title: GNI3_P188

city: Huddinge

first: Luca

last: Mazzurana

address: Alfred Nobels Aleè 8

institute: Karolinska Institutet

data_processing:
The reads were aligned to the human genome (hg19 –GRCh38) and spike-in sequences (from the External RNA Controls Consortium) using STAR v2.5.3a (Dobin et al., 2013), and filtered for uniquely mapping reads. Counts per gene were calculated for each transcript in Ensembl release 92 using rpkmforgenes (Ramsköld et al., 2009). The following rpkmforgenes options were used: -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendsceil
Genome_build: hg19 –GRCh38
Supplementary_files_format_and_content: Tab delimited files include metadata, barcodes and features of each plate. We also included a matrix containing estimated counts.

extract_protocol:
Sorted cells were processed using the Smart-seq2 protocol with minor changes (Picelli et al., 2013). Sequencing was done to the average depth of 0.7 million reads per cell with 43bp reads (single end) after demultiplexing. Blood samples were additionally sequenced for V(D)J analysis to and average depth of 0.84 million reads per cell with 150 bp reads (paired end) after demultiplexing.
Smart-Seq2

value: COLON

tag: Sex

value: F


title: HIEC DMSO #1

status: Public on Dec 14 2020

type: SRA

city: Ottawa

first: Yannick

middle: D.

last: Benoit

state: Ontario

address: 451 Smyth road

country: Canada

institute: University of Ottawa

description: processed data file: HT29_vs_HIEC.DMSO_all_salmon.txt

library_source: transcriptomic

data_processing:
Quantified transcripts from GENCODE v27 with salmon v0.9.1 using --gcBias flag.
Performed fold change analysis using DESeq2 as follows
Read transcript quantification data with tximport library and summarized to gene level quantification.
Filtered to retain genes with at least 5 reads assigned in at least two samples.
Constructed DESeqDataSet object with fourteen samples (two replicates of seven conditions), using the model ~condition (cell type/treatment).
Calculated fold changes using the lfcShrink() function with the apeglm method.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_quant.sf.txt: Salmon transcript quantification: Quantification of GENCODE v27 transcripts using salmon v0.9.1.
Supplementary_files_format_and_content: *_all.txt: DESeq2 fold change results: Results from the DESeq2 lfcShrink() function comparing two conditions, including results for all genes retained after filtering.

molecule: total RNA

organism: Homo sapiens

source_name: Intestinal epithelial crypt cells

extract_protocol:
RNA was extracted using the total RNA purification kit by Norgen Biotech Corp, following the manufacturer's guidelines. Quantification of total RNA samples was performed with a Qubit HS RNA assay (ThermoFisher Scientific) and fragment size was evaluated with a Fragment Analyzer HS NGS assay (AATI). A RNA Quality Number (RQN) of 8.0 or higher was considered satisfactory for library construction. Library construction was performed with a TruSeq RNA v2 (Illumina) with unique barcodes compatible with the Illumina NextSeq 500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: Intestinal epithelial crypt cells

tag: origin

value: 16-week fetal ileum

tag: treatment

value: 48 hours DMSO


title: AML3_noDNT_rep1

city: Toronto

first: Musaddeque

last: Ahmed

state: ON

address: 101 College St

institute: University health Network

description:
guide RNA
AML3_postDNT_vs_noDNT.gene_summary.txt

library_source: genomic

data_processing:
The fastq files were first converted to fasta file using custom shell script. For each sample, a custom bowtie database was generated by the command bowtie-build in bowtie suite (version 1.1.2). The library sgRNAs were mapped against the database for each sample using bowtie with the parameter v=0 and default values for other parameters.
The differential sgRNA abundance was estimated using the tool MAGeCK (Li et al., 2014).
Genome_build: Hg19
Supplementary_files_format_and_content: MAGeCK output for all cell lines. Please refer to MAGeCK documentation for output details.

molecule: genomic DNA

growth_protocol: AML2 and AML3 were cultured in alpha-MEM, KG1a and U937 in RPMI-1640, MV4-11 in IMDM, and TEX, all supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Genomic DNA was extracted from replicate samples (QIAamp Blood Midi kit) and sgRNA inserts were amplified by PCR
The sgRNAs were designed using the CRISPR-DO tool that accounted for sgRNA specificity and cutting efficiency. sgRNAs were synthesized as 73-mer oligonucleotides (CustomArray, USA), GAAAGGACGAAACACCGNNNNNNNNNNNNNNNNNNNNGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGC (N’s denote sgRNA 20 nucleotide target sequence; sense orientation) with a total of 12,472 sequences and amplified by PCR as a pool using the following primers: TAACTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTT GTGGAAAGGACGAAACACCG (Forward) and ACTTTTTCAAGTTGATAACG GACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAAC (Reverse). The PCR product was purified and cloned in the lentiGuide-Puro vector using BsmBI (NEB). Ligation was performed using the NEBuilder® HiFi DNA Assembly Cloning Kit and transformed into an electrocompetent strain (Stbl4; ThermoFisher, USA) to achieve ~300x coverage. Colonies were scraped off Agar plates using LB medium. Plasmid DNA was extracted using NA0310 Sigma GenElute™ HP Plasmid Maxiprep Kit and adequate library representation of each sgRNA was confirmed by NGS.
single end unstranded

treatment_protocol: we co-incubated the transduced AML3 cells with DNTs at a 1:1 E:T ratio for 2h to induce apoptosis in ~40-50% of the targets, depleted DNTs by magnetic separation (EasySep Human CD3 Positive Selection Kit), and performed FACS to separate Annexin V+ (live) and Annexin V- (dead or dying) target cells.

tag: source tissue

value: Blood

tag: expression

value: Cas9 expressing

tag: source type

value: Cell line


title: Liver, Control, Day 11 [VC46L]

type: RNA

city: Frederiksberg

first: Asma

middle: M

last: Karami

state: Denmark

address: Stigbojlen 7

country: Denmark

institute: University of Copenhagen

description: Replica 5

data_processing: All q-PCR assays exhibited efficiencies within 100% ± 5% so the simplified 2-ΔΔCq method was used for analysing data (Livak and Schmittgen, 2001). For normalization and as internal calibrator the average of three genes (ARP, ELF1α and β-actin) was chosen by using NormFinder (Andersen et al., 2004). For gene expression analyses, all challenged groups were compared to non-exposed time point controls using Student’s t-test. We considered differences to be significant when regulations were at least two-fold and p < 0.05. For four of the genes investigated in the non-exposed timepoint control groups less than three fish showed Cq values (excluding a t-test) and therefore we applied a qualitative assessment (presence/absence of Cq values) and analyzed data with the nonparametric Mann-Whitney test using a probability level of 5%.

label: FAM

organism: Oncorhynchus mykiss

source_name: Time point Control

label_protocol: cDNA synthesis was performed in T100 thermocycler, Biorad, Denmark, using Oligo d(T)16 primer and TaqMan® Reverse Transcription Reagents (cat.no. N8080234, Thermo Fischer Scientific, Denmark). Finally, cDNA was stored at −20°C until further use. Quantitative PCR assays were performed using an AriaMx Real-Time PCR machine (cat.no.G8830A-04R-010, AH diagnostics AS, Denmark). The cycling conditions were one cycle of predenaturation at 95°C for 3 min. This was followed by 40 cycles of denaturation at 94°C for 5 sec with a combined annealing/elongation process at 60°C for 15 sec with endpoint measurement. Primers and Taq-Man probes targeting immune-relevant rainbow trout genes were synthesized at TAG Copenhagen AS, Denmark. Reaction volumes were 12.5 μl (2.5 μl cDNA, 6.25 μl Brilliant III Ultra-Fast QPCR Master Mix (600881, AH Diagnostics AS, Denmark), 1.0 μl primer-probe mixture (forward primer, 10 μM and reverse primer, 10 μM), Taq-Man probe (5 μM), and 2.75 μl RNase-free water. Reverse transcriptase minus and negative controls were used for every plate setup. . NormFinder (Andersen et al., 2004) was applied to evaluate all combinations of three reference genes (Elongation factor (ELF) 1-α, β-actin and acidic ribosomal phosphoprotein P0 (ARP)) as endogenous control; the average of the three genes was chosen and stability values were 0.002, 0.005 and 0.002 for liver, spleen and gills, respectively.

growth_protocol: Fish were maintain in plastic tanks with low density. Water was recycled (20 L/min) by internal biofilters (EHEIM, Germany) applying 30% water replenishment daily. Water quality was monitored and kept constant at pH 7.6, nitrite < 0.01 mg/l, nitrate < 50 mg/l (TetraTest 6in1, cat.no. T704154, Eldorado A/S, Denmark) and ammonia < 0.5 mg/l (API Ammonia Test Strips, VioVet Ltd, UK). During the 14 days acclimation and 14 days experimental infection period, fish received commercial pelleted feed (1.5% biomass per day, INICIO 917, BioMar A/S, Denmark). After the pathogen exposure fish with clinical signs were euthanized with overdose (300 mg/L) of ethyl-3-aminobenzoate methanesulfonate (MS222) (cat.no. A5040, Sigma-Aldrich, Denmark)

extract_protocol: RNAlater fixed samples from fish (gills, liver and spleen) were homogenized (Tissue-lyser II, Qiagen, Denmark) using a homogenization buffer with 2-mercaptoethanol (Sigma-Aldrich). RNA was extracted using the GenEluteTM mammalian RNA kit (RTN350, Sigma-Aldrich, Denmark). Liver samples were pre-treated by Proteinase K (cat.no.P4850, Sigma-Aldrich, Denmark). DNase I (AMPD1, Sigma-Aldrich, Denmark) treatment was applied to remove genomic DNA. The concentration of RNA was determined in a NanoDrop 2000 spectrophotometer (Saveen & Werner, Denmark). Quality of RNA was evaluated by agarose (cat.no. 16500100, ThermoFisher Scientific, Denmark) gel electrophoresis. RNA was kept at −80°C until cDNA synthesis.

treatment_protocol: Tissue (liver, spleen, gills) samples were fixed in RNAlater (cat.no R0901, Sigma-Aldrich, Denmark), placed at 4°C for 24 h and subsequently stored at -20°C until further processing.

tag: organ

value: Liver

tag: pathogen

value: Uninfected

tag: time

value: Day 11


title: Liver, Control, Day 11 [VC45L]

description: Replica 5


title: GNI3_P187

country: Sweden

tag: tissue


title: GNI1_P004

value: M


title: Liver, Control, Day 11 [VC44L]

description: Replica 5


title: Liver,  Clinical Sign, Day 3 [V20L]

description: Replica 4

source_name: Clinical Sign

value: Vibrio anguillarum

value: Day 3


title: Liver,  Clinical Sign, Day 3 [V19L]

description: Replica 4


title: GNI2_P005


title: GNI2_P003


title: Liver,  Clinical Sign, Day 3 [V18L]

description: Replica 4


title: Liver,  Clinical Sign, Day 3 [V16L]

description: Replica 4


title: L4_P401

value: LUNG


title: GNI2_P002


title: Liver,  Clinical Sign, Day 3 [V15L]

description: Replica 4


title: shID1_3_S18

city: Pamplona

first: Silvestre

last: Vicent

state: Outside the US or Canada

address: 55 PIO XII Ave

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

data_processing:
The quality of the samples was verified using FastQC software.
FASTQ files were mapped to hg19 human assembly using STAR 2.5.2b using default parameters.
Gene expression quantification was carried out with featureCounts v1.5.0 using read counts of exonic gene regions.
The gene annotation reference was Gencode v19.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count values summarized by "featureCounts v1.5.0" for each gene

molecule: polyA RNA

source_name: H1792 cell line

extract_protocol: RNAseq (Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, Gennert D, Li S, Livak KJ, Rozenblatt-Rosen O, Dor Y, Regev A, Yanai I. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 2016; 17: 77.)

tag: cell line

value: lung adenocarcinoma

value: Infection with an inducible Id1 shRNA


title: Liver,  Clinical Sign, Day 3 [V14L]

description: Replica 4


title: Liver, Control, Day 11 [VC59L]

description: Replica 5


title: L2_P272


title: L3_P404


title: L1_P049


title: Liver,  Clinical Sign, Day 3 [V13L]

description: Replica 4


title: shID1_2_S17


title: Liver,  Clinical Sign, Day 3 [V8L]

description: Replica 4


title: shGFP_1_S13

value: Infection with an inducible GFP shRNA


title: Liver,  Clinical Sign, Day 3 [V11L]

description: Replica 4


title: WB1_P275

value: BLOOD


title: control rep3

city: Jinan

first: Xin

last: Zhang

state: Shandong

address: 107 Wenhua Xi Road

country: China

institute: Qilu Hospital, Shandong University

description: Small RNA

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

source_name: Cholangiocarcinoma cells

growth_protocol: QBC-939 was maintained in DMEM medium supplemented with 10% fetal bovine serum in 5% CO2 resuscitation.

