title: Female, KO, rep 4,run #3

library_source: transcriptomic single cell

data_processing:
The cell barcode and UMI are on Read 1. The structure of Read 1 is: [Barcode #1 7-10 bp] GA.T.A.+C.CC.T [Barcode #2 8 bp] [UMI 5bp]. The reads were filtered based on the presence of two sample barcode components separated by 22 bp in Read 1. The barcodes and UMI are the unique identifiers of each cell.
Reads were split into barcode-specific files (represnting an individual cell) and aligned using RSEM (v1.3.1) with --single-cell-prior option and Bowtie2 (v2.4.5) to the killifish genome. We used the output file to create a matrix of transcript per million (TPM) of each cell and each gene. The resulting matrix was analyzed in Python using scanpy package (v1.9.1).
Assembly: Nfu_20140520
Supplementary files format and content: Matrix table with TPM for every gene and every cell

molecule: polyA RNA

source_name: Ovary

growth_protocol: Male or female killifish were fed ad libidum.

extract_protocol:
Gonads were dissected from each fish according to (Astre, Moses & Harel, 2021) and kept on ice in full medium (L15, 1% penicillin-streptomycin, 50 μg/μl gentamicin, 15% FBS). When all dissections were complete, organs were washed once with L15, and media was replaced with digestion media (400 μl 0.25% trypsin) at 28°C for 2 hours. During the incubation, additional mechanical dissociation was applied by pipetting up and down periodically with a glass Pasteur pipette, followed by addition of 800μl of full medium to stop enzymatic digestion. Dissociated cells were passed through a 100μm cell strainer prior to FACS. For live/dead sorting by FACS, cells were stained with Propidium-iodide (PI, 1 μg/ml), incubated for 5 minutes, and live cells were sorted according to PI intensity using an Aria III Sorter (BD). Live cells were used for single cell RNA sequencing.
Microfluidic operations were performed using the Fluigent microfluidic pump system in a microfluidic device, that was fabricated by soft lithography following standard InDrop protocols (Klein et al., 2015; Mazutis et al., 2013), using some adaptations (Bavli et al., 2021; Sun et al., 2021). Cells were loaded at a concertation of 500,000 cells/ml in PBS, with a 10% v/v OptiPrep Density Gradient Medium (Sigma-Aldrich, cat #D1556), and were maintained in suspension using a magnetic micro-stirrer bar placed within the tube. Barcoded beads were prepared as previously described (Bavli et al., 2021; Sun et al., 2021). The reverse transcription/lysis mix consisted of 60 µL 5X First-Strand buffer (SuperScript™ III Reverse Transcriptase Kit, Invitrogen #18080044), 9 µL 10% (v/v) IGEPAL CA-630 (Sigma-Aldrich, Cat #I8896), 6 µL 25 mM dNTPs (NEB, Cat #N0446S), 10 µL 0.1 M DTT (SuperScript™ III Reverse Transcriptase Kit, Invitrogen Cat #18080044), 15 µL 1 M Tris-HCl (pH 8.0) (Sigma-Aldrich, Cat #T2319), 10 µL murine RNase inhibitor (NEB, Cat #M0314), 15 µL SuperScript™ III RT enzyme (200 U/µL, Invitrogen Cat #18080044), and 25 µL nuclease-free water (Sigma-Aldrich, Cat #W4502). The carrier oil was a mixture of HFE-7500 with 2% (w/w) fluorosurfactant (RAN Biotechnologies).   During a microfluidics run, all reagents, including the cell suspension, encapsulated cells, reverse transcription/lysis mix, and collection tubes were kept on ice. For each sample, three different collections were performed separately, to be used as technical replicates. Flow rates were 100 μL/h for both the cell suspension and reverse transcription/lysis mix, 25 μL/h for barcoded acrylamide beads (containing photocleavable barcoding poly-T primers), and 150 μL/h for carrier oil to produce 2 nL drops. Following the completion of the microfluidics stage, the collection tubes were exposed to UV for 10 min (6.5 J/cm2 of a 365-nm), to release photocleavable barcoding primers from the beads. Next, the UV-exposed emulsion was transferred to a reverse transcription reaction (50 °C for 2 h followed by 15 min at 70 °C for inactivation), and was demulsified to release the barcoded cDNA from the droplets by adding perfluoro-1-octanol (50 μl PFO, Sigma-Aldrich, cat #370533).   The upper aqueous phase containing the barcoded cDNA was transferred to a new well, followed by removal of unused primers and primer dimers by adding a 1:1 digestion mix (20 U/µL Exonuclease I, NEB, Cat #M0293; 20 U/µL HinfI enzyme, NEB, Cat #R0155; x1 Exonuclease I Reaction Buffer, NEB, Cat #B0293; x1 CutSmart buffer, NEB, Cat #B7204; and 30 μl of nuclease-free water). Samples were incubated for 1 h at 37 °C and 10 min at 80 °C, purified with AMPure XP beads (Beckman Coulter, Cat #A63882), and eluted in 13.5 μl TE buffer. Second strand synthesis was performed by the NEBNext mRNA Second Strand Synthesis Module (NEB, Cat #E6111) according to the recommended protocols (16 °C for 2.5 h, followed by 20 min at 65 °C). For linear amplification by in vitro transcription, second strand synthesis reaction products were combined with 24 μl T7 High Yield RNA Synthesis Kit (NEB, Cat #E2040) according to the recommended protocols. The reaction was incubated at 37 °C for 13 h, and the resulting RNA was purified with AMPure XP beads, and was used in subsequent library preparation steps.   Next, RNA was fragmented using an RNA fragmentation kit (Invitrogen, Cat #AM8740), followed by purification with AMPure XP beads. The resulting amplified and fragmented RNA was reverse transcribed using a random hexamer primer (PvG748-SBS12-RT (Alajem et al., 2021)). First-Strand synthesis was performed as previously described (Sun et al., 2021), using SuperScript™ III RT enzyme. Following reverse transcription, cDNA was purified with AMPure XP beads, and the resulting libraries were PCR amplified using standard PE1/PE2 full-length primer mix (2p fixed; 2p fixed (+barcode)), containing Illumina library indices for multiplexing, and using 14 amplification cycles (Sun et al., 2021). Amplified libraries were purified (AMPure XP beads), run in 2% agarose gels, and the desired 200-800 bp DNA library fragments were isolated using PureLink™ Quick Gel Extraction Kit (Invitrogen, cat #K210012). Library quality was confirmed by Agilent 2200 TapeStation nucleic acid system (Agilent) using the Agilent High Sensitivity D1000 DS DNA kit. The resulting libraries had an average size of 350-550 bp. Size-selected libraries were diluted to 4 nM, and combined into a pool for paired-end, single index sequencing on the Illumina NextSeq 550 instrument (Illumina 550 High Output v2, 75 cycle kit). Cycle distribution was 45 cycles for Read 1, 35 cycles for Read 2, and 8 cycles for library index read.

value: Ovary

tag: Sex

value: Female

value: One-month old

value: DND1 KO

tag: batch


title: GIST-T1, WT, H3K27ac, rep2

status: Public on Mar 06 2024

type: SRA

city: Boston

first: Kyung Lock

last: Kim

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

country: USA

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
ChIP-seq data were aligned to hg38 using BWA aln 0.7.4, requiring minimal mapping quality of 10
PCR duplicates were removed by Picard toolkit 2.9.2.
ChIP-Seq density tracks were generated by bedgraph to BigWig format after RPM normalization.
Peaks were called with MACS3, correcting against input controls.
Assembly: hg38
Supplementary files format and content: ChIP-seq density tracks in BigWig format

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: GIST-T1 cell line was obtained from Cosmo Biosciences. Cells were passaged in DMEM with 10% serum, 1X antibiotics and 1X Glutamax (Life Technologies).

extract_protocol:
For ChIP-seq, cultured cells were fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80ºC for at least overnight. Sonication of cultured cells was calibrated such that DNA was sheared to between 400bp and 2000bp. CTCF was immunoprecipitated with a monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling 3418). H3K27ac was immunoprecipitated with a polyclonal rabbit H3K27ac antibody from Active Motif (cat 39133).  H3K27me3 was immunoprecipitated with a polyclonal rabbit H3K27me3 antibody, clone C36B11 (Cell Signaling 9733).
ChIP DNA was used to generate sequencing libraries by NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

tag: cell line

tag: cell type

value: cell line established from a metastatic GIST

tag: genotype

value: WT


title: P124T1-577820 [D334T43 RNA-seq]

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

country: France

institute: Institut Curie

description: counts.RNA.Seq.FL.txt

library_source: transcriptomic

data_processing:
To analyze the iMEFs RNA-Seq libraries, adapters and low‐quality bases (<Q20) were removed from single- and paired-end reads with TrimGalore (v0.4.0) and Cutadapt (v1.8.2). Trimmed reads were then mapped to the mouse reference genome mm10 using the STAR (v2.7.0a) aligner and the corresponding gene annotation from GENCODE: release 23/GRCm38.p6. The following parameters were used for mapping of RNA-seq reads against the reference genome: --seedSearchStartLmax 20 --outSAMattributes NH HI NM MD --alignEndsType EndToEnd.
Gene counts were generated using FeatureCounts (Subread v1.5.1). Since iMEFs RNA-seq data include SE50 and PE100 datasets, we removed any potential batch effects with the removeBatchEffect function of the BioconductoR limma package prior to conducting the differential expression analysis with DESeq2.
Processing of FL RNA-Seq libraries was done similarly to that of iMEFs libraries, but reads were aligned to the human reference genome hg19 and annotated with the corresponding gene annotation from GENCODE (release 19/GRCh37.p13).
Assembly: mm10 for iMEFs libraries, hg19 for FL libraries
Supplementary files format and content: Processed data files include raw gene counts.

molecule: total RNA

source_name: Follicular lymphoma

growth_protocol: iMEFs were grown in Dulbecco’s Modified Eagle Medium (DMEM) high-glucose (4.5 g/L) supplemented with 10% fetal calf serum, nonessential amino acids and 2 mM L-glutamine at 37°C with 5% CO2 and 98% humidity.

extract_protocol:
To isolate RNA from MEFs, cells of all experimental conditions were grown simultaneously and RNA was extracted 3 days after plating 200,000 cells. Total RNA was isolated using Trizol-Chloroform extraction and isopropanol precipitation. cDNA was further obtained using the High Capacity cDNA RT kit.
RNA from FL samples was extracted using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. RNA quality was assessed on an automated Tapestation 4200 platform. RNA Integrity Numbers (RINs) were used to evaluate the integrity of RNA samples with > 7.0 considered intact and < 7.0 considered degraded.
iMEFs RNA-Seq libraries were prepared using the Swift Biosciences RNA library kit. FL RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA kit.

