-seq data was analyzed using a modified pipeline from GUIDE-seq. Firstly, we trimmed adapters using cutadapt, and reads without appropriate adapter was removed. Then the reads were mapped to the human genome (hg38) using bwa. Reads mapped to the same location and shared the same UMI were considered as PCR duplicates and merged in the following analysis. In order to fit in the target identification pipeline from GUIDE-seq, the reads name from bam files were modified, and the bam files from the forward and backward PCR were labeled and merged. Modifications were made to the GUIDE-Seq pipeline to remove reads originated from random priming. In summary, we normalized the reads number from the GUIDE-seq output file to reads per million and calculated the number of reads with correct primer extension. The candidate sites meet the following criteria: (1) no signal in the wild-type control sample; (2) the primer extension reads >= 1 at least at one direction; and (3) the geometric mean of the primer extension reads > 0.
Assembly: Site specific PCR amplicon, human

source_name: cellline

growth_protocol: HEK-293T cells were seeded in 12 well with DMEM(10%FBS,1%P/S)

extract_protocol:
Follow the TIANGEN DP304-03 manufacturer’s instructions
About 500ng extracted gDNA was digested with NotI then cleaned up with 0.5x AMPure XP beads to remove the carryover plasmids. The gDNA fragments were retained on the AMPure XP beads, and on-beads Tn5 digestion was performed at 55C for one hour and adaptors were inserted at the ends of the fragments. The Tn5 was expressed and embedded with the adaptors in-house. At the end of the Tn5 digestion, 6uL 0.2% SDS was added to terminate the reaction. The products were purified and size-selected by 1.5x AMPure XP beads and eluted in 50uL H2O. The 21bp insertion sequence was used to enrich the editing sites (both on-target and off-target) in the NGS library preparation. In the 1st round of the nested PCR, two separate reactions were performed. Each reaction used a 20uL template in a total of 50uL volume at ~30 cycles. One used the PEAC-seq insertion sequence as the forward primer binding site and the downstream Tn5 adaptor as the reverse primer binding site. Another used the upstream Tn5 adaptor as the forward primer binding site and the PEAC-seq insertion sequence as the reverse primer binding site. 1st round product were purified by 1.5x AMPure XP beads and eluted in 23 uL H2O .  The 20 uL eluted DNA was used as the template in the 2nd round amplification in a total of 50uL volume at 17 cycles, and Illumina adaptors were added. The amplicons were purified by AMPure XP beads using 0.6x+0.25x double size selection. The library was sequenced on the Illumina Novaseq platform as paired-end 150bp.
Amplicon sequencing

treatment_protocol: Transfection with the PEAC-seq plasmids

tag: cell line

tag: site

value: VEGFA TS2

tag: sgrna

value: GACCCCCTCCACCCCGCCTCCGG


title: Incisor Input

status: Public on Nov 14 2022

type: SRA

city: Farmington

first: Emma

middle: Wentworth

last: Winchester

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

country: USA

institute: UConn Health

library_source: genomic

data_processing:
Align to genome using bowtie 2.2.5 bowtie2 -p 6 -N 1 -X 2000 -t -x $sample.sam
Generate bam format and normalize with samtools 1.3 samtools view -@ 6 -b -F 4 -q 10 -o $sample_norm.bam $sample.sam
Sort bam with samtools 1.3 samtools sort -@ 6 -T $sample -o $sample.bam $sample_norm.bam
Index bam with samtools 1.3 samtools index $sample.bam
Convert to tagAlign format for size estimation samtools view -F 0x0204 -o - $sample.bam  | awk 'BEGIN{OFS="\t"}{if (and($2,16) > 0) {print $3,($4-1),($4-1+length($10)),"N","1000","-"} else {print $3,($4-1),($4-1+length($10)),"N","1000","+"} }' | gzip -c >  $sample.tagAlign.gz
Estimate fragment size using phantompeakqualtools Rscript ~/TOOLS/phantompeakqualtools/run_spp.R -c=../align/$sample.tagAlign.gz -i=../align$sample.tagAlign.gz -savp -rf -s=-500:5:500 -p=16 -out=$sample_fragment.txt -tmpdir=~ANALYSIS/ChIP/macs/tmp -filtchr=M -filtchr=Y
Call peaks with MACS2 2.1.1.20160309 macs2 callpeak -t ../align/$sample.bam -c ../align/Input_norm_sorted.bam -n $sample -f BAM -g mm --keep-dup all --nomodel -p 1e-2 --broad --nomodel --extsize 160 -B --SPMR --tempdir $sample_tmp
Generate p-value signals versus input with MACS2 2.1.1.20160309 macs2 bdgcmp -t $sample_treat_pileup.bdg -c $sample_control_lambda.bdg -o $sample_ppois.bdg -m ppois -S $sval
Convert to bedGraph to bigWig for display on UCSC genome browser bedGraphToBigWig $sample.pval.signal.bedGraph ~/GENOME/mm10/mm10.chrom.sizes  $sample.pval.signal.bigWig
Genome_build: mm10
Supplementary_files_format_and_content: bigWig for p-value ChIP-Seq Signals

molecule: genomic DNA

organism: Mus musculus

source_name: E13.5 Mandibular Incisor

growth_protocol: Samples flash frozen immediately after collection.

extract_protocol:
Cotney and Noonan, CSHL Protocols 2015.
Rubicon Genomics Thruplex 48S

treatment_protocol: Cotney and Noonan, CSHL Protocols 2015.

tag: strain

tag: antibody catalog/lot#


title: SCI rep3

city: Beijing

first: Yongjin

last: Li

state: China

address: Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing

department: Department of Orthopaedics

country: China

institute: Department of Orthopaedics, Xuanwu Hospital, Capital Medical University

library_source: transcriptomic

data_processing:
The quality of the sequencing raw data was assessed by FastQC, and we then performed mass clipping using Trimmomatic to get relatively accurate valid data. The data were aligned to the reference genome using bwa.
The data were aligned to the reference genome using bwa, and circRNAs were then identified by CIRI2. The origination of circRNAs were determined based on their location information and known gene annotations using BEDtools.
The expression of circRNAs was calculated by the reads per kilobase of transcript per million mapped reads (RPKM) formula based on BSJ reads.
The expression of mRNAs was calculated by the transcripts per kilobase of exon model per million mapped reads (TKM) formula.
The data processing were conducted using the R software package. The differentially expressed circRNAs (DECs) and differentially expressed mRNAs (DEMs) were analyzed using DESeq2 software. The screening criteria for DECs was |log2 fold-change (FC)| > 2 and P value < 0.05; and the screening criteria for DEMs was |log2 FC| > 5 and P.adj value < 0.01.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM and TKM values for each Sample

molecule: total RNA

source_name: spinal cord

extract_protocol:
RNA was harvested using TRlzol kit (B511311, Sangon, China) . 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The mice were anesthetized through intraperitoneal injection of 90 mg/kg ketamine and 10 mg/kg xylazine. Three control mice underwent a laminectomy at the T10 level without injury to the spinal cord, the other three experimental mice were placed on the NYU IMPACTOR MODEL-II spinal cord hitter platform after laminectomy at the T10 level, and the T10 spinal cord was hit with a hitting head weighing 10 grams to construct a SCI model. All the six mice were killed on the 4th day after surgery, and the spinal cord tissue about 4 cm long around the T10 level were collected for high-throughput RNA-sequencing.

tag: tissue

value: spinal cord

tag: genotype

value: WT

tag: treatment

value: laminectomy+hit spinal cord


title: GM19313

city: Copenhagen

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were trimmed to remove linker sequences, filtered for minimum sequence quality of Q30 in 50%, and rRNA reads matching U13369.1 were removed using rRNAdust (version 1.06 (FANTOM Consortium and the RIKEN PMI and CLST (DGT) et al. 2014))
Mapping to the human reference genome (hg38) was performed using BWA (version 0.7.15-r1140) allowing for max two mismatches per read. To limit mapping biases, reads were re-mapped using the WASP pipeline (van de Geijn et al. 2015) and BWA using the same parameters, taking into account biallelic SNVs (Lowy-Gallego et al. 2019). Reads with a mapping quality of at least 20 were retained for further analyses.
CAGE-defined transcription start sites (CTSSs) were identified from 5’ ends of CAGE read using CAGEfightR (version 1.10 (Thodberg et al. 2019))
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files of CAGE transcriptions start sites (CTSSs) with the score column containing the raw counts

organism: Homo sapiens

source_name: B-Lymphocyte

growth_protocol: Epstein-Barr virus immortalized LCLs were obtained from the NIGMS Human Genetic Cell Repository at Coriell Institute for Medical Research. Cells were incubated at 37°C at 5% carbon dioxide in the Roswell Park Memorial Institute (RPMI) Medium 1640 supplemented with 2mM L-glutamine and 20% of non-inactivated fetal bovine serum and antibiotics. Cell cultures were split every few days for maintenance. As these cell lines were freshly purchased, mycoplasma contamination screening was not undertaken.

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol, and gDNA was eliminated by treatment with the RNase-Free DNase Set (Qiagen).
CAGE libraries were prepared as described in (Takahashi et al, 2012, PMID: 22362160) with an input of 1.5mg of total RNA.

treatment_protocol: Samples were untreated.

value: untreated

tag: ethnicity

value: LWK

value: wildtype

tag: e-gel

value: No


title: WT_16_3

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

data_processing:
Reads were mapped to the genome with STAR (parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts in gene loci or exon only were calculated using htseq-count (parameters for genes: --stranded=reverse --order=name --type=gene --idattr=gene_id --mode=union; exon counts specific parameters: --type=exon --mode=intersection-strict).
Assembly: GRCm38
Supplementary files format and content: *.dat: Tab-delimited files containing raw read counts.

source_name: liver

growth_protocol: Mice were grown in 24h light-dark cycles. Time points represent Zeitgeber time when the light is switched on.

extract_protocol:
Snap-frozen liver tissues were homogenized in 5ml stench solution (guanidinium thiocyanate, Na-citrate, Na-acetate, beta-mercaptoethanol) followed by a standard phenol-chloroform RNA extraction protocol.
RNA-seq libraries were prepared from triplicates/condition according to standard protocols (TruSeq® Stranded Total RNA Library Prep Gold, Illumina) using 1 µg starting material.