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 libraries according 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.

treatment_protocol: QBC-939 was treated with Bmi1 shRNA or scrambled shRNA for 48h.

value: Cholangiocarcinoma

tag: knockdown

value: control


title: WB3_P405


title: WB2_P402

value: F


title: shGFP_3_S15


title: Liver,  Clinical Sign, Day 3 [V9L]

description: Replica 4


title: shID1_1_S16


title: Liver,  Clinical Sign, Day 3 [V7L]

description: Replica 4


title: CRNKL1 targeting gRNA, experiment 4

city: Erlangen

first: Han

last: Xiao

address: Schlossgarten 4

country: Germany

institute: Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg

data_processing:
Raw data were converted to reads including a quality score by Software bcl2fastq v2.17. Sequences matching Illumina TrueSeq adapters were masked. Low quality bases, poly-A or poly-T stretches as well as masked bases were trimmed in fqtrim v0.9.5.
For splicing and differential expression analysis of human genes, reads were aligned to the transcriptome using RSEM v1.2.20 (Li and Dewey, 2011) and Bowtie v1.1.2 (Li and Dewey, 2011) as read alignment program using default parameters.
Differential expression analysis was performed by DESeq2 v1.18.1 (Li and Dewey, 2011) using the RSEM output for read counts per gene. We considered genes that showed an absolute log2-transformed fold change greater than 1 and a adjusted p value (padj) of less than 0.1 as differentially expressed. To exclude lowly expressed genes, we only considered those with mean TPM greater than 1 in either untreated or knockdown samples. Gencode v19 annotation was used in all steps of the analysis, including in the definition of protein coding genes.
For the viral genome, reads were aligned to HIV-Dual-GT using hisat2 (Kim et al. 2019). Read counting for the different features was performed using samtools (Li et al. 2011) and regtools (Feng et al. 2018).
Differential splicing analysis was performed with SUPPA (Alamancos et al., 2015) using TPM values from the RSEM transcript isoform output. For PSI calculation, events were required to pass the expression filter of TPM greater than 1 (-f 1 parameter). We considered splicing events with adjusted p values (padj) lower than 0.01 and absolute deltaPSI greater than 0.25 as differentially included or excluded.
Genome_build: hg19
Genome_build: HIV-Dual-GT
Supplementary_files_format_and_content: RSEM_count_TPM_matrix_DESeq2.txt: Tab-delimited text file with counts and TPM per gene per sample obtained from RSEM together with the results of differential expression analysis (DESeq2, Li and Dewey, 2011)
Supplementary_files_format_and_content: SUPPA_differential_splicing_results.txt: Tab-delimited text file with the output obtained from SUPPA (Alamancos et al., 2015)

growth_protocol: The J-dual#3 reporter cell line generated by transducing Jurkat E61 (ATCC) cells with the HIV-dual-GT reporter construct was maintained  in RPMI 1640 medium supplemented with 10% FCS, 1% penicillin/streptomycin.

extract_protocol:
Cytoplasmic fractions were isolated from the control and sorted cells using NP-40 lysis buffer consisting of 10 mM Hepes (pH 7.8 adjusted by KOH); 10 mM KCl; 1 Mm DTT; 20% Glycerol; 0.25% NP40. Total RNA was extracted from supernatants with the Direct-zol RNA miniprep plus kit (Zymo Research).
Libraries were prepared from 500 ng RNA using the Illumina TruSeq stranded mRNA kit according to the manufacturers instructions and sequenced on an Illumina HiSeq 2500 platform as single end 101 bp reads

treatment_protocol: J-dual#3 cells were further transduced by lentivectors expressing SpCas9 and a CRNKL1-specific sgRNA (sequence: GCAGTTATCTGTACCTCAGC,  MOI of 3), or SpCas9 and a non-targetting (NT1) sgRNA (sequence: ATCGTTTCCGCTTAACGGCG, MOI of 3), or HIV-1 Rev protein (MOI of 1), respectively. Four days post superinfection, J-dual#3 cells expressing both DsRed and BFP were sorted from the cells knocked-down with CRNKL1 or overexpressing Rev. The SpCas9/NT-1 transduced cells were unsorted. Paired NT1 control and CRNKL1 knock-down experiments were repeated 4 times. The experiment with Rev overexpression was performed only once.

value: Jurkat, Clone E61 (ATCC) expressing the HIV-dual-GT reporter construct, clone 3

tag: crispr grna

value: CRNKL1 targeting

tag: lentiviral overexpression


title: TCs - 6sites_KO_KI (P234 Amplicon-Seq)

city: Loma Linda

first: Yawen

last: Fu

state: CA

address: 11234 Anderson St.

department: Department of Medicine

country: USA

institute: Loma Linda University

description:
PCR products of human gDNA
TCs CD326_GATA4_MYH6_HBG1_KO_KI total indel with HDR efficiencies and pattern details

data_processing:
The 150-bp paired-end high-throughput sequencing reads were merged into a single read with FLASH.
Demultiplex using the Barcode Splitter tool.
Using the web-based tool Cas-Analyzer to determine the editing efficiency and events by uploading the .fastq file for each amplicon.
Load the generated result text files to Microsoft Excel.
Use an in-house VB script to exclude sequencing errors and misalignment.

source_name: T cells

growth_protocol: iPSCs were cultured in a humidified atmosphere with 5% CO2 at 37 °C, and the medium was changed daily with fresh mTeSRTM E8 medium. K562 (ATCC) and U937 (ATCC) cells were cultured in RPMI-1640 medium (VWR) with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Invitrogen). Cells were maintained in a 37°C, 5% CO2, fully humidified incubator, and passaged twice weekly. T cells were grown at 37°C in a humidified incubator with 5% CO2. The medium was changed every two days, and the cell density was kept below 1 × 10e6 cells per ml.

extract_protocol:
Approximately 2 × 10e5 cells were harvested for genomic DNA extraction using 10 μl digestion buffer, which consisted of 100 mM NaCl, 10 mM Tris pH 8, 5 mM EDTA, 0.5% Tween 20 (Sigma), and 1% proteinase K (ABM; 10 mg/ml). Cells released gDNA after running the following program: 56°C for 60 min and 95°C for 10 min.
PCR amplicon libraries were prepared for sequencing using standard Illumina protocols
PCR Amplicon-Seq

treatment_protocol: The electroporations were performed using a Lonza 2b nucleofector according to the manufacturer’s instructions with modifications. 70 μl buffer per reaction was used. For K562 cells, the AmaxaTM Cell Line NucleofectorTM Kit V (Lonza) and program T-016 were used. For U937 cells, the AmaxaTM Cell Line NucleofectorTM Kit V (Lonza) and program W-001 were used. One to two million cells were used for each electroporation. For iPSCs, single-cell suspension of iPSCs was electroporated using Human Stem Cell NucleofectorTM Kit 2 with program B-016. We also added 0.5 μg BCL-XL plasmid to improve iPSC survival (13). After electroporation, the cuvette was incubated at 37 °C for ~5 minutes. During the first day after transfection, 10 μM ROCK inhibitor Y27632 was added to iPSC culture. For T cells, 3 d after initiating T-cell activation, the CD3/CD28 beads were magnetically removed, and 1 × 10e6 T cells were electroporated using the Lonza Nucleofector 2b (program B-016) and the Human T Cell Nucleofector Kit (VPA-1002, Lonza). Following electroporation, cells were cultured in fresh medium and incubated at 37 °C and 5% CO2.

value: PB-derived primary T cells

tag: editing

value: RNP-AAV


title: TCs - 6sites_KO_KI (P236 Amplicon-Seq)


title: sgENY2_rep1

description: total RNA

data_processing:
The raw sequencing data were mapped to human genome assembly GRCh38 using STAR with quantMode method against refGene gene annotation
The differential expression analyses were performed using DESeq2 package in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw count matrix of refGene genes in all samples

growth_protocol: 24hrs post-transduction, cells were selected with completed medium containing puromycin for 72hrs.

extract_protocol:
Total RNA was extracted from AML3 cells using the RNeasy Plus Mini Kit (Qiagen Cat. 74314) following manufacture’s guidelines
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (634418, Takara)

treatment_protocol: AML cells were transduced with sgRNAs targeting the genes or control

value: Blood

tag: sgrna


title: TCs - 6sites_KO_KI (P235 Amplicon-Seq)


title: Liver,  Clinical Sign, Day 3 [V5L]

description: Replica 4

value: Liver


title: REV overexpression

source_name: J-dual#3_REV overexpression

value: REV


title: CRNKL1 targeting gRNA, experiment 1


title: CRNKL1 targeting gRNA, experiment 3


title: K562 - 6sites_KO_KI_48h (P212 Amplicon-Seq)

description:
PCR products of human gDNA
K562 CD326_GATA4_MYH6_BCL11A_KO_KI_48h total indel with HDR efficiencies and pattern details

value: Erythroleukemia cell line


title: Non-targeting control gRNA, experiment 4

value: Non-targeting


title: K562 - 6sites_KO_KI_24h (P211 Amplicon-Seq)

description:
PCR products of human gDNA
K562 CD326_GATA4_MYH6_BCL11A_KO_KI_24h total indel with HDR efficiencies and pattern details


title: Liver,  Clinical Sign, Day 3 [V4L]

description: Replica 4

value: Vibrio anguillarum

value: Day 3


title: shGFP_2_S14

value: lung adenocarcinoma


title: Liver,  Clinical Sign, Day 3 [V2L]

description: Replica 4


title: Liver,  Clinical Sign, Day 3 [V3L]

description: Replica 4


title: Non-targeting control gRNA, experiment 3


title: Non-targeting control gRNA, experiment 1


title: Non-targeting control gRNA, experiment 2


title: TCs - BCL11A_KI_Drugs (P231 Amplicon-Seq)

description:
PCR products of human gDNA
TCs BCL11A_KI total indel with HDR efficiencies and pattern details with treatments of different drugs


title: Liver, No Clinical Sign, Day 3 [VT144L]

description: Replica 3

source_name: No Clinical Sign


title: K562 - 6sites_KO_KI_8h (P209 Amplicon-Seq)

description:
PCR products of human gDNA
K562 CD326_GATA4_MYH6_BCL11A_KO_KI_8h total indel with HDR efficiencies and pattern details


title: CRNKL1 targeting gRNA, experiment 2


title: Liver, No Clinical Sign, Day 3 [VT139L]

description: Replica 3


title: Liver, No Clinical Sign, Day 3 [VT148L]

description: Replica 3


title: Liver, No Clinical Sign, Day 3 [VT1410L]

description: Replica 3


title: Liver, No Clinical Sign, Day 3 [VT146L]

description: Replica 3


title: Liver, No Clinical Sign, Day 3 [VT143L]

description: Replica 3


title: Liver, No Clinical Sign, Day 3 [VT1310L]