tag: tissue

value: Follicular lymphoma

value: EZH2 mut.


title: GIST-T1, WT, H3K27ac, rep1


title: Female, KO, rep 3, run #4

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

organism: Nothobranchius furzeri

tag: age


title: EpiSC_rep1

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
EpiSC_rep1
RNA_TPM.tsv

data_processing:
10X Genomic single-cell 3' RNA-seq
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, default parameters).
For each experiment FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("count pipeline", default parameters).
Assembly: mm10
Supplementary files format and content: For all samples there is one tar gz archive containing the gene-barcode matrices as produced by the Cell Ranger pipeline. They contain the MEX-formatted UMI count matrices of each sample, or if multiple libraries where sequence, the aggregated gene-barcode matrix.
PolyA RNA-seq
All RNAseq samples were pre-processed using cutadapt to remove adapter and trim low quality bases.
Reads were subsequently aligned against the human reference genome mm10 using STAR (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie was used for calculation of strand-specific TPMs.
Assembly: mm10
Supplementary files format and content: tsv of TPM values
Total RNA-seq
All RNAseq samples were pre-processed using cutadapt to remove adapter and trim low quality bases.
To remove rRNA all reads were first aligned against the rDNA databank (rfam-5s-database-id98) using STAR and unmapped reads were kept for the next step.
Reads were subsequently aligned against the human reference genome mm10 using STAR (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie was used for calculation of strand-specific TPMs.
Assembly: mm10
Supplementary files format and content: tsv of TPM values
Bisulfite-Seq
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20. Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads, max 150 reads).
Assembly: mm10
Supplementary files format and content: bigWig file of 10X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

organism: Mus musculus

source_name: cell line

extract_protocol:
RNA was isolated from the samples according to the manufacturer's instructions using the RNeasy kit (74004, Qiagen).
1 µg RNA was used as input for the library preparation. Prior to the construction of the library, the integrity and quality of the RNA were evaluated using a 4200 Agilent TapeStation device and RNA ScreenTape reagents (Agilent). Samples having a RIN > 7.0 for RNA integrity were used. The library was generated with the TruSeq Stranded mRNA capture kit (20020594, KAP Biosystems) following the manufacturer's instructions, with the exceptions listed below. Unique Dual-Indexed (UDI, KAPA biosystems) adapters were ligated and the libraries were amplified for 8 cycles. Quality and concentration were measured using a 4200 Agilent TapeStation instrument and D5000 ScreenTape reagents (Agilent).
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

value: cell line

value: 2D epiblast stem cells

value: Mouse pluripotent stem cells

value: wild-type

tag: treatment

value: Conversion of ESCs via FGF2-ActivinA treatment


title: P119T1-561105 [D334T42 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: ESC3D_rep3

description:
ESC_3D_rep3
RNA_TPM.tsv

value: 3D epiblast stem cells

value: Cultured in 3D Matrigel with FGF2-ActivinA-XAV-Noggin


title: E3.5_rep2

description:
E3.5_ICM_rep2
RNA_TPM.tsv

source_name: Embryo

extract_protocol:
RNA was extracted from the epiblast of E3.5, E4.5, E5.5, E6.5, and E7.5 following the manufacturer's protocol (PicoPure RNA isolation kit; KIT0204; ThermoFisher Scientific) and eluted in 7 L elution buffer. The full eluate was utilized to prepare the library. Prior to the construction of the library, the integrity and quality of the RNA were evaluated using a 4200 Agilent TapeStation device and RNA ScreenTape reagents (Agilent). Samples having a RIN > 7.0 for RNA integrity were used.
The library was generated with the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input kit (634485, Takara Bio) following the manufacturer's instructions, with the exceptions listed below. To account for the input differences, fragmentation of RNA was done for 6 minutes at 85 °C on E3.5 and E4.5 epiblast samples, and for 4 minutes at 94 °C on E5.5, E6.5, and E7.5 epiblast samples. Adapters and indices from Illumina were added to distinguish the libraries (SMARTer RNA Unique Dual Index kit, 634451, Takara Bio). Instead of NucleoMag beads, the libraries were purified with AMPure XP beads (A63880, Beckman Coulter). ZapR v3 and R-probes v3 were used to deplete ribosomal cDNA (supplied with the kit). Libraries were amplified for thirteen cycles, purified, and analyzed for quality and concentration using a 4200 Agilent TapeStation instrument and D5000 ScreenTape reagents (Agilent).
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

value: Embryo

value: Strain:CD-1; embryo sex:male/female

value: no treatment


title: Female, KO, rep 3, run #3

value: Ovary

value: Female


title: ESC3D_rep2

description:
ESC_3D_rep2
RNA_TPM.tsv


title: GIST-T1, WT, CTCF, rep2


title: EpiSC_rep3

description:
EpiSC_rep3
RNA_TPM.tsv


title: Female, KO, rep 2, run #4

value: One-month old

value: DND1 KO


title: ESC3D_rep1

description:
ESC_3D_rep1
RNA_TPM.tsv


title: P14T3-599842 [D334T40 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: P93T2-418983 [D334T41 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: Female, KO, rep 1, run #2


title: GIST-T1, InsH, WCE, rep2

value: cell line established from a metastatic GIST

value: InsH


title: Embryo3D_rep3

description:
Embryo_3D_rep3
RNA_TPM.tsv


title: P3T2-495750 [D190T16 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: Follicular lymphoma

value: EZH2 mut.


title: Embryo3D_rep2

description:
Embryo_3D_rep2
RNA_TPM.tsv

value: cell line


title: Female, KO, rep 1, run #1


title: Male, KO, rep 4, run #4

source_name: Testis

value: Testis

value: Male


title: P99T1-492980 [D190T15 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: EZH2 WT


title: GIST-T1, InsF, WCE, rep2

value: InsF


title: Male, KO, rep 3, run #2


title: GIST-T1, InsE, WCE, rep2

value: InsE


title: P28T1-468558 [D190T13 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: scRNA_ESC

description: 10x Genomics

extract_protocol:
The single-cell suspension was washed three times in 0.4% BSA in 1X PBS by centrifugation at 4 °C for 5 minutes at 135 g in DNA Lobind tubes (0030108035, Eppendorf). The cells were counted with a hemocytometer (using Trypan blue staining), and the overall number was accounted for by counting dead cells as well. The number of input cells was determined following 10X genomics' recommendations for a sample recovery of 4,000 cells.
scRNAseq was performed on the cells using a 10X Genomics Chromium Single-cell 3' v2 kit. Except for the number of cycles used, single-cell libraries were generated according to the manufacturer's protocol. For cDNA amplification, 9 cycles in total were used. For library amplification, 8 cycles were used in total. The quality and concentration of cDNA and the library were assessed using a 4200 Agilent TapeStation device and D5000 ScreenTape reagents.
10X Genomic single-cell 3' RNA-seq
Accel-NGS Methyl-Seq DNA Library Kit (manufacturer's recommendation)

value: 3D epiblast stem cells

value: Mouse pluripotent stem cells

value: wild-type

value: Cultured in 3D Matrigel with FGF2-ActivinA-XAV-Noggin


title: GIST-T1, control, WCE, rep2

value: WT


title: Male, KO, rep 3, run #1

value: One-month old


title: Male, KO, rep 2, run #4

value: DND1 KO


title: P29T1-444287 [D190T12 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: scRNA_Embryo

description: 10x Genomics


title: Embryo3D_rep1

description:
Embryo_3D_rep1
RNA_TPM.tsv


title: GIST-T1, WT, CTCF, rep1

value: cell line established from a metastatic GIST


title: P25T1-438117 [D190T11 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: Male, KO, rep 1, run #3


title: P25T1-438117 H3K27me3 rep2 [D233C18]

data_processing:
Adapters and low‐quality bases (<Q20) were removed from Cut&Run-Seq reads with TrimGalore (v0.4.0) and Cutadapt (v1.8.2). Trimmed reads were mapped to the mouse reference genome mm10 with Bowtie2 (v2.2.5) using default parameters. PCR duplicates were with with Picard Tools MarkDuplicates (v1.97).
BigWig files were created using DeepTools bamCoverage (v3.0.2) with the following parameters: --normalizeUsingRPKM –ignoreForNormalization chrX chrY –samFlagInclude 64 –extendReads. Reads overlapping problematic, blacklisted regions (mm10-blacklist.v2.bed) were excluded from the computation of coverage with the option --blackListFileName.
In addition to scaling by library size, in order to remove any composition biases, we calculated a normalizing factor using the BioconductoR csaw::normFactors function. The normalization factor was passed onto DeepTools bamCoverage with the parameter --scaleFactor.
Processing of ChIP-Seq reads was done similarly to Cut&Run-Seq reads. Reads were however mapped to the human reference genome assembly hg19.
Assembly: mm10 for Cut&Run-Seq libraries; hg19 for ChIP-Seq libraries
Supplementary files format and content: BigWig files of genome-wide enrichment of the probed histone modification.

extract_protocol:
Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018).
In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes.
In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes.
Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction.
Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100).

tag: antibody


title: P23T1-436388 [D190T10 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: GIST-T1, InsF, WCE, rep1


title: P12T1-419652 [D190T08 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: GIST-T1, InsE, WCE, rep1


title: GIST-T1, InsH, WCE, rep1

value: InsH


title: GIST-T1, InsG, WCE, rep2

value: InsG


title: P13T1-422898 [D190T09 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: Follicular lymphoma


title: Female, WT, rep 3, run #3

value: Ovary

value: Female


title: RNAseq mouse 5

city: Shanghai

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

data_processing:
We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs, tsRNA (tRNA-derived small non-coding RNA), rsRNA (rRNA-derived small non-coding RNA), small snoRNAs, lncRNA, and mRNA, successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo-siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others.
We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM (transcripts per kilobase of exon model per million mapped reads) by StringTie.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include TPM values or raw counts for each Sample

source_name: oocyte

extract_protocol:
Total RNA from oocytes of different species were extracted with TRIzol Reagent (Ambion, USA), respectively.
Small RNA library construction. Briefly, the single oocytes were incubated at 72 °C for 3 min then cooled in ice. After 3′ adapter ligation, the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de-adenylates. Small RNAs were reverse-transcribed after 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel.
mRNA library construction. In brief, single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte, 1 μl of a 1/500,000-1/50,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, 4456740) was added. After reverse transcription and PCR pre-amplification, cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.

value: oocyte

value: female

tag: Stage

value: MII

value: wild type


title: Female, WT, rep 3, run #4


title: P16T1-477055 [D190T14 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: EZH2 WT


title: Female, WT, rep 2, run #2


title: P89T1-374818 [D190T07 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: EZH2 mut.


