title: MM099_3 (SNCL116)

first: Pietro

last: Berico

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

data_processing:
reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20).
reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis.
Reads were mapped onto the hg19 assembly of Homo sapiens genome using STAR version 2.5.3a. Gene expression quantiﬁcation was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 75 and “union” mode.
Only non-ambiguously assigned reads have been retained for further analyses. Read counts have been normalized across samples with the median-of-ratios method
Diﬀerential gene expression analysis was performed using the methodology implemented in the Bioconductor package DESeq2 version 1.16.1
P-values were adjusted for multiple testing by the method proposed by Benjamini and Hochberg
Deregulated genes were defined as genes with log2(foldchange) >1 or <-1 and adjusted p-value <0.05.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file with matrix table with raw gene counts, RPKM values, log fold change expression values between non treated and treated cells for every gene and every sample

source_name: Skin

extract_protocol:
total RNA was extracted using NucleoSpin RNAplus kit from Macherey-Nagel following manufacture instructions.
Total RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 8 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: cell line

value: Skin

tag: phenotype

value: drug-resistant

tag: treatment

value: nt


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C11_ad008

status: Public on Sep 18 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PIR

tag: Sex

value: male

tag: age

tag: strain


title: MM099_1 (SNCL114)

city: New York

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: MM099_2 (SNCL115)


title: WTD3_1

first: Xiaobin

middle: Summer

last: Wang

state: NEW YORK

address: 1130 Siant Nicholas Ave, Room 501

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

data_processing:
Library strategy: high-throughput genome translocation sequencing (HTGTS)
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 genome using Bowtie2. The best-path searching algorithm (related to YAHA; ref. 50) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads are then filtered to exclude mispriming events, germ-line (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. To plot all of the S-region junctions, including those in the repeats but unequivocally mapped to an individual switch region, we combined the ones filtered by a mappability filter but unequivocally mapped to S regions with “good” reads passing both the mappability (both deduplicated) filters (please see ref. 28 for simulation and details on plotting). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait and prey-break site. Blunt junctions are considered to have no MHs or insertions.
Genome_build: mm9
Supplementary_files_format_and_content: .xlsx files generated from tab-delimited text files after analysis for reads distribution

source_name: B cells

growth_protocol: Purified splenic B (CD43-) cells from mice carrying preassembled IgH and IgK loci (BL6 background) were cultured in RPMI mediume with cytokines (anti-CD40 (1 ng/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
Genomic DNA was extracted from day 4 cultured B cells.
Libraries were prepared according to protocol in (Hu J, et al. Nat Protoc 11:853–871.(2016)) Linear amplifications were performed using Sμ-specific biotin primer  5′/5BiosG/CAGACCTGGGAATGTATGGT3′) and followed by nesting PCR with (5′CACACAAAGACTCTGGACCTC3′)  AflII is used to remove germ-line sequence.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: Cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

tag: cell type

value: anti-CD40 and Il4 activated B cells

tag: genotype

value: wild type


title: 16_FO_P7_GTCGTA

city: Toronto

first: Patrick

middle: O

last: McGowan

state: ON

address: 1265, Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto

data_processing:
FastQ files were trimmed to remove low quality reads (q < 30) and adaptors, and later aligned to RGD Rnor_6.0
The average reads per sample was 20.8X106 with a mapping efficiency of 50-60 %
Differentially methylated regions (DMRs) were identified using a dynamic sliding window approach and annotated using the methylPipe 49 and compEpiTools R packages
The bisulfite conversion rate was >99 % for all samples
Regions were declared to be differentially methylated if the average methylation of at least 10 consecutive CpG sites within a 1 Kb region was ≥ 5 % between mHFD and mCHD with FDR < 0.05
Genome_build: Rnor6
Supplementary_files_format_and_content: The data are the methylation calls from the BAM files - specifically, the data is filtered out to only get reads that have 4X coverage in the CpG context of each subject. These methylation calls are then used for formal analysis via methylPipe R package, where they pool all of the respective calls together (ie. aP90 subjects are pooled together, and all P7 subjects are pooled together), to obtain the appropriate methylation level in each group. These methylation files are in .txt format.

organism: Rattus norvegicus

source_name: High fat diet,earlylife (P7)

extract_protocol:
gDNA was extracted using the ZR-Duet™DNA/RNA MiniPrep (D7005; Zymo Research) according to manufacturing instructions
Libraries were constructed using Ovation RRBS Methyl-Sequencing Kit (0553-32; NuGEN) as per the manufacturer's instructions.

treatment_protocol: Dams were on a high fat diet 4 weeks prior to pregnancy, during gestation, and lactation. The offspring were not directly on a high fat diet. Offspring used in the P90 condition was weaned off to a control diet. All animals were euthanized swiftly and brains were collected and stored at -80C. Brains were cryosectioned into 50 uM sections using Research Cryostat Leica CM3050 S (CM3050 S; Leica Biosystems) and the amygdala was microdissected using stereotaxic coordinates (P7: bregma: -0.20mm to -1.60 mm 38; P90 bregma: −1.72mmto −3.00mm

value: Amygdala

value: LongEvans

tag: diet

value: high fat


title: MM029_1 (SAMP9)


title: mouse119_liver_15sec_RiboSeq

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

description: ribosome footprints

data_processing:
Library strategy: Ribo-seq
To remove illumina adapter from Ribo-seq libraries run "cutadapt -u 1 -m 23 -a AGATCGGAAGAGCACACGTCT --discard-untrimmed -o output.fastq input.fastq"
mRNA-seq sequences were aligned with TopHat 2.1.0 using following settings: tophat --transcriptome-index --no-discordant --no-mixed --no-novel-juncs
The NCBI mouse genome build GRCm38.p3 and the Mus musculus Annotation Release 105 were used as a reference. When aligning mRNA-seq and ribosome profiling reads for expression and translation efficiency estimation we used the following strategy. Only full chromosomes were left and all non-chromosomal and mitochondrial records removed. Furthermore, only RefSeq and BestRefSeq records were left in the transcriptome annotation, while Gnomon predictions were discarded along with pseudogenes. Read count per gene was accessed by HTseq-count software
To plot time-dependent ribosome occupancy, we employed a different strategy. First, using a gene bank (gbk) file, which comes in a package with the genome assembly and annotation, we extracted RefSeq and BestRefSeq records for every gene including CDS, 5’-UTR and 3’-UTR lengths and sequences. Among them, we identified the longest isoform for every gene, prioritized as CDS > 5’UTR > 3’UTR. 5’-UTRs were trimmed by 100 nucleotides. If either or UTRs were shorter than 100 nucleotides, we filled it with up to 100 based on genomic coordinates. The full list of sequences is collected in the mRNA_100.fna file. To prepare a list of non-redundant genes, we run blast of all vs. all (blastall -p blastn -m 8 -b 500 -v 500 -e 0.001). Gene pairs that are too similar at the level of nucleotide sequence were excluded. In addition to the e-score, we enforced a requirement of the high-homology stretch being at least 50 nt long, and if it was longer, the similarity had to be at least 90% to treat these genes as homologous and redundant. A total of 13,685 genes passed every threshold. This reference set ensured unambiguous alignment of ribosome footprints. Resulting sequences are collected in the mRNA_100unique.fna file.
Custom Perl and R scripts were used to calculate the footprint coverage profiles of individual genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts contain raw read count of individual genes; footprint coverage contains gene coverage profiles

source_name: liver

extract_protocol:
Frozen tissue was lysed a glass-Teflon Dounce homogenizer: 20 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 1 mM DTT, 1% Triton-X100, 0.1 mg/ml cycloheximide. The lysate was incubated with 4:1 mixture of ribonucleases T1 and S7 for 30 min at room temperature with gentle agitation. Lysate fractionation was performed by ultracentrifugation for 3 h at 35.000 rpm in an SW41 rotor (Beckman, Optima L-20K) at 4⁰ C in 10-50% sucrose, 20 mM Tris-HCl pH 7.5, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide. After the centrifugation, gradients were passed through a UV detector (Bio-Rad) and the absorption at 254 nm was recorded. The fraction containing monosomes was collected in a single tube. The volume of the sample was brought to 50 ul by concentrating it using 100 kDa filters (Amicon Ultra, Millipore). Then, the sample was diluted to 500 ul with a buffer containing 10 mM Tris-HCl pH 7.5, 2 mM EDTA, 1% SDS. RNA was extracted by hot acid phenol (Ambion) and precipitated by the glycogen-ethanol method (1/10 volume of 3 M sodium acetate, 1/100 volume of glycogen, 2.5 volumes of pure ethanol, 1-hour incubation at -20 followed by centrifugation). RNA was loaded on a 15% polyacrylamide TBE-urea gel and the band containing ribosomal footprints around 28-30 nucleotides was cut.
DNA adapter (rApp-AGATCGGAAGAGCACACGTCT- ddC) was ligated to the 3' end of RNA footprint. Illumina flanking sequences were added through reverse transcription and consequent Circligation technique.

value: 72 weeks old mouse

tag: inhibitors

value: harringtonine 15 sec cycloheximide

tag: injection route

value: tail-vein

tag: internal animal id


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C10_ad004


title: mouse118_liver_30sec_RiboSeq

description: ribosome footprints

value: harringtonine 30 sec cycloheximide


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C10_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C10_ad006


title: 11_FO_P7_AGTGAG


title: MM074VR_2 (SAMP8)

value: Vemurafenib


title: 5_FO_P7_ACCTCA

source_name: Control diet, earlylife (P7)

value: control diet


title: 7_FO_P7_GTGCTT


title: 501_3 (SAMP27)

value: wild-type


title: mouse108_liver_15sec_RiboSeq

description: ribosome footprints


title: mouse107_liver_45sec_RiboSeq

description: ribosome footprints

value: harringtonine 45 sec cycloheximide


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C10_ad008


title: 501_2 (SAMP26)

value: Skin


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C10_ad001


title: mouse106_liver_30sec_RiboSeq

description: ribosome footprints


title: 3_FO_P7_AACCAG


title: MM029_2 (SAMP10)

value: drug-resistant

value: nt


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C10_ad012

value: PIR

value: male


title: 501_1 (SAMP25)


title: Untreated tumors Rep 3 - small

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

institute: University of Pittsburgh

data_processing:
STAR alignment
DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delim file of genes(rows) and cells (columns)

growth_protocol: KP mice were infected with Cre-ffluc-hROR1 lentivirus and, 13 weeks post-infection, were left untreated or treated with 3 weekly doses of oxaliplatin and cyclophosphamide. Tumors were excised 6 hours after OxCy treatment and RNA isolated for RNAseq analysis.