value: liver

tag: zeitgeber time

tag: replicate


title: PEAC-seq target VEGFA ts2 site and MLH1dn overexpression mdnPET2.15F


title: WT_16_2


title: GM19310

value: Yes


title: SCI rep1


title: PEAC-seq target EMX1 site and MLH1dn overexpression mdnPEEMX1.18R

description:
PEAC-seq target EMX1 site and MLH1dn overexpression
PEAC-seq target EMX1 site and MLH1dn overexpression

value: GAGTCCGAGCAGAAGAAGAAGGG


title: CML423-GO100

city: London

first: Eduardo

last: Gomez Castaneda

address: 30 Guilford Street

department: Institute of Child Health

country: United Kingdom

institute: UCL

data_processing:
Base calling
Trimming with cutadapt 2.10 (parametres -j 12 -m 20 -u -1 -U -1)
Alignment with STAR 2.7.3a
Count matrix generation with featureCounts (subread 2.0)
Assembly: Gencode v31 (Human GRCh38.primary_assembly)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: CML CD34+ cells

growth_protocol: Cells were resuspended at a density of 2x105cells/mL in SFM + physiological growth factors (0.2ng/mL SCF, 1ng/mL G-CSF, 0.2ng/mL GM-CSF, 1ng/mL IL6, 0.05ng/mL LIF, 0.2ng/mL MIP1α) and cultured at 37°C and 5% CO2

extract_protocol:
RNA was extracted using the Arcturus PicoPure kit for patients CML423 and CML460 and using the RNAeasy Micro kit for patient CML441. RNA was reverse transcribed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, Saint-Germain-en-Laye). cDNA library preparation was performed using Nextera library preparation kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GO

tag: patient

value: PicoPure


title: GM19307


title: control rep3

value: laminectomy


title: WT_16_1


title: GM19257

value: YRI


title: Incisor H3K27ac

tag: antibody


title: PEAC-seq target EMX1 site and MLH1dn overexpression mdnPEEMX1.15F


title: control rep2


title: MUT_16_3

value: smg6 flox/flox


title: MUT_16_2


title: GM19248


title: control rep1


title: GM19247


title: PEAC-seq target EMX1 site (sgRNA engineered with evopreQ1 aptamer) and MLH1dn overexpression mdnepegPEEMX1.18R

description:
PEAC-seq target EMX1 site (sgRNA engineered with evopreQ1 aptamer) and MLH1dn overexpression
PEAC-seq target EMX1 site (sgRNA engineered with evopreQ1 aptamer) and MLH1dn overexpression


title: MUT_16_1


title: GM19235


title: WT_12_3


title: GM19225


title: PEAC-seq target EMX1 site (sgRNA engineered with evopreQ1 aptamer) and MLH1dn overexpression mdnepegPEEMX1.15F


title: WT_12_2


title: PEAC-seq target VEGFA ts2 site (sgRNA engineered with evopreQ1 aptamer) epegPET2.18R

description:
PEAC-seq target VEGFA ts2 site (sgRNA engineered with evopreQ1 aptamer)
PEAC-seq target VEGFA ts2 site (sgRNA engineered with evopreQ1 aptamer)

value: VEGFA TS2


title: Control MPP mouse 3

city: Oslo

first: Lorena

last: Arranz

address: Forskningsveien 1

department: CRESCO - Centre for Embryology and Healthy Development

country: Norway

institute: University of Oslo

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
335_MPP

data_processing:
Fastq files were extracted and demultiplexed using bcl2fastq-1.8.4 pipeline.
Only reads overlapping coding sequences were counted.
All reads mapping to the same gene were summed.
Only reads with unique mapping positions and a mapping quality score of at least 1 were considered for read counting.
Supplementary alignments were ignored for read counting.
Paired-end reads that mapped to different chromosomes or with unexpected strandedness were ignored.
Paired-end reads were counted as single fragments.
Reads mapping to multiple genes were assigned to the gene with the largest number of overlapping bases.
Genome_build: Genome assembly GCF_000001635.25 and the associated annotation GRCm38.p5.
Supplementary_files_format_and_content: [Info_genomics_LArranz.pdf]  Eurofins analysis report
Supplementary_files_format_and_content: [SupplementaryInformation_Mapping.pdf]  Eurofins supplementary mapping report
Supplementary_files_format_and_content: [eurofins_normCPM.tab]  Normalized cpm tab delimited
Supplementary_files_format_and_content: [eurofins_rawCount.tab]  Raw counts tab delimited

source_name: Bone marrow

extract_protocol:
RNA was obtained using Picopure RNA isolation kit (Arcturus)
RNA amplification: RNA was amplified and prepared for RNA-Seq using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Library preparation: The RNA sequencing library was prepared with the Low Input Library Prep Kit v2 (Clontech) to construct index-tagged cDNA. The quality, quantity and the size distribution of the Illumina libraries were determined using the Fragment Analyzer High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical). Sequencing: Libraries were sequenced on the Illumina HiSeq 2500 (Illumina) following the standard sequencing protocol with the TruSeq SBS Kit v4 and the following software versions: HCS 2.2.58, RTA 1.18.64

tag: developmental stage

value: Adult

tag: cell type

value: Multipotent progenitors

value: Bone marrow

value: control

tag: time


title: WT_12_1

value: WT


title: NRAS-G12D+ MPP mouse 3

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
336_MPP


title: PEAC-seq target VEGFA ts2 site (sgRNA engineered with evopreQ1 aptamer) epegPET2.15F

tag: cell line

value: GACCCCCTCCACCCCGCCTCCGG


title: Control MPP mouse 2

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
340_MPP


title: Incisor H3K4me3


title: SCI rep2

value: spinal cord

value: laminectomy+hit spinal cord


title: GM19222

value: untreated

value: wildtype

value: No


title: PEAC-seq target VEGFA ts2 site (sgRNA engineered with evopreQ1 aptamer) and MLH1dn overexpression mdnepegPET2.18R

description:
PEAC-seq target VEGFA ts2 site (sgRNA engineered with evopreQ1 aptamer) and MLH1dn overexpression
PEAC-seq target VEGFA ts2 site (sgRNA engineered with evopreQ1 aptamer) and MLH1dn overexpression

tag: site


title: PEAC-seq target VEGFA ts2 site (sgRNA engineered with evopreQ1 aptamer) and MLH1dn overexpression mdnepegPET2.15F

tag: sgrna


title: MUT_12_3

value: liver


title: PEAC-seq target EMX1 site (sgRNA engineered with evopreQ1 aptamer) epegEMX1.18R

description:
PEAC-seq target EMX1 site (sgRNA engineered with evopreQ1 aptamer)
PEAC-seq target EMX1 site (sgRNA engineered with evopreQ1 aptamer)

value: GAGTCCGAGCAGAAGAAGAAGGG


title: NRAS-G12D+ MPP mouse 2

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
285_MPP

tag: strain


title: NRAS-G12D+ MPP mouse 1

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
276_MPP


title: MUT_12_2


title: GM19213


title: Control MPP mouse 1

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
312_MPP


title: Control ST-HSC mouse 3

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
335_ST

value: Short term HSC


title: MUT_12_1


title: D511 GEX jejunum

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description:
jej_D511
D492_D511.gex.matrix.txt

library_source: transcriptomic single cell

data_processing:
Pseudoalignment of the scRNA-seq reads to the GRCh38/Gencode v24 transcriptome was performed using kallisto v0.45.2 in “BUS” mode [Bray et al, Nat. Biotech, 2016; Melsted et al, Nat Biotech, 2021, Melsted et al, Bioinformatics, 2019]. A raw count matrix was generated using bustools v0.40.0  and filtered for high-confidence cell-associated barcodes using the EmptyDrops algorithm [Lun et al, Genome Biology, 2019]. Count matrices were then processed in the Python scanpy package. Events between 1000 and 25000 total counts, between 700 and 4000 genes, and less than 25% mitochondrial counts were kept.
For the scTCR-seq data, we used the 10x Genomics cloud-based analysis framework CellRanger pipeline (version 6.0.1) to define clonotypes, which are based on CDR3 sequences of both TCR alpha and beta chains. scTCR-seq libraries were aligned to the vdj_GRCh38_alts_ensembl-5.0.0 reference using Single Cell V(D)J R2-only chemistry.
Assembly: GRCh38
Supplementary files format and content: scRNA-seq: text file transcript counts; scTCR-seq: text file with amino acid CDR3 sequence, nucleotide CDR3 sequence, and clone ID

source_name: D511 organ donor

extract_protocol:
Tissue samples were maintained in cold saline or media and transported to the laboratory within 2-4 hrs of organ procurement. Tissue processing protocols were adapted from protocols previously described [Poon et al, Cell Reports, 2021; Carpenter et al, Am. J. Transplant, 2018; Senda et al, Mucuosal Immunol, 2019; Dogra et al, Cell, 2020; Poon et al, Sci Immunol, 2021], and processed in a timely manner, resulting in high yields of live leukocytes. Briefly, mononuclear cells were isolated from the blood and BM samples by density centrifugation using Lymphocyte Separation Medium (Corning, cat# 25-072-CI) or Ficoll-Paque PLUS (GE, cat# 17-1440-03). Spleen was processed using mechanical dissociation, followed by density centrifugation, as above. Lung, jejunum, and lymph node samples were processed using mechanical and enzymatic digestion, followed by density centrifugation, as previously described [Kumar et al, Immunity, 2018; Poon et al, Cell Reports, 2021; Senda et al, Mucosal Immunol, 2019; Poon et al, Sci Immunol, 2021; Wells et al, protocols.io, 2021]. Skin samples were carefully washed using cell culture medium, cleaned by scraping the subcutaneous fat with a scalpel, and washed with cell culture medium again. Then, skin samples were cut into pieces of approximately 4mm in width and digested overnight at 37ºC using the Human Skin Dissociation Kit (Miltenyi). The following day, mononuclear cells were washed and isolated.
Using the Chromium Next GEM single cell 5’ Reagent kit v2 (10X Genomics), sorted T cells from each tissue site were loaded onto separate lanes of the Next GEM Chromium Controller (10X Genomics) for encapsulation (target recovery of 5,000 cells for each sample). Single cell libraries were constructed using manufacturer's protocols. TCR sequencing libraries for TCRαβ were prepared with the V(D)J enrichment kit from 10X Genomics, following manufacturer's protocols.

value: jejunum

tag: Sex

value: male

tag: age

value: T cells


title: GM19210

value: YRI

tag: genotype


title: Control ST-HSC mouse 2

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
340_ST

value: Adult

tag: tissue


title: D511 GEX spleen

description:
spl_D511
D492_D511.gex.matrix.txt

value: spleen


title: Control ST-HSC mouse 1

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
312_ST

value: Bone marrow

value: control


title: GM19206

tag: treatment

tag: ethnicity


title: GM19207

tag: e-gel

value: Yes


title: WT_8_2

value: WT

tag: zeitgeber time

tag: replicate


title: NRAS-G12D+ ST-HSC mouse 3

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
336_ST


title: WT_8_1


title: NRAS-G12D+ ST-HSC mouse 2

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
285_ST


title: GM19204


title: MUT_8_3

value: smg6 flox/flox


title: D511 GEX lung

description:
lng_D511
D492_D511.gex.matrix.txt

value: lung


title: D511 GEX inguinal lymph node

description:
iln_D511
D492_D511.gex.matrix.txt

value: inguinal lymph node


title: GM19201

value: untreated

value: wildtype

value: No


title: GM19214


title: MUT_8_2

value: liver


title: PEAC-seq target EMX1 site (sgRNA engineered with evopreQ1 aptamer) epegEMX1.15F

value: GAGTCCGAGCAGAAGAAGAAGGG


title: WT_8_3


title: GM19223


title: NRAS-G12D+ ST-HSC mouse 1

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
276_ST

value: Short term HSC


title: GM19200


title: D511 GEX lung lymph node

description:
lln_D511
D492_D511.gex.matrix.txt

value: lung lymph node

value: male

value: T cells


title: GM19197

value: YRI


title: MUT_8_1


title: WT_4_3


title: D511 GEX mesenteric lymph node

description:
mln_D511
D492_D511.gex.matrix.txt

value: mesenteric lymph node


title: D511 GEX skin

description:
skn_D511
D492_D511.gex.matrix.txt

value: skin


title: D511 GEX blood

description:
bld_D511
D492_D511.gex.matrix.txt

value: blood


title: Control LT-HSC mouse 2

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
340_LT

value: Adult

value: Long term HSC

value: Bone marrow

value: control


title: GM19190

value: untreated


title: WT_4_2

value: WT


title: Control LT-HSC mouse 1

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
312_LT


title: NRAS-G12D+ LT-HSC mouse 3

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
336_LT


title: WT_4_1


title: D492 GEX mesenteric lymph node

description:
mln_D492
D492_D511.gex.matrix.txt

source_name: D492 organ donor


title: D492 GEX lung lymph node

description:
lln_D492
D492_D511.gex.matrix.txt


title: MUT_4_3

value: smg6 flox/flox


title: NRAS-G12D+ LT-HSC mouse 2

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
285_LT


title: GM19175

value: wildtype

value: Yes


title: MUT_4_2

value: liver


title: Control LT-HSC mouse 3

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
335_LT


title: MUT_4_1


title: GM19172

value: No


title: D492 GEX jejunum

description:
jej_D492
D492_D511.gex.matrix.txt

value: jejunum

value: male


title: CD63_769: IL-1rn-KO MSC mouse 6

data_processing:
Fastq files were extracted and demultiplexed using bcl2fastq-1.8.4 pipeline.
Only reads overlapping coding sequences were counted.
All reads mapping to the same gene were summed.
Only reads with unique mapping positions and a mapping quality score of at least 1 were considered for read counting.
Supplementary alignments were ignored for read counting.
Paired-end reads that mapped to different chromosomes or with unexpected strandedness were ignored.
Paired-end reads were counted as single fragments.
Reads mapping to multiple genes were assigned to the gene with the largest number of overlapping bases.
Genome_build: Genome assembly GCF_000001635.25 and the associated annotation GRCm38.p5.
Supplementary_files_format_and_content: eurofins_normCPM.tab: eurofins norm cpm as tab delimited
Supplementary_files_format_and_content: eurofins_rawCount.tab: eurofins raw counts as tab delimited
Supplementary_files_format_and_content: ReadMe.pdf: ReadMe results from eurofins
Supplementary_files_format_and_content: SupplementaryInformation_Mapping.pdf: Supplementary info from eurofins