title: RNAseq mouse 4


title: GIST-T1, InsH, H3K27me3, rep2


title: P59T2-571562 [D240T43 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: GIST-T1, control, WCE, rep1


title: Female, WT, rep 2, run #1


title: RNAseq mouse 2


title: GIST-T1, InsF, H3K27me3, rep2

value: InsF


title: GIST-T1, InsG, H3K27me3, rep2


title: RNAseq mouse 3


title: Female, WT, rep 1, run #4


title: P161T3-664187 [D240T41 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: Female, WT, rep 1, run #3


title: GIST-T1, InsG, WCE, rep1


title: P160T1-664100 [D240T40 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: GIST-T1, InsE, H3K27me3, rep2

value: InsE


title: P141T1-606917 [D240T39 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: Male, WT, rep 2, run #4

value: Testis

value: Male

value: WT


title: mouse control

value: control


title: GIST-T1, control, H3K27me3, rep2

value: cell line established from a metastatic GIST


title: mouse oxidation

value: NaIO4 oxidation


title: GIST-T1, InsH, H3K27me3, rep1

value: InsH


title: Male, WT, rep 2, run #3

value: One-month old


title: P122T2-565463 [D240T37 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: Follicular lymphoma


title: small RNA mouse 5

value: oocyte

tag: molecule subtype

value: small RNA


title: Male, WT, rep 3, run #2


title: GIST-T1, InsG, H3K27me3, rep1

value: InsG


title: small RNA mouse 4

value: female

value: MII

value: wild type


title: P162T1-667100 [D240T42 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: EZH2 WT


title: P123T3-574265 [D240T38 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: EZH2 mut.


title: P121T1-565213 [D240T36 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: Male, KO, rep 2, run #3

value: Testis

value: DND1 KO


title: GIST-T1, InsF, H3K27me3, rep1

value: InsF


title: Male, WT, rep 1, run #1

value: Male

value: WT


title: Male, WT, rep 1, run #4


title: GIST-T1, InsE, H3K27me3, rep1

value: cell line established from a metastatic GIST

value: InsE


title: small RNA mouse 2


title: small RNA mouse 3


title: P102T2-386667 [D240T35 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: RNAseq mouse 1


title: P100T2-525120 [D240T34 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: GIST-T1, control, H3K27me3, rep1


title: RNAseq guinea pig 2

organism: Cavia porcellus

value: GV


title: small RNA mouse 1


title: GIST-T1, InsH, H3K27ac, rep2

value: InsH


title: RNAseq guinea pig 1

value: oocyte


title: RNAseq pig 5

organism: Sus scrofa domesticus


title: P96T2-422698 [D240T33 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: Follicular lymphoma


title: GIST-T1, InsG, H3K27ac, rep2

value: InsG


title: P70T2-374143 [D240T32 RNA-seq]

description: counts.RNA.Seq.FL.txt


title: RNAseq pig 4

value: female


title: guinea pig oxidation

value: NaIO4 oxidation


title: guinea pig control

value: wild type

value: control


title: GIST-T1, InsF, H3K27ac, rep2


title: guinea pig PIWIL3 IP

value: PIWIL3 IP


title: RNAseq pig 2

value: MII


title: GIST-T1, control, H3K27ac, rep2


title: guinea pig PIWIL1 IP

value: PIWIL1 IP


title: M5

city: Stillwater,

first: Khursheed

last: Iqbal

state: OK

address: 310 N Monroe St,

institute: Oklahoma state university

description: Transcript profiles were generated from control shRNA and NOTUM shRNA exposures in CT27 human TS cells cultured in conditions promoting EVT cell differentiation (n=3 experiments per group, including separate transductions). Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer. Barcoded cDNA libraries were multiplexed onto a TruSeq paired-end flow cell and sequenced (100-bp paired-end reads) with a TruSeq 200-cycle SBS kit (Illumina). Samples were run on Illumina HiSeq2500 sequencers located at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 12.0 (Qiagen).

data_processing:
Reads from *.fastq files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Assembly: human reference genome (GRCh37)

source_name: human trophoblast stem cell

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (euglycemia vs hyperglycemia).

value: trophoblast stem cell

tag: shRNA


title: GIST-T1, InsE, H3K27ac, rep2


title: P20T1-432387 [D240T31 RNA-seq]

description: counts.RNA.Seq.FL.txt

value: EZH2 WT


title: M4


title: M6


title: pig oxidation


title: guinea pig lgG IP

value: lgG IP


title: RNAseq pig 1


title: GIST-T1, InsG, H3K27ac, rep1

value: cell line established from a metastatic GIST


title: M3


title: guinea pig input

value: input


title: pig control


title: M2


title: pig PWIL3 IP


title: small RNA guinea pig 4

value: GV

value: small RNA


title: GIST-T1, InsF, H3K27ac, rep1

value: InsF


title: GIST-T1, InsH, H3K27ac, rep1

value: InsH


title: GIST-T1, InsE, H3K27ac, rep1

value: InsE


title: M1


title: small RNA guinea pig 3

value: oocyte

value: female


title: RNAseq guinea pig 3

value: wild type


title: RNAseq pig 3


title: GIST-T1, control, H3K27ac, rep1

value: WT


title: CHIR3

description: Transcript profiles were generated from vehicle control and CHIR99021 (2 µM)  exposures in CT27 human TS cells cultured in conditions promoting EVT cell differentiation (n=3 experiments per group). Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer. Barcoded cDNA libraries were multiplexed onto a TruSeq paired-end flow cell and sequenced (100-bp paired-end reads) with a TruSeq 200-cycle SBS kit (Illumina). Samples were run on Illumina HiSeq2500 sequencers located at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 12.0 (Qiagen).


title: CHIR2


title: small RNA guinea pig 2


title: GIST-T1, InsG, CTCF, rep2

value: InsG


title: CHIR1


title: pig input

value: MII


title: small RNA guinea pig 1


title: GIST-T1, InsH, CTCF, rep2


title: EVT_CHIR_Vehicle3

value: control


title: WT_8.2

city: Seattle

first: Jennifer

last: Davis

state: WA

address: 815 Mercer Street D342

department: Bioengineering & Pathology & Laboratory Medicine

institute: University of Washignton

data_processing:
Raw reads were filtered by BGI to remove adapter sequences and low quality reads.
Cleaned reads were aligned to reference genomes (GRCm38/mm10) using STAR with de novo junction discovery and summarized at the gene level using featureCounts.
For analysis of RNAseq data, raw counts were normalized to transcripts per million (TPM) and the fraction of RNA remaining at 4 and 8 hours was calculated for each transcript with an average of >10 TPM at baseline. To account for differences in sequencing depth and RNA composition, RNA fractions were normalized using an adaptation of DESeq2’s median of ratios method in which the geometric mean of the fraction of remaining RNA was calculated for each transcript and then sample-specific normalization factors were determined by calculating the median ratio of all ratios of the fraction of RNA remaining. Subsequently, normalized fractions were calculated for each sample and a moderated t-test was implemented from the limma package to compare normalized fractions of RNA remaining between genotypes.
Assembly: GRCm38
Supplementary files format and content: "raw_counts.csv" = csv file containing raw counts for each gene for each sample.
Supplementary files format and content: "corrected_ratios.csv" = csv file containing normalized ratios of remaining transcript compared to baseline

source_name: isolated adult mouse cardiomyocyte

growth_protocol: Mouse ventricular myocytes were freshly isolated by Langendorff perfusion with Liberase TM (0.225mg/mL, Roche) in Krebs-Henseleit buffer (135mM NaCl, 4.7mM KCl, 0.6mM KH2PO4, 0.6mM Na2HPO4,1.2mM MgSO4, 20mM Hepes,10μM BDM, and 30mM Taurine) as previously described. Ventricular myocytes were mechanically dispersed and filtered through a 200μm nylon mesh then allowed to sediment for 5-10minutes. Sedimentation was repeated three times using increasing Ca2+ concentration from 0.125 to 0.25 to 0.5mmol/L. Myocytes were then resuspended in plating media (DMEM/10% FBS/10mM BDM) and plated on laminin-coated coverslips for 3 hours.

extract_protocol:
Total RNA was extracted using TRIzol and the Qiagen RNeasy kit.
Libraries were prepared at BGI using their standard approach based on the DNBseq platform.

treatment_protocol: Plating media was replaced with culture media (DMEM/10mM BDM/100mg/ml BSA with the addition of 2μg/mL Actinomycin D (ActD). Myocytes were harvested at baseline and 4- and 8-hours after initiating ActD Treatment.

value: isolated adult mouse cardiomyocyte

tag: hours after_actd


title: small RNA pig 4


title: WT_8.3


title: small RNA pig 5


title: GIST-T1, InsE, CTCF, rep2


title: WT_8.1


title: small RNA pig 3


title: pig PWIL1 IP

value: PIWIL1 IP


title: GIST-T1, control, CTCF, rep2


title: EVT_CHIR_Vehicle1

value: trophoblast stem cell


title: small RNA pig 2


title: RNAseq human 5


title: WT_4.1


title: small RNA pig 1


title: GIST-T1, InsG, CTCF, rep1

value: cell line established from a metastatic GIST


title: GIST-T1, InsH, CTCF, rep1


title: pig lgG IP

value: lgG IP


title: WT_0.3


title: RNAseq human 4

value: GV


title: RNAseq human 3


title: GIST-T1, InsF, CTCF, rep1


title: WT_0.2


title: border zone and injured ventricle tissues, mut

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw reads were aligned against the zebrafish genome (DanRer11) and counted by StarSolo.
Secondary analysis was performed in Annotated Data Format.
After preprocessing, cells were analyzed via the Scanpy framework.
Preprocessed counts were used to calculate quality metrics in order to estimate cell quality regarding ribosomal content, mitochondrial content, number of genes and total read count.
Doublets were removed by Scrublet.
Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance.
Assembly: DanRer11
Supplementary files format and content: Tab-separated files of barcodes, gene annotations and gene counts.

organism: Danio rerio

extract_protocol:
To isolate cells of wild-type and cd74a; cd74b mutant samples, the border zone and injured tissues of four ventricles (from two females and two males each) were used.  For both EdCs and whole border zones and injured tissues, dissociation was performed using the Pierce Primary Cardiomyocyte Isolation Kit, (Thermo Fisher Scientific) according to the manufacturer’s protocol and with a few modifications, as previously published (PMID: 34516874). Dead cells were removed using a LeviCell 1.0 (Levitas Bio), following tissue dissociation.
The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3? Reagent Kits v3.1 (10xGenomics). Single cell RNAseq library preparation was done using standard protocol. Sequencing was done on Nextseq2000.