extract_protocol:
RNA was extracted using the RNeasy Mini kit (QIAGEN) according to the manufactuer’s instructions. Total RNA integrity was checked using an Agilent 4200 TapeStation (Agilent Technologies) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences).
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina) and a Sciclone NGSx Workstation (PerkinElmer). Library size distributions were validated using an Agilent 4200 TapeStation. Additional library quality control, blending of pooled indexed libraries, and cluster optimization were performed using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). RNA-seq libraries were pooled (6- to 8-plex) and clustered onto a flow cell lane.

treatment_protocol: Tumors were excised from KP mice, pooled, and stored in RNA Later. Tumors were lysed in 1 ml buffer RLT (QIAGEN) using a gentleMACS Dissociator (Miltenyi). RNA was extracted using the RNeasy Mini kit (QIAGEN) according to the manufactuer’s instructions.

value: female

tag: transgene

value: Kras-LSLG12D/+; P53f/f


title: Untreated tumors Rep 2 - large


title: Untreated tumors Rep 3 - large


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C1_ad001


title: Untreated tumors Rep 1 - small


title: SD_NLS_3

city: CLEVELAND

first: Bibo

last: Li

state: OH

address: 2121 Euclid Avenue

department: Center for Gene Regulation in Health and Disease

institute: CLEVELAND STATE University

data_processing:
Base-calling using NovaSeq 6000 for Illumina sequencing
Raw reads were first processed with Novogene Perl Scripts (removing reads with low quality,  with adapters, and containing poly-N; calculating Q20, Q30 and GC contents).
Clean reads were mapped to T. brucei Lister 427 genome TriTrypDB-45_TbruceiLister427_2018_Genome.fasta and its annotation TriTrypDB-45_TbruceiLister427_2018.gff Idownloaded from the TriTryp DB) using HISAT2.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq R package (1.18.0)

molecule: polyA RNA

organism: Trypanosoma brucei brucei

source_name: TbRAP1-2SD (S742DS744D) rep 3

growth_protocol: bloodstream T. brucei cells were cultured in HMI9 medium with 10% FBS. All cells were maintained with medium containing 2 µg/ml G418, 4 µg/ml Hygromycin, 2 µg/ml of Phleomycin, 5 µg/ml blasticidin. TbRAP1F/-, TbRAP1F/5A, and TbRAP1F/2SD cells are also selected with 0.1 µg/ml Puromycin. At the time of adding 100 ng/ml doxycycline, Hygromycin and blasticidin were removed by washing cells 3 times.

extract_protocol:
Total RNA was isolated and purified through RNeasy columns (Qiagen). RNA samples were run on a BioAnalyzer 2100 (Agilent Technologies) using the Agilent RNA 6000 nano kit to verify the RNA quality before sent to Novogene, where RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) using 1 μg poly(A) RNA according to manufacturer’s protocol and index codes were added to attribute sequences to each sample.

treatment_protocol: 100 ng/ml doxycycline (to induce Cre expression) for 30 hrs

tag: background strain

value: lister 427

tag: genotype/variation

value: +Cre 30 hrs

value: cultured cells


title: SD_NLS_1

source_name: TbRAP1-2SD (S742DS744D) rep 1


title: SD_NLS_2

source_name: TbRAP1-2SD (S742DS744D) rep 2


title: MM074VR_1 (SAMP7)

tag: cell line


title: MM047THZR_1 (PRBC16)

tag: phenotype


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C1_ad012


title: 4_FO_P7_TGGTGA

value: Amygdala

value: LongEvans


title: MM047_2 (PRBC15)

tag: treatment


title: MM047THZR_2 (PRBC17)


title: Untreated tumors Rep 1 - large


title: NLS_5A_3

source_name: TbRAP1-5A (737RKRRR741 mutated to 737AAAAA741) rep 3


title: Ox/Cy treated tumors Rep 2 - small

treatment_protocol: Tumors were excised from KP mice 6 hours after treatment Ox/Cy, pooled, and stored in RNA Later. Tumors were lysed in 1 ml buffer RLT (QIAGEN) using a gentleMACS Dissociator (Miltenyi). RNA was extracted using the RNeasy Mini kit (QIAGEN) according to the manufactuer’s instructions.


title: MM047_1 (PRBC14)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C1_ad002

tag: brain region


title: NLS_5A_2

source_name: TbRAP1-5A (737RKRRR741 mutated to 737AAAAA741) rep 2


title: NLS_5A_1

source_name: TbRAP1-5A (737RKRRR741 mutated to 737AAAAA741) rep 1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C1_ad010

tag: Sex


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C1_ad004

tag: age


title: CKO_s_3

source_name: TbRAP1 CKO (conditional knockout) rep 3


title: Ox/Cy treated tumors Rep 2 - large

tag: strain


title: Ox/Cy treated tumors Rep 1 - small


title: CKO_s_2

source_name: TbRAP1 CKO (conditional knockout) rep 2

tag: tissue


title: Ox/Cy treated tumors Rep 1 - large


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C1_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C1_ad007


title: MM074_2 (PRBC11)


title: MM074THZR_2 (PRBC13)


title: CKO_s_1

source_name: TbRAP1 CKO (conditional knockout) rep 1


title: D0

description: D0 (pre-CAR infusion)

data_processing:
Cellranger3.0.0 default-parameters + aggregate
Monocle
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delim file of genes(rows) and cells (columns)

growth_protocol: For CAR-T cell infusion product, CD8+ T cells were enriched from spleens and lymph nodes of B6 CD45.1 mice using EasySep Mouse CD8 Enrichment kit (StemCell). Cells were stimulated with anti-CD3 and anti-CD28 and transduced with retrovirus encoding a ROR1 CAR co-expressed with truncated CD19 fused to GFP (tCD19-GFP) transduction marker, as described in Srivastava et al. On D5 after stimulation, CD8+ CAR-T cells were postivitely enriched using mouse CD19 microbeads (Miltenyi Biotec) and subsequently cryopreseerv\rve

extract_protocol:
Tumors were processed and captured using 10x genomics single cell platform
10x single cell 3' v2

treatment_protocol: Tumors were excised from KP mice on D0 prior to CAR-T cell infusion, pooled, and enzymatically digested into a single cell suspension using  Tumor Dissociation Kit (Miltenyi Biotec)


title: MM074_1 (PRBC10)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B9_ad008


title: melanoma cells input

data_processing:
Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2
Reads were mapped onto the hg19 assembly of the human genome. Peak detection was performed using MACS (http://liulab.dfci.harvard.edu/MACS/) under settings where the input fraction was used as negative control.
Peaks detected were annotated using HOMER (http://biowhat.ucsd.edu/homer/ngs/annotation.html) as well as TSS protein enrichment comparison.
As reference coordinates, we used the MACS-determined peaks or the annotated TSS/TTS of human genes as defined by RefSeq database.
Sequence enrichment was performed using RSAT (http://rsat.sb-roscoff.fr) with MACS-determined peaks as reference.
Genome_build: hg19

source_name: Human melanoma cells

extract_protocol:
Cells were grown on 15cm plates and, once reached 80% of confluence, were fixed with PBS + 0.4% formaldehyde solution for 10min. Subsequently fixation reaction was stopped with 2M Glycin pH 8. Cells were then pellet and re-suspended in lysis buffer (EDTA 10mM, Tris HCl pH8 50mM, SDS 1%) and sonicate with Covaris E220 AFA power 200Hz 6 cycles 200s to get a DNA fragmentation between 500 and 200bp. Chromatin was then diluted in 60ug aliquots with 8 volumes of ChIP dilution buffer (Tris HCl pH8 16.7mM, EDTA 1.2mM, NaCl 167mM, Triton X-100 1.1%, SDS 0.01%). The immunoprecipitations were done incubating between 1-5ug of antibody overnight and the complex antibody-chromatin was then captured with G protein sepharose beads (Sigma Aldrich) 1h at 4°C. Beads were washed 2 times with Low Salt Buffer (Trish HCl pH8 20mM, EDTA 2mM, NaCl 150mM, Triton X-100 1%, SDS 0.1%), High Salt Buffer (Trish HCl pH8 20mM, EDTA 2mM, NaCl 500mM, Triton X-100 1%, SDS 0.1%), LiCl buffer (Tris HCl pH8 500mM, EDTA 1mM, Na deoxycholate 1%, NP40 1%, LiCl 0.25M), TE buffer (Tris HCl pH8 10mM, EDTA 1mM) and DNA was eluted 30min at room temperature with Elution buffer (NaHCO3 0.1M, SDS 1%). DNA was finally purified through phenol-chloroform and resuspend in 100uL of water.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 1 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: no treatment


title: melanoma cells anti-FLAG-CDK7


title: MM074THZR_1 (PRBC12)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B9_ad007


title: CSKO_s_1

source_name: TbRAP1 CSKO (conditional single knockout) rep 1


title: RPE1 TRIM37 OE clone 5 DOX rep3

city: San Diego

first: Karen

last: Oegema

state: California

address: 9500 Gilman Drive, CMM East

institute: UCSD

data_processing:
STAR aligner
DEseq2
Supplementary_files_format_and_content: Differential Gene expression; CSV files

source_name: Human retinal pigmented epithelial cells

growth_protocol: hTERT RPE1 and CHP134 cells were grown in DMEM/F12 and RPMI, respectively, with 10% FBS (10%). Each growth medium was supplemented with 100 IU/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
RNeasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 1µM Doxycycline for 24h, if indicated.

tag: geneotype

value: Inducible TetOn-TRIM37 expresssion

tag: drug treatment

value: Doxycycline (1µM; 24h)


title: D10+CAR

description: early time point (D10 post-CAR treatment)

treatment_protocol: Tumors were excised from KP mice 10 days after treatment with Cy + ROR1 CAR-T cells, pooled, and enzymatically digested into a single cell suspension using  Tumor Dissociation Kit (Miltenyi Biotec)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B9_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: CARPRODUCT

description: T cell infusion product

treatment_protocol: CD8+ T cells were transduced with a construct encoding ROR1 CAR co-expressed with truncated CD19 fused to GFP (tCD19-GFP) and bead-enriched for transduced cells using CD19-microbeads to generate the CD8+ CAR-T cell infusion product

value: WT


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B9_ad001


title: CSKO_s_2

source_name: TbRAP1 CSKO (conditional single knockout) rep 2


title: WSB adipose 4 weeks (86)