value: Mesenchymal stromal cells

tag: genotype/variation

value: 20-25 weeks


title: WT_0_3


title: D492 GEX skin

description:
skn_D492
D492_D511.gex.matrix.txt

value: skin

value: T cells


title: WT_0_2


title: CD63_752: IL-1rn-KO MSC mouse 4

tag: developmental stage

value: Adult


title: NRAS-G12D+ LT-HSC mouse 1

description:
Gene expression profiling of bone marrow HSC from Mx1-Cre NRAS-G12D and NRAS-G12D controls, 6 weeks after Cre activation with pI:pC injection
eurofins_normCPM.tab, eurofins_rawCounts.tab
276_LT

tag: cell type

value: Long term HSC


title: D492 GEX spleen

description:
spl_D492
D492_D511.gex.matrix.txt

value: spleen


title: D492 GEX inguinal lymph node

description:
iln_D492
D492_D511.gex.matrix.txt

value: inguinal lymph node


title: WT_0_1


title: D492 GEX lung

description:
lng_D492
D492_D511.gex.matrix.txt

value: lung


title: GM19171

value: untreated

value: YRI


title: GM19184

value: wildtype


title: GM19185


title: CD63_C5: Control MSC mouse 6

value: Bone marrow

value: Control


title: CD63_C4: Control MSC mouse 5


title: MUT_0_3

value: liver

value: smg6 flox/flox


title: GM19153

value: No


title: GM19152


title: GM19147


title: MUT_0_2


title: CD63_C2: Control MSC mouse 4

value: Mesenchymal stromal cells


title: MUT_0_1


title: GM19146


title: Amplicon NGS: control.pnpla3.OT23

description: Section 5 processed data.xlsx

data_processing:
Library strategy: PEAC-seq
The PEAC-seq data was analyzed using a modified pipeline from GUIDE-seq. Firstly, we trimmed adapters using cutadapt, and reads without appropriate adapter was removed. Then the reads were mapped to the human or mouse genome (hg38, mm10) using bwa. Reads mapped to the same location and shared the same UMI were considered as PCR duplicates and merged in the following analysis. In order to fit in the target identification pipeline from GUIDE-seq, the reads name from bam files were modified, and the bam files from the forward and backward PCR were labeled and merged. Modifications were made to the GUIDE-Seq pipeline to remove reads originated from random priming. In summary, we normalized the reads number from the GUIDE-seq output file to reads per million and calculated the number of reads with correct primer extension. The candidate sites meet the following criteria: (1) no signal in the wild-type control sample; (2) the primer extension reads >= 1 at least at one direction; and (3) the geometric mean of the primer extension reads > 0.
For PCR validation, reads were align to the amplicon sequence by crispresso2 using --max_paired_end_reads_overlap 140 --min_paired_end_reads_overlap     10 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0.2
Genome_build: human or mouse genome (hg38, mm10)
Supplementary_files_format_and_content: Section 5 processed data.xlsx:  In vivo off-target sites called by PEACSeq 6 set primers

source_name: skin & muscle

extract_protocol:
Euthanize Pregnant mice at E14.5~E21, and then collect the fetuses from uterus, skin and muscle tissues of fetuses were collected, dissected and snap-frozen in liquid nitrogen.
PEAC-seq and NGS library prepration are same as in cell lines.
Amplicon library

treatment_protocol: The mixture of Cas9-MMLV mRNA (100ng/uL) and pegRNA (50ng/uL) was injected into the cytoplasm of the zygote.

value: skin & muscle

tag: development stage

value: wild type


title: CD63_758: IL-1rn-KO MSC mouse 5

value: 20-25 weeks


title: GM19144

tag: cell line


title: GM19159


title: E3_MPP: Control MPP mouse 3

value: Adult

value: Multipotent progenitors


title: Amplicon NGS: control.pnpla3.OT31

description: Section 5 processed data.xlsx

tag: site


title: E2_MPP: Control MPP mouse 2


title: GM19160

value: Yes


title: GM19143


title: 276_KO_MPP: IL-1rn-KO MPP mouse 3


title: Amplicon NGS: control.pnpla3.OT11

description: Section 5 processed data.xlsx


title: Amplicon NGS: control.pnpla3.OT12

description: Section 5 processed data.xlsx


title: GM19141


title: 274_KO_MPP: IL-1rn-KO MPP mouse 2


title: GM19138


title: Amplicon NGS: control.pnpla3.OT33

description: Section 5 processed data.xlsx


title: E3_ST: Control ST-HSC mouse 3

value: Short term HSC


title: GM19137


title: 226_KO_MPP: IL-1rn-KO MPP mouse 1


title: Amplicon NGS: control.pnpla3.OT10

description: Section 5 processed data.xlsx


title: GM19130


title: GM19121


title: E2_ST: Control ST-HSC mouse 2


title: GM19119


title: E1_MPP: Control MPP mouse 1


title: GM19118


title: 276_KO_ST: IL-1rn-KO ST-HSC mouse 3


title: E1_ST: Control ST-HSC mouse 1


title: Amplicon NGS: control.pnpla3.OT14

description: Section 5 processed data.xlsx


title: Amplicon NGS: control.pnpla3.OT18

description: Section 5 processed data.xlsx


title: Amplicon NGS: control.pnpla3.OT24

description: Section 5 processed data.xlsx


title: D492 GEX bone marrow

description:
bom_D492
D492_D511.gex.matrix.txt

value: bone marrow

value: male

value: T cells


title: 274_KO_ST: IL-1rn-KO ST-HSC mouse 2


title: 226_KO_ST: IL-1rn-KO ST-HSC mouse 1


title: GM19117

value: untreated

value: YRI

value: wildtype


title: E3_LT: Control LT-HSC mouse 3

value: Long term HSC

value: Bone marrow

value: Control


title: Amplicon NGS: control.pnpla3.OT21

description: Section 5 processed data.xlsx


title: GM19116

value: No


title: GM19114


title: Amplicon NGS: control.pnpla3.OT6

description: Section 5 processed data.xlsx

value: skin & muscle


title: E1_LT: Control LT-HSC mouse 1


title: E2_LT: Control LT-HSC mouse 2


title: GM19113


title: Amplicon NGS: control.pnpla3.OT16

description: Section 5 processed data.xlsx

value: wild type


title: Amplicon NGS: control.pnpla3.OT15

description: Section 5 processed data.xlsx


title: Amplicon NGS: control.pnpla3.OT3

description: Section 5 processed data.xlsx


title: GM19107


title: GM19108


title: 276_KO_LT: IL-1rn-KO LT-HSC mouse 3

value: 20-25 weeks


title: Amplicon NGS: control.pnpla3.OT13

description: Section 5 processed data.xlsx


title: 274_KO_LT: IL-1rn-KO LT-HSC mouse 2

value: Adult


title: Amplicon NGS: control.pnpla3.OT20

description: Section 5 processed data.xlsx


title: D511 TCR jejunum

description:
jej_D511
D492_D511.tcr.matrix.txt

value: jejunum


title: Amplicon NGS: control.pnpla3.OT4

description: Section 5 processed data.xlsx


title: Amplicon NGS: control.pnpla3.OT8

description: Section 5 processed data.xlsx


title: 226_KO_LT: IL-1rn-KO LT-HSC mouse 1


title: GM19099

value: Yes


title: GM19095


title: GM19098


title: Amplicon NGS: control.pnpla3.OT1

description: Section 5 processed data.xlsx


title: Amplicon NGS: control.pnpla3.OT2

description: Section 5 processed data.xlsx


title: GM19092


title: D511 TCR lung

description:
lng_D511
D492_D511.tcr.matrix.txt

value: lung


title: GM19044

value: LWK


title: D511 TCR inguinal lymph node

description:
iln_D511
D492_D511.tcr.matrix.txt

value: inguinal lymph node

value: male


title: Amplicon NGS: control.pnpla3.ON

description: Section 5 processed data.xlsx


title: D511 TCR lung lymph node

description:
lln_D511
D492_D511.tcr.matrix.txt

value: lung lymph node

value: T cells


title: Amplicon NGS: 31-OT31

description: Section 5 processed data.xlsx

source_name: whole embryo

value: whole embryo

tag: sgrna

value: GGGATTAGGCCAGAGAAGAGGGG

value: Zygote Injection (100ng/μL Cas9-MMLV mRNA + 50ng/μL pegRNA)


title: D511 TCR mesenteric lymph node

description:
mln_D511
D492_D511.tcr.matrix.txt

value: mesenteric lymph node


title: GM19038

value: untreated

value: wildtype


title: Amplicon NGS: 31-OT12

description: Section 5 processed data.xlsx

tag: strain


title: GM19037

value: No


title: GM19041


title: D511 TCR skin

description:
skn_D511
D492_D511.tcr.matrix.txt

value: skin

tag: Sex


title: GM19036


title: GM19102

value: YRI


title: Amplicon NGS: control.pnpla3.OT9

description: Section 5 processed data.xlsx

value: skin & muscle

value: wild type


title: Amplicon NGS: 31-OT11

description: Section 5 processed data.xlsx


title: D492 TCR spleen

description:
spl_D492
D492_D511.tcr.matrix.txt

value: spleen

tag: age


title: D511 TCR spleen

description:
spl_D511
D492_D511.tcr.matrix.txt


title: D511 TCR blood

description:
bld_D511
D492_D511.tcr.matrix.txt

value: blood


title: D492 TCR lung lymph node

description:
lln_D492
D492_D511.tcr.matrix.txt


title: Amplicon NGS: 31-OT10

description: Section 5 processed data.xlsx


title: Amplicon NGS: 31-OT33

description: Section 5 processed data.xlsx


title: GM19035

value: LWK

tag: genotype

value: Yes


title: GM19030


title: GM19031


title: D492 TCR mesenteric lymph node

description:
mln_D492
D492_D511.tcr.matrix.txt

tag: tissue

value: male


title: D492 TCR jejunum

description:
jej_D492
D492_D511.tcr.matrix.txt

value: jejunum

value: T cells


title: Amplicon NGS: 31-OT24

description: Section 5 processed data.xlsx

value: whole embryo

value: GGGATTAGGCCAGAGAAGAGGGG

tag: treatment


title: D492 TCR inguinal lymph node

description:
iln_D492
D492_D511.tcr.matrix.txt

value: inguinal lymph node


title: Amplicon NGS: 31-OT23

description: Section 5 processed data.xlsx

value: Zygote Injection (100ng/μL Cas9-MMLV mRNA + 50ng/μL pegRNA)