description: Replica 3


title: TCs - BCL11A_KI_Drugs (P230 Amplicon-Seq)


title: TBX5Het_day23_exon3_rep2

city: San Francisco

first: Benoit

last: Bruneau

address: 1650 Owens St

institute: Gladstone Institutes

data_processing:
Libraries were sequenced on Illumina Hiseq 2500 or Nextseq
Raw sequencing reads were converted to FASTQ files using Cellranger 2.0.2 mkfastq
Reads were aligned to hg19 v1.2.0 using the Cellranger 2.0.2 count
Cellranger 2.0.2 aggr was used to aggregate libraries from WTC11, TBX5Het and TBX5Hom.
Aggregated gene expression matrix was processed in Seurat 2.3.4. Briefly, cells with UMI counts between 10,000 and 80,000 were retained. Gene expression was normalized, scaled and mitochondrial reads and cell cycle genes were regressed. Cells were clustered based on the top 25-30 prinicipal components.
Cardiomyocyte clusters were extracted into a new Seurat object and analyzed as described previously.
Genome_build: hg19
Supplementary_files_format_and_content: Processed Seurat expression matrix as a csv file, with columns as cell barcodes and rows as genes

growth_protocol: iPSCs were maintained in mTeSR media on matrigel

extract_protocol:
Cells on day 23 were singularized using Trypsin 0.25% and 10,000 cells were loaded on a 10X Chromium chip
Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v2 was used to construct libraries

treatment_protocol: iPSC lines were differentiated to cardiomyocytes using the Stemdiff Cardiomyocyte Differentiation Kit

value: iPSC derived cardiomyocytes

tag: genotype/variation

tag: timepoint

value: Day 23


title: TCs - BCL11A_KO_KI (P207 Amplicon-Seq)

description:
PCR products of human gDNA
TCs BCL11A_KO_KI total indel with HDR efficiencies and pattern details

tag: cell type


title: WTC11_day23_exon3_rep2

value: wildtype/parental


title: TCs - BCL11A_KO_KI (P206 Amplicon-Seq)


title: TCs - BCL11A_KO_KI (P205 Amplicon-Seq)


title: Liver, No Clinical Sign, Day 3 [VT138L]

description: Replica 3


title: TBX5Hom_day23_exon7

data_processing:
Libraries were sequenced on Illumina Hiseq 2500 or Nextseq
Raw sequencing reads were converted to FASTQ files using Cellranger 2.0.2 mkfastq
Reads were aligned to hg19 v1.2.0 using the Cellranger 2.0.2 count
Cellranger 2.0.2 aggr was used to aggregate libraries from PGP1, TBX5Het_exon7 and TBX5Hom_exon7
Aggregated gene expression matrix was processed in Seurat 2.3.4. Briefly, cells with UMI counts between 10,000 and 80,000 were retained. Gene expression was normalized, scaled and mitochondrial reads and cell cycle genes were regressed. Cells were clustered based on the top 25-30 prinicipal components.
Genome_build: hg19
Supplementary_files_format_and_content: Processed Seurat expression matrix as a csv file, with columns as cell barcodes and rows as genes

source_name: iPSC derived cardiomyocytes


title: K562 - 6sites_KO_KI_12h (P210 Amplicon-Seq)

description:
PCR products of human gDNA
K562 CD326_GATA4_MYH6_BCL11A_KO_KI_12h total indel with HDR efficiencies and pattern details


title: K562 - 6sites_KO_KI_4h (P208 Amplicon-Seq)

description:
PCR products of human gDNA
K562 CD326_GATA4_MYH6_BCL11A_KO_KI_4h total indel with HDR efficiencies and pattern details


title: TBX5Het_day23_exon7


title: sgATXN7L3_rep2

description: total RNA


title: TBX5Hom_day23_exon3_dup2

data_processing:
Libraries were sequenced on Illumina Hiseq 2500 or Nextseq
Raw sequencing reads were converted to FASTQ files using Cellranger 2.0.2 mkfastq
Reads were aligned to hg19 v1.2.0 using the Cellranger 2.0.2 count
Cellranger 2.0.2 aggr was used to aggregate libraries from WTC11, Control, TBX5Het and TBX5Hom.
Aggregated gene expression matrix was processed in Seurat 2.3.4. Briefly, cells with UMI counts between 10,000 and 80,000 were retained. Gene expression was normalized, scaled and mitochondrial reads and cell cycle genes were regressed. Cells were clustered based on the top 25-30 prinicipal components.
Cardiomyocyte clusters were extracted into a new Seurat object and analyzed as described previously.

Please note that the same raw data from each timepoint (Day6_exon3lines, Day11_exon3lines, Day23_exon3lines_rep1) were combined and a different type of analysis called trajectory inference (using a package called URD) was performed to generate the Day6_Day11_Day23_matrix.csv (linked to the Day6_exon3lines Series records). URD (v1.0.2) was used for trajectory analysis. Seurat matrix was converted to an URD object, cell-to-cell transition probabilities were calculated by setting number of nearest neighbors to 211 and sigma of 8.  Pseudotime was then calculated by running 80 flood simulations with POU5F1+ clusters as the 'root' cells. Next, all day 23 clusters were set as ‘tip’ cells and biased random walks were simulated from each tip to build an URD tree.

Genome_build: hg19
Supplementary_files_format_and_content: Processed Seurat expression matrix as a csv file, with columns as cell barcodes and rows as genes


title: Liver, No Clinical Sign, Day 3 [VT137L]

description: Replica 3


title: Liver, No Clinical Sign, Day 3 [VT135L]

description: Replica 3


title: Liver, No Clinical Sign, Day 3 [VT136L]

description: Replica 3


title: TCs - BCL11A_KO_KI (P204 Amplicon-Seq)


title: iPSCs - GATA4_KO_KI_24h (P200 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs GATA4_KO_KI_24h total indel with HDR efficiencies and pattern details

source_name: iPSCs

value: PB-derived induced pluripotent stem cells

value: iPSC


title: TBX5Hom_day23_exon3_rep2


title: PGP1_day23


title: iPSCs - GATA4_KO_KI_8h (P198 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs  GATA4_KO_KI_8h total indel with HDR efficiencies and pattern details


title: iPSCs - GATA4_KO_KI_4h (P197 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs  GATA4_KO_KI_4h total indel with HDR efficiencies and pattern details


title: Liver, Survivor, Day 0 [V27L]

description: Replica 6

source_name: Survivor

value: Day 11


title: TBX5Het_day23_exon3_dup2


title: iPSCs - GATA4_KO_KI_12h (P199 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs GATA4_KO_KI_12h total indel with HDR efficiencies and pattern details


title: U937_TCs - BCL11A_AAVS1_KO_KI (P196 Amplicon-Seq)

description:
PCR products of human gDNA
U937 TCs - BCL11A_AAVS1_KO_KI total indel with HDR efficiencies and pattern details

source_name: U937_T cells

value: Erythroleukemia cell line_PB-derived primary T cells


title: U937_TCs - BCL11A_AAVS1_KO_KI (P195 Amplicon-Seq)


title: Liver, No Clinical Sign, Day 3 [VT131L]

description: Replica 3


title: Liver, No Clinical Sign, Day 3 [VT133L]

description: Replica 3


title: U937_TCs - BCL11A_AAVS1_KO_KI (P194 Amplicon-Seq)


title: Liver, No Clinical Sign, Day 3 [VT134L]

description: Replica 3


title: Control_day23_exon3_dup2


title: TBX5Het_day23_exon3_dup1


title: TBX5Hom_day23_exon3_dup1


title: Liver, Control, Day 3 [VC37L]

description: Replica 2

value: Uninfected


title: Control_day23_exon3_dup1


title: Liver, Control, Day 3 [VC36L]

description: Replica 2


title: U937_TCs - BCL11A_CD326_KO_KI_48h (P193 Amplicon-Seq)

description:
PCR products of human gDNA
U937 TCs - BCL11A_CD326_KO_KI_48h total indel with HDR efficiencies and pattern details

value: RNP-AAV


title: Liver, No Clinical Sign, Day 3 [VT132L]

description: Replica 3


title: Liver, Control, Day 3 [VC40L]

description: Replica 2


title: U937_TCs - BCL11A_CD326_KO_KI_24h (P192 Amplicon-Seq)

description:
PCR products of human gDNA
U937 TCs - BCL11A_CD326_KO_KI_24h total indel with HDR efficiencies and pattern details


title: WTC11_day23_exon3_dup1


title: U937_TCs - BCL11A_CD326_KO_KI_8h (P190 Amplicon-Seq)

description:
PCR products of human gDNA
U937 TCs - BCL11A_CD326_KO_KI_8h total indel with HDR efficiencies and pattern details


title: U937_TCs - BCL11A_CD326_KO_KI_12h (P191 Amplicon-Seq)

description:
PCR products of human gDNA
U937 TCs - BCL11A_CD326_KO_KI_12h total indel with HDR efficiencies and pattern details


title: Liver, Control, Day 3 [VC34L]

description: Replica 2


title: TBX5Hom_day11_exon3_dup2

data_processing:
Libraries were sequenced on Illumina Hiseq 2500 or Nextseq
Raw sequencing reads were converted to FASTQ files using Cellranger 2.0.2 mkfastq
Reads were aligned to hg19 v1.2.0 using the Cellranger 2.0.2 count
Cellranger 2.0.2 aggr was used to aggregate libraries from WTC11, Control, TBX5Het and TBX5Hom
Aggregated gene expression matrix was processed in Seurat 2.3.4. Briefly, cells with UMI counts between 10,000 and 80,000 were retained. Gene expression was normalized, scaled and mitochondrial reads and cell cycle genes were regressed. Cells were clustered based on the top 25-30 prinicipal components.
Cardiomyocyte clusters were extracted into a new Seurat object and analyzed as described previously.

Please note that the same raw data from each timepoint (Day6_exon3lines, Day11_exon3lines, Day23_exon3lines_rep1) were combined and a different type of analysis called trajectory inference (using a package called URD) was performed to generate the Day6_Day11_Day23_matrix.csv (linked to the Day6_exon3lines Series records). URD (v1.0.2) was used for trajectory analysis. Seurat matrix was converted to an URD object, cell-to-cell transition probabilities were calculated by setting number of nearest neighbors to 211 and sigma of 8.  Pseudotime was then calculated by running 80 flood simulations with POU5F1+ clusters as the 'root' cells. Next, all day 23 clusters were set as ‘tip’ cells and biased random walks were simulated from each tip to build an URD tree.

Genome_build: hg19
Supplementary_files_format_and_content: Processed Seurat expression matrix as a csv file, with columns as cell barcodes and rows as genes

extract_protocol:
Cells on day 11 were singularized using Trypsin 0.25% and 10,000 cells were loaded on a 10X Chromium chip
Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v2 was used to construct libraries

tag: genotype


title: Liver, Control, Day 3 [VC35L]

description: Replica 2


title: Liver, Control, Day 3 [VC33L]

description: Replica 2


title: TBX5Het_day11_exon3_dup2


title: TBX5Hom_day11_exon3_dup1


title: iPSCs - BCL11A_KI_48h (P183 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_48h total indel with HDR efficiencies and pattern details


title: Liver, Control, Day 3 [VC31L]

description: Replica 2


title: WTC11_day23_exon3_dup2


title: Control_day11_exon3_dup2


title: iPSCs - BCL11A_KI_12h (P181 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_12h total indel with HDR efficiencies and pattern details


title: TBX5Het_day11_exon3_dup1


title: Liver, Control, Day 3 [VC30L]

description: Replica 2


title: U937_TCs - BCL11A_CD326_KO_KI_4h (P189 Amplicon-Seq)

description:
PCR products of human gDNA
U937 TCs - BCL11A_CD326_KO_KI_4h total indel with HDR efficiencies and pattern details


title: Liver, Control, Day 3 [VC29L]

description: Replica 2


title: Liver, Control, Day 3 [VC32L]

description: Replica 2


title: Control_day11_exon3_dup1


title: iPSCs - BCL11A_KI_4h (P179 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_4h total indel with HDR efficiencies and pattern details


title: iPSCs - BCL11A_KI_24h (P182 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_24h total indel with HDR efficiencies and pattern details


title: WTC11_day11_exon3_dup1


title: iPSCs - BCL11A_KI_8h (P180 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_8h total indel with HDR efficiencies and pattern details


title: Liver, Control, Day 3 [VC27L]

description: Replica 2


title: WTC11_day11_exon3_dup2


title: TBX5Hom_day6_exon3_dup2

data_processing:
Libraries were sequenced on Illumina Hiseq 2500 or Nextseq
Raw sequencing reads were converted to FASTQ files using Cellranger 2.0.2 mkfastq
Reads were aligned to hg19 v1.2.0 using the Cellranger 2.0.2 count
Cellranger 2.0.2 aggr was used to aggregate libraries from WTC11, Control, TBX5Het and TBX5Hom
Aggregated gene expression matrix was processed in Seurat 2.3.4. Briefly, cells with UMI counts between 10,000 and 80,000 were retained. Gene expression was normalized, scaled and mitochondrial reads and cell cycle genes were regressed. Cells were clustered based on the top 25-30 prinicipal components.

