title: RPE1 WT rep2

data_processing:
Raw paired-end FASTQ files were aligned to the GRCh38 reference genome using bowtie2 version 2.4.4
BAM files were sorted and indexed with samtools version 1.6
Peaks were called using Macs3 version 3.0.0b1 with RPE1 WT set as the control and default settings
Peaks were filtered using the ENCODE blacklist v2 and manually inspected
Total read counts were calculated for each sample and used to generate comparable bigwig files for visualization using bamCoverage version 3.3.0 and the scaleFactor option
Assembly: GRCh38
Supplementary files format and content: Scaled bigwig coverage files for all samples
Supplementary files format and content: List of blacklist filtered peaks called using MACS3 against RPE1 WT


title: WA Control, Biol rep 1

status: Public on Feb 03 2025

type: SRA

city: Santiago

first: Benjamín

last: Szenfeld

state: Las Condes

address: Av Plaza 680

department: Genetics and Genomics

country: Chile

institute: Institute of Science and Innovation in Medicine

description: Library name: Sample 1

library_source: transcriptomic

data_processing:
Galaxy Europe was used to upload the RNA-seq FASTQ files and generate paired datasets for each sample (forward and reverse reads). Then, the Salmon tool was employed to map the sequences to the reference transcriptome and obtain expression quantifications per sample in the form of TPMs and counts.
Assembly: sacCer3
Supplementary files format and content: Tabular files include, for each gene, the raw counts, TPM, Length, and EffectiveLength.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: DBVPG6044 (West African, "WA")

growth_protocol: Yeast taken from patches on YPD plates were grown in triplicates at 28 °C.

extract_protocol:
Cells were centrifuged and treated with 2U zymolyase for 30 minutes at 37°C. RNA was extracted using the E.Z.N.A. Total RNA Kit I (OMEGA), according to the manufacturer's instructions. Subsequently, the samples were treated with DNase I (Promega) to eliminate genomic DNA contamination. RNA integrity was confirmed using a Fragment Analyzer (Agilent).
The samples were then sent to BGI, where the preparation of the libraries and sequencing were carried out employing DNBseqTM technology.

treatment_protocol: Control (5 mL of YNB medium) and treated with U18 (5 mL of YNB medium containing 200 mg/mL U18666A)

tag: cell line

value: DBVPG6044 (West African, "WA")

tag: genotype

value: WT (ho::NatMX, ura3::KanMX)

tag: treatment

value: Control


title: RPE1 WT rep3

city: Zürich

first: Markus

middle: S

last: Schröder

state: Zürich

address: Otto-Stern-Weg 7

department: Biology, Molecular Health Sciences

country: Switzerland

institute: ETH Zürich

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: RPE-1 TP53 KO

growth_protocol: Ten million cells for each condition were fixed in 1% formaldehyde at room temperature for 15 minutes. The fixation reaction was quenched with glycine to a final concentration of 125 mM. Cells were harvested and washed twice with chilled PBS, and pellets were snap frozen in a dry ice-ethanol bath before storing at -80°C.

extract_protocol:
When ready to process, cell pellets were thawed on ice and incubated with lysis buffer 1 on ice for 10 minutes. Cells were pelleted by centrifugation and incubated with LB2 for 5 minutes on ice. The extracted nuclei were pelleted by centrifugation and resuspended in LB3. Nuclei were sonicated using a Covaris S2 sonicator. Debris were pelleted by centrifugation at 4°C and the supernatant was transferred to a 5 mL tube. 100 µL of Dynabeads protein A that had been prebound with MRE11 antibody (Novus, Cat# NB100-142) were added to the cell lysate and samples were incubated at 4°C overnight with rotation. Beads were collected on a magnetic stand and washed with ice-cold RIPA buffer 6 times, followed by a final wash with TBS before resuspending beads in 200 µL of elution buffer (50 mM Tris–HCl, pH 8; 10 mM EDTA; 1% SDS). The bead slurries were incubated overnight at 65°C to reverse crosslinks. Samples were treated with 1 mg/mL RNaseA (Ambion, Cat# 2271) for 30 minutes at 37°C, followed by proteinase K treatment 20 mg/mL (Invitrogen, Cat# 25530-049) for 1 hour at 55°C.
DNA was then purified using a MinElute PCR Purification Kit (Qiagen, Cat# 28004) and sequencing libraries were prepared using a NEBNext Ultra II kit.

value: RPE-1 TP53 KO


title: bin2-RNAi-apex1-rep2

city: St. Louis

first: Andrea

last: Eveland

state: Missouri

address: 975 North Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints

data_processing:
Paired-end reads were first trimmed for adapter sequences using Cutadapt v2.3 and the wrapper tool TrimGalore v0.6.2 with default parameters except for --length 70 --trim-n --illumina.
Clean reads were used to quantify the maize B73 AGPv4 gene models with Salmon v1.4.0 using the selective alignment method with a decoy-aware transcriptome.
Supplementary_files_format_and_content: salmon_output.tgz:This file contains all the expression data generated with Salmon, the metadata file of the sample dataset and the script to import the data in R

molecule: polyA RNA

organism: Zea mays

growth_protocol: Plant materials were sown into cone trays (5 cm diameter, 11.5 cm depth, 142 ml total volume) in Metromix 360 - Turface blend and grown in controlled growth chambers at the Danforth Center’s growth facility with 14 hr days, 28° C / 24° C, 50% humidity and 450 µMol light. At 14 DAS, seedlings were transplanted to 3 gallon pots (9.5” by 11” diameter) with Berger 35% with 2 tsp corn top dressing, 3 seedlings per pot.