title: GM19027

value: untreated

tag: ethnicity

value: wildtype


title: D492 TCR skin

description:
skn_D492
D492_D511.tcr.matrix.txt

value: skin


title: GM19026

tag: e-gel

value: No


title: Amplicon NGS: 31-OT18

description: Section 5 processed data.xlsx


title: Amplicon NGS: 31-OT14

description: Section 5 processed data.xlsx


title: D492 TCR bone marrow

description:
bom_D492
D492_D511.tcr.matrix.txt

value: bone marrow


title: GM19028


title: Amplicon NGS: 31-OT6

description: Section 5 processed data.xlsx


title: D492 TCR lung

description:
lng_D492
D492_D511.tcr.matrix.txt

data_processing:
Pseudoalignment of the scRNA-seq reads to the GRCh38/Gencode v24 transcriptome was performed using kallisto v0.45.2 in “BUS” mode [Bray et al, Nat. Biotech, 2016; Melsted et al, Nat Biotech, 2021, Melsted et al, Bioinformatics, 2019]. A raw count matrix was generated using bustools v0.40.0  and filtered for high-confidence cell-associated barcodes using the EmptyDrops algorithm [Lun et al, Genome Biology, 2019]. Count matrices were then processed in the Python scanpy package. Events between 1000 and 25000 total counts, between 700 and 4000 genes, and less than 25% mitochondrial counts were kept.
For the scTCR-seq data, we used the 10x Genomics cloud-based analysis framework CellRanger pipeline (version 6.0.1) to define clonotypes, which are based on CDR3 sequences of both TCR alpha and beta chains. scTCR-seq libraries were aligned to the vdj_GRCh38_alts_ensembl-5.0.0 reference using Single Cell V(D)J R2-only chemistry.
Assembly: GRCh38
Supplementary files format and content: scRNA-seq: text file transcript counts; scTCR-seq: text file with amino acid CDR3 sequence, nucleotide CDR3 sequence, and clone ID
Library strategy: scTCR-seq

value: lung


title: GM19025


title: GM19019


title: GM19017


title: Amplicon NGS: 31-OT21

description: Section 5 processed data.xlsx


title: Amplicon NGS: 31-OT3

description: Section 5 processed data.xlsx


title: GM19024


title: Amplicon NGS: 31-OT16

description: Section 5 processed data.xlsx


title: GM18934

value: YRI


title: Amplicon NGS: 31-OT15

description: Section 5 processed data.xlsx


title: 32_72h_1262_stretch_4_S30

city: Helsinki

first: Lotta

last: Pohjolainen

address: Viikinkaari 5 E

country: Finland

institute: University of Helsinki

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GRCm38.p6 whole genome using STAR aligner (2.7.6a) in two-pass mode.
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id -a gencode.v34.annotation.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of sample-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance) results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Genome_build: Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13, GCA_000001405.28) from GENCODE release 34.
Supplementary_files_format_and_content: Raw count matrix of sequencing reads (featureCounts meta-feature level) as .xlsx

source_name: human induced pluripotent stem cell-derived cardiomyocytes

growth_protocol: The iPS(IMR90)-4 cells were differentiated to cardiomyocytes using CHIR99021 + Wnt-C59 induction followed by purification by glucose deprivation on days 11-15. The differentiation protocol produced ≥95% pure cardiomyocytes. HiPSC-CMs were seeded at a density of 700,000-800,000 cells/well in RB+ supplemented with 10% fetal bovine serum on collagen I-coated 6-well BioFlex® culture plates (Flexcell International Corporation) with additional Matrigel coating. The hiPSC-cardiomyocytes were allowed to attach for 48 h, after which the medium was changed to serum-free RB+. The experiments were started on days 29-43 of differentation.

extract_protocol:
Total RNA was isolated using a NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions. Cells were lysed in 350 µl of RA1 lysis buffer supplemented with 1% β-mercaptoethanol and stored at -80 °C (maximum one month) before RNA isolation. The RNA quality was analyzed with Agilent 4200 TapeStation.
Library was constructed using NEBNext Ultra Directional RNA Library Prep kit including rRNA depletion.

treatment_protocol: Equibiaxial stretch was applied with FX-5000 Tension System (Flexcell International Corporation) for 24 h, 48 h or 72 h in two-second cycles (0.5 Hz) to induce 10 to 21% stretch.

tag: stretching

value: stretched

tag: time point

tag: agent

value: 30 microM 1262

tag: sample pairing


title: Amplicon NGS: 31-OT13

description: Section 5 processed data.xlsx


title: GM18924


title: 30_72h_1262_stretch_3_S28


title: 29_72h_1262_ctrl_3_S27

value: unstretched


title: 31_72h_1262_ctrl_4_S29


title: 28_72h_1262_stretch_2_S26


title: GM18923


title: Amplicon NGS: 31-OT9

description: Section 5 processed data.xlsx


title: Amplicon NGS: 31-OT4

description: Section 5 processed data.xlsx


title: GM18917


title: 27_72h_1262_ctrl_2_S25


title: Amplicon NGS: 31-OT20

description: Section 5 processed data.xlsx


title: 26_72h_1262_stretch_1_S24


title: 25_72h_1262_ctrl_1_S23


title: GM18916


title: GM18915


title: Amplicon NGS: 31-OT1

description: Section 5 processed data.xlsx


title: 23_72h_DMSO_ctrl_4_S21

value: 0.3percent DMSO


title: Amplicon NGS: 31-OT2

description: Section 5 processed data.xlsx


title: GM18910

value: Yes


title: Amplicon NGS: 31-ON

description: Section 5 processed data.xlsx


title: 22_72h_DMSO_stretch_3_S20


title: GM18908


title: GM18909


title: 19_72h_DMSO_ctrl_2_S17


title: Amplicon NGS: 21-OT31

description: Section 5 processed data.xlsx

value: skin & muscle


title: GM18907


title: Amplicon NGS: 21-OT12

description: Section 5 processed data.xlsx


title: 21_72h_DMSO_ctrl_3_S19


title: GM18881


title: Amplicon NGS: 31-OT8

description: Section 5 processed data.xlsx

value: whole embryo


title: 17_72h_DMSO_ctrl_1_S15


title: Amplicon NGS: 21-OT10

description: Section 5 processed data.xlsx

value: GGGATTAGGCCAGAGAAGAGGGG


title: Amplicon NGS: 21-OT11

description: Section 5 processed data.xlsx


title: 18_72h_DMSO_stretch_1_S16


title: Amplicon NGS: 21-OT33

description: Section 5 processed data.xlsx


title: 16_48h_DMSO_stretch_4_S14


title: 20_72h_DMSO_stretch_2_S18


title: GM18877


title: 24_72h_DMSO_stretch_4_S22


title: GM18878


title: Amplicon NGS: 21-OT16

description: Section 5 processed data.xlsx


title: 15_48h_DMSO_ctrl_4_S13


title: GM18876


title: 14_48h_DMSO_stretch_3_S12


title: Amplicon NGS: 21-OT14

description: Section 5 processed data.xlsx


title: GM18912


title: Amplicon NGS: 21-OT24

description: Section 5 processed data.xlsx


title: GM18874


title: 12_48h_DMSO_stretch_2_S10


title: 13_48h_DMSO_ctrl_3_S11


title: GM18879


title: GM18873


title: Amplicon NGS: 21-OT18

description: Section 5 processed data.xlsx


title: 11_48h_DMSO_ctrl_2_S9


title: GM18868


title: GM18870


title: GM18865


title: 10_48h_DMSO_stretch_1_S8


title: GM18867


title: Amplicon NGS: 21-OT6

description: Section 5 processed data.xlsx


title: Amplicon NGS: 21-OT20

description: Section 5 processed data.xlsx


title: Amplicon NGS: 21-OT3

description: Section 5 processed data.xlsx


title: 9_48h_DMSO_ctrl_1_S7


title: Amplicon NGS: 21-OT21

description: Section 5 processed data.xlsx


title: 7_24h_DMSO_ctrl_4_S5


title: 4_24h_DMSO_stretch_2_S4


title: Amplicon NGS: 21-OT13

description: Section 5 processed data.xlsx


title: Amplicon NGS: 21-OT15

description: Section 5 processed data.xlsx


title: Amplicon NGS: 21-OT23

description: Section 5 processed data.xlsx


title: GM18861


title: GM18858


title: 3_24h_DMSO_ctrl_2_S3


title: 2_24h_DMSO_stretch_1_S2


title: GM18864


title: Amplicon NGS: 21-OT4

description: Section 5 processed data.xlsx


title: Amplicon NGS: 21-OT8

description: Section 5 processed data.xlsx


title: 1_24h_DMSO_ctrl_1_S1


title: Amplicon NGS: 21-OT1

description: Section 5 processed data.xlsx


title: GM18523


title: GM18520


title: 8_24h_DMSO_stretch_4_S6


title: Amplicon NGS: 21-ON

description: Section 5 processed data.xlsx


title: GM18519


title: Amplicon NGS: 21-OT2

description: Section 5 processed data.xlsx


title: GM18517


title: GM18516


title: Amplicon NGS: control.Pcsk9.OT20

description: Section 5 processed data.xlsx

value: wild type


title: GM18511


title: GM18856


title: Amplicon NGS: control.Pcsk9.OT21

description: Section 5 processed data.xlsx


title: GM18510


title: Amplicon NGS: 21-OT9

description: Section 5 processed data.xlsx

value: Zygote Injection (100ng/μL Cas9-MMLV mRNA + 50ng/μL pegRNA)


title: Amplicon NGS: control.Pcsk9.OT18

description: Section 5 processed data.xlsx


title: Amplicon NGS: control.Pcsk9.OT17

description: Section 5 processed data.xlsx


title: GM18853

value: untreated


title: GM18504

value: wildtype


title: GM18501


title: Amplicon NGS: control.Pcsk9.OT16

description: Section 5 processed data.xlsx


title: GM18499


title: AGS_500IND_3

city: Kolkata

first: Uday

last: Bandyopadhyay

state: WB

address: EN 80, Salt Lake, College More, EN Block, Sector V, Kolkata,

department: Division of Molecular Medicine

country: India

institute: Bose Institute

data_processing:
Bcl files were converted to Fastq files using Bcl2fastq tool and the data were subjected to quality check using FastQC v.0.11.7.
This was followed by adapter trimming with Cutadapt v1.16 using Illumina Universal Adapter.
Hisat2 2.1.0. was used to align the trimmed reads with Human hg38 reference genome .
Sorting of Bam files were performed with Samtools v1.19.
Next, gene count was performed with FeatureCounts followed by differential analysis with DESeq2.Differentially expressed genes with ≥  or ≤ 1.5-fold expression change and p value ≤ 0.05 and FDR ≤ 0.05 were filtered.
Supplementary files format and content: tab-delimited text files include Count values for each Sample

source_name: AGS (a human gastric adenocarcinoma cell line)

growth_protocol: AGS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA sequencing library preparation using TruSeq Stranded Total RNA Library preparation kit from Illumina. Briefly, total RNA was isolated from the tissue or cell samples using PureLink RNA Mini Kit (Thermo) following manufacturer’s guidelines. 45 mg of tissue or 107 cells per sample were used as the starting material. Quality and concentration of the isolated RNA samples were checked in Nanodrop 2000 (Thermo) and Agilent 2100 Bioanalyzer. Samples with RIN ≥ 7.0 were subsequently used for library preparation. Equal amount (200 ng) of RNA from each sample was first subjected to ribosomal RNA depletion using the Ribo-Zero Human/Mouse/Rat depletion module of the kit followed by purification and divalent cation-based fragmentation. The resulting fragments were purified and subjected to cDNA synthesis, A-tailing and dual index adapter ligation. The products were subsequently purified and PCR enriched. The resulting RNA libraries were checked in Agilent 2200 TapeStation (Agilent Technologies), quantified, normalized and subjected to equimolar pooling. The pooled libraries were finally loaded on sequencing run flow cell (Illumina) and subjected to 100 bp paired-end massively parallel sequencing in Novaseq 6000 sequencer (Illumina).
RNA libraries for RNA-seq were prepared using Illumina TrueSeq strand Library Prep Kit following manufacturer's protocols.

treatment_protocol: AGS cells were plated and allowed to grow over-night. Cells were treated with 0.5 mM indomethacin for 24 hrs. Then the cells were harvested and used for transcriptome analysis and protein expression profiling to capture the subtle effects on cellular metabolism.

tag: cell type

value: Indomethacin 0.5 mM

tag: time

value: 24 hrs


title: Amplicon NGS: control.Pcsk9.OT15

description: Section 5 processed data.xlsx

tag: development stage


title: hSAEpC at D28 post-ALI, biological replicate 2

type: RNA

city: Pittsburgh

first: Kambez

middle: Hajipouran

last: Benam

state: Pennsylvania

address: 200 Lothrop St, Rm E1144

institute: University of Pittsburgh

description: Gene expression data from hSAEpCs at D28 post-ALI (late stage of differentiation)

hyb_protocol: Following labeling, ssDNA was hybridized to the Human Gene 2.0 ST GeneChips® for 16 hr at 45C in an Affymetrix HybridizationOven 645. GeneChips® were washed and stained in the Affymetrix Fluidics Station 450 using the GeneChip® Hybridization, Wash, and Stain Kit (performed at Molecular Biology Core Facilities of Dana-Farber Cancer Institute at Harvard University (https://mbcf.dfci.harvard.edu)).