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

data_processing:
Fixed SNPs for each strain (wsb_snps.vcf.gz and gough_snps.vcf.gz are the annotations of SNPs relative to mm10) were used to create strain-specific reference genomes that were used for read alignment.
Reads were aligned to reference transcripts using Bowtie v1.1.1
Gene abundances were estimated using RSEM v1.2.21
Genome_build: mm10/GRCm38, Ensembl v79 annotation
Supplementary_files_format_and_content: The processed data file for each sample is the gene-level abundance output of RSEM and is a tab-delimited text file

organism: Mus musculus domesticus

source_name: adipose

extract_protocol:
Organs were removed, snap frozen in liquid nitrogen, and stored at −80° C until RNA extraction. Liver RNA was harvested using Trizol reagent; adipose and hypothalmus RNA was harvested using the Qiagen RNeasy Lipid Tissue Mini Kit (74804). 1 μg of DNase-treated and purified total RNA for each sample was used for RNA-seq library preparation and construction via Illumina TruSeq RNA Sample Prep kits (v2, sets A and B; RS-122-2001 and RS-122-2202).
Paired-end, 51-base pair RNA-seq libraries were generated using Illumina TruSeq RNA Sample Prep kits (v2, sets A and B; RS-122-2001 and RS-122-2202), TruSeq Rapid Cluster-HS kits (PE-402-4001), and Illumina TruSeq Rapid SBS kits (FC-402-4002).

value: WSB/EiJ

tag: id of strain

tag: sex id

value: 4 weeks

tag: age id

value: gonadal fat pad

tag: tissue id


title: RPE1 TRIM37 OE clone 5 DOX rep2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C1_ad008


title: D0+OxCy

description: D0 (pre-CAR infusion, 6hrs after OxCy)

treatment_protocol: Tumors were excised from KP mice on D0 prior to CAR-T cell infusion and 6 hours after OxCy treatment, pooled, and enzymatically digested into a single cell suspension using  Tumor Dissociation Kit (Miltenyi Biotec)

tag: transgene


title: WSB adipose 4 weeks (85)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B9_ad006


title: RPE1 TRIM37 OE clone 5 DOX rep1


title: uty_input

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 Pine Ave West

department: Institut de recherches cliniques de Montréal (IRCM)

institute: Université de Montréal

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the reference mouse genome version mm9 using BOWTIE2 version 2.2.6
Peak calling was performed on eahc sample using corresponding input with MACS2 2.0.10. Differential binding analysis was performed using MACS2 bdgdiff to identify specific and common peaks to each condition
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated using BedTools and BedGraphToBigWig from ENCODE project
Supplementary_files_format_and_content: Bed file represents specific peaks to b6 samples compared to uty identified by MACS bdgdiff function

source_name: cardiac left ventricular tissue

growth_protocol: adult male mice were used at 40 days of age to harvest cardiac tissues

extract_protocol:
Tissues were homogenized and cross-linked in 1% formaldehyde at room temperature for 10 minutes.   The reaction was stopped by adding glycine (125mM), followed by an additional incubation for 5 minutes.   Chromatin was prepared as described, with little modifications (21).  Nuclei were prepared by sequential   incubation and purification by centrifugation on ice for 5 min in buffer A [10 mM Tris-HCl (pH 8), 10mM EDTA  0.25% Triton X-100], and for 30 min in buffer B [10 mM Tris-HCl (pH 8), 1 mM EDTA, 200 mM NaCl] (all buffers  include protease inhibitors). Nuclei were resuspended in sonication buffer [10mMTris-HCl (pH 8), 1mMEDTA,   0.5% SDS, 0.5% Triton X-100, 0.05% NaDOC, 140 mM NaCl] and sonicated to obtain chromatin fragments of an average length of 500 bp. Sonicated chromatin was immunoprecipitated with either rabbit IgG (G2018, Sigma-Aldrich)  or ChIP grade ab4729 anti-H3K27 antibody from Abcam (Cambridge, MA).  The immunoprecipitate was collected using  protein-A/G beads (Santa Cruz Biotechnology). After washes and decrosslinking, DNA was purified using QIAquick columns following manufacturer’s directives (Qiagen, Mississauga, On)
Immunoprecipitated DNA was used to prepare sequencing libraries using the TruSeq DNA kit   from Illumina, according to the manufacturer's instructions.

value: cardiac left ventricular


title: uty_ech_2


title: RPE1 TRIM37 OE clone 5 rep3

value: No


title: WSB adipose 4 weeks (84)

value: male


title: D10+CAR+OxCy

description: early time point (D10 post-CAR+OxCy treatment)

treatment_protocol: Tumors were excised from KP mice 10 days after treatment with OxCy + ROR1 CAR-T cells, pooled, and enzymatically digested into a single cell suspension using  Tumor Dissociation Kit (Miltenyi Biotec)

value: female


title: uty_ech_1


title: CSKO_s_3

source_name: TbRAP1 CSKO (conditional single knockout) rep 3

tag: background strain


title: RPE1 TRIM37 OE clone 5 rep2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B9_ad012

value: PIR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B8_ad008


title: WSB adipose 4 weeks (76)


title: RPE1 TRIM37 OE clone 5 rep1


title: b6y129_ech_2


title: Gough adipose 4 weeks (22G)

value: Gough


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B8_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B8_ad002


title: RPE1 TRIM37 OE clone 4 DOX rep3


title: Gough adipose 4 weeks (21G)


title: b6y129_ech_1


title: RPE1 TRIM37 OE clone 4 DOX rep2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B9_ad010


title: Gough adipose 4 weeks (20G)


title: RPE1 TRIM37 OE clone 4 DOX rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B8_ad006


title: 071_vivo-Pr-fol-P3_rep3

city: Fukuoka

first: Nobuhiko

last: Hamazaki

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku,

department: Department of Developmental Stem Cell Biology

country: Japan

institute: Kyushu University

data_processing:
Fastq files from sequencing experiments were mapped to the mouse mm10 genome using default parameters for STAR (v2.6.0, Dobin et al., 2013)
Mapped reads were counted by featureCount (v1.6.0, Liao et al., 2014, -O -s 2).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including TPM values for each Sample.

growth_protocol: ESC lines were cultured in 2i plus LIF without feeders (Ying et al., 2008). PGCLC induction was performed as described (Hayashi and Saitou, 2013). PGCLCs were purified by FACSAria II or Fusion (BD Bioscience) and aggregated with E12.5 female gonadal somatic cells in a low-binding U-bottom 96-well plate (NUNC) for 2 days of culture in GK15 supplemented with 1 μM retinoic acid. To strictly remove residual PGCs from dissociated gonadal cells, both SSEA1 and CD31 antibodies (Miltenyi Biotech) were used according to the manufacturer’s instructions. 5,000 PGCLCs were cultured with 75,000 gonadal somatic cells to produce one reconstituted ovary. IVD culture was performed as described (Hikabe et al., 2016). rOvaries (5,000 PGCLCs and 75,000 gonadal somatic cells) were placed on Transwell-COL membranes soaked in αMEM-based IVDi medium: αMEM supplemented with 2% FCS, 150 μM ascorbic acid (Sigma), 1× Glutamax, 1× penicillin/streptomycin and 55 μM 2-mercaptoethanol (Life Technologies). At 4 days of culture, the culture medium was changed to StemPro-34-based IVDi medium: StemPro-34 SFM (Life Technologies) supplemented with 10% FCS, 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin, and 55 μM 2-mercaptoethanol. From 7 days to 10 days of culture, 500 nM ICI182780 was added to the StemPro-34-based IVDi medium. IVG culture was performed as described (Hikabe et al., 2016). Briefly, the isolated secondary follicles on the Transwell-COL membranes were soaked in IVG medium: αMEM supplemented with 5% FCS, 2% polyvinylpyrrolidone (Sigma), 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin, 100 μM 2-mercaptoethanol, 55 μg ml−1 sodium pyruvate (Nacalai Tesque), 0.1 IU ml−1 follicle-stimulating hormone (Follistim; MSD), 15 ng ml−1 BMP15 and 15 ng ml−1 GDF9 (R&D Systems). At 2 days of culture, BMP15 and GDF9 were withdrawn from the medium and then follicles were incubated in 0.1% TypeIV Collagenase (MP Biomedicals). After washing with αMEM supplemented with 5% FCS several times, the follicles were cultured in IVG-αMEM without BMP15 and GDF9. At 11 days of culture, cumulus-oocyte complexes grown on the membrane were picked up by a fine glass capillary. Cumulus–oocyte complexes were transferred to IVM medium: αMEM supplemented with 5% FCS, 25 μg ml−1 sodium pyruvate, 1× penicillin/streptomycin, 0.1 IU ml−1 follicular-stimulating hormone, 4 ng ml−1 EGF, and 1.2 IU ml−1 hCG (gonadotropin; ASKA). At 16 h of culture, swollen cumulus cells were stripped from the oocytes by treating with hyaluronidase (Sigma), and then MII oocytes were determined by 1st polar body extrusion. For direct induction of ngDIOs, 5x10^4 ESCs were transferred into a low-cell-binding U-bottom 96-well plate (NUNC) in S10 medium (StemPro-34 SFM (Life Technologies) supplemented with 10% FCS, 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin and 55 μM 2-mercaptoethanol) with 150 ng/ml SCF, 0.5 µM of Shield1 (Clontech), and 10 nM Y-27632 (Wako). For the extended culture, we transferred the aggregates onto Transwell-COL membranes using mouth pipet on day 2,  and cultured under normoxic conditions (20% O2 and 5% CO2 at 37 °C) for 2-4 weeks. For induction of GV and MII DIO, 5x10^4 ESCs were aggregated with 30,000-75,000 E12.5 female gonadal somatic cells in S10 medium with 0.5 µM of Shield1 and cultured for 2 days and transferred onto Transwell-COL membranes (Corning) soaked in S10 medium with 0.5 µM of Shield1 and cultured for 28 days. At 21-28 days of culture, individual follicles were manually isolated using sharpened tungsten needles. The Isolated follicles were further differentiated by IVG for 7-11 days and IVM culture and fertilized by IVF as previously described (Hayashi et al., 2017; Hikabe et al., 2016).