value: cd74a;cd74b mutant


title: border zone and injured ventricle tissues, wt

value: wild-type


title: GIST-T1, InsF, CTCF, rep2

value: InsF


title: RNAseq human 2


title: WT_0.1


title: KO_8.3

value: MBNL1 loss-of-function (KO)


title: EVT_CHIR_Vehicle2


title: GIST-T1, control, CTCF, rep1


title: Mut_biol_rep1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Reads with a quality drop below a mean of Q15 in a window of 5 nucleotides92 were trimmed using Trimmomatic version 0.39.  The analyses only included reads with a minimum of 15 nucleotides.
Trimmed reads were aligned against the Ensembl zebrafish genome version danRer11 (ensembl release 104) using STAR 2.7.9a with the parameters “--outFilterMismatchNoverLmax 0.1 --alignIntronMax 200000”
Reads aligning to genes were counted with featureCounts 2.0.2 from the Subread package.  Only reads mapping at least partially inside exons were admitted and aggregated per gene.  Reads overlapping multiple genes or aligning to multiple regions were excluded.
Identification of differentially expressed genes was performed using DESeq2 version 1.30.0.  Significantly DEGs were classified with Benjamini-Hochberg corrected p-value < 0.05 and −0.59≤ log2FC ≥+0.59.
The Ensemble annotation was enriched with UniProt data (release 12.04.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource [UniProt]).
Assembly: danRer11
Supplementary files format and content: libraray-size normalized counts

source_name: Heart ventricle

growth_protocol: Animal husbandry followed standard conditions in accordance with institutional (Max-Planck-Gesellschaft) and national ethical and animal welfare guidelines approved by the ethics committee for animal experiments at the Regierungspräsidium Darmstadt, Germany.  All efforts were made to minimize pain, distress, and discomfort.  Anesthesia was performed by incubating zebrafish in 0.6 mM tricaine solution (MS-222; Sigma-Aldrich).  Euthanasia was performed using a lethal dose of anesthetic.  Hearts were collected following euthanasia.

extract_protocol:
The RNA of single ventricles (one female and one male per condition) was isolated using the RNeasy Micro Kit (Qiagen), according to the manufacturer's instructions.  Trimmed reads were aligned against the Ensembl zebrafish genome version danRer11 (ensembl release 104) using STAR 2.7.9a with the parameters “--outFilterMismatchNoverLmax 0.1 --alignIntronMax 200000”
1µg of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme).

value: Heart ventricle

value: cd74a; cd74b mutant

value: Cryoinjury


title: RNAseq human 1

value: oocyte

value: female

value: wild type


title: Zebrafish heart 105275

data_processing:
Raw reads were aligned against the zebrafish genome (DanRer11) and counted by StarSolo.
Secondary analysis was performed in Annotated Data Format.
After preprocessing, cells were analyzed via the Scanpy framework.
Preprocessed counts were used to calculate quality metrics in order to estimate cell quality regarding ribosomal content, mitochondrial content, number of genes and total read count.
Doublets were removed by Scrublet.
Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance.
Assembly: DanRer11
Supplementary files format and content: Tab-separated files of barcodes, basic observations, variable annotations and gene counts.

source_name: heart ventricle

extract_protocol:
To isolate immune cells, pools of three whole ventricles from Tg(mhc2dab:EGFP); Tg(ptprc:DsRed) zebrafish (containing at least one female and one male) were used.  Ventricles were cut into small pieces and dissociated in a 1× PBS solution containing 200 µg/ml of Liberase DL (Roche) for 20 min at 33ºC with constant agitation.  The solution was gently pipetted up and down every 3 min to promote tissue disaggregation.  The cell suspensions were passed through a 35 µm nylon mesh by centrifugation into Falcon round bottom polystyrene test tube (Corning Inc.) at 300 g for 4 min at 4ºC. EGFP+ and/or DsRed+ cells were sorted using a FACSAria III (BD) sorter, following exclusion of dead cells using DAPI staining.  Cells were sorted into a 20% FBS solution (in 1× PBS) and subsequently used for scRNA-Seq analysis.
Single cell RNAseq was performed on ICELL8 platform (Takara Bio) using the V2 protocol with in-chip preamplifcation. Samples were pre-sorted into HBSS (Gibco) in a concentration of 20 cells/µl and stained with Hoechst dye (Invitrogen) for 5min at RT prior loading to MSND dispenser. For each sample 1 dispense (in ~630 wells) were made on one 5184 well chip resulting in 1479 wells containing a single cell after selection in CellSelect software (Takara Bio). Selected wells were processed for RT, in-chip preamplification and cDNA was pooled for final library preparation using standard Nextera protocol (Illumina). Library was checked in Labchip Gx touch 24 (Perkin Elmer) and sequenced on Nextseq500 (Illumina) using V2 chemistry and paired-end setup (11bp Read1, 80bp Read2). A total of 656M reads were obtained.

value: heart ventricle

value: immune cells

tag: time

value: mixed samples (6, 24, 72 hours post-cryoinjury (hpci) and 7, 14, 30 days post-cryoinjury (dpci))


title: human oxidation

value: NaIO4 oxidation


title: KO_8.2

value: isolated adult mouse cardiomyocyte


title: WT2_biol_rep2

treatment_protocol: Reads with a quality drop below a mean of Q15 in a window of 5 nucleotides92 were trimmed using Trimmomatic version 0.39.  The analyses only included reads with a minimum of 15 nucleotides.


title: WT_4.2

value: WT


title: human control

value: GV

value: control


title: KO_8.1


title: RNAseq dog only 3

organism: Canis lupus familiaris

extract_protocol:
Total RNA from oocytes of different species were extracted with TRIzol Reagent (Ambion, USA), respectively.
Small RNA library construction. Briefly, the single oocytes were incubated at 72 °C for 3 min then cooled in ice. After 3′ adapter ligation, the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de-adenylates. Small RNAs were reverse-transcribed after 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel.
mRNA library construction. In brief, single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte, 1 μl of a 1/500,000-1/50,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, 4456740) was added. After reverse transcription and PCR pre-amplification, cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.
miRNA-Seq and RNA-Seq

value: MII


title: WT1_biol_rep1


title: RNAseq dog only 2


title: small RNA human 4

value: small RNA


title: MC38 cells KOSRC-1_3

city: Xiamen

first: Yilin

last: Hong

address: Xiang'an South Road

institute: Xiamen University

data_processing:
Hisat2 for sequence alignment
Stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
Samtools tools for related file processing
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Xls file include expression  values for each sample

source_name: colorectal

growth_protocol: MC38 cells weremaintained in RPMI 1640 medium supplemented with 10% FBS  in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using the RNeasy Mini Kit (Qiagen, Carlsbad, USA) according to the manufacturer’s instructions
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: MC38 cells treated with IFNγ (100 ng/mL) for 24h.

value: colorectal

value: colorectal cancer cells

value: IFN-gamma


title: KO_4.3

value: MBNL1 loss-of-function (KO)


title: RNAseq dog only 1

value: oocyte


title: GIST-T1, InsE, CTCF, rep1

value: cell line established from a metastatic GIST

value: InsE


title: small RNA human 3

value: female

value: wild type


title: KO_4.2


title: Mut2_biol_rep2

value: Heart ventricle

value: cd74a; cd74b mutant

value: Cryoinjury


title: small RNA human 2


title: MC38 cells KOSRC-1_1


title: KO_4.1

value: isolated adult mouse cardiomyocyte


title: MC38 cells KOSRC-1_2


title: dog only oxidation

value: NaIO4 oxidation


title: small RNA dog only 3


title: small RNA human 1

value: GV


title: ΔSslac2-1 GMM, rep 3

city: Madison

first: Mehdi

last: Kabbage

state: Wisconsin

address: 583 Russell Labs, 1630 Linden Dr.

department: Plant Pathology

institute: University of Wisconsin - Madison

data_processing:
Original image data file from high-throughput sequencing was transformed to sequenced reads by CASAVA base recognition
Reads were mapped Sclerotinia sclerotiorum reference genome using HISAT2
Raw counts for each gene were generated using the feature Counts tool from Subread
Raw counts data were normalized with the DESeq normalization method using the DESeq2 package
The normalized gene counts were transformed to log2 scale using the voom method from the R Limma package and then used to generate differential expression (log2(fold change)) values
Assembly: Sclerotinia sclerotiorum 1980 UF-70
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Sclerotinia sclerotiorum

source_name: hyphae

growth_protocol: WT (1980) and mutant strains were grown in 1% GMM for 3 days.

extract_protocol:
Total RNA was extracted using the Maxwell RSC Plant RNA Kit
RNA libraries for RNA-seq were prepared using polyA selection

treatment_protocol: At the end of 3 days, cultures were moved to fresh medium containing 1% soybean SE and allowed to grow for 4h prior to flash freezing in liquid nitrogen.

tag: strain

value: hyphae

value: Sslac2 knockout

value: GMM


title: MC38 cells KOCtrl_2

value: colorectal

value: colorectal cancer cells

value: Ctrl


title: MC38 cells KOCtrl_3

value: IFN-gamma


title: dog only control

value: oocyte

value: MII

value: control


title: KO_0.2

value: MBNL1 loss-of-function (KO)


title: small RNA dog only 2

value: female

value: wild type


title: small RNA dog only 1


title: MC38 cells KOCtrl_1


title: ΔSslac2-1 GMM, rep 2


title: KO_0.3


title: ΔSslac2-1 GMM, rep 1


title: P1_Ctl4

data_processing:
Raw reads were filtered by BGI to remove adapter sequences and low quality reads.
Cleaned reads were aligned to reference genomes (GRCm38/mm10) using STAR with de novo junction discovery and summarized at the gene level using featureCounts.
Differential expression analysis was completed using DESeq2 using the standard workflow.
For alternative splicing analysis, reads were quantified at the transcript level using Salmon and alternative splicing analysis was completed using IsoformSwitchAnalyzeR.
Assembly: GRCm38
Supplementary files format and content: csv file containing raw counts for each gene for each sample.

source_name: Heart - ventricle

value: Heart - ventricle

value: Ctl

tag: time after_knockout


title: RNAseq dog 4

value: SF


title: Input

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the Star aligner (Dobin et al. 2013) and RPM normalized bedgraphs were generated using the Star –outWigNorm option. RPM normalized bedgraphs for IPs were converted to wigs, normalized to DNA input by subtraction saved in bedgraph format using Deeptools (Ramirez et al. 2016). Values that were negative after input subtraction were set to zero in the final bedgraph.