Please note that the same raw data from each timepoint (Day6_exon3lines, Day11_exon3lines, Day23_exon3lines_rep1) were combined and a different type of analysis called trajectory inference (using a package called URD) was performed to generate the Day6_Day11_Day23_matrix.csv (linked to the Day6_exon3lines Series records). URD (v1.0.2) was used for trajectory analysis. Seurat matrix was converted to an URD object, cell-to-cell transition probabilities were calculated by setting number of nearest neighbors to 211 and sigma of 8.  Pseudotime was then calculated by running 80 flood simulations with POU5F1+ clusters as the 'root' cells. Next, all day 23 clusters were set as ‘tip’ cells and biased random walks were simulated from each tip to build an URD tree.

Genome_build: hg19
Supplementary_files_format_and_content: Processed Seurat expression matrix as a csv file, with columns as cell barcodes and rows as genes

extract_protocol:
Cells on day 6 were singularized using Trypsin 0.25% and 10,000 cells were loaded on a 10X Chromium chip
Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v2 was used to construct libraries

value: Day 6


title: TBX5Hom_day6_exon3_dup1


title: Liver, Control, Day 3 [VC26L]

description: Replica 2

value: Liver


title: iPSCs - BCL11A_KO_24h (P177 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_24h total indel efficiencies and pattern details

value: RNP


title: iPSCs - BCL11A_KO_48h (P178 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_48h total indel efficiencies and pattern details


title: TBX5Het_day6_exon3_dup1


title: iPSCs - BCL11A_KO_12h (P176 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_12h total indel efficiencies and pattern details


title: iPSCs - BCL11A_KO_8h (P175 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_8h total indel efficiencies and pattern details


title: Liver, Control, Day 3 [VC25L]

description: Replica 2


title: Liver, Control, Day 0 [VC19L]

description: Replica 1

value: Day 0


title: Liver, Control, Day 0 [VC20L]

description: Replica 1


title: Liver, Control, Day 3 [VC22L]

description: Replica 2


title: Control_day6_exon3_dup1


title: iPSCs - BCL11A_KO_4h (P174 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_4h total indel efficiencies and pattern details


title: Control_day6_exon3_dup2


title: iPSCs - AAVS1_KO_Drugs (P168 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1_KO  total indel efficiencies and pattern details with treatments of different drugs


title: iPSCs - AAVS1_KI_Drugs (P169 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1_KI total indel with HDR efficiencies and pattern details with treatments of different drugs


title: Liver, Control, Day 0 [VC18L]

description: Replica 1


title: WTC11_day6_exon3_dup2


title: iPSCs - AAVS1_KI_Drugs (P167 Amplicon-Seq)


title: Liver, Control, Day 0 [VC13L]

description: Replica 1


title: WTC11_day6_exon3_dup1

data_processing:
Libraries were sequenced on Illumina Hiseq 2500 or Nextseq
Raw sequencing reads were converted to FASTQ files using Cellranger 2.0.2 mkfastq
Reads were aligned to hg19 v1.2.0 using the Cellranger 2.0.2 count
Cellranger 2.0.2 aggr was used to aggregate libraries from WTC11, Control, TBX5Het and TBX5Hom
Aggregated gene expression matrix was processed in Seurat 2.3.4. Briefly, cells with UMI counts between 10,000 and 80,000 were retained. Gene expression was normalized, scaled and mitochondrial reads and cell cycle genes were regressed. Cells were clustered based on the top 25-30 prinicipal components.

Please note that the same raw data from the Day6_exon3lines, Day11_exon3lines, Day23_exon3lines_rep1 datasets were combined and a different type of analysis called trajectory inference (using a package called URD) was performed to generate the Day6_Day11_Day23_matrix.csv (linked to the Day6_exon3lines Series records). URD (v1.0.2) was used for trajectory analysis. Seurat matrix was converted to an URD object, cell-to-cell transition probabilities were calculated by setting number of nearest neighbors to 211 and sigma of 8.  Pseudotime was then calculated by running 80 flood simulations with POU5F1+ clusters as the 'root' cells. Next, all day 23 clusters were set as ‘tip’ cells and biased random walks were simulated from each tip to build an URD tree.

Genome_build: hg19
Supplementary_files_format_and_content: Processed Seurat expression matrix as a csv file, with columns as cell barcodes and rows as genes


title: TTX_5

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

data_processing:
All FASTQ files were aligned using the HISAT2 alignment program (version 2.1.0) to the Rattus norvegicus (UCSC version rn6) reference genome.
The files were then assembled into potential transcripts using the StringTie assembler program (version 1.3.3).
Next, the potential transcripts were passed to the prepDE program to generate read counts.
Differential gene expression was then tested using DESeq2 (Bioconductor version 3.10).
To identify genes encoding secreted proteins, the highly regulated genes were filtered according to the MetazSecKB database for R. norvegicus based on curated evidence of secretio.
Genome_build: rn6
Supplementary_files_format_and_content: Table with raw counts and expression for each gene from each sample

organism: Rattus norvegicus

source_name: Cultured hippocampal cells

growth_protocol: Sprague–Dawley rat embryos were sacrificed on embryonic day 18. The hippocampus was dissected, and hippocampal cells were dissociated with trypsin. Hippocampal cells were seeded at 5 × 10^5 cells per 35-mm dish, and maintained in neurobasal medium  supplemented with 2% B27 and 0.5 mM L-glutamine and incubated at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
Total RNA was extracted using the Qiagen RNA extraction kit according to the manufacturer’s instructions.
Total RNA with an RNA integrity number greater than 9.0  were subjected to RNA sequencing library preparation using the RNA Library Prep Kit for Illumina according to the manufacturer’s directions.

treatment_protocol: Cultured rat hippocampal cells at 19 DIV were treated with TTX (1 μM) or vehicle (Con) for 24 h

tag: developmental stage

value: 20 days in vitro

tag: treatment

value: TTX (1 μM)

tag: strain

value: Sprague-Dawley


title: Liver, Control, Day 0 [VC16L]

description: Replica 1

tag: organ


title: TBX5Het_day6_exon3_dup2


title: iPSCs - AAVS1_KO_Drugs (P166 Amplicon-Seq)


title: Liver, Control, Day 0 [VC11L]

description: Replica 1

tag: pathogen


title: Liver, Control, Day 0 [VC10L]

description: Replica 1

tag: time


title: TTX_4

institute: Hong Kong University of Science and Technology


title: Liver, Control, Day 3 [VC24L]

description: Replica 2

value: Day 3


title: TTX_3


title: U937 - BCL11A_KO (P152 Amplicon-Seq)

description:
PCR products of human gDNA
U937 BCL11A_KO total indel efficiencies and pattern details

value: Pro-monocytic human myeloid leukemia cell line


title: Liver, Control, Day 0 [VC9L]

description: Replica 1


title: K562 - BCL11A_KI (P151 Amplicon-Seq)

description:
PCR products of human gDNA
K562 BCL11A_KI total indel with HDR efficiencies and pattern details

value: Erythroleukemia cell line


title: TTX_2


title: K562 - BCL11A_KO (P150 Amplicon-Seq)

description:
PCR products of human gDNA
K562 BCL11A_KO total indel efficiencies and pattern details


title: TTX_1


title: Liver, Control, Day 0 [VC6L]

description: Replica 1


title: U937 - BCL11A_KI (P149 Amplicon-Seq)

description:
PCR products of human gDNA
U937 BCL11A_KI total indel with HDR efficiencies and pattern details


title: Con_4

value: vehicle


title: Con_5


title: Liver, Control, Day 0 [VC5L]

description: Replica 1


title: U937 - BCL11A_KO (P148 Amplicon-Seq)


title: K562 - BCL11A_KO_48h (P147 Amplicon-Seq)

description:
PCR products of human gDNA
K562 BCL11A_KO_48h total indel efficiencies and pattern details


title: Liver, Control, Day 0 [VC4L]

description: Replica 1


title: Liver, Control, Day 0 [VC3L]

description: Replica 1


title: Con_3


title: K562 - AAVS1_KO_KI (P165 Amplicon-Seq)

description:
PCR products of human gDNA
K562 AAVS1_KO_KI total indel with HDR efficiencies and pattern details


title: K562 - BCL11A_KO_24h (P146 Amplicon-Seq)

description:
PCR products of human gDNA
K562 BCL11A_KO_24h total indel efficiencies and pattern details


title: Con_2


title: K562 - BCL11A_KO_12h (P145 Amplicon-Seq)

description:
PCR products of human gDNA
K562 BCL11A_KO_12h total indel efficiencies and pattern details


title: Con_1


title: K562 - BCL11A_KO_4h (P143 Amplicon-Seq)

description:
PCR products of human gDNA
K562 BCL11A_KO_4h total indel efficiencies and pattern details


title: Liver, Control, Day 0 [VC8L]

description: Replica 1


title: dme_Piwi_IP_RK_ov_1

city: Baltimore

first: Manolis

last: Maragkakis

state: MD

address: 251 Bayview Blvd

institute: National Institute on Aging

data_processing:
Adaptor trimming: The adaptor was trimmed with cutadapt v2.3
Remove duplicates (only for libraries with 8 random nucleotides at the end of reads): Remove duplicate sequences from the fastq and then trim the 8 nt from the 3' end of reads
Alignment: Reads were aligned using STAR v2.4.2a to the genome (dm3) and to consensus transposon sequences.
Aligned reads were loaded into a SQLite3 database for further processing with CLIPSeqTools and annotated with information whether they overlap with elements from RepeatMasker (downloaded from UCSC) and genes (from UCSC gene model annotation file).
Genome_build: dm3
Supplementary_files_format_and_content: Processed files are TAB delimited files quantifying the number of reads on the sense and antisense strands of the consensus transposon sequences. Files contain the following columns: sample (sample name), category (sense or antisense), ref (transposon_name), count (number of collapsed reads), copyNumber (number of reads) , celltype

organism: Drosophila melanogaster

source_name: Ovaries

growth_protocol: Fly strains were grown on standard cornmeal molasses at 25°C, with 70% relative humidity in a 12-h light–dark cycle.

extract_protocol: Small RNAs were Trizol extracted from immunopurified PIWI clade proteins isolated from fly ovary lysates.

treatment_protocol: Fly ovaries were dissected in cold PBS from 2-5 day old yeast fed flies.