extract_protocol:
IVD culture was performed as described previously (Hikabe et al., 2016, Nature). rOvaries (5,000 PGCLCs and 75,000 gonadal somatic cells) were placed on Transwell-COL membranes soaked in αMEM-based IVDi medium: αMEM supplemented with 2% FCS, 150 μM ascorbic acid (Sigma), 1× Glutamax, 1× penicillin/streptomycin and 55 μM 2-mercaptoethanol (Life Technologies). At 4 days of culture, the culture medium was changed to StemPro-34-based IVDi medium: StemPro-34 SFM (Life Technologies) supplemented with 10% FCS, 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin, and 55 μM 2-mercaptoethanol. From 7 days to 10 days of culture, 500 nM ICI182780 was added to the StemPro-34-based IVDi medium.Ovaries (in vivo) and rOvaries (in vitro) at each developmental stage were treated with CTK solution (0.1 mg/ml collagenase IV, 0.25% trypsin, 20% KSR and 1 mM CaCl2 in PBS) for 30 minutes at 37°C, then transferred into Accutase (Nacalai Tesque) and incubated at 37°C for 15 minutes. The IVD day11 or day13 SC+oocytes were isolated by FACS-sorting. For FACS preparation, the cells were dissociated by gentle pipetting and filtered by using a 70 μm-pored nylon mesh to remove cell clumps.
Ovaries (in vivo) and rOvaries (in vitro) at each developmental stage were treated with CTK solution (0.1 mg/ml collagenase IV, 0.25% trypsin, 20% KSR and 1 mM CaCl2 in PBS) for 30 minutes at 37°C, then transferred into Accutase (Nacalai) and incubated at 37°C for 15 minutes. The IVD day11 or day13 SC+oocytes were isolated by FACS-sorting. For FACS preparation, the cells were dissociated by gentle pipetting and filtered by using a 70 μm-pored nylon mesh to remove cell clumps. Collected samples were transferred into a 1.5 ml DNA LoBind tube (Eppendorf). Directional RNA-seq libraries were prepared as described previously (Hamazaki et al., 2015). Briefly, polyA-tailed RNA were extracted by Dynabeads mRNA Purification Kit.
Extracted polyA+RNA were converted to cDNA libraries by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

tag: genotype

value: Blimp1-Venus and Stella-CFP

tag: cell type

value: in vivo oocytes


title: 070_vivo-Pr-fol-P3_rep2


title: WSB adipose 4 weeks (77)


title: Gough adipose 4 weeks (18G)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B8_ad010


title: RPE1 TRIM37 OE clone 4 rep3

tag: cell line


title: 069_vivo-Pr-fol-P3_rep1


title: RPE1 TRIM37 OE clone 4 rep2


title: 068_vivo-incomp-GV_rep3


title: b6y129_input


title: WSB adipose 4 weeks (83)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B8_ad012


title: RPE1 TRIM37 OE clone 4 rep1


title: Gough adipose 4 weeks (19G)


title: WSB adipose 4 weeks (82)


title: CHP134 TRIM37 MT clone 2 rep3

source_name: Neuroblastoma cells

value: Partial TRIM37 knockout


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B7_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B7_ad007


title: 067_vivo-incomp-GV_rep2


title: CHP134 TRIM37 MT clone 2 rep2


title: 066_vivo-incomp-GV_rep1


title: WSB adipose 4 weeks (81)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B8_ad007


title: WSB adipose 4 weeks (80)


title: CHP134 TRIM37 MT clone 2 rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B7_ad001


title: WSB adipose 4 weeks (78)


title: CHP134 TRIM37 MT clone 1 rep3


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B7_ad002


title: Gough adipose 4 weeks (47G)


title: 064_vivo-comp-GV_rep2


title: CHP134 TRIM37 MT clone 1 rep2


title: 065_vivo-comp-GV-2_rep3


title: Gough adipose 4 weeks (46G)


title: CHP134 TRIM37 MT clone 1 rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B7_ad010


title: 063_vivo-comp-GV_rep1


title: Gough adipose 4 weeks (45G)


title: 038_d13_KO_Dynll1_rep2

value: in vitro oocytes


title: 037_d13_KO_Noto_rep2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B7_ad006


title: Gough adipose 4 weeks (35G)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B6_ad012


title: CHP134 rep2

description:
CHP134-CHP134-TRIM37ko-31
CHP134-CHP134-TRIM37ko-63

value: Wild type


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B7_ad008


title: Gough adipose 4 weeks (28G)


title: 035_d13_KO_Nobox_rep2


title: CHP134 rep1


title: 036_d11_KO_Stat3_rep2


title: WSB hypothalamus 4 weeks (56H)

source_name: hypothalamus

value: hypothalamus


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B6_ad001


title: 034_d13_KO_Kdm1b_rep2


title: WSB hypothalamus 4 weeks (42H)


title: RPE1 TRIM37 KO rep8

value: TRIM37 knockout


title: RPE1 TRIM37 KO rep9


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B6_ad008


title: 032_d11_KO_Sub1_rep2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B7_ad012


title: CHP134 rep3


title: 031_d13_KO_Sfr1_rep2


title: RPE1 TRIM37 KO rep7


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B6_ad002


title: WSB hypothalamus 4 weeks (31H)


title: RPE1 TRIM37 KO rep6


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B6_ad004


title: 030_d13_KO_Ccnk_rep2


title: WSB hypothalamus 4 weeks (27H)


title: 029_d13_KO_Mef2b_rep2


title: Gough hypothalamus 4 weeks (22H)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B6_ad010


title: RPE1 TRIM37 KO rep4


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B6_ad007


title: Gough hypothalamus 4 weeks (21H)


title: 033_d13_KO_Tcf25_rep2


title: RPE1 TRIM37 KO rep3


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B5_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B5_ad007


title: WSB hypothalamus 4 weeks (32H)


title: 028_d13_KO_Foxr1_rep2


title: RPE1 TRIM37 KO rep2


title: Gough hypothalamus 4 weeks (20H)


title: 027_d13_KO_Ell3_rep2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B5_ad001


title: Gough hypothalamus 4 weeks (19H)


title: RPE1 TRIM37 KO rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B5_ad008


title: Gough hypothalamus 4 weeks (18H)


title: RPE1 rep3-3


title: 025_d13_KO_Thap7_rep2


title: RPE1 rep3-2


title: RPE1 TRIM37 KO rep5


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B5_ad012


title: RPE1 rep3-1


title: WSB hypothalamus 4 weeks (26H)


title: 022_d11_KO_Lhx8_rep2


title: RPE1 rep2-3


title: 026_d13_KO_Ybx3_rep2


title: 021_d13_WT_rep2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B5_ad006


title: WSB hypothalamus 4 weeks (24H)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B5_ad010


title: RPE1 rep2-2


title: RPE1 rep2-1


title: 020_d11_WT_rep2


title: 019_d13_KO_Dynll1_rep1


title: 024_d13_KO_Tbpl2_rep2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B4_ad008


title: WSB hypothalamus 4 weeks (64H)


title: Gough hypothalamus 4 weeks (47H)


title: WSB hypothalamus 4 weeks (23H)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B4_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B4_ad007


title: 018_d13_KO_Noto_rep1


title: RPE1 rep1-2


title: 017_d11_KO_Stat3_rep1


title: Gough hypothalamus 4 weeks (45H)


title: WSB hypothalamus 4 weeks (25H)


title: RPE1 rep1-1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B4_ad001


title: 016_d13_KO_Nobox_rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B4_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B4_ad006


title: Gough hypothalamus 4 weeks (35H)


title: 015_d13_KO_Kdm1b_rep1


title: Human day 15 biorep 2

city: London

first: Teresa

last: Rayon

address: Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
expression_matrix.human.abundance.tsv
expression_matrix.human.counts.tsv

data_processing:
basecalling with bcl2fastq v2.20.0
alignment and quantification with BABS-RNASeq (https://github.com/crickbabs/BABS-RNASeq) and default parameters
Genome_build: GRCh38 Ensembl release-89
Supplementary_files_format_and_content: tab-delimited expression matrices from RSEM

source_name: Neural progenitor cells day 15

growth_protocol: For human motor neuron differentiation, cells were split with Versene and plated as clumps of ~50 cells on 1ug/cm2 fibronectin-coated (Millipore FC010) wells in N2B27 medium supplemented with 3 µM CHIR99021, 5ng/ml bFGF (100-18B Peprotech), 10uM SB431542 (LT S0400), 2uM DMH1 (A12820 Adooq Bioscience), and 10 µM ROCK inhibitor (Y-27632 Tocris) from days -3 to -1. Rock inhibitor was removed after 48 hours. On day 0 the cells were dissociated using accutase (A1110501 ThermoFisher Scientific) and 175,000 cells were plated per fibronectin-coated 35mm dish on N2B27 medium containing 100nM RA (R2625 Sigma Aldrich) and 500nM SAG (566660 Calbiochem) with10 µM ROCK inhibitor (Y-27632 Tocris). Rock inhibitor was removed 48h after plating and medium was replaced every other day.

extract_protocol:
Qiagen RNeasy Plus Micro Kit
KAPA mRNA

value: ES-derived neural progenitor cells

tag: starting conditions

value: differentiation from neuromesodermal progenitors

tag: treatment

value: RA and SAG

tag: time

value: day 15


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B4_ad010

tag: brain region

tag: Sex

tag: age


title: Gough hypothalamus 4 weeks (28H)

tag: strain

value: 4 weeks

tag: tissue


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B4_ad012


title: 013_d11_KO_Sub1_rep1


title: Human day 14 biorep 3

source_name: Neural progenitor cells day 14

value: day 14


title: Gough hypothalamus 4 weeks (46H)


title: WSB liver 4 weeks (42L)

source_name: liver

value: WSB/EiJ

tag: id of strain

value: male

value: left lobe of liver


title: WSB liver 4 weeks (32L)

tag: sex id


title: 012_d13_KO_Sfr1_rep1


title: Human day 14 biorep 2


title: 011_d13_KO_Ccnk_rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B3_ad002

value: PIR


title: Human day 15 biorep 3


title: WSB liver 4 weeks (31L)

tag: age id


title: CEMBA181008_5G_1_CEMBA181008_5G_2_C10_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B3_ad008


title: Human day 13 biorep 3

source_name: Neural progenitor cells day 13

value: day 13


title: 014_d13_KO_Tcf25_rep1

value: Blimp1-Venus and Stella-CFP


title: 010_d13_KO_Mef2b_rep1


title: Human day 15 biorep 1


title: Gough liver 4 weeks (22L)

value: Gough

tag: tissue id


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B3_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B3_ad004


title: 009_d13_KO_Foxr1_rep1

value: in vitro oocytes


title: 008_d13_KO_Ell3_rep1


title: Human day 13 biorep 1


title: WSB liver 4 weeks (27L)


title: Gough liver 4 weeks (21L)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B3_ad006


title: Human day 13 biorep 2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B3_ad001


title: Gough liver 4 weeks (20L)


title: Human day 12 biorep 3

source_name: Neural progenitor cells day 12

value: day 12


title: Human day 14 biorep 1


title: WSB liver 4 weeks (56L)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B3_ad012