organism: Schizosaccharomyces pombe

growth_protocol: Growth in YEA 30°C

extract_protocol:
Cells were crosslinked using 1% formaldehyde at room temperature for 20 min. Cells were spun at 2,000g for 10 min and pellets were lysed using glass beads and lysis buffer (50mM Hepes/KOH, 140mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% DOC plus protease inhibitors). Cell lysates were sheared using a Bioruptor-300 (Diagenode) to an approximate size of 300–600 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

value: h+ ura4-D18 lys1-131 Z:NAT>Padh31:tetR-tdTomato cen2:tetO>ura4+ leu1-32

tag: chip antibody

value: Abcam anti-GFP 290

tag: growth

value: Growth in YEA 30C

tag: fixation

value: 1% Formaldehyde

tag: condition

value: Input control


title: P1_Ctl3


title: Scm3-∆CYS

value: h+ ura4-D18 lys1-131 Z:NAT>Padh31:tetR-tdTomato cen2:tetO>ura4+ leu1+>pDUAL-nmt41-GFP-scm3-dCYS

value: Scm3-dCYS IP


title: ΔSslac2-1 Green Stem Extract, rep 3

tag: cell type

value: hyphae

value: Sslac2 knockout

value: Green Stem Extract


title: RNAseq dog 3

value: oocyte

tag: Sex

tag: genotype


title: ΔSslac2-1 Green Stem Extract, rep 2


title: P1_Ctl2

tag: tissue

tag: age


title: RNAseq dog 2


title: ΔSslac2-1 Green Stem Extract, rep 1

tag: treatment


title: P1_Ctl1


title: Untagged

value: Notag control


title: RNAseq dog 1

value: female

tag: Stage


title: WT (1980) GMM, rep 3

value: WT

value: GMM


title: P7_Ctl3

value: Heart - ventricle

value: Ctl


title: RNAseq Chinese hamster 5

organism: Cricetulus griseus

value: GV

value: wild type


title: KO_0.1

value: isolated adult mouse cardiomyocyte

value: MBNL1 loss-of-function (KO)


title: RNAseq Chinese hamster 4


title: WT (1980) GMM, rep 1


title: WT (1980) GMM, rep 2


title: P7_Ctl2


title: dog control

value: SF

value: control


title: P7_Ctl1


title: RNAseq Chinese hamster 3


title: WT (1980) Green Stem Extract, rep 3


title: WT (1980) Green Stem Extract, rep 2


title: small RNA dog 3

tag: molecule subtype

value: small RNA


title: RNAseq Chinese hamster 2


title: small RNA dog 4


title: P7_Tg3

value: MBNL1 gain-of-function (Tg)


title: small RNA dog 2


title: Scm3-FL

value: h+ ura4-D18 lys1-131 Z:NAT>Padh31:tetR-tdTomato cen2:tetO>ura4+ leu1+>pDUAL-nmt41-GFP-scm3+

value: Abcam anti-GFP 290

value: Growth in YEA 30C

value: 1% Formaldehyde

value: Scm3-FL IP


title: RNAseq Chinese hamster 1

value: oocyte

value: female


title: P7_Tg2

value: Heart - ventricle


title: small RNA dog 1


title: Female, dnd1 mutant, old sample 23

description:
Female, dnd1 mutant, old
Female, DND1 KO, old

data_processing:
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8), multiQC (v1.12), fastx-toolkits (v0.0.13), Trim Galore! (v0.6.4), and Cutadapt (v3.4). Options were set to remove Illumina TruSeq adapters and end sequences to retain high-quality bases with phred score > 20 and a remaining length > 20 bp. Successful processing was verified by re-running FastQC. Reads was mapped and quantified to the killifish genome Nfu_20140520 using STAR 2.7.6a. Differential gene expression as a function of genotype was performed using the edgeR package (v3.32.1).
Assembly: Nfu_20140520
Supplementary files format and content: CSV file included raw counts for each sample.

source_name: Liver

extract_protocol:
Fish were euthanized in 500 mg/L of Tricaine (Sigma-Aldrich, A5040) in system water. Dissections were carried out under a stereo binocular (Leica S9D) at room temperature. Livers were collected and flash frozen in liquid nitrogen and kept in -80°C until use. Tissues were homogenized by metal beads in 300 μl of TRI reagent (Sigma-Aldrich, T9424), using a TissueLyzer LT (QIAGEN, #85600) with a dedicated adaptor (QIAGEN, #69980). RNA purification was performed using the Direct-zol RNA Miniprep kit (Zymo, R2052) according to the manufacturer’s instructions. RNA concentration and quality were determined by using an Agilent 2100 bioanalyser (Agilent Technologies).
Library preparation was performed using KAPA Stranded mRNA-Seq Kit (ROCHE-07962193001) according to the recommended protocols. Library quantity and pooling were measured by Qubit (dsDNA HS, Q32854), Size selection at 4% agarose gel. Library quality was measured by Tape Station (HS, 5067-5584). Libraries were sequenced by NextSeq 2000 P3, 50 cycle, 70 bp single-end (Illumina, 20046810) with ~35 million reads per sample.

value: Liver

value: Female

value: 25-week old

value: dnd1 mutant

tag: batch


title: P7_Tg1


title: dog oxidation

value: wild type

value: NaIO4 oxidation


title: Female, dnd1 mutant, old sample 14


title: P60_Ctl7

value: Ctl


title: small RNA Chinese hamster 4

value: GV

value: small RNA


title: P7_Tg4

value: MBNL1 gain-of-function (Tg)


title: Ascl1_filtered_feature_bc_matrix

first: Michael

last: Schappe

address: 240 Longwood

institute: Harvard Medical School

description: 10X Genomics

data_processing:
CellRanger pipeline v3.1.0
Assembly: mm10-1.2.0
Supplementary files format and content: 10X Genomics v3, Ascl1-CreER;Ai14
Supplementary files format and content: 10X Genomics v3, Calca-Egfp

source_name: Lung

extract_protocol:
Collected cells were individually encapsulated in nanodroplets using the 10X Genomics platform (v3 chemistry) and single-cell cDNA was prepared according to the manufacturer's protocol
10X Genomics v3 chemistry

value: Lung

value: Ascl1-CreER; Ai14


title: P60_Ctl6


title: P60_Ctl5


title: L211220MM01

city: Bern

first: Mojgan

last: Masoodi

address: Freiburgstrasse 18

department: Institute of Clinical Chemistry

country: Switzerland

institute: Inselspital, Bern University Hospital

data_processing:
BRB-seq libraries are multiplexed paired-end libraries containing multiple barcoded samples that need to be demultiplexed
Barcodes were demultiplexed using the barcode mapping file barcodes_96_V5A_brb.txt
We used STAR v2.7.9a (in STARsolo mode) to align, demultiplex (using a barcode mapping file), and produce read counts as well as UMI count matrix for all samples
STARsolo was used with the following extra parameters: --soloUMIdedup NoDedup 1MM_Directional --soloCBmatchWLtype 1MM --clipAdapterType CellRanger4 --outSAMmapqUnique 60 --runThreadN  --soloStrand Forward --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13 --soloUMIlen 9 --soloCellFilter None --soloCBwhitelist barcodes_96_V5A_brb.txt --soloFeatures Gene --outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM --outFilterMultimapNmax 1
Read count normalization (DESEq2) was performed using R
Assembly: mm10 (Ensembl GRCm38 r102)
Supplementary files format and content: Tab-delimited text files including raw counts and UMI values for each sample

extract_protocol:
RNA was harvested using the Rneasy mini kit (Qiagen).
The libraries were generated using MERCURIUS BRB-seq kit (PN 10813, Alithea) following the user guide. In brief, the RNA samples were reverse transcribed using barcoded oligo-dT primers. Illumina libraries were prepared with cDNA following tagmentation protocol and sequencing on the Illumina Nextseq instrument (Alpern et al, 2019).
RNA-seq (paired-end, multiplexed, including UMI)

value: WT

tag: diet

value: mixed sample (non-demultiplexed)


title: small RNA Chinese hamster 3

value: oocyte


title: E16.5_Mammary_Mes_rep5

city: Bristol

first: Qiang

last: Lan

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

data_processing:
All sequencing reads were processed for quality control, removal of low-quality reads, adaptor sequence and ribosomal RNA using fastqc version 0.11.8 , multiqc version 1.9 , Trimmomatic version 0.39  and SortMeRNA version 2.1 accordingly.
The filtered reads were mapped to the reference genome (mm10) using Salmon version 0.99.0
Read counts were extracted and normlized using tximport (1.15.10) and DESeq2 (3.15).
Assembly: mm10
Supplementary files format and content: tab separated, normalized counts file
Supplementary files format and content: rds file

source_name: E16.5 Mammary mesenchyme

extract_protocol:
Samples were lysed immediately after collection and stored in TRI Reagent (T9424, Sigma) at -80 °C. Total RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research, Irvine, CA) with DNase treatment according to the manufacturer's instructions. RNA quality was assessed with 2100 Bioanalyzer (Agilent, Santa Clara, CA) using Agilent RNA 6000 Pico Kit or Agilent RNA 6000 Nano Kit (Agilent, Santa Clara, CA). RNA concentration was determined using Qubit RNA HS Assay Kit (Q32855, Thermo Fisher) with Qubit 4 Fluorometer (Thermo Fisher).
cDNA libraries were prepared with Ovation SoLo RNA-seq System (NuGen/Tecan Genomics) according to manufacturer's instructions

value: E16.5 Mammary mesenchyme

tag: developmental stage


title: P60_KO9

value: Heart - ventricle

value: MBNL1 loss-of-function (KO)


title: E16.5_Mammary_Mes_rep4

tag: strain

value: Female


title: WT (1980) Green Stem Extract, rep 1

value: hyphae

value: Green Stem Extract


title: small RNA Chinese hamster 2

value: female

value: wild type


title: P60_KO8

tag: time after_knockout


title: Chinese hamster oxidation

value: NaIO4 oxidation


title: Female, dnd1 mutant, young sample 21

description:
Female, dnd1 mutant, young
Female, DND1 KO, young

value: Liver

value: 5-week old

value: dnd1 mutant


title: small RNA Chinese hamster 1

value: GV

value: small RNA


title: Female, dnd1 mutant, young sample 1


title: Chinese hamster control

value: control


title: RNAseq goat 3

organism: Capra hircus

value: MII


title: E16.5_Mammary_Mes_rep2


title: E16.5_Mammary_Mes_rep3


title: Male, dnd1 mutant, old sample 24

description:
Male, dnd1 mutant, old
Male, DND1 KO, old

value: Male

value: 25-week old


title: P60_KO7

value: Heart - ventricle


title: Calca_filtered_feature_bc_matrix

description: 10X Genomics

value: Lung

value: Calca-Egfp


title: Female, dnd1 mutant, old sample 12

value: Female


title: small RNA Chinese hamster 5

value: oocyte


title: E16.5_Mammary_Mes_rep1

value: E16.5 Mammary mesenchyme


title: P60_KO6

value: MBNL1 loss-of-function (KO)