extract_protocol:
Poly-A+ RNA-seq libraries were generated from pools of hand-dissected inflorescence primordia and shoots (apex1 and apex2) from wild-type (B73) and maize mutants. RNA isolation from tassel material was performed using the PicoPure RNA isolation kit (ThermoFisher Scientific) according to manufacturer's instructions with the following adjustments: 40 µl and 60 µl of RNA extraction buffer were added respectively to stage 1 and stage 2 ground tassels. After 30 min incubation at 42°C, samples were centrifuged at 800g for 2 min. Equal volume of 70% EtOH was added to samples and processed according to kit directions. RNA isolation from shoot apex samples was performed using the Zymo quick-RNA plant kit according to manufacturer instructions with following adjustments: Lysis buffer was added directly to the ground tissue and centrifuged, supernatant was added directly to the filtration column.
Library preparation was outsourced to Novogene (USA).
RNA-seq libraries were processed using an Illumina HiSeq 4000 platform at Novogene with a 150 bp paired-end sequencing design.

tag: developmental stage


title: SA Control, Biol rep 3

description: Library name: Sample 6

source_name: Y12 (Sake, "SA")

value: Y12 (Sake, "SA")


title: FANCM-depleted rep2

source_name: RPE-1 TP53 KO FANCM KO

value: RPE-1 TP53 KO FANCM KO


title: PrS-MOW20012-WT1-hyp, WT

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: EPAS1_W_WT_1_3__GT24-02454_GACCTGAA-CTCACCAA_S33
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: featureCounts.csv genesCounts.csv genesRawCounts.csv genesTPM.csv stats.csv txCounts.csv txRawCounts.csv txTPM.csv

extract_protocol:
Arcturus PicoPure RNA isolation Kit Applied biosystems RNeasy Mini Kit QIAGEN NucleoSpin RNA Plus MACHEREY-NAGEL
KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina NovaSeq X

tag: cell type

value: iPSC

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: parental cell_line


title: doubles rep1

data_processing:
Raw paired-end FASTQ files were aligned to the GRCh38 reference genome using bowtie2 version 2.4.4
BAM files were sorted and indexed with samtools version 1.6
Total read counts were calculated for each sample and used to generate comparable bigwig files for visualization using bamCoverage version 3.3.0 and the scaleFactor option
Assembly: GRCh38
Supplementary files format and content: Scaled bigwig coverage files for all samples

source_name: RPE-1 TP53 KO FANCM KO SMARCAL1 KO

value: RPE-1 TP53 KO FANCM KO SMARCAL1 KO


title: SMARCAL1KO_X rep1

source_name: RPE-1 TP53 KO SMARCAL1 KO

value: RPE-1 TP53 KO SMARCAL1 KO


title: RPE1 WT rep1


title: FANCM-depleted rep3


title: WA Control, Biol rep 2

description: Library name: Sample 2


title: PrS-MOW20012-WT3-nor, WT

description:
Library name: EPAS1_W_WT_3_20__GT24-02462_CGGCGTGA-ACAGGCGC_S11
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: PrS-MOW20012-WT1-nor, WT

description:
Library name: EPAS1_W_WT_1_20__GT24-02460_TGACGAAT-GCCTACTG_S29
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: WA Control, Biol rep 3

description: Library name: Sample 3


title: SMARCAL1 KO rep2


title: Double-SDel-sgFM rep3


title: PrS-MOW20022-A07, WT

description:
Library name: GRHL1_W2_PTC_A07_GT24-02445_CCGCGGTT-CTAGCGCT_S27
WIBJ2.2J derived knockout cell line, GRHL1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon


title: BYBX_MII_LACE-seq_2

city: Nanning

first: liu

last: shaoyuan

address: Guangxi province of china

country: China

institute: Guangxi university

data_processing:
*library strategy: linear amplification of complementary DNA ends and sequencing (LACE-seq)
The adapter sequences and low-quality bases of raw reads were removed using trim-galore (v.0.6.7)
Clean reads were first aligned to mouse pre-rRNA using Bowtie software (v.2.3.5.1)
The remaining unmapped reads were then aligned to the mouse (mm10) reference genome by hisat2 (v.2.2.1)
Then the PCR duplicates were removed by sambamba (v.0.7.1)
The correlation between LACE-seq replicates was calculated as following: the LACE-seq correlation was calculated by deepTools (v.3.5.1)
Assembly: mm10
Supplementary files format and content: bigWig files for each Sample

organism: Mus musculus

source_name: Ovary

extract_protocol:
LACE-seq experiments were carried out according to the published protocol. In short, 50 oocytes were collected in 1.5 mL Eppendorf LoBind microcentrifuge tubes and quickly spun down to the bottom with a mini centrifuge. Samples were lysed on ice using 50 μl wash buffer for 10 min. Next, 1 μl SUPERase·In RNase inhibitor (Ambion, AM2696) and 4 μl RQ1 DNase (Promega, M6101) were applied to the lysate and incubated at 37 °C for 3 min. After snap-chilling the tube on ice for 3 min, 2 μg ac4c antibody and rotated at 4 °C for 1 h. Next, the samples were irradiated twice with UV-C light on the ice at 400 mJ, then 10 μl protein A/G beads were added to the sample and rotated for 2 h at 4 °C. After extensive wash steps, the immunoprecipitated RNAs were fragmented, and experienced 3′-dephosphorylation and linker ligation, followed by reverse transcription on-beads. Then, first-strand cDNAs were derived from protein A/G beads and further captured by streptavidin C1 beads for pre-PCR and added 3’-cDNA linker to produce dsDNA as the template for in vitro transcription (IVT). IVT products were purified by the removals of the DNA template using Turbo DNase and further purified by Agencourt RNA Clean beads based on the instructions of the manufacturer.
Then, linear amplified RNA was transformed into cDNA and amplified by PCR with P7 and barcoded P5 index primers. Final PCR products with a size of 250–500 bp were excised from a 2% agarose gel and purified by a gel purification kit (Qiagen, Catalog # 28604) as per the manufacturer's instructions.