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B3_ad010


title: Human day 12 biorep 2


title: Gough liver 4 weeks (19L)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B5_ad004


title: Human day 12 biorep 1


title: WSB liver 4 weeks (64L)

value: female


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B2_ad010


title: 005_d13_KO_Tbpl2_rep1


title: 004_d13_KO_Hes6_rep1


title: 003_d11_KO_Lhx8_rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B2_ad002


title: Gough liver 4 weeks (18L)


title: 007_d13_KO_Ybx3_rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B2_ad008


title: WSB liver 4 weeks (26L)


title: 002_d13_WT_rep1


title: Human day 11 biorep 2

source_name: Neural progenitor cells day 11

value: day 11


title: Human day 11 biorep 3

value: ES-derived neural progenitor cells


title: WSB liver 4 weeks (25L)


title: 006_d13_KO_Thap7_rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B2_ad001


title: WSB liver 4 weeks (24L)


title: Human day 10 biorep 3

source_name: Neural progenitor cells day 10

value: differentiation from neuromesodermal progenitors

value: day 10


title: Human day 11 biorep 1

value: RA and SAG


title: 001_d11_WT_rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B2_ad012


title: WSB liver 4 weeks (23L)

value: 4 weeks


title: Human day 10 biorep 2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B2_ad004


title: Gough liver 4 weeks (47L)


title: Human day 10 biorep 1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B2_ad007


title: CFPAC1.HNF1B-KO #03

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to human genome build GRCh38/hg38 using using START version 2.6.0c. Only uniquely mapped reads were retained
Gene expression counts were estimated using featureCounts  v0.6.1 (Rsubread version 1.6.1) , summarized across all exons , with option “largestOverlap”.
Differentially expressed genes were identified using EdgeR R-package v3.2.2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: The file gene.counts.txt contains the raw read counts for each samples.

source_name: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

growth_protocol:
IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep
See additional columns of the SAMPLES section

extract_protocol: 10^6 cells are lysed and processed according to SMART-Seq2 protocol. Briefly, 5 ng of poly-A containing mRNA molecules are copied into first strand cDNA by reverse transcription and template-switching using oligo(dt) primers and LNA-containing template-switching oligo (TSO). cDNA is pre-amplified using limited number of cycles, purified and tagmented with Tn5 transposase. cDNA fragments generated after tagmentation are gap-repaired, enriched by PCR and purified to create the final cDNA library for Illumina sequencing.

treatment_protocol:
Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting HNF1B gene
See additional columns of the SAMPLES section

value: CFPAC1 genome-edited clonal cell line


title: CFPAC1.HNF1B-KO #02


title: Human day 9 biorep 3

source_name: Neural progenitor cells day 9

value: day 9


title: CFPAC1.HNF1B-WT #03

treatment_protocol:
Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961)
See additional columns of the SAMPLES section

value: CFPAC1 clonal cell line


title: Gough liver 4 weeks (46L)

value: left lobe of liver


title: CFPAC1.HNF1B-KO #01


title: Gough liver 4 weeks (45L)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B2_ad006

value: PIR

value: male


title: Human day 9 biorep 2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B12_ad007


title: Gough liver 4 weeks (35L)


title: Human day 9 biorep 1


title: CFPAC1.HNF1B-WT #02


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B12_ad010


title: CFPAC1.HNF1B-WT #01


title: Human day 8 biorep 3

source_name: Neural progenitor cells day 8

value: day 8


title: Gough liver 4 weeks (28L)

value: Gough


title: WSB liver 2 weeks (59)

value: WSB/EiJ

value: 2 weeks


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B12_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: CFPAC1.ChIP.FOS.Rep2

description: Chromatin IP against FOS

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38),  then reads were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 200” and “--qvalue 0.05” flags and arguments. Each IP was compared to input DNA.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

extract_protocol: ChIP lysates were generated from 50x10^6 cells. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by AMPure XP SPRI (Beckman Coulter) and quantified using Quantifluor (Promega). ChIP DNA was prepared for HiSeq2000 or NextSeq500 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

tag: antibody

value: Anti-FOS (Antibody Sigma HPA018531 - Lot E106326 )


title: Human day 8 biorep 2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B12_ad006


title: WSB liver 2 weeks (41)


title: Human day 8 biorep 1


title: CFPAC1.ChIP.FOS.Rep1

description: Chromatin IP against FOS


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B12_ad001


title: Human day 7 biorep 3

source_name: Neural progenitor cells day 7

value: day 7


title: WSB liver 2 weeks (40)


title: HPAF2.InP

description: Control IP DNA

growth_protocol:
RPMI supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep
See additional columns of the SAMPLES section

treatment_protocol:
Original cell line
See additional columns of the SAMPLES section

value: HPAF2 cell line


title: WSB liver 2 weeks (39)


title: Human day 7 biorep 2

value: ES-derived neural progenitor cells

value: differentiation from neuromesodermal progenitors


title: WSB liver 2 weeks (5)


title: HPAF2.ChIP.MYRF.Rep1

description: Chromatin IP against MYRF

value: Anti-MYRF (Home made)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B11_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B12_ad012


title: Human day 7 biorep 1

value: RA and SAG


title: HPAF2.ChIP.MYRF.Rep2

description: Chromatin IP against MYRF


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B11_ad010


title: CFPAC1.ChIP.MYRF.Rep1

description: Chromatin IP against MYRF

value: CFPAC1 cell line


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B11_ad006


title: Human day 6 biorep 2

source_name: Neural progenitor cells day 6

value: day 6


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B11_ad012


title: Human day 6 biorep 3


title: Human day 6 biorep 1


title: Gough liver 2 weeks (17)


title: S09_NSuBi

city: Calgary

first: Leili

last: Rohani

state: Alberta

address: 405J, 1919 University Drive, NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

data_processing:
The constructed libraries sequenced on an Illumina NextSeq500 generated 75 bp, single-end reads. To process the samples, the quality of raw sequenced reads was checked with FastQC v0.11.5 program. No adapter or very highly overrepresented sequences were found, and the quality of sequencing was very high. RNA-seq reads were pseudoaligned to the human Ensembl RefSeq transcript database; GRCh38 (latest Ensembl human transcript reference) using Kallisto 0.42.4. For the parametric analysis, DESeq (an R/Bioconductor package) was used for differential gene expression using static/static suspension/stirred suspension bioreactor as the explanatory variable.DESeq results were filtered by Adj-p (corrected p-value) < 0.01.
Ingenuity Pathway Analysis (IPA) and its z-score algorithm was used to identify enriched canonical pathways that are more or less active (positive or negative z-score) according to IPA database and our RNA-seq data.
Genome_build: GRCh38 (latest Ensembl human transcript reference)
Supplementary_files_format_and_content: Raw count table (csv. Format) contains the number of transcripts in each sample. RNA-seq reads were pseudoaligned to the human Ensembl RefSeq transcript database; GRCh38 (latest Ensembl human transcript reference) using Kallisto 0.42.4.

source_name: Human embryonic stem cell line_H9

growth_protocol: For static culture, the primed hESC line H9 was converted to naïve pluripotency using RSeT™ Medium according to manufacturer’s instructions (Stem Cell Technologies, 5970). Briefly, once the primed hESCs reached to 70 – 80% confluency, they were passaged as small clumps (approximately 50 - 200 µm in size) using Dispase (1 U/mL) (Stem Cell Technologies, 7923), and were transferred onto mitomycin C treated-mitotically inactivated MEFs (iMEFs)-coated plates containing mTeSR™1 medium. The cells were incubated at 37°C for 24 - 36 hours under normoxic conditions (20% O2, 5% CO2) in mTeSR™1 medium. The mTeSR™1 medium was then replaced with RSeT™ medium and a daily full medium change with RSeT™ was done during the reversion to naïve hPSCs. Upon the appearance of domed-shaped and tightly-packed colonies (after 3-4 days in RSeT™ Medium), the colonies were typically ready to be passaged. The culture was passaged using StemPro® Accutase® Cell Dissociation Reagent (Thermo Fisher Scientific, A1110501), and seeded on new iMEFs containing RSeT™ medium supplemented with Y-27632 (Stem Cell Technologies, 72304) to a final concentration of 10 µM. During the first passages and reversion in RSeT™ condition, the cells were split at a ratio of 1:6. Once the culture was established, cells were split at a ratio of 1:10 every 3 days. Naïve hPSCs from passage 4 of static cuture were used for RNAseq analysis and for inoculation into the stirred suspension bioreactors and static suspension well-plates. For cell inoculation into stirred suspension bioreactors and static suspension well-plates, naïve hPSCs from passage 4 of static culture, were inoculated into 100 ml stirred suspension bioreactors (NDS Technologies, Vinland, NJ, USA) and 6-well static suspension plates at the density of 5E4 cells/ml and 2E5 cells/ml, respectively. For inoculation procedure, confluent naïve hPSCs from the static culture were enzymatically dissociated into single cells using StemPro® Accutase® Cell Dissociation Reagent and mechanical pipetting. Following dissociation into single cells, the naïve hESC and iMEF mixture were seeded onto gelatin (Sigma-Aldrich, G1890) coated dishes with complete RSeT™ medium for a period of 45 mins – 1 h. During this time, the iMEFs would adhere to the gelatin coated dishes while the naïve hESCs remained suspended. The naïve hESC suspension was aspirated from the dishes and centrifuged at 200 g for 5 mins. The desired cell concentration was then added to 6-well static suspension culture dishes (Greiner Bio-One, 657185) containing 2 ml of complete RSeT™ medium supplemented with 10 µM Y-27632. Following 1 hr of static suspension, small cell clumps were observed in the culture wells. These clumps were gently pipetted up and down several times and added to either 100 ml stirred suspension bioreactors or 6-well static suspension plates containing RSeT™ medium supplemented with 10 µM Y-27632 and 0.1 nM Rapamycin (Sigma Aldrich, R8781). The agitation rate of 100 rpm was used for naïve hPSCs cultured in 100 ml stirred suspension bioreactor. Naïve hESCs were cultured in 100 ml bioreactors and 6-well suspension plates for a period of 4 days under fed-batch condition (60% media change, 48h post-inoculation) before collecting for RNAseq analysis.