tag: antibody

value: a-Piwi-N7 Mourelatos lab

tag: tissue

value: Ovaries


title: dme_Aub_IP_WT_ov_1

value: a-Aub-83 Mourelatos lab


title: iPSCs - BCL11A_KO_48h (P142 Amplicon-Seq)

value: PB-derived induced pluripotent stem cells

tag: cell line

value: iPSC


title: Gill, Survivor, Day 0 [V40G]

description: Replica 6

value: Gill

value: Vibrio anguillarum

value: Day 11


title: Liver, Control, Day 0 [VC2L]

description: Replica 1

value: Liver

value: Uninfected


title: Gill, Survivor, Day 0 [V37G]

description: Replica 6


title: iPSCs - BCL11A_KO_24h (P141 Amplicon-Seq)

value: RNP


title: iPSCs - BCL11A_KO_12h (P140 Amplicon-Seq)


title: iPSCs - BCL11A_KO_8h (P139 Amplicon-Seq)


title: Gill, Survivor, Day 0 [V35G]

description: Replica 6


title: dme_Ago3_IP_RK_ov_1

value: aAgo3-380 Mourelatos lab


title: Gill, Survivor, Day 0 [V36G]

description: Replica 6


title: SLE Patient 2

city: Stanford

first: Kartik

last: Bhamidipati

state: California

address: 269 Campus Drive, Rm 4135

institute: Stanford University School of Medicine

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger mkfastq function from 10X Genomics 2.2.0 and aligned to the GCRhg38 genome supplied by 10X Genomics.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_gene_bc_matrices-*.tar are tar archives that include genes.tsv, barcordes.tsv and matrix.mtx files.

source_name: Peripheral Blood Mononuclear Cells (PBMCs)

extract_protocol:
B cells were isolated from HC and SLE PBMCs using a negative selection kit. Cell suspensions were subsequently subject to single-cell RNA sequencing using the 10X Genomics platform. Library preparation was performed using Single Cell 35 Reagent Kits v2 (10x Genomics) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: diagnosis

value: SLE

value: B Cell


title: Gill, Survivor, Day 0 [V34G]

description: Replica 6


title: SLE Patient 1


title: SLE Patient 3


title: K562 - BCL11A_KO_8h (P144 Amplicon-Seq)

description:
PCR products of human gDNA
K562 BCL11A_KO_8h total indel efficiencies and pattern details


title: Gill, Survivor, Day 0 [V33G]

description: Replica 6


title: Gill, Survivor, Day 0 [V32G]

description: Replica 6


title: iPSCs - BCL11A_KI_48h (P137 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_48h total indel with HDR efficiencies and pattern details

value: RNP-AAV


title: Liver, Control, Day 0 [VC1L]

description: Replica 1

value: Day 0


title: Healthy Control 2

value: Healthy


title: Gill, Survivor, Day 0 [V38G]

description: Replica 6


title: Gill, Survivor, Day 0 [V31G]

description: Replica 6


title: iPSCs - BCL11A_KI_12h (P135 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_12h total indel with HDR efficiencies and pattern details


title: dme_Aub_IP_RK_ov_1


title: dme_Ago3_IP_yw_ov_1


title: Healthy Control 1


title: OXO-PCR Patient 1031 sample 3E1

city: Oxford

first: Zhiyuan

last: Hu

address: John Radcliffe Hospital/Headley Way

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: HGSOC sample from the OXO-PCR cohort for validation

hyb_protocol: 70 μL hybridisation buffer was added to Reporter CodeSet to make the master mix. Master Mix, total RNA and water were added to PCR tubes to be hybridised at 65°C for 19 hours.

scan_protocol: The hybridization product was loaded onto the cartridge and scanned by the nCounter SPRINT profiler.

data_processing: Processed by using the nSolver analysis software (version 4.0.7) and normalized by the default setting

source_name: Pre-chemotherapy HGSOC

label_protocol: not provided

extract_protocol: For HH corhort, frozen tumor piece was placed into a tube containing 500 μl RLT buffer from RNeasy kit (QIAGEN) and one Retsch 6 mm steel core bead. Tubes were placed into well adapters of a Tissuelyser II (QIAGEN) and tissues were lysed at 15 Hz for 2 min. Tubes were centrifuged briefly and 320 μl was removed for subsequent RNA extraction using the RNeasy kit (QIAGEN) according to the manufacturer’s instructions. RNA concentrations were quantified using the Bioanalyzer system (Agilent). For OXO-PCR cohort, frozen tumor samples were embedded in OCT (NEG-50, Richard-Allan Scientific) and 10 μm sections were taken using MB DynaSharp microtome blades (ThermoFisher Scientific) in a CryoStar cryostat microtome (ThermoFisher Scientific). Scrolls were also collected to be used for bulk RNA-seq. Bulk scrolls were immediately processed for RNA extraction using the RNeasy Mini kit (Qiagen). The extraction procedure was performed according to the manufacturer’s instructions, including DNase digestion, after which RNA integrity was evaluated using the 2200 TapeStation (Agilent). The KAPA mRNA HyperPrep Kits (Roche) were use for the bulk scrolls.

value: Pre-chemotherapy high grade serous ovarian cancer

tag: pfs

tag: histology

value: Serous

tag: age

tag: grade

value: high

tag: Stage


title: iPSCs - BCL11A_KO_4h (P138 Amplicon-Seq)

tag: cell type

value: PB-derived induced pluripotent stem cells

tag: editing


title: Gill, Survivor, Day 0 [V29G]

description: Replica 6


title: Gill, Survivor, Day 0 [V30G]

description: Replica 6


title: iPSCs - BCL11A_KI_4h (P133 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_4h total indel with HDR efficiencies and pattern details

value: iPSC


title: iPSCs - BCL11A_KO_48h (P132 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_48h total indel efficiencies and pattern details


title: Gill, Survivor, Day 0 [V26G]

description: Replica 6

value: Gill


title: Gill, Survivor, Day 0 [V27G]

description: Replica 6

value: Vibrio anguillarum


title: OXO-PCR Patient 1031 sample 3E2


title: iPSCs - BCL11A_KI_24h (P136 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_24h total indel with HDR efficiencies and pattern details


title: OXO-PCR Patient 1027 sample 3D2


title: iPSCs - BCL11A_KO_8h (P129 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_8h total indel efficiencies and pattern details


title: OXO-PCR Patient 1027 sample 3D1


title: iPSCs - BCL11A_KO_4h (P128 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_4h total indel efficiencies and pattern details


title: iPSCs - BCL11A_KI_8h (P134 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KI_8h total indel with HDR efficiencies and pattern details


title: Gill, Control, Day 11 [VC59G]

description: Replica 5

value: Day 11


title: iPSCs - GATA4_KO_KI_48h (P127 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs GATA4_KO_KI_48h total indel with HDR efficiencies and pattern details


title: OXO-PCR Patient 1027 sample 3C9


title: OXO-PCR Patient 1015 sample 1F3


title: Gill, Control, Day 11 [VC57G]

description: Replica 5


title: Gill, Control, Day 11 [VC58G]

description: Replica 5


title: Gill, Survivor, Day 0 [V21G]

description: Replica 6


title: iPSCs - GATA4_KO_KI_24h (P126 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs GATA4_KO_KI_24h total indel with HDR efficiencies and pattern details


title: OXO-PCR Patient 1008 sample 1C9


title: Gill, Control, Day 11 [VC55G]

description: Replica 5


title: OXO-PCR Patient 1008 sample 1C7


title: Gill, Control, Day 11 [VC52G]

description: Replica 5


title: iPSCs - BCL11A_KO_24h (P131 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_24h total indel efficiencies and pattern details


title: iPSCs - GATA4_KO_KI_12h (P125 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs GATA4_KO_KI_12h total indel with HDR efficiencies and pattern details


title: OXO-PCR Patient 1002 sample 3F8


title: iPSCs - BCL11A_KO_12h (P130 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_12h total indel efficiencies and pattern details


title: Gill, Survivor, Day 0 [V24G]

description: Replica 6


title: iPSCs - GATA4_KO_KI_4h (P123 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs GATA4_KO_KI_4h total indel with HDR efficiencies and pattern details


title: iPSCs - GATA4_KO_KI_8h (P124 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs GATA4_KO_KI_8h total indel with HDR efficiencies and pattern details


title: Gill, Control, Day 11 [VC51G]

description: Replica 5


title: OXO-PCR Patient 1002 sample 3F6


title: iPSCs - CD326_BCL11A_KO_KI_48h (P122 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs CD326_BCL11A_KO_KI_48h total indel with HDR efficiencies and pattern details


title: Gill, Control, Day 11 [VC49G]

description: Replica 5


title: HH-150

scan_protocol: Not provided

data_processing: Processed by using nSolver.

source_name: Ovarian tumour

label_protocol: Not provided

extract_protocol: Frozen tumor piece was placed into a tube containing 500 μl RLT buffer from RNeasy kit (QIAGEN) and one Retsch 6 mm steel core bead. Tubes were placed into well adapters of a Tissuelyser II (QIAGEN) and tissues were lysed at 15 Hz for 2 min. Tubes were centrifuged briefly and 320 μl was removed for subsequent RNA extraction using the RNeasy kit (QIAGEN) according to the manufacturer’s instructions. RNA concentrations were quantified using the Bioanalyzer system (Agilent).

value: HGS

value: late


title: iPSCs - CD326_BCL11A_KO_KI_12h (P120 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs CD326_BCL11A_KO_KI_12h total indel with HDR efficiencies and pattern details


title: iPSCs - CD326_BCL11A_KO_KI_24h (P121 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs CD326_BCL11A_KO_KI_24h total indel with HDR efficiencies and pattern details


title: HH-147


title: HH-148


title: iPSCs - CD326_BCL11A_KO_KI_4h (P118 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs CD326_BCL11A_KO_KI_4h total indel with HDR efficiencies and pattern details


title: Gill, Control, Day 11 [VC48G]

description: Replica 5

data_processing: All q-PCR assays exhibited efficiencies within 100% ± 5% so the simplified 2-ΔΔCq method was used for analysing data (Livak and Schmittgen, 2001). For normalization and as internal calibrator the average of three genes (ARP, ELF1α and β-actin) was chosen by using NormFinder (Andersen et al., 2004). For gene expression analyses, all challenged groups were compared to non-exposed time point controls using Student’s t-test. We considered differences to be significant when regulations were at least two-fold and p < 0.05. For four of the genes investigated in the non-exposed timepoint control groups less than three fish showed Cq values (excluding a t-test) and therefore we applied a qualitative assessment (presence/absence of Cq values) and analyzed data with the nonparametric Mann-Whitney test using a probability level of 5%.