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (performed at Molecular Biology Core Facilities of Dana-Farber Cancer Institute at Harvard University (https://mbcf.dfci.harvard.edu)).

data_processing: The raw intensities of the CEL files were normalized with RMA (Affymetrix Expression Console). Unlabeled genes were removed and duplicates were averaged.

label: Biotin

label_protocol: The targets were prepared using the Affymetrix WT Plus assay and labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent (performed at Molecular Biology Core Facilities of Dana-Farber Cancer Institute at Harvard University (https://mbcf.dfci.harvard.edu))

growth_protocol: hSAEpCs isolated from a healthy normal subject were cultured on top of porous transwell inserts and guided to full differentiation into mucociliated epithelium under ALI.

extract_protocol: Cells were lysed in situ using RLT buffer, and Qiagen RNeasy Mini kit was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: None. We compared various days post-ALI. No treatment was applied to our cell cultures.

tag: developmental stage

value: Healthy normal

tag: disease

value: adult


title: GM18489

value: YRI

tag: cell line

value: No


title: AGS_500IND_2

value: AGS (a human gastric adenocarcinoma cell line)


title: hSAEpC at D28 post-ALI, biological replicate 3

source_name: hSAEpCs at D28 post-ALI (late stage of differentiation)


title: Amplicon NGS: control.Pcsk9.OT19

description: Section 5 processed data.xlsx

tag: strain

tag: site


title: hSAEpC at D21 post-ALI, biological replicate 1

description: Gene expression data from hSAEpCs at D21 post-ALI (late stage of differentiation)


title: Amplicon NGS: control.Pcsk9.OT14

description: Section 5 processed data.xlsx


title: AGS_500IND_1


title: GM18488

tag: genotype


title: hSAEpC at D28 post-ALI, biological replicate 1


title: hSAEpC at D21 post-ALI, biological replicate 2

source_name: hSAEpCs at D21 post-ALI (late stage of differentiation)


title: hSAEpC at D21 post-ALI, biological replicate 3


title: Amplicon NGS: control.Pcsk9.OT13

description: Section 5 processed data.xlsx

tag: tissue


title: hSAEpC at D10 post-ALI, biological replicate 3

description: Gene expression data from hSAEpCs at D10 post-ALI (intermediate stage of differentiation)


title: AGS_Control_3

tag: treatment

value: Indomethacin 0 mM


title: hSAEpC at D14 post-ALI, biological replicate 1

description: Gene expression data from hSAEpCs at D14 post-ALI (intermediate stage of differentiation)


title: GM18487

tag: ethnicity


title: hSAEpC at D14 post-ALI, biological replicate 2

source_name: hSAEpCs at D14 post-ALI (intermediate stage of differentiation)


title: AGS_Control_2


title: Amplicon NGS: control.Pcsk9.OT11

description: Section 5 processed data.xlsx


title: GM18486

tag: e-gel


title: Amplicon NGS: control.Pcsk9.OT10

description: Section 5 processed data.xlsx


title: Amplicon NGS: control.Pcsk9.OT12

description: Section 5 processed data.xlsx


title: CAGE_VRQ4_Pool_88_H6

data_processing:
Reads were trimmed to remove linker sequences, filtered for minimum sequence quality of Q30 in 50%, and rRNA reads matching U13369.1 were removed using rRNAdust (version 1.06 (FANTOM Consortium and the RIKEN PMI and CLST (DGT) et al. 2014))
Mapping to the human reference genome (hg38) was performed using BWA (version 0.7.15-r1140) allowing for max two mismatches per read. Reads with a mapping quality of 30 were retained for further analyses.
CAGE-defined transcription start sites (CTSSs) were identified from 5’ ends of CAGE read using CAGEfightR (version 1.10 (Thodberg et al. 2019))
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files of CAGE transcriptions start sites (CTSSs) with the score column containing the raw counts

growth_protocol: Epstein-Barr virus immortalized GM12878 cells were obtained from the NIGMS Human Genetic Cell Repository at Coriell Institute for Medical Research. Cells were incubated at 37°C at 5% carbon dioxide in the Roswell Park Memorial Institute (RPMI) Medium 1640 supplemented with 2mM L-glutamine and 20% of non-inactivated fetal bovine serum and antibiotics. Cell cultures were split every few days for maintenance. As these cell lines were freshly purchased, mycoplasma contamination screening was not undertaken.

treatment_protocol: untreated and 25ng/ml TNF-α for 6h GM12878 (4 replicates each)

value: CEU


title: translocation amplicon NGS library2 [DSB.S2]

description: Validation for translocation peak2 called by PEACSeq

data_processing:
library strategy: Amplicon sequencing
The PEAC-seq data was analyzed using a modified pipeline from GUIDE-seq. Firstly, we trimmed adapters using cutadapt, and reads without appropriate adapter was removed. Then the reads were mapped to the human or mouse genome (hg38, mm10) using bwa. Reads mapped to the same location and shared the same UMI were considered as PCR duplicates and merged in the following analysis. In order to fit in the target identification pipeline from GUIDE-seq, the reads name from bam files were modified, and the bam files from the forward and backward PCR were labeled and merged. Modifications were made to the GUIDE-Seq pipeline to remove reads originated from random priming. In summary, we normalized the reads number from the GUIDE-seq output file to reads per million and calculated the number of reads with correct primer extension. The candidate sites meet the following criteria: (1) no signal in the wild-type control sample; (2) the primer extension reads >= 1 at least at one direction; and (3) the geometric mean of the primer extension reads > 0.
For PCR validation, reads were align to the amplicon sequence by crispresso2 using --max_paired_end_reads_overlap 140 --min_paired_end_reads_overlap     10 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0.2
Genome_build: Site specific PCR amplicon, human

source_name: translocation amplicon NGS library2

extract_protocol:
Follow the TIANGEN DP304-03 manufacturer’s instructions
About 500ng extracted gDNA was digested with NotI then cleaned up with 0.5x AMPure XP beads to remove the carryover plasmids. The gDNA fragments were retained on the AMPure XP beads, and on-beads Tn5 digestion was performed at 55C for one hour and adaptors were inserted at the ends of the fragments. The Tn5 was expressed and embedded with the adaptors in-house. At the end of the Tn5 digestion, 6uL 0.2% SDS was added to terminate the reaction. The products were purified and size-selected by 1.5x AMPure XP beads and eluted in 50uL H2O. The 21bp insertion sequence was used to enrich the editing sites (both on-target and off-target) in the NGS library preparation. In the 1st round of the nested PCR, two separate reactions were performed. Each reaction used a 20uL template in a total of 50uL volume at ~30 cycles. One used the PEAC-seq insertion sequence as the forward primer binding site and the downstream Tn5 adaptor as the reverse primer binding site. Another used the upstream Tn5 adaptor as the forward primer binding site and the PEAC-seq insertion sequence as the reverse primer binding site. 1st round product were purified by 1.5x AMPure XP beads and eluted in 23 uL H2O .  The 20 uL eluted DNA was used as the template in the 2nd round amplification in a total of 50uL volume at 17 cycles, and Illumina adaptors were added. The amplicons were purified by AMPure XP beads using 0.6x+0.25x double size selection. The library was sequenced on the Illumina Novaseq platform as paired-end 150bp.

treatment_protocol: HEK-293T cells were seeded in a 12-well plate and grow till ~80% confluency. Each well was transfected with 3ug plasmids by Lipofectamine 3000. The post-transfection cells were collected after 48 hours. The cell sorter (SONY MA900) was used to sort about 100,000 GFP positive cells.

value: VEGFA TS3

tag: sgrna

value: GGTGAGTGAGTGTGTGCGTGTGG


title: CAGE_M4R3_Pool_87_E2


title: hSAEpC at D14 post-ALI, biological replicate 3


title: translocation amplicon NGS library1 [DSB.S1]

description: Validation for translocation peak1 called by PEACSeq

source_name: translocation amplicon NGS library1


title: Amplicon NGS: control.Pcsk9.OT9

description: Section 5 processed data.xlsx

value: skin & muscle


title: Amplicon NGS: control.Pcsk9.ON

description: Section 5 processed data.xlsx


title: site called by GUIDESeq but not called by PEACSeq [guide-site8]

value: VEGFA TS1

value: GGGTGGGGGGAGTTTGCTCCTGG


title: CAGE_AF7N_Pool_81_A3


title: Amplicon NGS: control.Pcsk9.OT5

description: Section 5 processed data.xlsx

value: wild type


title: site called by GUIDESeq but not called by PEACSeq [guide-site7]


title: Amplicon NGS: control.Pcsk9.OT4

description: Section 5 processed data.xlsx


title: CAGE_KSHX_Pool_85_D3


title: CAGE_SEFE_Pool_82_G6


title: site called by GUIDESeq but not called by PEACSeq [guide-site5]


title: Amplicon NGS: control.Pcsk9.OT3

description: Section 5 processed data.xlsx


title: site called by GUIDESeq but not called by PEACSeq [guide-site4]


title: Amplicon NGS: control.Pcsk9.OT2

description: Section 5 processed data.xlsx


title: CAGE_AF7N_Pool_81_A2


title: Amplicon NGS: control.Pcsk9.OT1

description: Section 5 processed data.xlsx


title: AGS_Control_1


title: CAGE_FN4E_Pool_86_B3


title: CAGE_HCSX_Pool_83_C6


title: hFK3

city: Ramat Gan

first: Tomer

last: Kalisky

address: Max and Anna Webb

department: Electrical Engineering

country: Israel

institute: Bar Ilan University

data_processing:
Mapping to hg19 using TopHat v2.1.0 python 2.7.5
Indexing bam file created by tophat:  'samtools index'
Sorting bam file for later use by htseq-count:  'samtools sort -n'
Counting genes using htseq-count  version HTSeq-0.6.1p1-py2.7-linux-x86_64  on python 2.7.5  '  htseq-count -f bam -s no -a 10 '
Normalizing counts using DESeq2 on R
Genome_build: hg19
Supplementary_files_format_and_content: Excel tables containing raw and normalized counts

molecule: polyA RNA

source_name: Cells from a human fetal kidney

growth_protocol: Human fetal kidney cells were collected from elective abortions at fetal gestational age between 15 to 19 weeks. The kidneys were dissociated into single-cell suspensions, resuspended in serum-free medium (SFM), plated in flasks, and cultured until reaching 80% confluence. FACS was used to isolate three cell fractions representing progressive developmental stages of the human fetal kidney: hFK1 (NCAM1+/CD133–), hFK2 (NCAM1+/CD133+), and hFK3 (NCAM1–/CD133+). All assays were conducted with low passage cultured cells (passage 0).     Three blastemal-predominant Wilms’ tumor xenografts (WT-PDX) originating from three different patients (WT11, WT14, and WT37) were established, propagated in mice, and collected. The xenografts were then dissociated into single-cell suspensions, resuspended in serum-containing medium (SCM), plated in flasks, and cultured overnight.