tag: tissue

value: Ovary

value: Oocyte

value: WT

value: Treat


title: PrS-MOW20012-B03-nor, WT

description:
Library name: EPAS1_W_PTC_B03_20__GT24-02459_CAGTAGGC-ATTCGTCA_S32
WIBJ2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: SMARCAL1 KO rep1


title: PrS-MOW20012-B03-hyp, WT

description:
Library name: EPAS1_W_PTC_B03_3__GT24-02453_AGTTCAGG-TCTGTTGG_S28
WIBJ2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: FANCM-depleted rep1


title: PrS-MOW20012-WT2-nor, WT

description:
Library name: EPAS1_W_WT_2_20__GT24-02461_TAATACAG-GTGAATAT_S10
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: S2D2, mDPCs from Dmp1-Cre; Setd2fl/fl mice

city: Wuhan

first: 佳欣

last: 牛

state: 洪山区

address: State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology

institute: Wuhan University

description:
Library name: Sample 5
processed data.xls: S2D2

data_processing:
Bowtie2 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2. FPKM Reads Count for each gene in each sample was counted by HTSeq, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample. DEGseq was used for differential gene expression analysis between two samples with non biological replicates. Genes with q≤0.05 and |log2Foldchange |≥0.58 are identified as differentially expressed genes (DEGs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed using Database for Annotation, Visualization, and Integrated Discovery (https://david.ncifcrf.gov). To provide a visual representation of the data, an online platform for data analysis and visualization, https://www.bioinformatics.com.cn (last accessed on 20 Feb 2024), was used.
Assembly: Ensembl; Mus_musculus.GRCm39
Supplementary files format and content: 1. Gene: Gene name. 2. *_count: Reads count for sample *. 3. *_normalize/baseMean: Normalized result for group * / Weighted mean after normalization in DESeq2 comparison groups. 4. FoldChange: Ratio of normalized values between two groups. 5. Log2FoldChange: Log2 value of the ratio of normalized values between two groups. 6. pval: Calculated p-value. 7. padj: Adjusted p-value after correction. 8. Up/Down: Indicates upregulation or downregulation of expression (Up for upregulation, Down for downregulation). 9. Significant: Whether the difference is significant. 10. GeneName: Name of the gene. 11. Biotype: Type of the gene. 12. Position: Genomic coordinates of the gene. 13. NR:Seq-id : Optimal alignment result of the gene with the NR database. 14. NR:Score : Alignment score of the gene with the NR database. 15. NR:Evalue : E-value of the gene's alignment with the NR database. 16. NR:Description : Functional description of the gene in the NR database. 17. NT:Seq-id : Optimal alignment result of the gene with the NT database. 18. NT:Score : Alignment score of the gene with the NT database. 19. NT:Evalue : E-value of the gene's alignment with the NT database. 20. NT:Description : Functional description of the gene in the NT database. 21. Uniprot:UniProtKB-AC : Optimal alignment result of the gene with the Uniprot database. 22. Uniprot:Score : Alignment score of the gene with the Uniprot database. 23. Uniprot:Evalue : E-value of the gene's alignment with the Uniprot database. 24. Uniprot:Description : Functional description of the gene in the Uniprot database. 25. COG:gene : Gene name aligned with the COG database. 26. COG:Score : Alignment score with the COG database. 27. COG:Eval : E-value of the alignment with the COG database. 28. COG:num : Gene ID aligned with the COG database. 29. Pfam:pfam_ID : Gene ID aligned with the Pfam protein family database. 30. Pfam:pfam_Name : Gene name aligned with the Pfam protein family database. 31. Pfam:pfam_Description : Functional description of the gene aligned with the Pfam protein family database. 32. GO:biological_process : GO-Term describing the annotated biological process. 33. GO:cellular_component : GO-Term describing the annotated cellular component. 34. GO:molecular_function : GO-Term describing the annotated molecular function. 35. KEGG:KO : Annotated ID in the KEGG database. 36. KEGG:Description : Functional description in the KEGG database.

source_name: mouse dental papilla cells

extract_protocol:
The mDPCs were isolated from control mice and Dmp1-Cre;Setd2fl/fl mice at P6. Total RNAs were extracted from mDPCs using Trizol reagent (Takara) and then subjected to PE150 Hiseq, which was performed by Anoroad in Wuhan. Each sample contained pooled RNAs from 3 biological replicates and was mixed with an equal mass of RNAs to minimize variation across samples. After the samples were qualified, 1~3 μg total RNAs of each sample was used as the starting material to construct a transcriptome sequencing library.
> Library examination  RNA concentration of library was measured using QubitR RNA Assay Kit in  Qubit® 3.0 to preliminary quantify and then dilute to 1ng/ul. Insert size was assessed  using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and  qualified insert size was accurate quantification using StepOnePlusTM Real-Time PCR  System (Library valid concentration> 10 nM).  > Library clustering and sequencing  The clustering of the index-coded samples was performed on a cBot cluster  generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the  manufacturer's instructions. After cluster generation, the libraries were sequenced on  an Illumina platform and 150 bp paired-end reads were generated.

value: mouse dental papilla cells

value: Dmp1-Cre; Setd2 fl/fl mice


title: MII_LACE-seq_2

value: Control


title: Double-SDel-sgFM rep2


title: PrS-MOW20012-A03-hyp, WT

description:
Library name: EPAS1_W_PTC_A03_3__GT24-02451_CAAGCTAG-CGCTATGT_S8
WIBJ2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: IgG_LACE-seq


title: SMARCAL1 KO rep3


title: PrS-MOW20012-B02-nor, WT

description:
Library name: EPAS1_W_PTC_B02_20__GT24-02458_TTGGACTC-CTGCTTCC_S14
WIBJ2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: Double-SDel-sgFM rep1


title: BYBX_MII_LACE-seq_1


title: MII+BYBX_1

data_processing:
For RNA-seq data analysis the raw data were removed adapter by trim-galore (v.0.6.7) and aligned to the mouse (mm10) reference genome by hisat2 (v.2.2.1) with default parameters. Uniquely mapped reads were assembled into transcripts guided by reference annotation (University of California at Santa Cruz [UCSC] gene models) using Cufflinks (v2.2.1). The level of expression of each gene was quantified as the FPKM and normalized to the ERCC spike-in. Samples prepared in different batches were normalized to GV-stage oocyte samples from each batch. Statistical analyses were performed using the R software (http://www.rproject.org). Functional annotation was performed using the R package Clusterprofiler (v.4.0)
Assembly: mm10
Supplementary files format and content: Raw fastq and FPKM data

extract_protocol:
Oocytes were collected at the indicated time after DMSO and BYBX treatment (10 oocytes per sample). Each sample was lysed using 4 μl lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 100 pg external RNA controls consortium (ERCC) mRNA spike-in) and immediately used for cDNA synthesis based on Smart-seq2 method.
Sequencing libraries were constructed from 500 pg of amplified cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme; TD503) according to the manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform using 150 bp paired-end reads.