value: Uninfected


title: iPSCs - CD326_BCL11A_KO_KI_8h (P119 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs CD326_BCL11A_KO_KI_8h total indel with HDR efficiencies and pattern details


title: Gill, Control, Day 11 [VC47G]

description: Replica 5


title: iPSCs - CD326_GATA4_KI_Drugs (P115 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs CD326_GATA4_KI total indel with HDR efficiencies and pattern details with treatments of different drugs


title: HH-146


title: HH-144


title: HH-145


title: iPSCs - CD326_GATA4_KI_Drugs (P114 Amplicon-Seq)


title: Gill, Control, Day 11 [VC50G]

description: Replica 5


title: Gill, Control, Day 11 [VC44G]

description: Replica 5


title: Gill, Control, Day 11 [VC45G]

description: Replica 5


title: iPSCs - CD326_GATA4_KO_Drugs (P112 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs CD326_GATA4_KO total indel efficiencies and pattern details with treatments of different drugs

value: RNP


title: Gill, Control, Day 11 [VC41G]

description: Replica 5


title: HH-149


title: iPSCs - CD326_GATA4_KO_Drugs (P113 Amplicon-Seq)


title: HH-143


title: HH-142


title: iPSCs - CD326_GATA4_KI_Drugs (P111 Amplicon-Seq)


title: HH-140


title: Gill,  Clinical Sign, Day 3 [V19G]

description: Replica 4

value: Day 3


title: Gill, Control, Day 11 [VC42G]

description: Replica 5


title: Gill, Control, Day 11 [VC46G]

description: Replica 5


title: Gill,  Clinical Sign, Day 3 [V16G]

description: Replica 4


title: iPSCs - CD326_GATA4_KI_Drugs (P110 Amplicon-Seq)


title: Gill,  Clinical Sign, Day 3 [V17G]

description: Replica 4


title: iPSCs - CD326_GATA4_KO_Drugs (P108 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs  CD326_GATA4_KO total indel efficiencies and pattern details with treatments of different drugs


title: iPSCs - CD326_MYH6_KO_KI (P104 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs CD326_MYH6_KO_KI total indel with HDR efficiencies and pattern details at different time points


title: Gill,  Clinical Sign, Day 3 [V14G]

description: Replica 4


title: HH-137


title: HH-138

value: Endometrial serous carcinoma


title: iPSCs - CD326_GATA4_KO_Drugs (P109 Amplicon-Seq)


title: Gill,  Clinical Sign, Day 3 [V13G]

description: Replica 4


title: HH-136


title: iPSCs - BCL11A_KO_48h_GATA4_KI (P101 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_48h_GATA4_KI total indel with HDR efficiencies and pattern details at different time points

value: RNP-AAV


title: HH-135


title: iPSCs - CD326_KO (P102 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs CD326_KO total indel efficiencies and pattern details


title: Gill,  Clinical Sign, Day 3 [V9G]

description: Replica 4


title: HH-141


title: Gill,  Clinical Sign, Day 3 [V11G]

description: Replica 4


title: Gill,  Clinical Sign, Day 3 [V8G]

description: Replica 4


title: HH-134


title: iPSCs - BCL11A_KO_24h_GATA4_KO (P100 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_24h_GATA4_KO total indel efficiencies and pattern details


title: HH-133


title: iPSCs - BCL11A_KO_12h (P99 Amplicon-Seq)


title: HH-132


title: Gill,  Clinical Sign, Day 3 [V6G]

description: Replica 4


title: HH-139


title: HH-131


title: iPSCs - BCL11A_KO_4h (P97 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_4h total indel efficiencies and pattern details


title: iPSCs - BCL11A_KO_8h (P98 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_KO_8h total indel efficiencies and pattern details


title: iPSCs - AAVS1_HBG_KO_KI (P95 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1_HBG_KO_KI total indel with HDR efficiencies and pattern details at different time points


title: Gill,  Clinical Sign, Day 3 [V5G]

description: Replica 4


title: Gill,  Clinical Sign, Day 3 [V4G]

description: Replica 4


title: Gill,  Clinical Sign, Day 3 [V3G]

description: Replica 4


title: iPSCs - AAVS1_HBG_KO_KI (P94 Amplicon-Seq)


title: HH-128


title: Gill,  Clinical Sign, Day 3 [V7G]

description: Replica 4


title: HH-127


title: Gill,  Clinical Sign, Day 3 [V2G]

description: Replica 4


title: HH-126


title: Gill, No Clinical Sign, Day 3 [VT1410G]

description: Replica 3


title: iPSCs - AAVS1_HBG_KO_KI (P93 Amplicon-Seq)


title: HH-124


title: Gill, No Clinical Sign, Day 3 [VT148G]

description: Replica 3


title: iPSCs - AAVS1_HBG_KO_KI (P92 Amplicon-Seq)


title: K562 - BCL11A_KO_4h (P89 Amplicon-Seq)

description:
PCR products of human gDNA
K562 BCL11A_KO_4h total indel efficiencies and pattern details

value: Erythroleukemia cell line


title: K562 - BCL11A_KO_8h (P90 Amplicon-Seq)

description:
PCR products of human gDNA
K562 BCL11A_KO_8h total indel efficiencies and pattern details


title: HH-125


title: HH-123


title: iPSC - BCL11A48h_KO (P88 Amplicon-Seq)

description:
PCR products of human gDNA
iPSC BCL11A 48h_KO total indel efficiencies and pattern details


title: Gill, No Clinical Sign, Day 3 [VT146G]

description: Replica 3


title: Gill, No Clinical Sign, Day 3 [VT147G]

description: Replica 3


title: HH-121


title: Gill, No Clinical Sign, Day 3 [VT144G]

description: Replica 3


title: HH-122


title: Gill, No Clinical Sign, Day 3 [VT145G]

description: Replica 3


title: Gill, No Clinical Sign, Day 3 [VT143G]

description: Replica 3


title: HH-130


title: HH-129


title: K562_iPSCs - AAVS1_HBG_KI_BCL11A24h_KO (P87 Amplicon-Seq)

description:
PCR products of human gDNA
K562 iPSCs - AAVS1_HBG_KI_BCL11A24h_KO total indel efficiencies and pattern details

value: Erythroleukemia cell line_PB-derived induced pluripotent stem cells


title: K562_iPSCs - AAVS1_HBG_BCL11A4h_KO (P84 Amplicon-Seq)

description:
PCR products of human gDNA
K562 iPSCs - AAVS1_HBG_BCL11A4h_KO total indel efficiencies and pattern details


title: Gill, No Clinical Sign, Day 3 [VT142G]

description: Replica 3


title: K562_iPSCs - AAVS1_HBG_BCL11A12h_KO (P86 Amplicon-Seq)

description:
PCR products of human gDNA
K562 iPSCs - AAVS1_HBG_BCL11A12h_KO total indel efficiencies and pattern details


title: K562_iPSCs - AAVS1_HBG_KI_BCL11A8h_KO (P85 Amplicon-Seq)

description:
PCR products of human gDNA
K562 iPSCs - AAVS1_HBG_KI_BCL11A8h_KO total indel efficiencies and pattern details


title: HH-120


title: HH-119


title: iPSCs - AAVS1_CD326_GATA4_MYH6_KI (P72 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs - AAVS1_CD326_GATA4_MYH6_KI total indel with HDR efficiencies and pattern details


title: HH-118

value: Serous carcinoma


title: Gill, No Clinical Sign, Day 3 [VT139G]

description: Replica 3


title: Gill, No Clinical Sign, Day 3 [VT1310G]

description: Replica 3


title: HH-117

value: Serous


title: Gill, No Clinical Sign, Day 3 [VT138G]

description: Replica 3


title: iPSCs - AAVS1_CD326_GATA4_MYH6_KO (P71 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1_CD326_GATA4_MYH6_KO total indel efficiencies and pattern details


title: iPSCs_U937 - HBG_KI_48h (P70 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs U937  HBG_KI_48h HDR efficiencies and pattern details

value: PB-derived induced pluripotent stem cells_Pro-monocytic human myeloid leukemia cell line


title: HH-116

value: low


title: Gill,  Clinical Sign, Day 3 [V1G]

description: Replica 4


title: HH-113

value: high


title: iPSCs - BCL11A_MYH6_KO_KI_24h (P61 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_MYH6_KO_KI_24h total indel with HDR efficiencies and pattern details

value: PB-derived induced pluripotent stem cells

value: iPSC


title: HH-112


title: U937 - HBG_KI (P68 Amplicon-Seq)

description:
PCR products of human gDNA
U937 HBG_KI HDR efficiencies and pattern details

value: Pro-monocytic human myeloid leukemia cell line


title: iPSCs - BCL11A_MYH6_KO_KI_4h (P58 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_MYH6_KO_KI_4h total indel with HDR efficiencies and pattern details


title: Gill, Control, Day 3 [VC38G]

description: Replica 2

value: Gill


title: Gill, Control, Day 3 [VC34G]

description: Replica 2


title: Gill, Control, Day 3 [VC35G]

description: Replica 2


title: HH-107

value: late


title: Gill, No Clinical Sign, Day 3 [VT134G]

description: Replica 3

value: Vibrio anguillarum


title: HH-108


title: iPSCs - HBG_KI (P69 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs HBG_KI HDR efficiencies and pattern details


title: HH-106


title: Gill, Control, Day 3 [VC36G]

description: Replica 2

value: Uninfected


title: HH-114

value: early


title: iPSCs - AAVS1_CD326_GATA4_KO_KI_12h (P53 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1_CD326_GATA4_KO_KI_12h  total indel with HDR efficiencies and pattern details


title: iPSCs - BCL11A_MYH6_KO_KI_12h (P60 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_MYH6_KO_KI_12h total indel with HDR efficiencies and pattern details


title: iPSCs - BCL11A_MYH6_KO_KI_8h (P59 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_MYH6_KO_KI_8h total indel with HDR efficiencies and pattern details


title: Gill, Control, Day 3 [VC37G]

description: Replica 2

value: Day 3


title: HH-115


title: Gill, No Clinical Sign, Day 3 [VT135G]

description: Replica 3


title: Gill, Control, Day 3 [VC39G]

description: Replica 2


title: HH-111

value: Serous Papillary


title: Gill, No Clinical Sign, Day 3 [VT133G]

description: Replica 3


title: iPSCs - BCL11A_MYH6_KO_KI_48h (P62 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A_MYH6_KO_KI_48h total indel with HDR efficiencies and pattern details

value: RNP-AAV


title: iPSCs - AAVS1_CD326_GATA4_KO_KI_48h (P55 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1_CD326_GATA4_KO_KI_48h  total indel with HDR efficiencies and pattern details


title: iPSCs - AAVS1_CD326_GATA4_KO_KI_24h (P54 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1_CD326_GATA4_KO_KI_24h  total indel with HDR efficiencies and pattern details


title: HH-109


title: Gill, No Clinical Sign, Day 3 [VT132G]

description: Replica 3


title: HH-110

value: Serous adenocarcinoma


title: iPSCs - AAVS1_CD326_GATA4_KO_KI_8h (P52 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1_CD326_GATA4_KO_KI_8h  total indel with HDR efficiencies and pattern details


title: Gill, Control, Day 3 [VC33G]

description: Replica 2


title: iPSCs_U937 - BCL11A_HBG_MYH6_KO_24h (P44 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs U937 - BCL11A HBG MYH6_KO_24h  total indel efficiencies and pattern details

value: RNP


title: HH-105

value: Serous


title: HH-104


title: Gill, Control, Day 3 [VC32G]

description: Replica 2


title: iPSCs_U937 - BCL11A_HBG_MYH6_KO_12h (P43 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs U937 - BCL11A HBG MYH6_KO_12h  total indel efficiencies and pattern details

value: PB-derived induced pluripotent stem cells_Pro-monocytic human myeloid leukemia cell line


title: HH-103


title: iPSCs - AAVS1_CD326_GATA4_KO_KI_4h (P51 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1_CD326_GATA4_KO_KI_4h  total indel with HDR efficiencies and pattern details


title: HH-101


title: Gill, Control, Day 3 [VC31G]

description: Replica 2


title: HH-102


title: U937 - BCL11A_HBG_KO_6h (P35 Amplicon-Seq)

description:
PCR products of human gDNA
U937 BCL11A_HBG_KO_6h total indel efficiencies and pattern details


title: HH-099


title: HH-100


title: Gill, Control, Day 3 [VC25G]

description: Replica 2


title: Gill, Control, Day 3 [VC30G]

description: Replica 2


title: Gill, Control, Day 3 [VC26G]

description: Replica 2


title: iPSCs_U937 - BCL11A_HBG_MYH6_KO_4h (P41 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs U937 - BCL11A HBG MYH6_KO_4h  total indel efficiencies and pattern details


title: HH-096


title: Gill, Control, Day 3 [VC27G]

description: Replica 2


title: iPSCs - BCL11A_HBG_KO_72h (P34 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A HBG_KO_72h total indel efficiencies and pattern details


title: iPSCs_U937 - BCL11A_HBG_MYH6_KO_8h (P42 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs U937 - BCL11A HBG MYH6_KO_8h  total indel efficiencies and pattern details


title: iPSCs - BCL11A_HBG_KO_24h (P33 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A HBG_KO_24h total indel efficiencies and pattern details