extract_protocol:
RNA-seq analysis was done in collaboration with the Centre for Health Genomics and Informatics at the University of Calgary. Naïve hPSCs from static, static suspension  and stirred suspension cultures were collected and the total RNA was extracted using PureLink™ RNA Mini Kit (Thermo Fisher Scientific, 12183018A), according to the manufacturers’ protocol, including DNAse I digestion using DNAse I Amplification Grade (Thermo Fisher Scientific, 18068015). Concentration and quality of the total extracted RNA was checked using Qubit Fluorometer (QubitR RNA HS high sensitivity assay Thermo Fisher) and TapeStation assay (Agilent 4200 TapeStation System), respectively. The total RNA was depleted of ribosomal RNA using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB, E6310L) and 500 ng of the remaining RNA was purified, fragmented, and used for cDNA synthesis and library preparation.
The Illumina sequencing library preparation was done using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) according to manufacturer’s protocol.

value: Inner cell mass (ICM) of blastocyte, human embryo

value: Human embryonic stem cell

value: Female

tag: protocol

value: stirred suspension


title: Gough liver 2 weeks (16)

value: male

value: left lobe of liver


title: S08_NSuBi


title: Human day 5 biorep 3

source_name: Neural progenitor cells day 5

value: day 5


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B11_ad002

value: PIR


title: S07_NSuBi


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B11_ad004


title: Gough liver 2 weeks (15)

value: Gough

value: 2 weeks


title: CFPAC1.ChIP.MYRF.Rep2

description: Chromatin IP against MYRF


title: WSB liver 2 weeks (63)

value: WSB/EiJ

value: female


title: S06_NSuSt

value: static suspension


title: Human day 5 biorep 1

value: ES-derived neural progenitor cells

value: differentiation from neuromesodermal progenitors


title: WSB liver 2 weeks (62)


title: Gough liver 2 weeks (38)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B11_ad008


title: Human day 5 biorep 2

value: RA and SAG


title: Human day 4 biorep 3

source_name: Neural progenitor cells day 4

value: day 4


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B10_ad004


title: S05_NSuSt

value: Inner cell mass (ICM) of blastocyte, human embryo


title: Human day 4 biorep 2


title: WSB liver 2 weeks (60)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B10_ad001


title: S04_NSuSt

value: Human embryonic stem cell


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B10_ad012


title: S03_NSt

value: Female

value: static


title: Human day 4 biorep 1


title: WSB liver 2 weeks (6)


title: S02_NSt


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B10_ad002

value: male


title: Human day 2 biorep 3

source_name: Neural progenitor cells day 2

value: day 2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B11_ad007


title: Gough liver 2 weeks (55)

value: left lobe of liver


title: Human day 2 biorep 2


title: S01_NSt


title: Human day 2 biorep 1


title: 023_d13_KO_Hes6_rep2

tag: genotype

value: Blimp1-Venus and Stella-CFP

value: in vitro oocytes


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B10_ad006

value: PIR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B10_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B1_ad010


title: Gough liver 2 weeks (53)

value: Gough

value: 2 weeks


title: Gough liver 2 weeks (54)

value: female


title: Human day 1 biorep 3

source_name: Neural progenitor cells day 1

tag: cell type

value: ES-derived neural progenitor cells

value: day 1


title: RPE1 rep1-3

source_name: Human retinal pigmented epithelial cells

tag: cell line

tag: geneotype

value: Wild type

tag: drug treatment

value: No


title: Human day 1 biorep 2

tag: starting conditions

value: differentiation from neuromesodermal progenitors

tag: treatment

value: RA and SAG

tag: time


title: Gough liver 2 weeks (52)

source_name: liver

tag: Sex

tag: age


title: Gest-zBr15dpf12

city: Philadelphia

first: Bushra

last: Raj

address: 421 Curie Boulevard

institute: University of Pennsylvania

description:
F12.GestMaster.txt
zfAllMerge-FILTEREDUSEME.xlsx

data_processing:
Single-cell RNA Sequencing data (FASTQ files) were processed using Cell Ranger v2.0.2 to generate count matrices
Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 (release-86) genome assembly. File uploaded as Danio_rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates (marked as *b in raw files) and the processing was done using the combination of all data (processed data files have comb* prefix)
scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping
Genome_build: GRCz10
Supplementary_files_format_and_content: *barcodes.tsv files contain 10X Genomics cell barcodes, *genes.tsv files contain gene names, *matrix.mtx contain transcriptome count data, *web_summary.html contain summary statistics for transcript mapping, .rds files are the processed R objects, .txt files contain marker genes identified for each cluster in the dataset, URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus.
Supplementary_files_format_and_content: scGESTALT data:  Gest-zBr15dpf8 and Gest-zBr15dpf9 correspond to two samples from the same zebrafish (ZF1). Gest-zBr15dpf10 and Gest-zBr15dpf11 correspond to two samples from the same zebrafish (ZF2). Gest-zBr15dpf12 and Gest-zBr15dpf13 correspond to two samples from the same zebrafish (ZF3). Gest-zBr15dpf14 and Gest-zBr15dpf15 correspond to two samples from the same zebrafish (ZF4).
Supplementary_files_format_and_content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers (CellBarcode and CellUMI) that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences (HMID column) , the t-SNE cluster membership number (ClusterIdent column), and unique identifier (Readname). zfAllMerge-FILTEREDUSEME.xlsx contains the merged statistics of all samples, filtered to contain high confidence barcodes, the barcode sequence aligned to a reference unedited sequence (mergedRead column), mutations at each target site (target[X] columns) and the edited sequences at each target site (sequence[X] columns) were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping

organism: Danio rerio

source_name: zebrafish brain

extract_protocol:
Gestalt barcode was PCR amplified. Sample indices and flow cell adaptors were then added by PCR.
Single-cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single-cell cDNA libraries and prepared for sequencing

tag: tissue

value: brain

tag: developmental stage


title: Gough liver 2 weeks (51)

tag: strain

tag: sex id


title: Gest-zBr15dpf15

description:
F15.GestMaster.txt
zfAllMerge-FILTEREDUSEME.xlsx


title: Gest-zBr15dpf14

description:
F14.GestMaster.txt
zfAllMerge-FILTEREDUSEME.xlsx


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B1_ad007

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B1_ad008


title: WSB liver E16.5 (W8C)

value: WSB/EiJ

tag: id of strain

tag: age id

tag: tissue id


title: WSB liver 2 weeks (61)


title: Human day 0 biorep 3

source_name: Neural progenitor cells day 0

tag: cell type

value: control

value: day 0


title: Gest-zBr15dpf11

description:
F11.GestMaster.txt
zfAllMerge-FILTEREDUSEME.xlsx


title: Gest-zBr15dpf10

description:
F10.GestMaster.txt
zfAllMerge-FILTEREDUSEME.xlsx


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B1_ad006

value: male


title: WSB liver E16.5 (W8B)

value: left lobe of liver


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B1_ad001


title: Gest-zBr15dpf13

description:
F13.GestMaster.txt
zfAllMerge-FILTEREDUSEME.xlsx


title: Human day 0 biorep 2

tag: cell line


title: Gest-zBr15dpf9

description:
F9.GestMaster.txt
zfAllMerge-FILTEREDUSEME.xlsx


title: Gest-zBr15dpf8

description:
F8.GestMaster.txt
zfAllMerge-FILTEREDUSEME.xlsx


title: WSB liver E16.5 (W8A)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B1_ad002


title: Human day 1 biorep 1


title: WSB liver E16.5 (W6C)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_B1_ad012


title: zBr15dpf21_S1

description:
zf15dpf_PCAALL.rds
zf15dpf_PCALL_cc_filt_MarkRes5.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds

extract_protocol:
Libraries were prepared as described in manufacturer's protocol for v2 kits
Single-cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single-cell cDNA libraries and prepared for sequencing


title: WSB liver E16.5 (W6B)


title: KPL 160424S3

first: Yaohe

address: John Vane Science Centre,  Charterhouse Square

department: Centre for Molecular Oncology

institute: Barts Cancer Institute

data_processing:
RNA-Seq reads were aligned to mm10 using Hisat2
Reads were processed with Samtools.
Count files were generated by mapping reads to the mouse genome (GRCm38) version9 (Ensembl 84) using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content:  [.txt] files are tab formatted text files containing counts on the mouse genome (GRCm38) version9 (Ensembl 84)

source_name: KP mice-derived lung cancer cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10%FBS in 37º CO2 incubator.

extract_protocol: Samples' total RNA was extracted by Trizol and 200ng total RNA sample was purified by oligo-dT beads.mRNA isolation and fragmentation: 200ng total RNA sample was purified by oligo-dT beads, then poly (A)-containing mRNA were fragmented into small pieces with Elute, Prime, Fragment Mix . cDNA synthesis: First-strand cDNA was generated by First Strand Master Mix and Super Script II(Invitrogen) reverse transcription(Reaction condition：25℃ for 10 min；42℃ for 50 min；70℃for 15 min). Then adding Second Strand Master Mix to synthes the second-strand cDNA (16℃1h). End repair, add A and adaptor ligation: the purified Fragmented cDNA combine with End Repair Mix, incubate at30℃ 30min. Purify the end-repaired DNA with Ampure XP Beads (AGENCOURT). Then add A-Tailing Mix , mix well by pipetting, incubate at 37℃ 30 min. Adapter Ligation : Combine the Adenylate 3'Ends DNA, RNA Index Adapter and Ligation Mix, mix well by pipetting. Incubate the ligate reaction at 30℃ 10 min. Purify the end-repaired DNA with Ampure XP Beads (AGENCOURT). RCR: Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix were performed to enrich the cDNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT).

treatment_protocol: No special treatment

value: KP cell line

tag: genotype/variation

value: With Kras G12D and p53 R172H mutation


title: KPL 160424S2


title: KPL 160424S1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A9_ad007

value: PIR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A9_ad001


title: Gough liver E16.5 (G6E)

value: Gough


title: zBr15dpf19_S3


title: zBr15dpf20_S2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A9_ad004


title: KPL 160302S3


title: zBr15dpf18_S4


title: Gough liver E16.5 (G6C)


title: KPL 160302S2


title: Human day 0 biorep 1


title: zBr15dpf17_S5


title: zBr15dpf16_S6


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A9_ad002


title: KPL 160302S1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A9_ad012


title: KP-LC3

source_name: Regrogrammed somatic cells-derived lung cancer cells

value: WT somatic cells reprogrammed cell line, modified K and P


title: Gough liver E16.5 (G4B)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A9_ad008


title: Gough liver E16.5 (G6A)


title: Gough liver 2 weeks (30)

value: 2 weeks


title: KP-LC2


title: Gough liver E16.5 (G6D)


title: WSB liver E16.5 (W7B)

value: female


title: zBr15dpf14_S3


title: zBr15dpf15_S4


title: WSB liver E16.5 (W6D)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A9_ad006