value: BYBX


title: GV_LACE-seq_2


title: S2D1, mDPCs from Dmp1-Cre; Setd2fl/fl mice

description:
Library name: Sample 4
processed data.xls: S2D1


title: S2D, mDPCs from Dmp1-Cre; Setd2fl/fl mice

description:
Library name: Sample 6
processed data.xls: S2D3


title: MII_LACE-seq_1


title: GV_LACE-seq_1


title: PrS-MOW20012-A03-nor, WT

description:
Library name: EPAS1_W_PTC_A03_20__GT24-02457_CCAAGTCT-TCATCCTT_S26
WIBJ2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: PrS-MOW20012-B02-hyp, WT

description:
Library name: EPAS1_W_PTC_B02_3__GT24-02452_TGGATCGA-TATCGCAC_S25
WIBJ2.2J derived knockout cell line, EPAS1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: MII+BYBX_2


title: CTR, mDPCs from control mice

description:
Library name: Sample 3
processed data.xls: CTR3

value: Wild type


title: GV_2

value: NO


title: PrS-MOW20026-WT3, WT

description:
Library name: PPARG_W2_WT_3_GT24-01968_GCTTGTCA-GTATGTTC_S16
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC


title: PrS-MOW20026-D08, WT

description:
Library name: PPARG_W2_PTC_D08_GT24-01965_GGACTTGG-CGTCTGCG_S25
WIBJ2.2J derived knockout cell line, PPARG PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: PPARG


title: MII_3

value: DMSO


title: PrS-MOW20026-B10, WT

description:
Library name: PPARG_W2_PTC_B10_GT24-01964_TTATAACC-TCGATATC_S26
WIBJ2.2J derived knockout cell line, PPARG PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: day 6

value: primitive syncytium


title: flox_MI_1

city: Hangzhou

first: Mo

last: Li

address: Jiefang road 88

department: Department of Cardiology of The Second Affiliated Hospital, School of Medicine

institute: Zhejiang University

description:
Library name: Sample 1
10×Genomics

library_source: transcriptomic single cell

data_processing:
The 10x Genomics cellranger v7.2.0 pipeline was employed to align the raw sequencing data to the reference transcriptome, utilizing mm10 for mouse samples
Initial quality control and clustering analysis were conducted using Seurat (v.4.4.0)
Assembly: Mouse mm10
Supplementary files format and content: Cellranger files

source_name: Heart

extract_protocol:
The heart tissues were minced using scalpel blades and subsequently digested using the Multi Tissue Dissociation Kit 2 (Miltenyi Biotec, 130-110-203). Then, cells derived from mouse heart tissue were filtered through a 100 μm cell strainer to obtain a single-cell suspension. The suspension was then centrifuged at 300x g for 10 minutes to pellet the cells. To remove red blood cells, Red Blood Cell Lysis Solution (Miltenyi Biotec, 130-094-183) was utilized. Subsequently, cell debris was eliminated using the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101).
Cells were processed using the Chromium Single Cell 3' Reagent v3 Kits from 10x Genomics. The workflow included reverse transcription, barcoding, complementary DNA amplification, and purification for library preparation, following the Chromium 3′ V3.1 protocol.

treatment_protocol: myocardial infaction

value: Heart

value: myocardial infarction


title: CTR2, mDPCs from control mice

description:
Library name: Sample 2
processed data.xls: CTR2


title: MII_2

value: Ovary


title: Nanopore-sequenced hMeDIP-seq of mouse cerebellum_replicate 3

city: Bath

first: Adele

last: Murrell

address: Claverton Down

department: Life Sciences Department

institute: University of Bath

description: Library name: cbm1_hmedip_3

data_processing:
Base-calling and aligment was performed using dorado basecaller
Sorting and indexing of alignment files using samtools
Extraction of modified bases using modkit pileup
Peak calling was performed using MACS2 callpeak with --gsize 'mm'
Assembly: mm39 (GRcm39)
Supplementary files format and content: GZIP compressed narrowPeak files containing significant  (q-val<0.05) peaks and peak enrichment values.
Supplementary files format and content: GZIP compressed bed files (bedMethyl) produced by Oxford Nanopore Technologies Modkit pileup. Contain all directly modified base detections (5mC and 5hmC) within the peak regions provided.