title: HH-095


title: HH-097


title: iPSCs - BCL11A_HBG_KO_6h (P32 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs BCL11A HBG_KO_6h total indel efficiencies and pattern details


title: iPSCs - AAVS1_CD326_GATA4_MYH6_KO_24h (P30 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1, CD326, GATA4, MYH6, KO24h total indel efficiencies and pattern details


title: Gill, Control, Day 0 [VC19G]

description: Replica 1

value: Day 0


title: Gill, Control, Day 3 [VC23G]

description: Replica 2


title: Gill, Control, Day 0 [VC20G]

description: Replica 1


title: Gill, Control, Day 3 [VC21G]

description: Replica 2


title: Gill, Control, Day 0 [VC17G]

description: Replica 1


title: HH-098

value: high


title: iPSCs - AAVS1_CD326_GATA4_MYH6_KO_6h (P29 Amplicon-Seq)

description:
PCR products of human gDNA
iPSCs AAVS1, CD326, GATA4, MYH6, KO6h total indel efficiencies and pattern details

value: PB-derived induced pluripotent stem cells


title: Gill, Control, Day 0 [VC18G]

description: Replica 1


title: HH-094


title: HH-091


title: HH-092


title: HH-093


title: Gill, Control, Day 0 [VC15G]

description: Replica 1


title: Gill, Control, Day 0 [VC16G]

description: Replica 1


title: HH-090


title: Gill, Control, Day 0 [VC14G]

description: Replica 1


title: HH-089


title: Gill, Control, Day 0 [VC12G]

description: Replica 1


title: HH-088


title: HH-087


title: Gill, Control, Day 0 [VC11G]

description: Replica 1


title: HH-086


title: Gill, Control, Day 0 [VC10G]

description: Replica 1


title: Gill, Control, Day 0 [VC13G]

description: Replica 1


title: HH-085


title: Gill, Control, Day 0 [VC9G]

description: Replica 1


title: HH-084


title: HH-083


title: Gill, Control, Day 0 [VC2G]

description: Replica 1


title: HH-082


title: MDAMB231 cells, SKP2-2, rep 3

city: Durham

first: Wei

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

data_processing:
NovaSeq Control Software (Application Version: 1.7.0, RTA Version: v3.4.4)
Illumina NovaSeq 6000 reads were processed using the TrimGalore toolkit v0.4.1 to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis. Read quality was checked for each sample using FastQC v0.11.2.
Reads were mapped to the GRCh38v93 version of the human genome and transcriptome using the STAR RNA-seq alignment tool v2.5.0c.  Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool v0.6.1.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package v1.16.1 with the R statistical programming environment v3.4.1_3.
Genome_build: GRCh38v93
Supplementary_files_format_and_content: htseq read count text file

source_name: triple negative breast cancer

growth_protocol: Cells were cultured at 37'C with 5%CO2 in DMEM (with FBS and penicillin/streptomycin)

extract_protocol:
RNeasy mini kit and DNase I treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA for 96 h by reverse transfection

value: breast

value: SKP2 siRNA_2

tag: genotype

value: SKP2 knockdown


title: MDAMB231 cells, SKP2-2, rep 2

tag: treatment


title: T74_P003

data_processing:
The reads were aligned to the human genome (hg19 –GRCh38) and spike-in sequences (from the External RNA Controls Consortium) using STAR v2.5.3a (Dobin et al., 2013), and filtered for uniquely mapping reads. Counts per gene were calculated for each transcript in Ensembl release 92 using rpkmforgenes (Ramsköld et al., 2009). The following rpkmforgenes options were used: -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendsceil
Genome_build: hg19 –GRCh38
Supplementary_files_format_and_content: Tab delimited files include metadata, barcodes and features of each plate. We also included a matrix containing estimated counts.

extract_protocol:
Sorted cells were processed using the Smart-seq2 protocol with minor changes (Picelli et al., 2013). Sequencing was done to the average depth of 0.7 million reads per cell with 43bp reads (single end) after demultiplexing. Blood samples were additionally sequenced for V(D)J analysis to and average depth of 0.84 million reads per cell with 150 bp reads (paired end) after demultiplexing.
Smart-Seq2

value: TONSIL

tag: Sex

value: M


title: HH-080


title: Gill, Control, Day 0 [VC1G]

description: Replica 1

source_name: Time point Control

tag: organ

value: Gill

value: Uninfected


title: dme_Aub_IP_csul_ov_1

tag: strain

value: a-Aub Siomi lab

value: Ovaries


title: T74_P002


title: dme_Aub_IP_w_ov_1


title: Gill, Control, Day 0 [VC7G]

description: Replica 1

tag: pathogen

tag: time


title: dme_Ago3_IP_w_ov_1

tag: antibody

value: a-Ago3 Siomi lab

tag: tissue


title: T74_P001


title: T74_P004


title: MDAMB231 cells, SKP2-1, rep 3

tag: cell line

value: SKP2 siRNA_1


title: HH-079

tag: pfs

value: late


title: dme_Ago3_IP_csul_ov_1


title: HH-078

tag: histology

value: Serous


title: HH-081

tag: age

value: early


title: HH-077

tag: grade


title: MDAMB231 cells, SKP2-1, rep 2


title: T86_P002

value: F


title: MDAMB231 cells, SKP2-1, rep 1


title: T75_P004


title: noAA_CB839_ox_rep2

city: New York

first: Bryan

last: King

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

description:
noAA6hr_CB839_io4_IGO_09008_8_S8
noAA6hr_CB839_io4

data_processing:
library strategy: CHARGE-seq
Raw sequence data (.bcl files) generated from Illumina MiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Unique sequences from the mouse gtRNAdb (http://gtrnadb.ucsc.edu/) were appended with a 3’ CCA and used to create a reference assembly with the ‘bowtie2-build’ function. Paired-end 75-bp reads were trimmed of Illumina adapters and aligned to the reference assembly with ‘bowtie2’ run in ‘very-sensitive’ mode, allowing 1 mismatch to account for degeneracy that occurs at methylated adenine bases.
Aligned reads were sorted and indexed with ‘samtools’ and a custom R script was used to assign gene alignments to each tRNA isodecoder. Reads were normalized by library size and the yeast phenylalanine tRNA spike-in counts prior to determining charge ratios.
Genome_build: mm10/mouse gtrnadb
Supplementary_files_format_and_content: tab-delimited txt file of normalized counts aligning to tRNA isodecoder genes

organism: Mus musculus

growth_protocol: MEFs were cultured in complete or amino-acid free DMEM medium for 6h.

extract_protocol:
Cells were lysed with cold TRIzol (15596018, Life Technologies) on ice. Lysates were shaken with chloroform 5:1, centrifuged at 18,600g and precipitated with 2.7x volumes of cold ethanol in presence of 30 μg of GlycoBlue Coprecipitant (AM9515, ThermoFisher) overnight. Samples were resuspended in 0.3M acetate buffer (pH = 4.5) with 10 mM EDTA and precipitated again. Next day, samples were resuspended in 10 mM acetate buffer with 1 mM EDTA. 2 ug of each RNA sample was treated with 10 mM of either sodium periodate (“oxidized sample”) or sodium chloride (“non-oxidized sample”) and incubated for 20 min at room temperature in the dark. Reactions were quenched with glucose for 15 min. Yeast tRNAPhe (R4018, Sigma-Aldrich) was added to each sample, after which samples were precipitated with ethanol. Samples were resuspended in 50 mM Tris buffer (pH=9) and incubated for 50 min at 37C, quenched with acetate buffer and precipitated
Samples were resuspended in RNAse-free water and subjected to a ligation to a 5’-adenylated DNA adaptor (5′-/5rApp/TGGAATTCTCGGGTGCCAAGG/3ddC/-3′), using truncated KQ mutant T4 RNA ligase 2 (M0373, New England Biolabs), for 3 hours at room temperature. Reverse transcription was performed with SuperScript IV reverse transcriptase (18090050, Thermo Scientific) according to the manufacturer’s instructions, with a primer complementary to the DNA adaptor. After the reverse transcription step, 3’ end of cDNA was ligated to a 5’-phosphorylated DNA adaptor (5’-/5phos/AGATCGGAAGAGCGTCGTGTAGGGA/3ddC/-3’) using T4 RNA ligase 1 (M0437, New England Biolabs) in presence of 20% PEG, 1 mM ATP and 30 mM hexammine cobalt(III) chloride (H7891, Sigma-Aldrich). Ligation products were subjected to 8 cycles of PCR with primers containing 8-mer barcodes and p5 and p7 Illumina adaptors. PCR products were run out on an agarose gel and ~190 bp bands were excised, purified and subjected to MiSeq paired-end Illumina sequencing.

treatment_protocol: Cells were treated with 1µM CB-839 (glutaminase inhibitor) or vehicle.

value: SV40-immortalized mouse embryonic fibroblasts (MEFs)

tag: medium

value: AA-free

tag: oxidation

value: oxidized

tag: molecule type

value: tRNA


title: noAA_CB839_rep2

description:
noAA6hr_CB839_cl_IGO_09008_4_S4
noAA6hr_CB839_cl

tag: cell type

value: non-oxidized


title: T86_P004

value: TONSIL


title: HH-076

value: high

tag: Stage


title: T75_P003

tag: Sex

value: M


title: MDAMB231 cells, NC, rep 3

value: breast

tag: treatment

value: nontargeting control siRNA

tag: genotype

value: control


title: T86_P001


title: MDAMB231 cells, SKP2-2, rep 1

value: SKP2 siRNA_2

value: SKP2 knockdown


title: MDAMB231 cells, NC, rep 2


title: HH-075

value: late


title: noAA_veh_rep2

description:
noAA6hr_DMSO_cl_IGO_09008_3_S3
noAA6hr_DMSO_cl

value: vehicle


title: HH-074

value: Serous


title: MDAMB231 cells, NC, rep 1


title: Comp_CB839_ox_rep2

description:
compl_CB839_io4_IGO_09008_6_S6
comp_CB839_io4

value: complete


title: HH-073


title: WB3_P405_VDJ

value: BLOOD


title: HH-072


title: Comp_veh_ox_rep2

description:
compl_DMSO_io4_IGO_09008_5_S5
comp_DMSO_io4

value: SV40-immortalized mouse embryonic fibroblasts (MEFs)


title: WB2_P402_VDJ

value: F


title: T75_P001


title: noAA_veh_ox_rep2

description:
noAA6hr_DMSO_io4_IGO_09008_7_S7
noAA6hr_DMSO_io4

value: AA-free

value: oxidized

value: tRNA


title: T86_P003

value: TONSIL


title: HH-070

value: high


title: T75_P002

value: M


title: Comp_CB839_rep2

description:
compl_CB839_cl_IGO_09008_2_S2
comp_CB839_cl

value: non-oxidized


title: HH-071


title: 320449: EtOH_0

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d
Gene level expression quantification is generated with RNA-SeQC (v2.3.3) and RSEM (v1.3.1). RPKM and TPM for transcript isoforms are quantitated on the merged lane-level data with RSEM (v1.3.1). Gene-level RPKMs are quantitated with RNA-SeQC (v2.3.3) on a standard collapsed reference annotation
Genome_build: GrCh38, GENCODE release 29
Supplementary_files_format_and_content: "Pheno.csv" contains sample metadata, "Etoh_Counts.csv" contains raw counts, "SummaryStats.csv" contains the number and percentages of reads mapped for each samples

source_name: Colon Organoid

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of either distal or proximal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol:
For RNA isolation, media was gently removed and 200μl RNA lysis Solution RA1 with TCEP (Machery-Nagel; Cat No: 740902.50) was added to each well. The lysate was collected in a 1.5ml Eppendorf tube. Each tube was vortexed vigorously and placed on ice. Further steps were carried out according to manufacturer’s protocol of the Machel-Nagel RNA XS kit. RNA was checked for quality using the Agilent 4200 Tapestation. Samples with RIN > =8.5 were considered for library preparation and sequencing using the Illumina NovoSeq
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II).  Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.
Libraries were multiplexed and sequenced on Illumina Novaseq6000 to generate 100bp PE reads.