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A9_ad010


title: KP-LC1


title: WSB liver E16.5 (W6A)


title: RNaseL KO BMM nsp15 9hpi rep1 cyclic phosphate

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description:
RNaseL_nsp15_9_rep1_cp
cyclic phosphate sequencing libraries

data_processing:
Data analysis pipeline and custom scripts are provided in a github repository (https://github.com/hesselberthlab/endoU). Cyclic phoshate libraries were preprocessed to extract UMI sequences which were appended to the fastq reads using UMI-tools (v0.5.4) (Smith 2017). Reads were next aligned with Bowtie2 to a to the MHV genome alone (GenBank accession: NC_001846.1) and a combined reference including the MHV genome, Mus musculus rRNA and U6 snRNA references (GenBank accession numbers: NR_003278.3, NR_003279.1, NR_003280.2, NC_000074.6, NR_003027.2), and annotated ORFs from the Mouse ORFeome collection (MGC full-cds collection for Mus musculus). Aligned reads were de-duplicated using UMI-tools to remove PCR duplicated reads. De-duplicated reads were converted to bedGraph format using BEDTools (v2.26.0) to report the number of reads at each single base cleavage position, including for sense and antisense sequences for the MHV aligned reads (39). Reads at each cleavage position were normalized by library size (Quinlan 2012).
RNA-seq libraries were preprocessed to trim Illumina adaptor sequences from the fastq reads using Cutadapt (v 1.16) (Martin 2011). Trimmed reads were aligned to a combined MHV (GenBank accession: NC_001846.1) and Mus musculus genome reference (Ensemble GRCm38.p6) and bedGraph coverage files were generated from each alignment using STAR (v 2.7.1a) (Dobin 2002) and featureCounts (from subread v 1.6.2) was used to assign counts to murine and viral RNAs.
Genome_build: NC_001846.1, NR_003278.3, NR_003279.1, NR_003280.2, NC_000074.6, NR_003027.2, GRCm38.p6, mouse orfeome collection
Supplementary_files_format_and_content: Bedgraphs files containing counts for the cylic phosphate libraries per position and a text file containing counts per gene/feature combined for all RNAseq libraries are provided

source_name: RNaseL-/- bone marrow macrophage: nsp15 mutant MHV infection: 9 hours post infection

extract_protocol:
Bone marrow macrophages were infected and RNA isolated from the cells using Trizol
Total RNA was DNased for 30 min prior to 3´-adaptor ligation  to cyclic phosphate containing molecules using Rtcb. Ligated molecules were chemically fragmented Ambion fragmentation reagent) for 4 min and 65℃ and gel purified to remove excess adaptor. Purified RNAs were 5´-adaptor ligated using Rtcb and ligated RNAs were purified using Streptavidin beads (Invitrogen). cDNA was prepared using an Illumina-compatible primer complimentary to the 3´-adaptor. cDNA was PCR amplified using Truseq barcoded F and R oligos for 18 cycles with 1 unit of  Phusion. PCR results were confirmed  by gel electrophoresis and the remaining sample was Ampure XP purified at a ratio of 1.8x bead.pcr volume. Samples were eluted in 10 ul and molarity was determined using a Qbit and submitted for sequencing.

tag: genotype

value: RNaseL-/-

value: nsp15 mutant MHV infection:9 hours post infection

value: bone marrow macrophage


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A8_ad001


title: zBr15dpf12_S1


title: RNaseL KO BMM ns2 9hpi rep1 cyclic phosphate

description:
RNaseL_ns2_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: RNaseL-/- bone marrow macrophage: ns2 mutant MHV infection: 9 hours post infection

value: ns2 mutant MHV infection:9 hours post infection


title: WSB liver E16.5 (W5C)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A8_ad010


title: zBr15dpf11_S4

value: brain


title: WSB liver E16.5 (W5A)

value: WSB/EiJ


title: zBr15dpf10_S3


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A8_ad006


title: Gough liver E16.5 (G6B)


title: RNaseL KO BMM MHV(V) 9hpi rep1 cyclic phosphate

description:
RNaseL_MHVV_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: RNaseL-/- bone marrow macrophage: WT MHV infection: 9 hours post infection

value: WT MHV infection:9 hours post infection


title: zBr15dpf9_S2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A8_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: zBr15dpf13_S2


title: zBr15dpf8_S1


title: Gough liver E16.5 (G4E)


title: Gough liver E16.5 (G4D)


title: IFNAR KO BMM nsp15 9hpi rep1 cyclic phosphate

description:
IFNAR_nsp15_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: nsp15 mutant MHV infection: 9 hours post infection

value: IFNAR-/-


title: Gough liver E16.5 (G3E)


title: zBr15dpf7e_S6


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A8_ad012

value: male


title: zBr15dpf6_S3


title: IFNAR KO BMM MHV(S) 9hpi rep1 cyclic phosphate

description:
IFNAR_MHVS_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: WT MHV infection: 9 hours post infection


title: RNaseL KO BMM MHV(S) 9hpi rep1 cyclic phosphate

description:
RNaseL_MHVS_9_rep1_cp
cyclic phosphate sequencing libraries


title: IFNAR KO BMM ns2 9hpi rep1 cyclic phosphate

description:
IFNAR_ns2_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: ns2 mutant MHV infection: 9 hours post infection


title: IFNAR KO BMM MHV(V) 9hpi rep1 cyclic phosphate

description:
IFNAR_MHVV_9_rep1_cp
cyclic phosphate sequencing libraries


title: zBr15dpf5_S1


title: IFNAR KO BMM mock 9hpi rep1 cyclic phosphate

description:
IFNAR_mock_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: mock infection: 9 hours post infection

value: mock infection:9 hours post infection


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A8_ad004


title: zBr15dpf4_S3


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A7_ad007


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A7_ad012


title: zBr15dpf3e_S2


title: WT BMM nsp15 9hpi rep1 cyclic phosphate

description:
B6_nsp15_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: nsp15 mutant MHV infection: 9 hours post infection


title: crp1 mutant_rep1

city: Pusan

first: Eon-Min

last: Ko

address: pusandaehak-ro

country: South Korea

institute: Pusan national university

data_processing:
The quality of the obtained data was checked by determining the phred quality score using FastQC v0.11.5.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.32, then mapped to the whole genome of M. smegmatis using bowtie v1.1.2 with default setting.
Mapped reads per annotated gene were counted by Bam2readcount.
Counted values were nomalized in the RPKM method.
Genome_build: Mycobacterium smegmatis MC2 155 (GCF_000015005.1_ASM1500v1)
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each sample

organism: Mycolicibacterium smegmatis

source_name: in vitro aerobic culture of the crp1 mutant strain

growth_protocol: The M. smegmatis strains were grown aerobically in Middlebrook 7H9 medium supplemented with 0.2% glucose and 0.02% Tween 80 (vol/vol) on a gyratory shaker (200 rpm) at 37°C.

extract_protocol:
The stains were grown until an optical density at 600 nm reached 2.0 to 2.1. Cells were harvested by centrifugation at 4°C with 3500×g for 3 min. The cell pellets were resuspended with 1 ml TRIzol (Invitrogen). Procedures of total RNA extract from the cell pellets were performed using TRIZol purchased from Invitrogen and followed the instructions provided to users. Six ibraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq2000 instrument.
The RNA sequencing libraries were created using a TruSeq RNA Sample Prep Kit v2 (Illumina) with the standard low-throughput protocol.

tag: strain background

tag: conditions

value: in vitro


title: RNaseL KO BMM mock 9hpi rep1 cyclic phosphate

description:
RNaseL_mock_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: RNaseL-/- bone marrow macrophage: mock infection: 9 hours post infection

tag: treatment


title: zBr15dpf2_S2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A8_ad007

first: Joseph

institute: HHMI-Salk-Institute

tag: Sex


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A7_ad004

tag: age


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A8_ad002


title: WT_rep3

source_name: in vitro aerobic culture of the wild type strain

value: wild type


title: Gough liver E16.5 (G3B)

source_name: liver

tag: tissue

value: left lobe of liver


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A7_ad002

value: PIR


title: zBr15dpf1_S1

source_name: zebrafish brain

tag: developmental stage


title: WT BMM MHV(S) 9hpi rep1 cyclic phosphate

description:
B6_MHVS_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: WT MHV infection: 9 hurs post infection

value: WT MHV infection:9 hurs post infection


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A7_ad008

tag: strain


title: crp1 mutant_rep3


title: WT_rep2


title: WT BMM MHV(V) 9hpi rep1 cyclic phosphate

description:
B6_MHVV_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: WT MHV infection: 9 hours post infection


title: crp1 mutant_rep2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A7_ad001


title: zBr8dpf12_S3

description:
zf8dpf_cc_filt.cluster4.rds
zf8dpf_cc_filt_MarkRes6v4.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds


title: WT BMM mock 9hpi rep1 cyclic phosphate

description:
B6_mock_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: mock infection: 9 hours post infection


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A7_ad006


title: RNaseL KO BMM nsp15 12hpi rep1 cyclic phosphate

description:
RNaseL_nsp15_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: RNaseL-/- bone marrow macrophage: nsp15 mutant MHV infection: 12 hours post infection

value: nsp15 mutant MHV infection:12 hours post infection


title: zBr8dp11_S7


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A7_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A6_ad006


title: Stimulated - CD8+ - MC CAR - Donor 1

city: Memphis

middle: Allen

last: Schreiner

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Children's Research Hospital

data_processing:
Read alignment was performed using STAR and BWA software
Gene level quantification was performed by HTSeq
Differentially expressed genes were identified using limma voom
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: Osteosarcoma cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from whole blood of healthy donors by Lymphoprep gradient centrifugation, stimulated with CD3/CD28 antibodies, and transduced with retroviral vectors encoding EphA2 Delta-, CD28 zeta-, 41BB zeta-, and MyD88.CD40 (MC) zeta-CARs. The resulting CAR T cells were maintained in RPMI with 10% FBS, 10 ng/mL IL-7 and 5 ng/mL IL-15.

extract_protocol:
poly-A selected
stranded mRNA

treatment_protocol: CAR T cells were taken directly from culture or stimulated with LM7 tumor cells at a 2:1 T cell:tumor cell ratio for 24 hours before being sorted (FACS) into CD4+transgene+ and CD8+transgene+ populations.