title: Male, dnd1 mutant, old sample 20


title: RNAseq goat 1

value: female

value: wild type


title: P60_Ctl4

value: Ctl


title: Female, dnd1 mutant, old sample 13

value: Liver

value: dnd1 mutant


title: RNAseq goat 2


title: P60_Ctl3


title: Female, dnd1 mutant, young sample 26

value: 5-week old


title: E16.5_Fatpad_rep4

source_name: E16.5 Fatpad

value: E16.5 Fatpad


title: Male, dnd1 mutant, old sample 19


title: Male, dnd1 mutant, young sample 28

description:
Male, dnd1 mutant, young
Male, DND1 KO, young


title: P60_Ctl2


title: goat oxidation

value: MII

value: NaIO4 oxidation


title: goat control

value: control


title: E16.5_Fatpad_rep3


title: P60_Ctl1

value: Heart - ventricle


title: goat PIWIL3 IP

value: PIWIL3 IP


title: E16.5_Fatpad_rep2


title: Male, dnd1 mutant, young sample 25

value: Male


title: P60_KO5


title: goat PIWIL1 IP

value: PIWIL1 IP


title: Male, dnd1 mutant, young sample 27


title: goat lgG IP

value: oocyte

value: lgG IP


title: P60_KO4

value: MBNL1 loss-of-function (KO)


title: Male, dnd1 mutant, young sample 2


title: E13.5_Salivary_Mes_rep5

source_name: E13.5 Salivary Mesenchyme

value: E13.5 Salivary Mesenchyme

value: not applicable


title: Female, WT, old sample 9

description:
Female, WT, old
Female, WT, old

value: Female

value: 25-week old

value: WT


title: E13.5_Salivary_Mes_rep4


title: small RNA goat 3

value: female

value: wild type

value: small RNA


title: P60_KO2


title: Female, WT, old sample 11

description:
Female, WT, old
Female, WT, old

value: Liver


title: E13.5_Salivary_Mes_rep3


title: E16.5_Fatpad_rep5

value: E16.5 Fatpad


title: Female, WT, old sample 10

description:
Female, WT, old
Female, WT, old


title: goat  input

value: MII

value: input


title: small RNA goat 2


title: Female, WT, young sample 8

description:
Female, WT, young
Female, WT, young

value: 5-week old


title: P60_KO1

value: Heart - ventricle


title: E13.5_Salivary_Mes_rep2


title: small RNA goat 1

value: oocyte


title: E13.5_Salivary_Mes_rep1


title: RNAseq monkey 3

organism: Macaca fascicularis


title: Female, WT, young sample 7

description:
Female, WT, young
Female, WT, young


title: RNAseq monkey 4


title: RNAseq rabbit 4

organism: Oryctolagus cuniculus

value: GV


title: E16.5_Fatpad_rep1


title: Female, WT, young sample 6

description:
Female, WT, young
Female, WT, young


title: RNAseq monkey 2


title: E13.5_Ventral_Skin_Mes_rep5

source_name: E13.5 Ventral skin mesenchyme

value: E13.5 Ventral skin mesenchyme


title: RNAseq rabbit 3


title: P60_KO3

value: MBNL1 loss-of-function (KO)


title: Female, WT, young sample 22

description:
Female, WT, young
Female, WT, young


title: E13.5_Ventral_Skin_Mes_rep3

value: not applicable


title: RNAseq monkey 1


title: monkey oxidation

value: NaIO4 oxidation


title: RNAseq rabbit 2


title: E13.5_Ventral_Skin_Mes_rep4


title: E13.5_Ventral_Skin_Mes_rep2


title: Male, WT, old sample 18

description:
Male, WT, old
Male, WT, old

value: Male

value: 25-week old


title: monkey control

value: female

value: control


title: rabbit oxidation

value: wild type


title: RNAseq rabbit 1


title: Male, WT, old sample 16

description:
Male, WT, old
Male, WT, old

value: Liver

value: WT


title: small RNA monkey 5

value: MII

value: small RNA


title: rabbit control


title: E13.5_Mammary_Mes_rep5

source_name: E13.5 Mammary mesenchyme

value: E13.5 Mammary mesenchyme


title: small RNA monkey 4


title: Male, WT, old sample 15

description:
Male, WT, old
Male, WT, old


title: E13.5_Ventral_Skin_Mes_rep1


title: E13.5_Mammary_Mes_rep4


title: small RNA monkey 3


title: Male, WT, young sample 5

description:
Male, WT, young
Male, WT, young

value: 5-week old


title: E13.5_Mammary_Mes_rep3


title: small RNA rabbit 3

value: oocyte


title: Male, WT, young sample 4

description:
Male, WT, young
Male, WT, young


title: small RNA rabbit 2

value: GV


title: E13.5_Mammary_Mes_rep2


title: small RNA monkey 1


title: small RNA rabbit 1


title: Male, WT, young sample 3

description:
Male, WT, young
Male, WT, young


title: E13.5_Mammary_Mes_rep1


title: Male, WT, old sample 17

description:
Male, WT, old
Male, WT, old


title: CD81_opAsCas12a-gCH29

status: Public on Mar 05 2024

city: Palo Alto

first: Chris

last: Hsiung

state: CA

address: 3181 Porter Dr

institute: Arc Institute

description: gCH29 = crCD81-1

data_processing:
Raw fastq files were aligned to reference sequences using CRISPResso2, as detailed in the associated manuscript.
Assembly: hg19
Supplementary files format and content: Quantification of percentage of reads containing indels overlapping each position in the PCR amplicon

growth_protocol: K562 cells were cultured at 37deg. C with 5% CO2 in tissue culture incubators. Culture media consists of RPMI-1640 (Gibco cat# 22400121) containing 25 mM HEPES, 2mM L-glutamine, and supplemented with 10% FBS (VWR), 100 units/mL streptomycin, and 100 mg/mL penicillin. During the screen, K562 cells were cultured in flasks in a shaking incubator and the culture media was supplemented with 0.1% Pluronic F-127 (Thermo Fisher P6866).

extract_protocol:
For analysis at the CD55 and CD81 loci, genomic DNA was isolated using NucleoSpin Blood (Macherey-Nagel, Catalog no. 740951.50). For analysis at the KIT locus, cell lystates were generated using QuickExtract DNA Solution (Lucigen) and directly subjected to PCR amplification.
For analysis of CD55 and CD81 loci, PCRs for loci of interest were run using Amplicon-EZ (Genewiz) partial Illumina adapters and amplicons were processed using NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel, Catalog no. 740609.250). Paired end (2 x 250 bp) sequencing was completed at GENEWIZ (Azenta Life Sciences). For analysis of the KIT locus, cell lysates were subjected to 15 cycles of PCR to introduce Illumina sequencing primer binding sites and 0-8 staggered bases to ensure library diversity. After reaction clean-up using ExoSAP-IT kit (Thermo Fisher 78201), an additional 15 cycles of PCR was used to introduce unique dual indices and Illumina P5 and P7 adaptors. Libraries were pooled and purified by SPRIselect magnetic beads before paired-end sequencing using an Illumina MiSeq. Sequencing primer binding sites, unique dual indices (from Illumina TruSeq kits), P5 and P7 adaptor sequences are from Illumina Adaptor Sequences Document # 1000000002694 v16.
PCR amplicon sequencing

treatment_protocol: K562 cell lines engineered with the corresponding Cas12a protein constructs were transduced with crRNAs, sorted for transduced cells based on GFP-positivity. 200,000 cells were collected on day 14 after crRNA transduction.

tag: cell line


title: CD81_denAsCas12aKRAB-gCH29

description: gCH29 = crCD81-1


title: CD81_parental-gCH29

description: gCH29 = crCD81-1


title: CD81_multiAsCas12aKRAB-gCH29

description: gCH29 = crCD81-1


title: CD55_multiAsCas12aKRAB-gCH27

description: gCH27 = crCD55-4


title: CD55_denAsCas12aKRAB-gCH27

description: gCH27 = crCD55-4


title: CD55_opAsCas12a-gCH27

description: gCH27 = crCD55-4


title: small RNA rabbit 4


title: KIT_multiAsCas12a-gCH130

description: gCH130 = crCD55-4_crB2M-1_crKIT-2_crCD81-1


title: KIT_opAsCas12a-gCH130


title: KIT_denAsCas12aKRAB-gCH130


title: KIT_multiAsCas12aKRAB-gCH130


title: KIT_multiAsCas12a-gCH134

description: gCH134 = crCD55-4_crB2M-1_crB2M-3_crKIT-2_crKIT-3_crCD81-1


title: CD55_parental-gCH27

description: gCH27 = crCD55-4


title: KIT_denAsCas12aKRAB-gCH134


title: KIT_parental-none

description: K562 parental cells, no crRNA


title: Tracer TLS Multiseq - Multiseq barcodes

description: Multiseq barcodes library of the Tracer TLS pool

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
Processed using the deMULTIplex R pacakge for MULTI-seq sample barcode FASTQ alignment. In brief: The R functions found in 'MULTIseq.Align.Suite.R' can be used to convert MULTI-seq sample barcode FASTQ files into a sample barcode UMI count matrix. Think of this pipeline as 'CellRanger' for sample barcode data. This pre-processing pipeline can be split into four distinct steps: (1) Split raw FASTQs into cell barcode, UMI, and sample barcode sequences associated with a user-defined set of cell barcodes; (2) Remove reads that do not align with >1 mismatch to any MULTI-seq sample barcode reference sequence; (3) Remove reads representing duplicated UMIs on a cell-by-cell basis; (4) Convert this parsed read table to a sample barcode UMI count matrix.
Assembly: mm10
Supplementary_files_format_and_content:  TSV file with "<final.calls>\t<cellBC>\t<MultiSeqBCseq>\t<MultiSeqGroup>" represeting an entry for every cell containing a label for a MultiSeqGroup (final.calls), the cell barcode, the MultiSeq barcode sequence and the assigend MultiSeq group.
Library strategy: Amplicon-seq