source_name: Cerebellum

extract_protocol:
High molecular weight genomic DNA was extracted from these cerebella using the QIAGEN MagAttract HMW DNA Kit (QIAGEN, 67563) using a modified protocol available from the Oxford Nanopore Technologies Community website74. Quality control was performed on a DeNovix DS-11 FX+ Spectrofluorometer.
DNA from mouse cerebellum was sheared to a target of 6 kb using a Covaris g-TUBE (Covaris, 520079). An aliquot was sequenced as a control on an R10.4.1 MinION flow cell (Oxford Nanopore Technologies, FLO-MIN114) using Ligation Sequencing (SQK-LSK114) Kit 14 following the associated protocol. Sheared DNA was sonicated in triplicate using a Bioruptor® Pico sonication device (Diagenode, B0106001) in a 1.5 mL Bioruptor® Pico Microtube with cap (Diagenode, C30010016) to target fragment lengths < 500bp. A 2200 TapeStation system (Agilent, G2991A) with D1000 ScreenTapes (Agilent, 5067-5582) and associated reagents (Agilent, 5067-5583) was used to assess the fragment size distribution of each replicate (mean 362 bp). 5hmC immunoprecipitation was performed based on Nestor and Meehan23. 1 μg sonicated dsDNA was incubated overnight at 4°C rotating in IP buffer (10 mM Na-phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100) with 2 μL of either whole serum α-5hmC antibody (ActiveMotif, 39769) or IgG-purified α-5hmC antibody (ActiveMotif, 39791). Samples were then incubated with 40 μL equilibrated Dynabeads Protein G (Invitrogen, 10003D) for 1 hour while rotating at 4°C and washed three times in ice-cold IP buffer for 5 minutes at room temperature. Bound DNA was eluted in digestion buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5% SDS) and 200 ng proteinase K (ThermoFisher Scientific, EO0491) for 3 hours at 50 °C on a shaker at 800 rpm. Immunoprecipitated DNA was purified using the QIAQuick PCR Purification kit (QIAGEN, 28104) following manufacturer instructions and eluted into 50 μL elution buffer before sequencing. The eluate was prepared for sequencing following the MinION protocol SQK-LSK114. Libraries were loaded onto three R10.4.1 MinION flow cells and sequenced, generating 154-382 Mb of sequence data per flow cell.

value: Cerebellum

tag: age

value: 8 weeks

tag: strain

tag: Sex

value: Female

tag: chip antibody


title: Nanopore-sequenced hMeDIP-seq of mouse cerebellum_replicate 2

description: Library name: cbm1_hmedip_2

value: IgG-purified α-5hmC antibody (ActiveMotif, 39791)


title: MII_1

value: Oocyte


title: CTR1, mDPCs from control mice

description:
Library name: Sample 1
processed data.xls: CTR1

value: mouse dental papilla cells


title: CBO-MOK20074P-WT3, WT

description:
Library name: NR2F1_WT3_GT24-06992_CATAGAGT-TGGTGGCA_S195
KOLF2.2J differentiated to cortical brain organoid

extract_protocol:
mRNA was captured using magnetic oligo-dT beads according to KAPA mRNA HyperPrep Kit
KAPA mRNA HyperPrep Kit Illumina NovaSeq X

value: Not applicable

value: day 22

value: Cortical brain (dorsal forebrain patterning)


title: swine-6-LV

city: hangzhou

first: jiuxiao

last: zhao

state: zhejiang

address: Yuhangtang Road, Hangzhou 310058

institute: zhejiang university

description: Library name: Sample5

data_processing:
Linux and R
Assembly: GRCH38
Supplementary files format and content: csv files normalised by DESeq2 for each sample

organism: Sus scrofa

source_name: Left ventricle

extract_protocol:
We extracted total RNA from pig ventricular myocardium tissues and human cardiomyocytes differentiated from H7 human ESCs using TRIzol (Invitrogen, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit of Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °C before PCR.

value: Left ventricle

value: somatic cell

value: heart cells

value: KCNH2 mutation


title: PrS-MOW20026-WT1, WT

description:
Library name: PPARG_W2_WT_1_GT24-01966_AAGTCCAA-TACTCATA_S20
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: day 6

value: primitive syncytium


title: GV_1

value: Ovary

value: Control

value: NO


title: flox_MI_2

description:
Library name: Sample 2
10×Genomics

value: Heart

value: myocardial infarction


title: swine-2-LV

description: Library name: Sample2

value: wt


title: Nanopore-sequenced hMeDIP-seq of mouse cerebellum_replicate 1

description: Library name: cbm1_hmedip_1

value: Cerebellum

value: 8 weeks

value: Female

value: Whole serum α-5hmC antibody (ActiveMotif, 39769)


title: swine-9-LV

description: Library name: Sample8

value: Left ventricle

value: KCNH3 mutation


title: swine-8-LV

description: Library name: Sample7

value: somatic cell

value: heart cells


title: CBO-MOK20074P-WT1, WT

description:
Library name: NR2F1_WT1_GT24-06990_GACGTCTT-GGTGAACC_S197
KOLF2.2J differentiated to cortical brain organoid

value: iPSC

value: Not applicable

value: day 22

value: Cortical brain (dorsal forebrain patterning)


title: LNI-DDRR-iMN

city: Cambridge

first: Kate

middle: E

last: Galloway

state: MA

address: 25 Ames St

department: Chemical Engineering

institute: MIT

description:
Library name: LNIx3HARIDD-14dpi-iMN-1
10x Genomics

data_processing:
We used the cellranger count pipeline (10x Genomics, v6.1.1) to align and quantify single cell expression for each library. Only protein coding genes and lncRNAs were used for quantification.
A custom genome for alignment was created using cellranger mkref (10x Genomics, v6.1.1) to enable alignment of eGFP transcripts for the Hb9::GFP reporter. Briefly, GRCm39 as a base genome was used, and eGFP transgene was concatenated on as a protein coding gene.
Cells were filtered for < 8% mitochondrial reads, and between 200 and 10,000 features. The SCTransform function was used to normalize libraries.
Assembly: Custom genome: GRCm39 with eGFP transgene appended to detect Hb9::GFP
Supplementary files format and content: Tab-separated values files (tsv) for barcodes and features; matrix files (mtx) for matrix values

source_name: LNI-DDRR-iMN

extract_protocol:
Intermediate conversion subpopulations at 4 dpi were dissociated by 0.025% trypsin-EDTA. Final converted populations at 14 dpi were dissociated by DNAse (>1,000 U/vial) and papain (>100 U/vial) dissolved into 6 mL DMEM/F-12. Cells were spun down, washed, and resuspended in DMEM/F-12 for FACS isolation. Intermediate conversion subpopulations were identified by low CellTrace-FarRed intensity (hyper-proliferative) at 4 dpi. Hb9::GFP+ at 14 dpi cells were identified relative to Hb9::GFP negative control. 1:1000 Zombie NIR™ was spiked in prior to flow to sort for live cells. Cell subpopultions were then sorted and collected into collection buffer (DMEM/F-12 supplemented with N2, B27, and glutamax) in tubes pre-coated with 7.5% BSA/PBS. Cell suspensions were then spun down and resuspended in PBS. Cell suspension viability was confirmed >90% viable by Trypan Blue staining prior to loading into chip for library construction.
Libraries were prepared using 10X Genomics NextGEM 3' v3.1 reagents following manufacturers protocols using 12 cycles of amplification in cDNA generation. Sequencing generated approximately 30-60k reads/cell for each library. Intermediate converting 4 dpi populations had less reads at ~5k reads/cell, presumably due to their lower global transcriptional activity.