extract_protocol:
Bulk total RNA was prepared from ~1.5*10^5 cells using the Direct-zol RNA MiniPrep kit (R2050, Zymo Research) according to the manufacturer’s instructions and stored in − 80 °C.
RNA was quantified on an Agilent BioAnalyzer (Agilent Technologies) and aliquots of 270–500 ng were made into cDNA libraries using the TruSeq mRNA-Seq library kit (Illumina).    All 6 libraries (hFK1, hFK2, hFK3, WT11, WT14, and WT37) were sequenced paired-end 2 × 126 bases on an Illumina HiSeq 2500 platform in the Israel National Center for Personalized Medicine (G-INCPM). For each sample we obtained approximately 40 million paired-end reads.

value: Kidney

value: late


title: site called by GUIDESeq but not called by PEACSeq [guide-site3]


title: Amplicon NGS: 12-OT21

description: Section 5 processed data.xlsx

value: AGCAGCAGCGGCGGCAACAGCGG

value: Zygote Injection (100ng/μL Cas9-MMLV mRNA + 50ng/μL pegRNA)


title: site called by GUIDESeq but not called by PEACSeq [guide-site2]


title: site called by GUIDESeq but not called by PEACSeq [guide-site6]


title: site called by GUIDESeq but not called by PEACSeq [guide-site1]


title: hFK2

value: intermediate


title: hFK1

value: early


title: PEACSeq unique 2 [peac-site16]

description: PEACSseq unique site2 called by PEACSeq

source_name: PEACSeq unique 2


title: WT37

source_name: Cells from a blastemal-predominant Wilms’ tumor patient-derived xenograft

value: blastemal-predominant Wilms' tumor


title: WT14


title: Amplicon NGS: 12-OT18

description: Section 5 processed data.xlsx


title: Amplicon NGS: 12-OT20

description: Section 5 processed data.xlsx


title: wildtype 293T PEACSeq FANCF 5F [WTT6.5F]

description: wildtype 293T PEACSeq FANCF 5F

source_name: wildtype 293T PEACSeq FANCF 5F

value: Wildtype


title: WT11


title: PEACSeq unique 1 [peac-site15]

description: PEACSseq unique site1 called by PEACSeq

source_name: PEACSeq unique 1


title: Amplicon NGS: 12-OT19

description: Section 5 processed data.xlsx


title: Amplicon NGS: 12-OT17

description: Section 5 processed data.xlsx


title: hSAEpC at D8 post-ALI, biological replicate 3

description: Gene expression data from hSAEpCs at D8 post-ALI (early stage of differentiation)

value: Healthy normal

value: adult


title: NRAS-G12D+ mouse 2 [NRAS_TG_rep1]

description:
NRAS_LEUK_rep2
Gene expression profiling of Nes-gfp enriched cells from bone marrow of leukemic and control mice.

data_processing:
Raw fastq files were extracted and demultiplexed using bcl2fastq.
Raw fastq files were trimmed for adapters using flexbar v3.5.0 as recommended by the NEBNext Single Cell/Low Input cDNA kit workflow.
Transcript quantification of fastq files were performed using Salmon v1.1.0 with the commands --numBootstraps 100 --seqBias --gcBias --validateMappings --minScoreFraction 0.2 --consensusSlack 0.1.
Gene level estimation was performed with Sleuth v0.30.0.
Genome_build: GRCm38.p6 ENSEMBL v98
Supplementary_files_format_and_content: DGE_normCounts.txt

source_name: Bone marrow

extract_protocol:
RNA was obtained using Picopure RNA isolation kit (Arcturus)
RNA was amplified using NEBNext Single Cell/Low input RNA library kit v. 3.0 (NEB #E6420) using the protocol for low input RNA. This protocol was follwed to the fragmentation step which was performed with Covaris M220 with target size of 150 bp. Sequencing libraries were prepared using TruSeq RNA Library Preparation Kit V.2.0 (# RS-122-2001) starting from "perform end repair" to final library.
RNA-Sequencing with Illumina NextSeq 550 on a Mid flow cell (150 cycles) paired-end reads, and with an input of 1.5 pM.

tag: strain background

tag: age

value: Adult

tag: genotype/variation

value: Nes-gfp

value: transplanted with bone marrow cells from previously leukemic (Mx1-Cre-positive NRAS-G12D-positive) mice

value: Bone marrow Nes-gfp-positive mesenchymal stromal cells


title: wildtype 293T PEACSeq RNF2 5F [WTT5.5F]

description: wildtype 293T PEACSeq RNF2 5F

source_name: wildtype 293T PEACSeq RNF2 5F


title: hSAEpC at D10 post-ALI, biological replicate 1

source_name: hSAEpCs at D10 post-ALI (intermediate stage of differentiation)


title: NRAS-G12D+ mouse 1 [NRAS_TG_rep1]

description:
NRAS_LEUK_rep1
Gene expression profiling of Nes-gfp enriched cells from bone marrow of leukemic and control mice.

tag: cell type


title: wildtype 293T PEACSeq RNF2 10F [WTT5.10F]

description: wildtype 293T PEACSeq RNF2 10F

source_name: wildtype 293T PEACSeq RNF2 10F


title: Amplicon NGS: 12-OT16

description: Section 5 processed data.xlsx

source_name: skin & muscle

value: skin & muscle


title: Amplicon NGS: 12-OT15

description: Section 5 processed data.xlsx


title: hSAEpC at D8 post-ALI, biological replicate 1

source_name: hSAEpCs at D8 post-ALI (early stage of differentiation)


title: Amplicon NGS: 12-OT14

description: Section 5 processed data.xlsx


title: Hi-C WT MEF 4OHT No AsISI Rep1

first: Jennifer

last: Zagelbaum

address: 1130 Saint Nicholas

institute: Columbia

data_processing:
To be updated.
Assembly: mm10
Supplementary files format and content: mcool

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Mouse embryonic fibroblast (MEF) were cultured in high-glucose Dulbecco’s modified Eagle’s medium supplemented with L-glutamine, 10% fetal bovine serum, and 1% penicillin-streptomycin

extract_protocol:
Genomic DNA was extracted using phenol/chloroform extraction
Libraries were constructed using standardized HTGTS and Hi-C protocols

tag: assay

value: Hi-C

value: WT


title: Hi-C WT MEF 4OHT NU7441 Rep2


title: wildtype 293T PEACSeq EMX1 5F [WTT4.5F]

description: wildtype 293T PEACSeq EMX1 5F

source_name: wildtype 293T PEACSeq EMX1 5F


title: hSAEpC at D8 post-ALI, biological replicate 2


title: Amplicon NGS: 12-OT13

description: Section 5 processed data.xlsx

tag: development stage


title: hSAEpC at D6 post-ALI, biological replicate 3

description: Gene expression data from hSAEpCs at D6 post-ALI (early stage of differentiation)

tag: developmental stage


title: hSAEpC at D6 post-ALI, biological replicate 2

source_name: hSAEpCs at D6 post-ALI (early stage of differentiation)

tag: disease


title: hSAEpC at D0 post-ALI, biological replicate 3

description: Gene expression data from hSAEpCs just before introducing ALI (D0)


title: hSAEpC at D4 post-ALI, biological replicate 3

description: Gene expression data from hSAEpCs at D4 post-ALI (very early stage of differentiation)


title: hSAEpC at D2 post-ALI, biological replicate 2

description: Gene expression data from hSAEpCs at D2 post-ALI (very early stage of differentiation)


title: hSAEpC at D10 post-ALI, biological replicate 2


title: Hi-C WT MEF 4OHT No AsiSI Rep2


title: Hi-C WT MEF 4OHT NU7441 Rep1


title: wildtype 293T PEACSeq EMX1 10F [WTT4.10F]

description: wildtype 293T PEACSeq EMX1 10F

source_name: wildtype 293T PEACSeq EMX1 10F

tag: cell line


title: Control mouse 1 [NRAS_WT_rep1]

description:
NRAS_C_rep1
Gene expression profiling of Nes-gfp enriched cells from bone marrow of leukemic and control mice.

value: transplanted with bone marrow cells from previously pI-pC induced control (Mx1-Cre-negative NRAS-G12D-positive) mice


title: Amplicon NGS: 12-OT12

description: Section 5 processed data.xlsx

tag: strain


title: Control mouse 2 [NRAS_WT_rep2]

description:
NRAS_C_rep2
Gene expression profiling of Nes-gfp enriched cells from bone marrow of leukemic and control mice.


title: hSAEpC at D6 post-ALI, biological replicate 1


title: Hi-C WT MEF 4OHT CK666 Rep2


title: hSAEpC at D4 post-ALI, biological replicate 2

source_name: hSAEpCs at D4 post-ALI (very early stage of differentiation)


title: hSAEpC at D0 post-ALI, biological replicate 2

source_name: hSAEpCs just before introducing ALI (D0)


title: hSAEpC at D2 post-ALI, biological replicate 3

source_name: hSAEpCs at D2 post-ALI (very early stage of differentiation)


title: wildtype 293T PEACSeq T3 5F [WTT3.5F]

description: wildtype 293T PEACSeq T3 5F

source_name: wildtype 293T PEACSeq T3 5F

tag: site


title: hSAEpC at D4 post-ALI, biological replicate 1


title: hSAEpC at D0 post-ALI, biological replicate 1


title: atx4/5_repeat2

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using HISAT2 version 2.2.0 with the default parameters.
The differentially expressed genes and transposable elements were identified with |log2FC| >1 and P value<0.01 using edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long-day (LD) photoperiod (23℃, 16 h light/ 22℃, 8 h darkness).

extract_protocol:
Total RNA was isolated from 11-day-old seedlings in LD using Trizol reagent.
Sequencing libraries were built for RNA-seq (the 150 bp paired-end or the single-ended 50-bp strategy).