tag: agent

value: Stimulated - CD8+ - MC CAR


title: RNaseL KO BMM ns2 12hpi rep1 cyclic phosphate

description:
RNaseL_ns2_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: RNaseL-/- bone marrow macrophage: ns2 mutant MHV infection: 12 hours post infection

value: RNaseL-/-

value: ns2 mutant MHV infection:12 hours post infection


title: Stimulated - CD8+ - MC CAR - Donor 2


title: WT BMM ns2 9hpi rep1 cyclic phosphate

description:
B6_ns2_9_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: ns2 mutant MHV infection: 9 hours post infection

value: bone marrow macrophage


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A6_ad001

city: La Jolla

last: Ecker

address: 10010 North Torrey Pines Road

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region


title: zBr8dpf8_S4


title: zBr8dpf9_S5


title: zBr8dpf10_S6


title: Stimulated - CD4+ - MC CAR - Donor 3

value: Stimulated - CD4+ - MC CAR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A6_ad002


title: Stimulated - CD4+ - MC CAR - Donor 2


title: RNaseL KO BMM MHV(V) 12hpi rep1 cyclic phosphate

description:
RNaseL_MHVV_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: RNaseL-/- bone marrow macrophage: WT MHV infection: 12 hours post infection

value: WT MHV infection:12 hours post infection


title: zBr8dpf7_S3

value: brain


title: RNaseL KO BMM mock 12hpi rep1 cyclic phosphate

description:
RNaseL_mock_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: RNaseL-/- bone marrow macrophage: mock infection: 12 hours post infection

value: mock infection:12 hours post infection


title: zBr8dpf6_S6


title: WT_rep1


title: Stimulated - CD4+ - MC CAR - Donor 1


title: Stimulated - CD8+ - MC CAR - Donor 3


title: zBr8dpf13_S1


title: RNaseL KO  BMM mock 0hr for 9hpi rep1 cyclic phosphate

description:
RNaseL_mock_09_rep1_cp
cyclic phosphate sequencing libraries

source_name: RNaseL-/- bone marrow macrophage: mock infection: 0 hr mock for 9 hours post infection

value: mock infection:0 hr mock for 9 hours post infection


title: Stimulated - CD8+ - 41BB CAR - Donor 2

value: Stimulated - CD8+ - 41BB CAR


title: IFNAR KO BMM mock 0hr for 9hpi rep1 cyclic phosphate

description:
IFNAR_mock_09_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: mock infection: 0 hr mock for 9 hours post infection

value: IFNAR-/-


title: Stimulated - CD8+ - 41BB CAR - Donor 3


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A6_ad010

value: male


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A6_ad007


title: Stimulated - CD8+ - 41BB CAR - Donor 1


title: zBr8dpf4_S4


title: WT BMM mock 0hr for 9hpi rep1 cyclic phosphate

description:
B6_mock_09_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: mock infection: 0 hr mock for 9 hours post infection


title: RNaseL KO BMM MHV(S) 12hpi rep1 cyclic phosphate

description:
RNaseL_MHVS_12_rep1_cp
cyclic phosphate sequencing libraries


title: Stimulated - CD4+ - 41BB CAR - Donor 3

value: Stimulated - CD4+ - 41BB CAR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A6_ad012


title: RNaseL KO BMM mock 0hr for 12hpi rep1 cyclic phosphate

description:
RNaseL_mock_012_rep1_cp
cyclic phosphate sequencing libraries

source_name: RNaseL-/- bone marrow macrophage: mock infection: 0 hr mock for 12 hours post infection

value: mock infection:0 hr mock for 12 hours post infection


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A5_ad012

value: PIR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A6_ad008


title: IFNAR KO BMM mock 0hr for 12hpi rep1 cyclic phosphate

description:
IFNAR_mock_012_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: mock infection: 0 hr mock for 12 hours post infection


title: Stimulated - CD4+ - 41BB CAR - Donor 2


title: zBr8dpf1_S1


title: Stimulated - CD4+ - 41BB CAR - Donor 1


title: WT BMM mock 0hr for 12hpi rep1 cyclic phosphate

description:
B6_mock_012_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: mock infection: 0 hr mock for 12 hours post infection


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A5_ad008


title: zBr5dpf9_S6

description:
zf5dpf_cc_filt.cluster.rds
zf5dpf_cc_filt_MarkRes5.5.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds

source_name: zebrafish brain


title: zBr8dpf5_S5


title: IFNAR KO BMM nsp15 12hpi rep1 cyclic phosphate

description:
IFNAR_nsp15_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: nsp15 mutant MHV infection: 12 hours post infection


title: Stimulated - CD8+ - CD28 CAR - Donor 3

value: Stimulated - CD8+ - CD28 CAR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A5_ad004


title: zBr5dpf8_S5


title: Stimulated - CD8+ - CD28 CAR - Donor 2


title: Stimulated - CD8+ - CD28 CAR - Donor 1


title: zBr8dpf2_S2


title: zBr5dpf7_S4


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A5_ad001


title: IFNAR KO BMM MHV(S) 12hpi rep1 cyclic phosphate

description:
IFNAR_MHVS_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: WT MHV infection: 12 hours post infection


title: zBr8dpf3_S3

description:
zf8dpf_cc_filt.cluster4.rds
zf8dpf_cc_filt_MarkRes6v4.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds


title: Stimulated - CD4+ - CD28 CAR - Donor 3

value: Stimulated - CD4+ - CD28 CAR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A5_ad006


title: zBr5dpf6_S3


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A5_ad010


title: IFNAR KO BMM mock 12hpi rep1 cyclic phosphate

description:
IFNAR_mock_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: mock infection: 12 hours post infection


title: Stimulated - CD4+ - CD28 CAR - Donor 2


title: zBr5dpf4_S1


title: IFNAR KO BMM MHV(V) 12hpi rep1 cyclic phosphate

description:
IFNAR_MHVV_12_rep1_cp
cyclic phosphate sequencing libraries


title: Stimulated - CD4+ - CD28 CAR - Donor 1


title: WT BMM nsp15 12hpi rep1 cyclic phosphate

description:
B6_nsp15_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: nsp15 mutant MHV infection: 12 hours post infection

value: nsp15 mutant MHV infection:12 hours post infection


title: Stimulated - CD8+ - 4H5D CAR - Donor 3

source_name: Osteosarcoma cells

value: Stimulated - CD8+ - 4H5D CAR


title: zBr5dpf3_S4


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A4_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A4_ad007


title: WT BMM ns2 12hpi rep1 cyclic phosphate

description:
B6_ns2_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: ns2 mutant MHV infection: 12 hours post infection

value: ns2 mutant MHV infection:12 hours post infection


title: zBr5dpf2_S3


title: IFNAR KO BMM ns2 12hpi rep1 cyclic phosphate

description:
IFNAR_ns2_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: IFNAR-/- bone marrow macrophage: ns2 mutant MHV infection: 12 hours post infection

value: bone marrow macrophage


title: Stimulated - CD8+ - 4H5D CAR - Donor 2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A5_ad007

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A4_ad006


title: WT BMM MHV(S) 12hpi rep1 cyclic phosphate

description:
B6_MHVS_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: WT MHV infection: 12 hurs post infection

value: WT MHV infection:12 hurs post infection


title: zBr5dpf1_S7


title: WT BMM MHV(V) 12hpi rep1 cyclic phosphate

description:
B6_MHVV_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: WT MHV infection: 12 hours post infection

value: WT MHV infection:12 hours post infection


title: Stimulated - CD4+ - 4H5D CAR - Donor 3

value: Stimulated - CD4+ - 4H5D CAR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A5_ad002


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A4_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A4_ad008


title: Stimulated - CD4+ - 4H5D CAR - Donor 2


title: WT BMM mock 12hpi rep1 cyclic phosphate

description:
B6_mock_12_rep1_cp
cyclic phosphate sequencing libraries

source_name: C57BL/6 bone marrow macrophage: mock infection: 12 hours post infection

value: mock infection:12 hours post infection


title: zBr5dpf5_S2

value: brain


title: zBr3dpf6_S8

description:
zf3dpf_cc_filt.cluster.rds
zf3dpf_cc_filt_MarkRes5.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds


title: uty_f

description: cytoplasmic RNA

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the reference mouse genome version GRCm38 using STAR version 2.5.1b
Raw counts for each feature from GRCm38 ENSEMBL v93 annotation  file were extracted using FeatureCounts v1.6.0
DESeq2 version 1.22.2 was used to normalize gene readcounts and compute differential expression between uty and b6 experimental conditions.
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file including normalized readcounts values for each sample from DESeq2 analysis

source_name: adult cardiomyocytes isolated by heart retrograde perfusion and maintained in culture for 4 hours

growth_protocol: Adult male mice were to obtain hearts for digestion.  After isolation, the cells were plated on laminin-coated dishes, and used 4 hours after plating for RNA isolation

extract_protocol:
Qiagen Rneasy micro RNA kit with Dnase treatment
Illumina TruSeq Stranded RNA Kit, after ribodepletion with Fast Select mouse RNA removal kit (Qiagen).

value: cardiomyocytes

tag: type of data

value: adult cardiomyocytes


title: Stimulated - CD4+ - 4H5D CAR - Donor 1


title: uty_e

description: cytoplasmic RNA


title: zBr3dpf4_S6


title: Stimulated - CD8+ - 4H5D CAR - Donor 1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A4_ad001

value: male


title: zBr3dpf3_S5


title: zBr3dpf5_S7


title: Unstimulated - CD8+ - MC CAR - Donor 3

value: Unstimulated - CD8+ - MC CAR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A3_ad010


title: uty_d

description: cytoplasmic RNA


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A3_ad006


title: zBr3dpf2_S2


title: b6_g

description: cytoplasmic RNA


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A3_ad001


title: zBr3dpf1_S1


title: b6_f

description: cytoplasmic RNA


title: Unstimulated - CD8+ - MC CAR - Donor 1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A3_ad007


title: zBr2dpf6_S4

description:
zf2dpf_cc_filt.cluster.rds
zf2dpf_cc_filt_MarkRes6.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds


title: b6_e

description: cytoplasmic RNA


title: Unstimulated - CD4+ - MC CAR - Donor 3

value: Unstimulated - CD4+ - MC CAR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A3_ad008

value: PIR


title: zBr2dpf5_S3


title: Unstimulated - CD4+ - MC CAR - Donor 2


title: Unstimulated - CD8+ - MC CAR - Donor 2


title: Unstimulated - CD4+ - MC CAR - Donor 1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A3_ad002