treatment_protocol: Cells were collected at different points in conversion. Specific populations were identified and collected via FACS (BD FACSAria) and all cells were sorted to obtain viable single cell suspensions.

value: 14 dpi

value: LNI-DDRR-iMN

tag: batch


title: PrS-MOW20026-WT2, WT

description:
Library name: PPARG_W2_WT_2_GT24-01967_ATCCACTG-ACGCACCT_S18
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: cell line

value: day 6

value: primitive syncytium


title: AGO3-loaded piRNA, rep3

city: Tokyo

first: Yurika

last: Namba

state: --- Select a state ---

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biological Sciences, Graduate School of Science

country: Japan

institute: The University of Tokyo

description: Library name: Ago3-piRNA_rep3

library_source: other

data_processing:
After removing adaptor sequences using Cutadapt (version 4.6) (Martin 2011), 22-35 nt reads were mapped against the p50T.SilkBase using Bowtie (version 1.3.1) (Langmead et al. 2009) in random and multiple counting modes not allowing mismatch. Genome-mapped reads were remapped against transposon library containing the Cd sequence using Bowtie in random and multiple counting modes allowing up to two mismatches. Reads mapped to the Cd sequence were processed using SAMtools and BEDTools (version 2.31.1) (Quinlan and Hall 2010) and normalized against the number of genome-mapped reads to RPM. Distribution of piRNAs were visualized using karyoploteR (version 1.8.4) (Gel and Serra 2017). The Ping-Pong Z score was calculated as the difference of the score at the 5'-to-5' distance of 10 nt and the mean scores of background distances, divided by the standard deviation of the scores of background distances, defined as distances of 0-9 and 11-20 nt. Sequence logos were generated using ggseqlogo (version 0.2) (Wagih 2017).
Assembly: the Bombyx mori genome assembly (Nov 2016) (Kawamoto et al. 2019) from the SilkBase database
Supplementary files format and content: Tab-separated text files contain normalized read counts (RPM) mapped to the p50T.SilkBase for each sequence.

molecule: other

organism: Bombyx mori

growth_protocol: B.mori ovary-derived cultured germ cells (BmN4 cells) were cultured in EX-CELL 420 serum-free medium for insect cells (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1× penicillin-streptomycin-glutamine (Gibco) at 37°C and with 5% CO2.

extract_protocol:
Dynabeads Protein G (Thermo Fisher Scientific) and antibodies were incubated with 0.02% Tween-20 in PBS. Anti-Siwi and anti-AGO3 (Nishida et al. 2015) antibodies were used. The cells were lysed at 4°C with immunoprecipitation (IP) buffer [30 mM HEPES-KOH (pH 7.3), 150 mM KOAc, 2 mM Mg(OAc)2, 5 mM DTT, 0.1% NP-40, 2 µg/mL pepstatin, 2 µg/mL leupeptin, and 0.5% aprotinin] supplemented with RNasin Plus Ribonuclease Inhibitor (Promega). After the cell debris was removed by centrifugation, the cell lysates were incubated with antibody-conjugated beads at 4°C. After protein-antibody binding, the beads were washed once with IP buffer containing 500 mM NaCl and then extensively washed with IP buffer. Protein-bound RNAs were purified from the beads using proteinase K (Roche) treatment followed by phenol/chloroform treatment, and precipitated with ethanol.
Small RNA libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) and sequenced on the MiSeq platform (Illumina) to obtain 51 nt single-end reads.

treatment_protocol: To deplete endogenous proteins, the cells (1×10^6 cells) suspended in 100 μL of EP buffer [2.1 mM HEPES-KOH (pH 7.1), 137 mM NaCl, 5 mM KCl, and 0.5 mM Na2HPO4] were transfected with 500 pmol siRNA duplex by electroporation with Nucleofector 2b (Lonza). Luciferase (Luc) siRNA was used as a control.

value: Cultured germ cell derived from ovary

value: RNAi


title: PrS-MOW20026-A10, WT

description:
Library name: PPARG_W2_PTC_A10_GT24-01963_CCGCGGTT-CTAGCGCT_S24
WIBJ2.2J derived knockout cell line, PPARG PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: PPARG

value: Termination codon


title: AGO3-loaded piRNA, rep2

description: Library name: Ago3-piRNA_rep2


title: LNI-DDRR-4dpi

description:
Library name: LNIx3HARIDD-4dpi-CTFR-lo-1
10x Genomics

value: 4 dpi

tag: genotype


title: swine-7-LV

description: Library name: Sample6

value: Left ventricle

value: KCNH2 mutation


title: LNI-DDRR-nosupplements

description:
Library name: LNIx3HARIDD-14dpi-noNT-1
10x Genomics

source_name: LNI-DDRR-nosupplements

value: LNI-DDRR-nosupplements

tag: treatment

value: No supplements


title: AGO3-loaded piRNA, rep1

description: Library name: Ago3-piRNA_rep1


title: swine-5-LV

description: Library name: Sample4

value: somatic cell

value: heart cells

value: wt


title: Naïve, rep 1

city: Washington

first: George

last: Melchor

state: DC

address: 3700 O St NW

department: Biology

institute: Georgetown University

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, alignment and transcript counting were accomplished using Cell Ranger (v7.1.0, 10x Genomics).
Raw feature bc matrices were denoised and cell/nuclei calling was performed with CellBender (v0.3.0, Fleming et al., 2023).
Assembly: mm10-2020-A
Supplementary files format and content: .h5 singular files per sample containing processed gene expression matrices and default metadata.