value: Arabidopsis seedlings

tag: growth conditions

value: long day (16 h light, 8 h dark)

tag: genotype


title: Amplicon NGS: 12-OT10

description: Section 5 processed data.xlsx

tag: tissue

value: AGCAGCAGCGGCGGCAACAGCGG

tag: treatment

value: Zygote Injection (100ng/μL Cas9-MMLV mRNA + 50ng/μL pegRNA)


title: wildtype 293T PEACSeq T25F [WTT2.5F]

description: wildtype 293T PEACSeq T25F

source_name: wildtype 293T PEACSeq T25F


title: Amplicon NGS: 12-OT11

description: Section 5 processed data.xlsx


title: hSAEpC at D2 post-ALI, biological replicate 1


title: wildtype 293T PEACSeq T3 10F [WTT3.10F]

description: wildtype 293T PEACSeq T3 10F

source_name: wildtype 293T PEACSeq T3 10F


title: atx4/5_repeat1


title: atx4/5;jmj24_repeat2


title: Hi-C WT MEF 4OHT DMSO Rep2


title: Amplicon NGS: 12-OT9

description: Section 5 processed data.xlsx


title: wildtype 293T PEACSeq T210F [WTT2.10F]

description: wildtype 293T PEACSeq T210F

source_name: wildtype 293T PEACSeq T210F


title: Hi-C WT MEF ND CK666 Rep2

value: No Damage/CK-666


title: atx4/5;jmj24_repeat1


title: wildtype 293T PEACSeq T1 5F [WTT1.5F]

description: wildtype 293T PEACSeq T1 5F

source_name: wildtype 293T PEACSeq T1 5F


title: Amplicon NGS: 12-ON

description: Section 5 processed data.xlsx


title: atx2/3/4/5_repeat2


title: Amplicon NGS: 12-OT5

description: Section 5 processed data.xlsx


title: Hi-C WT MEF 4OHT CK666 Rep1


title: wildtype 293T PEACSeq T1 10F [WTT1.10F]

description: wildtype 293T PEACSeq T1 10F

source_name: wildtype 293T PEACSeq T1 10F


title: Amplicon NGS: 12-OT4

description: Section 5 processed data.xlsx


title: Hi-C WT MEF ND DMSO Rep2

value: No Damage/DMSO


title: atx2/3/4/5_repeat1


title: atx1/2_repeat2


title: wildtype 293T PEACSeq 15F [WT.15F]

description: wildtype 293T PEACSeq 15F

source_name: wildtype 293T PEACSeq 15F

value: Wildtype


title: atx1/2/4/5_repeat2


title: wildtype 293T PEACSeq 19R [WT.19R]

description: wildtype 293T PEACSeq 19R

source_name: wildtype 293T PEACSeq 19R


title: Amplicon NGS: 5-OT21

description: Section 5 processed data.xlsx

source_name: skin & muscle


title: Hi-C WT MEF ND DMSO Rep1

source_name: Mouse Embryonic Fibroblasts


title: HTGTS WT MEF 4OHT NU7441 Control Rep 1

data_processing:
Fastq files were used as input of HTGTS pipeline https://github.com/robinmeyers/transloc_pipeline with default parameters.
Assembly: mm10
Supplementary files format and content: tlx
Library strategy: HTGTS

growth_protocol: Mouse embryonic fibroblast (MEF) and U2OS cell lines were cultured in high-glucose Dulbecco’s modified Eagle’s medium supplemented with L-glutamine, 10% fetal bovine serum, and 1% penicillin-streptomycin

value: HTGTS


title: Amplicon NGS: 12-OT3

description: Section 5 processed data.xlsx


title: Hi-C WT MEF 4OHT DMSO Rep1


title: Amplicon NGS: 12-OT2

description: Section 5 processed data.xlsx


title: atx1/2/4/5_repeat1


title: wildtype 293T PEACSeq 18R [WT.18R]

description: wildtype 293T PEACSeq 18R

source_name: wildtype 293T PEACSeq 18R


title: WDR5A_RNAi_repeat2


title: atx1/2_repeat1


title: FANCF  PEACSeq 19R [T6.19R]

description: FANCF  PEACSeq 19R

source_name: FANCF  PEACSeq 19R

value: FANCF

value: GGAATCCCTTCTGCAGCACCAGG


title: FANCF PEACSeq 18R [T6.18R]

description: FANCF PEACSeq 18R

source_name: FANCF PEACSeq 18R


title: HTGTS WT MEF 4OHT NU7441 Rep 3


title: HTGTS WT MEF 4OHT NU7441 Rep 2


title: WDR5A_RNAi_repeat1


title: Amplicon NGS: 5-OT20

description: Section 5 processed data.xlsx


title: Hi-C WT MEF ND CK666 Rep1


title: jmj24_repeat2


title: FANCF PEACSeq 15F [T6.15F]

description: FANCF PEACSeq 15F

source_name: FANCF PEACSeq 15F


title: Amplicon NGS: 12-OT1

description: Section 5 processed data.xlsx


title: Amplicon NGS: 5-OT18

description: Section 5 processed data.xlsx


title: Amplicon NGS: 5-OT19

description: Section 5 processed data.xlsx


title: HTGTS WT MEF 4OHT NU7441 Rep 1


title: FANCF  PEACSeq 5F [T6.5F]

description: FANCF  PEACSeq 5F

source_name: FANCF  PEACSeq 5F


title: HTGTS WT MEF 4OHT NU7441 Control Rep 2


title: jmj24_repeat1


title: jmj24/26/28_repeat2


title: HTGTS WT MEF Cas9 CK666 Rep3


title: RNF2  PEACSeq 5F [T5.5F]

description: RNF2  PEACSeq 5F

source_name: RNF2  PEACSeq 5F

value: GTCATCTTAGTCATTACCTGTGG


title: FANCF PEACSeq 10F [T6.10F]

description: FANCF PEACSeq 10F

source_name: FANCF PEACSeq 10F


title: Amplicon NGS: 5-OT16

description: Section 5 processed data.xlsx


title: jmj24/26/28_repeat1

source_name: Arabidopsis seedlings


title: Amplicon NGS: 5-OT17

description: Section 5 processed data.xlsx


title: HTGTS WT MEF Cas9 DMSO Rep3


title: RNF2 PEACSeq 15F [T5.15F]

description: RNF2 PEACSeq 15F

source_name: RNF2 PEACSeq 15F


title: RNF2  PEACSeq 19R [T5.19R]

description: RNF2  PEACSeq 19R

source_name: RNF2  PEACSeq 19R


title: RNF2 PEACSeq 18R [T5.18R]

description: RNF2 PEACSeq 18R

source_name: RNF2 PEACSeq 18R


title: HTGTS WT MEF Cas9 DMSO Rep2


title: Amplicon NGS: 5-OT14

description: Section 5 processed data.xlsx


title: RNF2 PEACSeq 10F [T5.10F]

description: RNF2 PEACSeq 10F

source_name: RNF2 PEACSeq 10F


title: HTGTS WT MEF Cas9 CK666 Rep1


title: Col-0_repeat3

value: wild type


title: EMX1  PEACSeq 5F [T4.5F]

description: EMX1  PEACSeq 5F

source_name: EMX1  PEACSeq 5F

value: GAGTCCGAGCAGAAGAAGAAGGG


title: HTGTS WT MEF Cas9 DMSO Rep1


title: Col-0_repeat2


title: Col-0_repeat1


title: HTGTS WT MEF Cas9 CK666 Rep2


title: Amplicon NGS: 5-OT11

description: Section 5 processed data.xlsx

value: skin & muscle


title: HTGTS WT MEF 4OHT Actin-R62D-NLS Control Rep2


title: Col-0_repeat4


title: EMX1  PEACSeq 19R [T4.19R]

description: EMX1  PEACSeq 19R

source_name: EMX1  PEACSeq 19R


title: jmj24/26/28_H3K4me3_repeat2

data_processing:
Basecalls performed using bcl2fastq version 2.16.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2 allowing one mismatch.
The SICER was used to identify ChIP-enriched peaks between wild type and mutant.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

extract_protocol:
Chromatin isolated from 11-day-old seedlings in LD were subjected to sonication and immunoprecipitation with the anti-H3K4me2 or anti-H3K4me3 antibody.
Libraries were built for ChIP-seq (Illumina HiSeq X Ten; 150-bp paired-end sequencing)

tag: chip antibody

value: Millipore, 07-473


title: HTGTS WT MEF 4OHT Actin-R62D-NLS Control Rep1

value: WT


title: EMX1 PEACSeq 18R [T4.18R]

description: EMX1 PEACSeq 18R

source_name: EMX1 PEACSeq 18R

tag: sgrna


title: HTGTS WT MEF 4OHT NU7441 Control Rep 3


title: jmj24/26/28_H3K4me3_repeat1


title: HTGTS WT MEF 4OHT Actin-R62D-NLS Rep2


title: Amplicon NGS: 5-OT10

description: Section 5 processed data.xlsx

source_name: skin & muscle


title: Amplicon NGS: 5-OT9

description: Section 5 processed data.xlsx


title: Amplicon NGS: 5-OT13

description: Section 5 processed data.xlsx


title: atx1/2/4/5_H3K4me3_repeat2


title: HTGTS WT MEF 4OHT Actin-R62D-NLS Rep1

source_name: Mouse Embryonic Fibroblasts


title: Amplicon NGS: 5-ON

description: Section 5 processed data.xlsx


title: EMX1 PEACSeq 10F [T4.10F]

description: EMX1 PEACSeq 10F

source_name: EMX1 PEACSeq 10F


title: Amplicon NGS: 5-OT15

description: Section 5 processed data.xlsx


title: Amplicon NGS: 5-OT12

description: Section 5 processed data.xlsx


title: atx1/2/4/5_H3K4me2_repeat2

value: Abcam, ab7766


title: VEGFA TS3  PEACSeq 5F [T3.5F]

description: VEGFA TS3  PEACSeq 5F

source_name: VEGFA TS3  PEACSeq 5F

value: VEGFA TS3

value: GGTGAGTGAGTGTGTGCGTGTGG


title: atx1/2/4/5_H3K4me3_repeat1

value: Arabidopsis seedlings

value: long day (16 h light, 8 h dark)


title: HTGTS WT MEF 4OHT Wiskostatin Control Rep2


title: EMX1 PEACSeq 15F [T4.15F]

description: EMX1 PEACSeq 15F

source_name: EMX1 PEACSeq 15F


title: Amplicon NGS: 5-OT5

description: Section 5 processed data.xlsx

value: AGCAGCAGCGGCGGCAACAGCGG

value: Zygote Injection (100ng/μL Cas9-MMLV mRNA + 50ng/μL pegRNA)


title: Amplicon NGS: 5-OT4

description: Section 5 processed data.xlsx


title: HTGTS WT MEF 4OHT Wiskostatin Control Rep1


title: VEGFA TS3  PEACSeq 19R [T3.19R]

description: VEGFA TS3  PEACSeq 19R

source_name: VEGFA TS3  PEACSeq 19R


title: Amplicon NGS: 5-OT3

description: Section 5 processed data.xlsx


title: atx1/2_H3K4me3_repeat2


title: atx1/2/4/5_H3K4me2_repeat1


title: Amplicon NGS: 5-OT2

description: Section 5 processed data.xlsx


title: VEGFA TS3 PEACSeq 18R [T3.18R]

description: VEGFA TS3 PEACSeq 18R

source_name: VEGFA TS3 PEACSeq 18R


title: HTGTS WT MEF 4OHT Wiskostatin Rep1


title: atx1/2_H3K4me3_repeat1


title: VEGFA TS3 PEACSeq 10F [T3.10F]

description: VEGFA TS3 PEACSeq 10F

source_name: VEGFA TS3 PEACSeq 10F


title: Control shared by Pcsk9 and Pnpla3 edition

description: Section 5 processed data.xlsx


title: Col-0_H3K4me3_repeat5


title: Amplicon NGS: 5-OT1

description: Section 5 processed data.xlsx


title: HTGTS WT MEF 4OHT CK666 Rep 5

data_processing:
Library strategy: HTGTS
Fastq files were used as input of HTGTS pipeline https://github.com/robinmeyers/transloc_pipeline with default parameters.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: tlx

extract_protocol:
Genomic DNA was extracted using phenol/chloroform extraction
Libraries were constucted using standardized HTGTS and Hi-C protocols

value: Mouse Embryonic Fibroblasts


title: HTGTS WT MEF 4OHT CK666 Rep 6

value: HTGTS


title: Control for Pcsk9 edition

description: Section 5 processed data.xlsx

value: Control for Pcsk9 edition


title: Col-0_H3K4me3_repeat4


title: VEGFA TS2  PEACSeq 5F [T2.5F]

description: VEGFA TS2  PEACSeq 5F

source_name: VEGFA TS2  PEACSeq 5F

value: VEGFA TS2

value: GACCCCCTCCACCCCGCCTCCGG


title: HTGTS WT MEF 4OHT CK666 Rep 4


title: Control for Pnpla3 edition

description: Section 5 processed data.xlsx

value: Control for Pnpla3 edition


title: Col-0_H3K4me3_repeat3

source_name: Arabidopsis seedlings

value: wild type


title: VEGFA TS2 PEACSeq 18R [T2.18R]

description: VEGFA TS2 PEACSeq 18R

source_name: VEGFA TS2 PEACSeq 18R


title: Col-0_H3K4me3_repeat2


title: VEGFA TS2 PEACSeq 15F [T2.15F]