organism: synthetic construct

source_name: Tracer TLS Multiseq - Multiseq barcodes

growth_protocol: Trunk-Like Structures (TLS) have been generated as previously described (Veenvliet, Bolondi et al 2020; Bolondi et al 2021) with some modifications to induce Cas9-based molecular recording. Briefly, mESCs were trypsinized on the feeder plate as described above and washed with ES+LIF. Cells were pelleted by centrifugation at 1000rpm for 5 minutes at room temperature and resuspended in 2ml ES+LIF. On three gelatinized (0.1% gelatin) wells of a 6-well plate, cells were sequentially plated for 25 minutes, 20 minutes and 15 minutes during which cells were kept in the incubator at 37°C and 5% or 7.5% CO2. With each transfer, cells were triturated to maintain a single cell suspension. Feeder-freed mESCs were then washed once in 5ml pre-heated (37°C) PBS containing MgCl2 and CaCl2 (Sigma D8662) and once in pre-incubated (37°C, 5% or 7.5% CO2) 5ml NDiff227 (Takara Y40002). mESCs were then pelleted by centrifugation for 5 minutes at 1000rpm and resuspended in 500µl of NDiff227. 10µl of the cell suspension was mixed with 10µl of Trypanblue (Bio-Rad 1450021) for automated cell counting with Luna Automated Cell Counter. 1x106 live cells were then used for nucleofection using the Amaxa 4D-Nucleofector X Kit for mESCs (Lonza V4XP-3012) in combination with 10µg of Cre-expressing plasmid DNA (Addgene #13775) using the manufacturer instruction and the CG-104 program. Nucleofected cells were then washed with 10ml pre-warmed N2Diff227, resuspended in 1ml N2Diff227 and counted again using the automated cell counting with Luna Automated Cell Counter. 500 cells were then plated in a volume of 30 to 40µl NDiff227 into each well of a 96-well round bottom, low attachment plate (Costar 7007 ultra-low attachment 96 well plate (7007)). Cells were then allowed to aggregate for 48 h. After these 48h cells were pulsed with 3µM CHIR99021 (CHIR, Merck Millipore) in 150µl NDiff227. After 72h, medium was refreshed by removing 150µl of the old media and adding the same volume of new, pre-incubated (37°C and 5% or 7.5% CO2) NDiff227. At 96h, structures were then embedded in 5% Growth-Factor-Reduced Matrigel (MG) (Corning 356231). To this end, fresh NDiff227 medium was pre-incubated for at least 20 minutes at 37°C and 5% or 7.5% CO2. Pre-incubated medium was then put on ice for 5 minutes, after which MG was added to achieve a final concentration of 5% in the culture wells. Medium was then put at room temperature for 5 minutes, during which 150µl of old medium was removed from the aggregates. New medium with MG (150µl) was then added, and the cultures were returned to the incubator and further cultured at 37°C and 5% or 7.5% CO2. Tracer TLS cultures were allowed to settle for at least 30 minutes before proceeding to further experimentation. For Tracer TLS treated with CHIR+LDN (Tracer TLSCL), 5µM CHIR together with 600nM LDN was added prior to MG and left from 96h to 120h.

extract_protocol:
Single-cell RNAseq (scRNA-seq) experiments have been performed as previously described (Veenvliet, Bolondi et al 2020). Briefly, Tracer TLS were generated as described above. Two individual 120h TLS (Tracer TLS 1 and 2) were selected based on the presence of one axis of elongation, clear formation of a neural tube domain and segmentation. Individual structures were picked with a p200 with the pipette tip cut-off at the 50µl mark, and serially washed through pipette transferring (cut 200µl tip) in wells filled with 200µl of 1xPBS/0.4%BSA (5 transfers) to get rid of the Matrigel. Each structure was then dissociated in 200µl TrypLE Express (Gibco) for 25 minutes at 37ºC, with pipetting every 5 minutes intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40µm. Cells were washed twice with 1ml 1xPBS/0.4%BSA with centrifugation steps performed for 5 minutes at 1200rpm in low DNAbind Eppendorf tubes. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomics, Chromium™ Single Cell 3’ v3.1; one structure per reaction). Single-cell libraries were generated according to the manual, with one modification: fewer PCR cycles (n=8) were ran than recommended during cDNA amplification or library generation/sample indexing to increase library complexity. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were sequenced with a minimum of 400 million paired end fragments according to parameters described in the manual.
Lineage tracing barcodes (intBCs) libraries were prepared for all samples via PCR amplification from the double stranded 10x cDNA. Briefly, 100ng of 10x cDNA was used to prepare 4x25µl PCR reactions for each sample. Amplification was carried out using Q5 2X MasterMix (NEB; M0492S) with the following steps: 98ºC 30sec/ 98ºC 10sec – 68ºC 30sec – 72ºC 40sec (10 cycles)/ 72ºC 2 minutes/ 4ºC hold. Next, the four reactions for each sample were pooled together and a double-sided AMPure XP beads (Beckman, A63881) cleanup (0.45X/0.7X) was performed to purify the intBCs libraries. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using asymmetric end sequencing (150 cycles kit; 28/91 FC-410-1002) on a Novaseq platform at a minimum of 100 million fragments per sample.

value: synthetic

value: LSL-Cas9-GFP-Tracer BC library + LentiBC


title: KIT_opAsCas12a-gCH134


title: small RNA monkey 2


title: Tracer TLS #2 - Lineage tracing

description: Lineage barcodes library of one Tracer TLS

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
First, Reads were aligned against the mouse genome (mm10 with additional chromosomes for GFP and mCherry), and barcodes and unique molecular identifiers were counted using ‘cellranger count’. The lineage tracing data for the TLS#1 and the Multiseq experiment were sequenced on the same flow cell. However, the indices could not be determined fully, and reads were merged between the two lineage tracing experiments. We went through a stringed filtering strategy based on the cell-barcode information to recover the data. First, we extracted the cell barcodes discovered in the associated scRNAseq data set. We then determined unique cell barcodes for each of the two datasets and filtered the lineage tracing information down to those cells with experiment-specific cell barcodes.
FASTQ files were processed using the Cassiopeia python package for  preprocessing for phylogeny-inference algorithms. In brief: the steps of the Cassiopeia pipeline are 1) converts the BAM files into an unmapped BAM, 2) collapses reads together into UMIs, 3) aligns sequences onto the reference target site sequence, and finally 4) calls alleles and lineage information at specific sites within the aligned target site.
Assembly: mm10
Supplementary_files_format_and_content: TSV of indel information for each target site in each cell barcode.
Library strategy: Amplicon-seq

source_name: Tracer TLS #2 - Lineage tracing

value: LSL-Cas9-GFP-Tracer BC library


title: Tracer TLS #1 - Lineage tracing

source_name: Tracer TLS #1 - Lineage tracing


title: KIT_enAsCas12a-gCH130


title: Tracer TLS Multiseq - Lenti barcodes

description: Lenti barcodes library of the Tracer TLS pool

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).Raw reads (fastq) were generated using Cell Ranger (v.4) from 10x Genomics Inc. with the command 'cellranger mkfastq.' Reads from all timepoints were aligned against the mouse genome (mm10 with additional chromosomes for GFP and mCherry), and barcodes and unique molecular identifiers were counted using 'cellranger count'.
The unaligned reads were extracted from the BAM file using samtools (-bh -f 4) and tranformed into a fastq file (bedtools bamtofastq).
The known pre- and suffix (ACCTCCCTAGCAAACTGGGGCACAAGAT and GTACCTTTAAGACCAATGACTT) were trimmed away using cutadapt and only resulting reads with the correct pattern (....CT....AC....TC....GT....TG....CA....C) and length (n=41) were kept for further processing (LentiBCs). Based on the read name, the LentiBCs and cell BC joined, resulting in a table containing read name, cell BC and LentiBCs.
Assembly: mm10
Supplementary_files_format_and_content: TSV file with "<readID>\t<cellBC>\t<lentiBC>"
Library strategy: Amplicon-seq

source_name: Tracer TLS Multiseq - Lenti barcodes


title: Tracer TLS Multiseq - Lineage tracing

description: Lineage barcodes library of the Tracer TLS pool

source_name: Tracer TLS Multiseq - Lineage tracing


title: KIT_multiAsCas12aKRAB-gCH134


title: Female Uterus, 300 mg/kg/day MOPA, Animal 209

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_209u

data_processing:
Raw sequencing reads (FASTQ files) were aligned to known probe sequences listed in the TempO-Seq probe manifest using HISAT2 to compute a matrix of read counts for each probe in each sample.
Assembly: TempO-seq Rat S1500+ v1.2
Supplementary files format and content: Count table CSV files contain a row for each known probe and a column for each sample. Each cell contains the number of reads from a single cell uniquely aligned to a single probe sequence
Supplementary files format and content: Probe manifest CSV file contains a row for each known probe with the probe name, sequence, and target gene

organism: Rattus norvegicus

source_name: Uterus

growth_protocol: Male and female Sprague Dawley (Crl:CD IGS, Charles River Laboratory) rats are purchased at 6 – 8 weeks of age. Upon receipt, the animals are placed on a standard, purified laboratory diet and reverse osmosis treated drinking water ad libitum. The specific brand and type of food and source of the water should be noted in Appendix II (Detailed Animal Study Report) of the individual assessment. After a 7- to 14-day quarantine and acclimation period, the animals are weighed and randomly assigned by weight to chemical exposure and control groups. Only clinically healthy animals are used in the study. The target age for initiating exposure is 8 - 10 weeks.

extract_protocol:
Treated and control animals are necropsied approximately 24 hours after the last exposure. Carbon dioxide asphyxiation is used as the method of euthanasia, with death confirmed by a secondary method such as exsanguination or cervical dislocation. The following tissues were dissected from each animal: kidney, liver, adrenal gland, brain, heart, lung, ovary (females), spleen, testis (males), thyroid, thymus, and uterus (females). Tissue samples were collected within ten minutes of termination. The left liver lobe, right kidney, left lung, both testis, uterus, heart, spleen, thymus and whole brain were sectioned into 5mm^3 pieces. Samples from these larger tissues were then individually divided into at least 3 cryovials. At least two of the samples from each tissue in each animal were preserved in RNAlater™ (Thermo Fisher Scientific) at 4°C overnight and then frozen at approximately -20°C for up to 3 weeks before transferring to approximately -80°C. At least one sample from each larger tissue is frozen immediately in liquid nitrogen and stored at approximately -80°C.   The smaller bilateral tissues: adrenal glands, thyroid gland, and ovaries (female) are placed into two cryovials and preserved in RNALater with the left side of the tissue or gland going into the first cryovial and the right side going into the second cryovial. The first tube of RNALater preserved tissue is submitted for sequencing. For each tissue undergoing transcriptomic analysis, total RNA is extracted from one of the aliquots stored in RNAlater™.
The isolated total RNA is used to perform targeted RNA sequencing (RNA-seq) using the BioSpyder TempO-Seq rat S1500+ assay (v1.2) according to manufacturer’s instructions. No specific RNA purity or integrity criteria are applied to the RNA samples as the TempO-Seq assay has been designed to provide high quality gene expression measurements on whole cell lysates, purified RNA, and formalin-fixed paraffin embedded tissue.