source_name: spinal cord

extract_protocol:
To visualize the lesion, mice were injected with 1% neutral red solution (500µL, intraperitoneal, prepared in PBS), approximately 2 hours prior to intracardiac perfusion with PBS. The spinal cord was extracted from perfused mice. Lesions demarcated with neutral red, rostral nonlesioned white matter tissue, and naive spinal cord white matter tissue were microdissected and collected according to experimental batch. Each lesioned and nonlesioned sequencing sample is the result of 3-4 microdissected  pooled  samples from lesioned mice ensuring large biological variability.  Single nucleus suspensions were created utilzing the Nuclei PURE lysis kit (Signma #646563),  with a sucrose density gradient and ultracentrifugation (30,000 rcf, 15,600 rpm). Nuclei pellets were washed, filtered at 40µm, and visualized under brightfield for intact nucleus morphology.
Sequencing libraries were prepared according to library batch number, following the protocol for 10x Genomics Chromium next GEM Single Cell 3' v3.1 Dual Index. Briefly, 10,000 nuclei per sample was loaded into Chromium Single Cell 3’ Chip G wells and placed in the Chromium controller for GEM generation as outlined in 10x Genomics User Guide (CG000315. Rev A) for a targeted recovery of 5,000 nuclei per sample. GEMs were incubated in the thermal cycler for cDNA barcoding, followed by GEM-RT cleanup and cDNA amplification using v3.1 Chromium GEM kit. Total cDNA concentration was measured by Qubit dsDNA HS and 25% of the total cDNA was used for 3' gene expression library construction using Dual Index Kit TT Set A. The resulting sequencing libraries was assessed for quality using the BioAnalyzer 2100 with a High Sensitivity DNA kit (Agilent), and quantified using the KAPA Library Quantification Kit, Illumina Platforms (KAPA Biosystems) according to manufacturer's protocol. Libraries were sequenced on a S4 flow cell to an average depth of 400 million reads per sample.

treatment_protocol: Demyelinated lesions were created with the injection of 1% LPC into the ventral white matter of the mouse spinal cord  (approx. T12 vertebral area).

value: spinal cord

value: Naïve

tag: experimental batch

tag: library batch

tag: sequencing batch

value: Wildtype

tag: disease state

value: Female


title: CBO-MOK20074P-WT2, WT

description:
Library name: NR2F1_WT2_GT24-06991_TGCGAGAC-CAACAATG_S196
KOLF2.2J differentiated to cortical brain organoid

tag: cell type

value: iPSC

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

value: day 22

value: Cortical brain (dorsal forebrain patterning)


title: Siwi-loaded piRNA, rep3

description: Library name: Siwi-piRNA_rep3

value: Cultured germ cell derived from ovary

value: RNAi


title: swine-4-LV

description: Library name: Sample3

tag: tissue

value: Left ventricle


title: Cre_MI_1

description:
Library name: Sample 3
10×Genomics

value: Heart

value: CD248 cKO

value: myocardial infarction


title: CBO-MOK20074P-C11, KO

description:
Library name: NR2F1_PTC_C11_GT24-06989_AGTACTCC-AACAGGTT_S198
KOLF2.2J derived knockout cell line, NR2F1 PTC, differentiated to cortical brain organoid

value: Termination codon

tag: time

tag: model system

tag: parental cell_line


title: swine-1-LV

description: Library name: Sample1

value: somatic cell

value: heart cells


title: Siwi-loaded piRNA, rep2

description: Library name: Siwi-piRNA_rep2


title: B73-apex2-rep1

description:
Library name: B73-atac-apex2-rep1
apex2_atac.tar.gz

data_processing:
Cleaned ATAC-seq reads were mapped to the maize AGPv4 genome using bowtie2 v2.4.5 with default parameters except for --very-sensitive -X 2000 --dovetail. Reads mapped to mitochondria and chloroplast together with PCR duplicates and low mapping quality reads (mapping score < 10) were removed. Peaks were called using MACS2 v2.1.2 94 with the parameters -f BAMPE --shift -100 --extsize 200 --nomodel -B --SPMR -g 2106338117. Consensus peaks were generated using the Bioconductor package GenomicRanges. BigWig files were generated using bamCoverage with the parameters --binSize 1 --normalizeUsing RPKM.
Assembly: Mazie AGPv4
Supplementary files format and content: bed and bigWig

extract_protocol:
Flash frozen and ground shoot apex 2 tissue (~0.25 g) was resuspended in 4 mL of 1x nuclei isolation buffer (16 mM HEPES; pH8, 200 mM sucrose, 0.8 mM MgCl2, 4 mM KCl, 32% Glycerol, 0.25% Triton X100, 1x complete protease inhibitor, 0.1% 2-ME, 0.1 mM PMSF), shaken at 4°C for 20 minutes and then filtered through 2 sheets of miracloth. Nuclei were centrifuged at 1,000 x g at 4°C for 15 minutes. Nuclei were resuspended in 800 µL, 400 µL, and finally 100 µL 1x TB (tagmentation buffer; 10 mM Tris Base, 5 mM MgCl2, 10% v/v dimethylformamide) and centrifuged for 5 min at 1000 x g at 4°C between each resuspension.
Libraries were generated using reagents from the Illumina DNA Library Prep Kit (FC-121-1031). 2.5 µL Tn5 enzyme, 2.5 µL of 2x TB and 20 µL of nuclei were incubated for 1 hr at 37°C. 22 µL of H2O, 2.5 µL 10% SDS, and 0.5 µL of Proteinase K was added to the reaction and incubated at 55 °C for 1 hour. Tagmented libraries were purified using the Zymo clean and concentrator kit, eluting with RSB. 25 ng of tagmented DNA was combined with 2.5 µL of both index primers (Illumina; FC-121-1011), 7.5 µL PCR master mix, 2.5 µL NPM and filled to 25 µL with RSB buffer. ATAC-seq libraries were PCR amplified for 11 cycles, diluted to 50 µL and cleaned up with a two-sided Ampure XP bead size selection. A 0.5:1 bead:sample ratio followed by a 1.2:1 bead:sample ratio was used to select ~200-1000 bp libraries. ATAC-seq libraries were processed using an Illumina NovaSeq 6000 platform with a 150 bp paired-end sequencing design.