treatment_protocol: For this experiment, cells were treated with fresh growth media plus ethanol (Sigma Aldrich; Cat No: E7023) (2μl per 1ml of growth media), or fresh growth media plus 2μl cell culture grade distilled water as a control. Media (with or without ethanol) was replaced every 24 hours for 3 days in order to replace evaporating ethanol.

value: Colon Organoid

tag: gender

value: Female

value: EtOH

value: Distal

tag: sample type

value: RNA-sequencing


title: noAA_CB839_ox_rep1

description:
08_noAA6hr_CB839_io4_IGO_09008_B_8_S8
noAA6hr_CB839_io4


title: Comp_veh_rep2

description:
compl_DMSO_cl_IGO_09008_1_S1
comp_DMSO_cl

value: vehicle


title: noAA_CB839_rep1

description:
04_noAA6hr_CB839_cl_IGO_09008_B_4_S4
noAA6hr_CB839_cl


title: noAA_veh_ox_rep1

description:
07_noAA6hr_DMSO_io4_IGO_09008_B_7_S7
noAA6hr_DMSO_io4


title: HH-067

value: Serous

value: late


title: 320446: CTL_1

value: Male

value: CTL

value: Proximal


title: HH-066


title: 320447: EtOH_1


title: 320445: EtOH_2


title: HH-068


title: Comp_CB839_rep1

description:
02_compl_CB839_cl_IGO_09008_B_2_S2
comp_CB839_cl

value: SV40-immortalized mouse embryonic fibroblasts (MEFs)

value: complete


title: WB1_P275_VDJ

value: BLOOD


title: noAA_veh_rep1

description:
03_noAA6hr_DMSO_cl_IGO_09008_B_3_S3
noAA6hr_DMSO_cl

value: AA-free

value: tRNA


title: 320444: CTL_2


title: Comp_veh_ox_rep1

description:
05_compl_DMSO_io4_IGO_09008_B_5_S5
comp_DMSO_io4

value: oxidized


title: Comp_CB839_ox_rep1

description:
06_compl_CB839_io4_IGO_09008_B_6_S6
comp_CB839_io4


title: HH-064

value: high


title: 320443: EtOH_3

value: Colon Organoid

value: Female


title: HH-069

value: early


title: 320442: CTL_3

value: Distal

value: RNA-sequencing


title: Comp_veh_rep1

description:
01_compl_DMSO_cl_IGO_09008_B_1_S1
comp_DMSO_cl

value: vehicle

value: non-oxidized


title: 320448: CTL_0


title: 320441: EtOH_4

value: Male

value: EtOH


title: 320439: EtOH_5

value: Proximal


title: HH-060

value: Serous

value: late


title: HH-062


title: HH-059


title: HH-063


title: HH-061


title: HH-065


title: HH-058


title: 320437: EtOH_6


title: 320436: CTL_6

value: CTL


title: 320435: EtOH_7


title: HH-057


title: HH-056


title: 320440: CTL_4


title: HH-055


title: HH-054


title: 320433: EtOH_8


title: 320434: CTL_7


title: 320431: EtOH_9


title: HH-052


title: 320438: CTL_5


title: HH-051


title: MOLM14 cell transfected with shCALCRL rep2

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

hyb_protocol: GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays has been used and cartridges have been washed and stained using the Fluidic Protocol FS450_0002

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing:
8 CEL (2 conditions, n=8 each) files generated after array scanning were imported into R/CRAN environment (R version 3.4.0) and preprocess with rma function of oligo package.
pd.hugene.2.0.st (https://bioconductor.org/packages/release/data/annotation/html/pd.hugene.2.0.st.html)
hugene20sttranscriptcluster.db (https://bioconductor.org/packages/release/data/annotation/html/hugene20sttranscriptcluster.db.html)

label: biotin

source_name: shCALCRL-F

label_protocol: GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays protocol has been used with 100ng of total RNA as starting amount

growth_protocol: MOLM14 cells were maintained in RPMI-media (Gibco) supplemented with 10% FBS (Invitrogen) in the presence of 100 U/mL of penicillin and 100μg/mL of streptomycin, and were incubated at 37°C with 5% CO2. The cultured cells were split every 2 to 3 days and maintained in an exponential growth phase.

extract_protocol: mRNA from 2.106 of cells was extracted using RNeasy (Qiagen). RNA purity was monitored with NanoDrop 1ND-1000 spectrophotometer and RNA quality was assessed through Agilent 2100 Bionalyzer with RNA 6000 Nano assay kit. No RNA degradation or contamination were detected (RIN > 9). 100 ng of total RNA were analyzed on Affymetrix GeneChip© Human Gene 2.0 ST Array using the Affymetrix GeneChip© WT Plus Reagent Kit according to the manufacturer’s instructions (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays P/N 703174 Rev. 2).

treatment_protocol: Mixing 2.106 cells in 2ml of freshly thawed lentivirus and Polybrene (Sigma-Aldrich, Cat# 107689) at a final concentration of 8 ug/ml. At 3 days post infection, transduced cells were selected using 1 μg/ml puromycin. CALCRL MISSION shRNA (shCALCRL#1, Sigma-Aldrich, Cat# TRCN0000356798; shCALCRL#2, Sigma-Aldrich, Cat# TRCN0000356736)

tag: batch

value: shCALCRL


title: 12_105a_a VPS39 3d.rma-gene-full-Signal

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

institute: Lund University

hyb_protocol: according to the manufacturer’s recommendations

data_processing: Expression Console Software v1.4.1.46 was used for quality analyses and data were processed using Robust Multi-array Analysis (RMA) and log2 transformed. Paired t-tests were used when comparing Control vs siVPS39.

source_name: muscle cells

growth_protocol: Briefly, myoblasts were cultured in growth medium (HAM’s/F10 supplemented with 20% fetal bovine serum (FBS), 1% penicillin/streptomycin and 1% Amphotericin B). To induce differentiation, cells were incubated in differentiation medium 1 (DMEM with 1.0 g/l glucose supplemented with 10% FBS and 1% penicillin/streptomycin) for 2 days, followed by differentiation medium 2 (DMEM with 4.5 g/l glucose supplemented with 2% horse serum and 1% penicillin/streptomycin) until cells were fully differentiated, as determined by visual confirmation of myotube formation (>3 nuclei per myotube in approximately 70% of cells) on day 7.

extract_protocol: RNA from VPS39-silenced cells was extracted using RNeasy mini kit (Qiagen #74104)

treatment_protocol: Primary human myoblasts (at 70-90% confluence) were transfected with ON-TARGETplus human set of four siRNA molecules (Dharmacon, Lafayette, CO, USA) targeting VPS39 (LQ-014052-01) or a negative control (Non-targeting plus #D-001810-10).

tag: genotype/variation


title: MOLM14 cell transfected with shCALCRL rep3

source_name: shCALCRL-G


title: MOLM14 cell transfected with shcontrol rep4

source_name: shCTRL-D

value: shCTRL


title: MOLM14 cell transfected with shcontrol rep2

source_name: shCTRL-B


title: HH-050


title: MOLM14 cell transfected with shCALCRL rep4

source_name: shCALCRL-H


title: MOLM14 cell transfected with shcontrol rep1

source_name: shCTRL-A


title: 320430: CTL_9

tag: tissue


title: 8_105a_2 VPS39 3d.rma-gene-full-Signal

scan_protocol: according to the manufacturer’s recommendations


title: 10_105a_b VPS39 3d.rma-gene-full-Signal

label_protocol: according to the manufacturer’s recommendations


title: 320429: EtOH_10


title: erk7 starved rep4

city: Helsinki

first: Krista

last: Kokki

address: Viikinkaari 9, Biocenter 1, Institute of Biotechnology P.O.Box. 56

department: Department of Biosciences (Genetics)

country: Finland

institute: University of Helsinki

description:
all_comparisons.txt
S 16

data_processing:
Sequenced reads were trimmed with Trimmomatic with parameters ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36
Sequences were mapped using TopHat (v2.1.0) to dmel R6.10 with parameter -p 4 and quantified with HTSeq (v2.7.6) with parameters -m HTSeq.scripts.count -m union -s reverse -a 10 -t exon -i Parent
Differentially expressed genes were calculated with R package limma with Benjamini-Hochberg correction, with genes with low counts (cpm<1 in more than one replicate) filtered
Genome_build: Flybase Drosophila melanogaster R6.10
Supplementary_files_format_and_content: tab delimited.txt file includes read counts for expressed genes for all samples and their statistics

source_name: whole larvae

growth_protocol: Control and ERK7 mutant flies were kept in egg laying champers with apple juice plates and yeast paste for 3 hours. 24 hours later the 1st instar larvae were transferred to standard lab food. 48 hours later larvae were transferred to either PBS + 0.5% agarose food or a fresh standard lab food. 6 hours later, larvae were collected from both food types for RNA extraction.

extract_protocol:
Larvae were frozen in liquid nitrogen and homogenized with a pestle and mortar in lysis buffer and vortexed. Samples were frozen for complete lysis of the tissue. Total RNA was extracted with Nucleospin RNA II kit according to manufacturer's protocol. Elution was done with water and the samples stored at -80°C. Library construction was performed by DNA sequencing and genomics lab at the Institute of Biotechnology with the following protocol: the total RNA samples were first treated with Dnase I. Then the mRNA was enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments. The first stand of cDNA was synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with magnetic beads. End reparation and 3'-end single nucleotide A addition was performed. Finally, sequencing adaptors were ligated to the fragments and fragment enrichment was done by PCR amplification.
Library construction was performed by DNA sequencing and genomics lab at the Institute of Biotechnology with the following protocol: mRNA was enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments. The first stand of cDNA was synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with magnetic beads. End reparation and 3'-end single nucleotide A addition was performed. Finally, sequencing adaptors were ligated to the fragments and fragment enrichment was done by PCR amplification.

value: erk7 mutant

value: whole larvae

tag: developmental stage

value: 3rd instar larvae


title: MOLM14 cell transfected with shCALCRL rep1

source_name: shCALCRL-E


title: 320428: CTL_10

value: Colon Organoid

value: Female


title: HH-049

tag: pfs

tag: histology

value: high

value: early


title: MOLM14 cell transfected with shcontrol rep3

source_name: shCTRL-C


title: 6_92a_2 VPS39 3d.rma-gene-full-Signal


title: HH-048

tag: age

tag: grade

value: low


title: 320432: CTL_8

value: RNA-sequencing


title: HH-053


title: 4_105a VPS39 3d.rma-gene-full-Signal


title: 320427: EtOH_11

value: Male


title: erk7 starved rep2

description:
all_comparisons.txt
S 14


title: 320426: CTL_11


title: HH-047


title: 2_92a VPS39 3d.rma-gene-full-Signal


title: erk7 starved rep1

description:
all_comparisons.txt
S 13


title: HH-046


title: erk7 starved rep3

description:
all_comparisons.txt
S 15


title: control starved rep4

description:
all_comparisons.txt
S 12

value: wild type


title: 320424: CTL_12

value: Distal


title: 320423: EtOH_13

value: EtOH


title: HH-043

value: Serous


title: HH-044

value: late


title: 9_105a_a SCR 3d.rma-gene-full-Signal

value: Control


title: HH-045


title: 320421: EtOH_14


title: control starved rep1

description:
all_comparisons.txt
S 9


title: 11_105a_b SCR 3d.rma-gene-full-Signal


title: control starved rep2

description:
all_comparisons.txt
S 10


title: control starved rep3

description:
all_comparisons.txt
S 11


title: 7_105a_2 SCR 3d.rma-gene-full-Signal


title: 3_105a SCR 3d.rma-gene-full-Signal