treatment_protocol: For oral gavage studies, at least four male and four female rats per dose group receive the vehicle alone or test article in vehicle via gavage (5 or 10 ml/kg) for five days. Animals are weighed daily prior to administration and are observed twice daily, once during administration and once in the late afternoon, at least six hours apart, for assessment of moribundity and mortality. Formal clinical observations are performed on the first day post-dosing and prior to necropsy. Moribund animals or animals exhibiting overt clinical toxicity are removed from the study. The temperature in the experimental animal room is maintained at a target of 22°C (± 3°C) with a relative humidity that is ideally between 50-60% but is at least 30% and preferably not to exceed 70% other than during room cleaning. Lighting is artificial with a sequence of 12 hours light, 12 hours dark. Animals are housed individually or caged in small groups of no more than three animals of the same sex in accordance with local institutional animal care and use requirements.

value: Female

value: Uterus

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: 300 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:300 mg/kg/day

value: dose group:9

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage

tag: sample qc_issue

value: No Issue


title: Female Uterus, 10 mg/kg/day MOPA, Animal 196

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_196u

value: 10 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:10 mg/kg/day

value: dose group:6


title: Female Uterus, 100 mg/kg/day MOPA, Animal 205

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_205u

value: 100 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:100 mg/kg/day

value: dose group:8


title: Female Uterus, 10 mg/kg/day MOPA, Animal 197

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_197u


title: Female Uterus, 100 mg/kg/day MOPA, Animal 207

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_207u


title: Female Uterus, 300 mg/kg/day MOPA, Animal 208

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_208u


title: Female Uterus, 100 mg/kg/day MOPA, Animal 206

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_206u


title: Female Uterus, 30 mg/kg/day MOPA, Animal 200

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_200u

value: 30 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:30 mg/kg/day

value: dose group:7


title: Female Uterus, 100 mg/kg/day MOPA, Animal 204

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_204u

value: Female

value: Uterus

value: Sprague Dawley


title: Female Uterus, 10 mg/kg/day MOPA, Animal 194

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_194u

value: 10-12 weeks post acclimation


title: Female Uterus, 30 mg/kg/day MOPA, Animal 201

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_201u


title: Female Uterus, 30 mg/kg/day MOPA, Animal 199

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_199u


title: KIT_enAsCas12a-gCH134

description: gCH134 = crCD55-4_crB2M-1_crB2M-3_crKIT-2_crKIT-3_crCD81-1


title: Female Uterus, 10 mg/kg/day MOPA, Animal 195

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_195u


title: Female Uterus, 30 mg/kg/day MOPA, Animal 202

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_202u


title: Female Uterus, 300 mg/kg/day MOPA, Animal 210

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_210u

value: 300 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:300 mg/kg/day

value: dose group:9


title: Female Uterus, 300 mg/kg/day MOPA, Animal 211

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_211u

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage

value: No Issue


title: Female Uterus, 100 mg/kg/day MOPA, Animal 203

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_203u


title: Female Uterus, 10 mg/kg/day MOPA, Animal 193

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_193u

value: 10 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:10 mg/kg/day

value: dose group:6


title: Female Uterus, 3 mg/kg/day MOPA, Animal 191

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_191u

value: 3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:3 mg/kg/day

value: dose group:5


title: Female Uterus, 3 mg/kg/day MOPA, Animal 189

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_189u


title: Female Uterus, 3 mg/kg/day MOPA, Animal 190

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_190u


title: Female Uterus, 30 mg/kg/day MOPA, Animal 198

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_198u

value: 30 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:30 mg/kg/day

value: dose group:7


title: Female Uterus, 3 mg/kg/day MOPA, Animal 192

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_192u

value: Female

value: Uterus

value: Sprague Dawley


title: Female Uterus, 3 mg/kg/day MOPA, Animal 188

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_188u

value: 10-12 weeks post acclimation


title: Female Uterus, 1 mg/kg/day MOPA, Animal 187

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_187u

value: 1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:1 mg/kg/day

value: dose group:4


title: Female Uterus, 1 mg/kg/day MOPA, Animal 186

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_186u

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage

value: No Issue


title: Female Uterus, 1 mg/kg/day MOPA, Animal 183

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_183u


title: Female Uterus, 1 mg/kg/day MOPA, Animal 184

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_184u


title: Female Uterus, 1 mg/kg/day MOPA, Animal 185

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_185u


title: Female Uterus, 0.3 mg/kg/day MOPA, Animal 182

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_182u

value: 0.3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.3 mg/kg/day

value: dose group:3


title: Female Uterus, 0.3 mg/kg/day MOPA, Animal 181

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_181u


title: Female Uterus, 0.1 mg/kg/day MOPA, Animal 173

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_173u

value: 0.1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.1 mg/kg/day

value: dose group:2


title: Female Uterus, 0.1 mg/kg/day MOPA, Animal 175

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_175u


title: Female Uterus, 0.3 mg/kg/day MOPA, Animal 178

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_178u


title: Female Uterus, 0.01 mg/kg/day MOPA, Animal 172

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_172u

value: 0.01 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.01 mg/kg/day

value: dose group:1


title: Female Uterus, 0.1 mg/kg/day MOPA, Animal 176

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_176u

value: Female

value: Uterus

value: Sprague Dawley


title: Female Uterus, 0.1 mg/kg/day MOPA, Animal 174

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_174u

value: 10-12 weeks post acclimation


title: Female Uterus, Vehicle Control, Animal 166

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_166u

value: Deionized water control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: dose group:0


title: Female Uterus, 0.01 mg/kg/day MOPA, Animal 169

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_169u

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage

value: No Issue


title: Female Uterus, 0.01 mg/kg/day MOPA, Animal 168

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_168u


title: Female Uterus, 0.3 mg/kg/day MOPA, Animal 180

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_180u

value: 0.3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.3 mg/kg/day

value: dose group:3


title: Female Uterus, 0.3 mg/kg/day MOPA, Animal 179

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_179u


title: Female Uterus, 0.1 mg/kg/day MOPA, Animal 177

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_177u

value: 0.1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.1 mg/kg/day

value: dose group:2


title: Female Uterus, 0.01 mg/kg/day MOPA, Animal 170

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_170u

value: 0.01 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.01 mg/kg/day

value: dose group:1


title: Female Uterus, Vehicle Control, Animal 167

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_167u

value: Female

value: Uterus

value: Sprague Dawley


title: Female Uterus, Vehicle Control, Animal 165

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_165u

value: 10-12 weeks post acclimation

value: Deionized water control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: Outlier sample removed


title: Female Uterus, Vehicle Control, Animal 164

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_164u

value: dose group:0

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage

value: No Issue


title: Female Uterus, Vehicle Control, Animal 163

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_163u


title: Female Ovary, 300 mg/kg/day MOPA, Animal 211

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_211o

source_name: Ovary

value: Ovary

value: 300 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:300 mg/kg/day

value: dose group:9


title: Female Uterus, Vehicle Control, Animal 160

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_160u


title: Female Uterus, Vehicle Control, Animal 162

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_162u


title: Female Ovary, 300 mg/kg/day MOPA, Animal 209

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_209o


title: Female Ovary, 300 mg/kg/day MOPA, Animal 210

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_210o


title: Female Ovary, 100 mg/kg/day MOPA, Animal 206

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_206o

value: 100 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:100 mg/kg/day

value: dose group:8


title: Female Ovary, 100 mg/kg/day MOPA, Animal 207

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_207o

value: Female


title: Female Ovary, 300 mg/kg/day MOPA, Animal 208

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_208o

value: Sprague Dawley


title: Female Uterus, 0.01 mg/kg/day MOPA, Animal 171

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_171u

value: Uterus

value: 10-12 weeks post acclimation

value: 0.01 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.01 mg/kg/day

value: dose group:1


title: Female Ovary, 100 mg/kg/day MOPA, Animal 204

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_204o

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: Female Ovary, 100 mg/kg/day MOPA, Animal 205

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_205o

value: route of_exposure:Oral gavage


title: Female Ovary, 100 mg/kg/day MOPA, Animal 203

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_203o

value: No Issue


title: Female Ovary, 30 mg/kg/day MOPA, Animal 202

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_202o

value: Ovary

value: 30 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:30 mg/kg/day

value: dose group:7


title: Female Ovary, 30 mg/kg/day MOPA, Animal 201

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_201o


title: Female Ovary, 30 mg/kg/day MOPA, Animal 199

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_199o


title: Female Ovary, 10 mg/kg/day MOPA, Animal 193

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_193o

value: 10 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:10 mg/kg/day

value: dose group:6


title: Female Ovary, 10 mg/kg/day MOPA, Animal 195

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_195o

value: Female


title: Female Ovary, 30 mg/kg/day MOPA, Animal 198

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_198o

value: Sprague Dawley


title: Female Ovary, 10 mg/kg/day MOPA, Animal 197

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_197o


title: Female Ovary, 10 mg/kg/day MOPA, Animal 196

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_196o


title: Female Ovary, 30 mg/kg/day MOPA, Animal 200

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_200o


title: Female Ovary, 10 mg/kg/day MOPA, Animal 194

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_194o


title: Female Ovary, 3 mg/kg/day MOPA, Animal 191

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_191o

value: 3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:3 mg/kg/day

value: dose group:5

value: Outlier sample removed


title: Female Ovary, 3 mg/kg/day MOPA, Animal 190

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_190o

value: 10-12 weeks post acclimation


title: Female Ovary, 3 mg/kg/day MOPA, Animal 189

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_189o

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: Female Uterus, Vehicle Control, Animal 161

description:
etap_mopa_uterus_female_counts.csv
Plate_42_MOPA_uterif_161u

value: Uterus

value: Deionized water control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: dose group:0

value: route of_exposure:Oral gavage


title: Female Ovary, 3 mg/kg/day MOPA, Animal 188

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_188o

value: Ovary

value: No Issue


title: Female Ovary, 1 mg/kg/day MOPA, Animal 185

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_185o

value: 1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:1 mg/kg/day

value: dose group:4


title: Female Ovary, 1 mg/kg/day MOPA, Animal 183

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_183o

value: Female

value: Sprague Dawley


title: Female Ovary, 1 mg/kg/day MOPA, Animal 184

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_184o


title: Female Ovary, 1 mg/kg/day MOPA, Animal 186

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_186o


title: Female Ovary, 0.3 mg/kg/day MOPA, Animal 182

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_182o

value: 0.3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.3 mg/kg/day

value: dose group:3


title: Female Ovary, 0.3 mg/kg/day MOPA, Animal 179

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_179o

value: 10-12 weeks post acclimation


title: Female Ovary, 0.3 mg/kg/day MOPA, Animal 180

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_180o

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: Female Ovary, 0.3 mg/kg/day MOPA, Animal 178

description:
etap_mopa_ovary_female_counts.csv
Plate_41_MOPA_ovaryf_178o