description: VEGFA TS2 PEACSeq 15F

source_name: VEGFA TS2 PEACSeq 15F


title: Col-0_H3K4me3_repeat1


title: HTGTS WT MEF 4OHT CK666 Rep 2


title: HTGTS WT MEF 4OHT Wiskostatin Rep2


title: Pcsk9 PEAC-seq Rep1

description: Section 5 processed data.xlsx

value: skin & muscle


title: HTGTS WT MEF 4OHT CK666 Rep 1


title: VEGFA TS3 PEACSeq 15F [T3.15F]

description: VEGFA TS3 PEACSeq 15F

source_name: VEGFA TS3 PEACSeq 15F


title: VEGFA TS2 PEACSeq 10F [T2.10F]

description: VEGFA TS2 PEACSeq 10F

source_name: VEGFA TS2 PEACSeq 10F


title: HTGTS WT MEF 4OHT DMSO Rep 6


title: Pnpla3 PEAC-seq Rep2

description: Section 5 processed data.xlsx

source_name: whole embryo

value: whole embryo

value: GGGATTAGGCCAGAGAAGAGGGG


title: VEGFA TS1  PEACSeq 5F [T1.5F]

description: VEGFA TS1  PEACSeq 5F

source_name: VEGFA TS1  PEACSeq 5F

value: VEGFA TS1

value: GGGTGGGGGGAGTTTGCTCCTGG


title: Col-0_H3K4me2_repeat2

value: Abcam, ab7766


title: VEGFA TS1  PEACSeq 19R [T1.19R]

description: VEGFA TS1  PEACSeq 19R

source_name: VEGFA TS1  PEACSeq 19R


title: HTGTS WT MEF 4OHT DMSO Rep 5

value: WT


title: HTGTS WT MEF 4OHT DMSO Rep 4


title: HTGTS WT MEF 4OHT CK666 Rep 3


title: HTGTS WT MEF 4OHT DMSO Rep 3


title: atx1/2/4/5_repeat2

data_processing:
Basecalls performed using bcl2fastq version 2.16.
For analysis of whole-genome DNA methylation data, the mapping, duplication filtering, and methylation extracting were all performed using the standard procedure of Bismark (v0.22.3).
The clean reads were mapped to the Arabidopsis genome (TAIR10) using Bismark and allowing one mismatch.
After duplications were removed, DNA methylation at CG, CHG, and CHH sites was calculated separately.
For the identification of different types of DMRs, the genome was divided in 200-bp bins, and the CG, CHG, and CHH methylation levels in each bin were calculated and compared between the WT and the atx1/2/4/5 mutants. Bins that showed differences in DNA methylation levels (CG > 0.2, CHG > 0.1, CHH > 0.05) were recorded and filtered based on Fisher’s exact test and BH method adjusted p values (cutoff = 0.01).
Assembly: TAIR10
Supplementary files format and content: BigWig format files for each cytosine context (CG, CHG, CHH or CX) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level.

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with 16 h of light at 23ºC and 8 h of darkness at 21ºC.

extract_protocol:
Genomic DNA was extracted from 11-day-old Arabidopsis seedlings by CTAB and purified with phenol: chloroform (1:1).
DNA libraries were prepared for sequencing using standard Illumina protocols (paired-end 150).

treatment_protocol: The 11-day-old seedlings grown on MS plates were harvested and subjected to DNA extraction.

value: Arabidopsis seedlings


title: VEGFA TS1 PEACSeq 18R [T1.18R]

description: VEGFA TS1 PEACSeq 18R

source_name: VEGFA TS1 PEACSeq 18R


title: Col-0_H3K4me2_repeat1

value: long day (16 h light, 8 h dark)


title: atx1/2/4/5_repeat1


title: VEGFA TS2  PEACSeq 19R [T2.19R]

description: VEGFA TS2  PEACSeq 19R

source_name: VEGFA TS2  PEACSeq 19R


title: ELL_Niclosamide

city: Pullman

first: Kanako

last: Hayashi

state: WA

address: BLS345, 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

description: single-cell RNA-seq

data_processing:
Basecalling and demultiplexing done by Cell Ranger mkfastq v3.1.0
Custom reference made with NCBI's GRCm38 mouse genome and gene model annotation 108 using cellranger mkref v.3.1.0
Alignment to custom reference done with cellranger count v3.1.0 and argument --expect-cells=6000
The resulting filtered count matrix for each sample t was imported into R (v3.6.1), and analyzed with Seurat (v3.1.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: tar archive of cellranger's filtered_feature_bc_matrix output folder including barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files.

source_name: peritoneal cells

extract_protocol:
Peritoneal cells were recovered by lavage (4mLx2 of ice-cold PBS). Red blood cells were lysed and single cell suspensions were used for the analysis
The libraries were constructed with the Chromium Single-Cell Gene Expression kit V3

treatment_protocol: Three weeks after the induction of ELL or Sham, niclosamide was orally dosed at 0 or 200 mg/kg/day for a total of 3 weeks

tag: Sex

value: female

value: 4 months

tag: samples

value: peritoneal lavage (cells)

tag: sample group

value: ELL with 200 mg/kg/day of niclosamide


title: ELL

description: single-cell RNA-seq

tag: age

value: ELL


title: Pcsk9 PEAC-seq Rep2

description: Section 5 processed data.xlsx

source_name: skin & muscle

value: AGCAGCAGCGGCGGCAACAGCGG

value: Zygote Injection (100ng/μL Cas9-MMLV mRNA + 50ng/μL pegRNA)


title: Col-0_repeat2

value: wild type


title: Sham_Niclosamide

description: single-cell RNA-seq

value: sham with 200 mg/kg/day of niclosamide


title: VEGFA TS1 PEACSeq 15F [T1.15F]

description: VEGFA TS1 PEACSeq 15F

source_name: VEGFA TS1 PEACSeq 15F


title: HTGTS WT MEF 4OHT DMSO Rep 2

source_name: Mouse Embryonic Fibroblasts

tag: cell type

value: Mouse Embryonic Fibroblasts

tag: assay

value: HTGTS


title: Col-0_repeat1


title: HTGTS WT MEF 4OHT DMSO Rep 1


title: Sham

description: single-cell RNA-seq

value: sham


title: Pnpla3 PEAC-seq Rep1

description: Section 5 processed data.xlsx

value: skin & muscle

tag: development stage

value: GGGATTAGGCCAGAGAAGAGGGG


title: 3D-Plasma-V1-3D_98

status: Public on Nov 13 2022

city: Chicoutimi

first: Luigi

last: Bouchard

state: Quebec

address: 305 rue Saint-Vallier, Pavillon des Augustines

department: Biochimie et génomique fonctionnelle

country: Canada

institute: Université de Sherbrooke

description:
98
3D-Plasma-V1-3D_98
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with FASTX-Toolkit. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using STAR. As rRNA contamination was almost inexistant in our samples (average of 1.04±0.90% of total mapped reads based on metrics from STAR), the mapping step to the rRNA was removed to speed tup the process.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple sample (PMID : 30956140).
Samples with < 1M miRNAs reads were considered outliers and removed from the downstream analysis (differential analysis using DESeq2 package).
DESeq2 function collapseReplicates was used to combined technical replicates in the analysis for data that were extracted and sequenced twice. Technical replicate have the same ID and fastq files contains either "pilote" or "projet". Technical replicate are identified in the technical replicates column (N = 12 originally, 9 gave consent for genetic data sharing)
Assembly: GRCh37
Supplementary files format and content: tab-seperated value files include raw read counts (non-normalized) for each Sample

source_name: Plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from either 500μl of plasma kept at −80 °C until extraction. Seventy-five μl of nuclease-free water was used to eluate total RNA which was then precipitated following the method described by Burgos et al. (PMID: 23525801). Briefly, 35 μl of cold (4°C) 7 M ammonium acetate solution (ThermoFisher Scientific, catalogue # 02002268) were added to 70μl of total RNA. This was followed by the addition of 420μl of chilled (−20°C) absolute ethanol (Commercial Alcohols, ON, Canada; catalogue # P006EAAN) and overnight precipitation at −20°C. The mix was then centrifuged at 16 000g at 4°C for 30 min. RNA pellets were then washed twice with 200 μl of cold 80% ethanol followed by centrifugation at 16 000g at 4°C for 5min. It was then dried for 30min at room temperature and 5μl of nuclease-free water was added. The total volume was used for library preparation.
Samples were randomized before library preparation. An adapted version of the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) protocol from Burgos et al. (PMID: 23525801) was used to manage low concentrated miRNA samples. In this protocol, half of the standard volumes were used for ligation (3′ and 5′ ends) of RNA sample (5μl), reverse transcription, barcoding (index 1-20: one index per sample) and PCR amplification (15 cycles) to preserve the ratio between RNA amount (which is lower in plasma samples) and the reagents. Purification and size-selection (145-160bp) of the libraries were done by migration on a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, catalogue # EC6265BOX) followed by elution in 300 μl of nuclease-free water and overnight incubation at 500 RPM at room temperature on an incubating microplate shaker (VWR, ON, Canada, catalogue #12620-930). The libraries were then precipitated according to the manufacturer's instructions (including incubation of the precipitation mix at −80°C for 30min) and were resuspended in 25 μl of 10 mM Tris-HCI pH 8.5 buffer. Library sequencing, including quality control and sample pooling, was performed at the McGill University and Génome Québec Innovation Centre (Québec, Canada). Libraries were first quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) and the average size fragment was determined using a LabChip GX II (PerkinElmer) instrument. The libraries were normalized and pooled before being denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 225pM on an Illumina NovaSeq S1 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 1x100 cycles (single-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads. Ten samples were extracted and sequenced twice to account for batch preparation and to confirm standardization.

value: Plasma

tag: pregnancy status_1

value: Normal


title: 3D-Plasma-V1-3D_96

description:
96
3D-Plasma-V1-3D_96
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Gestational diabetes mellitus


title: 3D-Plasma-V1-3D_95

description:
95
3D-Plasma-V1-3D_95
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: female


title: control sample 1 miRNA-seq

city: WuXi

first: Tao

last: Zheng

address: No.69, Xuejiali, Nanquan Town, Binhu District, Wuxi City, Jiangsu Province, China

institute: Wuxi Fisheries College, Nanjing Agricultural University

data_processing:
Subsequently, unique sequences with length in 18~25 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 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles

organism: Tachysurus fulvidraco x Tachysurus vachelli

source_name: Intestine

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Intestine

value: untreated


title: 3D-Plasma-V1-3D_94

description:
94
3D-Plasma-V1-3D_94
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: control sample 3 miRNA-seq


title: control sample 2 miRNA-seq


title: Transport 16h- samples 1 miRNA-seq

value: transport 16h


title: Transport 16h- samples 2 miRNA-seq


title: 3D-Plasma-V1-3D_99

description:
99
3D-Plasma-V1-3D_99
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_92

description:
92
3D-Plasma-V1-3D_92
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_97

description:
97
3D-Plasma-V1-3D_97
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_91

description:
91
3D-Plasma-V1-3D_91
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_9

description:
9
3D-Plasma-V1-3D_9
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: Transport 16h- samples 3 miRNA-seq


title: 3D-Plasma-V1-3D_93

description:
93
3D-Plasma-V1-3D_93
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_88

description:
88
3D-Plasma-V1-3D_88
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_89

description:
89
3D-Plasma-V1-3D_89
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_8

description:
8
3D-Plasma-V1-3D_8
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.


title: 3D-Plasma-V1-3D_84

description:
84
3D-Plasma-V1-3D_84
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.

value: Other pregnancy complications


title: 3D-Plasma-V1-3D_85

description:
85
3D-Plasma-V1-3D_85
3D_Plasma_miRNA_v1_geo_rawcounts_part2.txt
The Pregnancy Status 1 column contains the pregnancy status of the women. If a second pregnancy status was also present, it is recorded in the Pregnancy Status 2 column.