title: CBO-MOK20077P-WT2, WT

description:
Library name: SIX3_WT_2_GT24-05568_CGTCTGCG-ATTGTGAA_S192
KOLF2.2J differentiated to cortical brain organoid

value: day 8


title: NUGC-3 Xenograft, PC14586, QDx6, 24h, bio rep 2

city: Princeton

first: Lizhong

last: Xu

state: NJ

address: 400 Alexander Park Drive, Suite 301

institute: PMV Pharmaceuticals, Inc.

data_processing:
DESeq2 (version 1.34.0)
Paired-end reads were aligned to the human genome GRCh38 using STAR aligner (version 2.7.7a).
Fragments were assigned to the genes (GENCODE annotation) using featureCounts (version 1.4.6-p5).
Differential expression analysis was performed using R (version 4.1.3) package DESeq2 (version 1.34.0) testing for the fold change significantly >1.5 to identify differentially expressed genes (DEGs).
Fragments per kilobase of transcript per million mapped reads (FPKM) values were computed using edgeR package (version 3.36.0) using the TMM normalization method. Transcripts per million (TPM) values were computed from FPKM values assuming that the abundance of each transcript is proportional to its FPKM value.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values (TSV) files include TPM values for each Sample.

source_name: Xenografted tumor

growth_protocol: Tumors were grown after injecting 1x106 NUGC-3 cells suspended in 0.1 ml of 50% PBS:50% Matrigel Matrix (Corning) subcutaneously into the dorsal flank of female Balb/c nude mice aged 4–6 weeks, which were kept in ambient temperatures at 68–72 °F, 30–70 % humidity, and a dark/light cycle of 12 h.

extract_protocol:
Total RNA was extracted from the liquid nitrogen flash-frozen tumor samples by TissueLyser LT (Qiagen), and purified by using QIAcube (Qiagen) with DNase I digestion, following the manufacturer's protocols.
After rRNA depletion by using Fastselect HMR kit (Qiagen), strand-specific RNA sequencing libraries were prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB), following manufacturers’ instructions.

treatment_protocol: Xenografted tumors, after whose sizes reached ~300 mm3, were treated by orally administering the mice with either the vehicle (2% Klucel hydroxypropylcellulose (HPC), 0.5% Tween 80, v/w in water) or PC14586 (100 mg/kg) formulated in the vehicle (protected from light at room temperature), as indicated. QD, once daily; 2QD, twice daily.

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma

tag: model

value: NUGC-3 xenografted to Mus musculus

value: Day6, 24h


title: NL, 20dpl, rep 1

description: 10x Genomics

value: spinal cord

value: Wildtype

value: Nonlesion

tag: Sex

value: Female


title: Les, 20dpl, rep 1

description: 10x Genomics

value: Lesion


title: NUGC-3 Xenograft, PC14586, QDx6, 24h, bio rep 4

tag: cell line


title: B73-apex2-rep2

description:
Library name: B73-atac-apex2-rep2
apex2_atac.tar.gz

tag: genotype


title: Les, 20dpl, rep 2

description: 10x Genomics


title: CBO-MOK20077P-WT3, WT

description:
Library name: SIX3_WT_3_GT24-05569_TCGATATC-ACTCGTGT_S178
KOLF2.2J differentiated to cortical brain organoid

value: iPSC

value: Not applicable

value: Cortical brain (dorsal forebrain patterning)


title: Siwi-loaded piRNA, rep1

description: Library name: Siwi-piRNA_rep1

value: Cultured germ cell derived from ovary

tag: treatment

value: RNAi


title: CBO-MOK20074P-B12, KO

description:
Library name: NR2F1_PTC_B12_GT24-06988_TGGCCGGT-GCGCTCTA_S194
KOLF2.2J derived knockout cell line, NR2F1 PTC, differentiated to cortical brain organoid

value: Termination codon

value: day 22


title: NUGC-3 Xenograft, PC14586, QDx6, 24h, bio rep 3


title: CBO-MOK20077P-WT1, WT

description:
Library name: SIX3_WT_1_GT24-05567_TACTCATA-GCCACAGG_S185
KOLF2.2J differentiated to cortical brain organoid

value: day 8


title: WT_MH_replicate2

city: paris

first: Zeynep

last: Baharoglu

address: 25 rue du dr roux

country: France

institute: Institut Pasteur

description: Vibrio cholerae N16961 hapR+

data_processing:
Count data were analyzed using R version 3.2.0 and the Bioconductor package DESeq2 version 1.8.1
Data were normalized with DESeq2 and the “shorth” parameter
The dispersion estimation and statistical test for differential expression were performed with default parameters
The generalized linear model was set with a single covariate corresponding to the biological condition, biological replicates being included into each condition
Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.001 were considered differentially expressed.
Assembly: V. cholerae N16961 accession numbers AE003852 and AE003853
Supplementary files format and content: excel files containing number of reads and differencial expression values

organism: Vibrio cholerae

source_name: bacterial culture

growth_protocol: growth in liquid MH up to OD 0,25

extract_protocol:
Cultures were centrifuged, and RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit (20020595) was used with 7 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Krin et al., 2018, PMID: 29783948)

treatment_protocol: tobramycin 0,4 µg/ml

value: bacterial culture

tag: growth phase

value: exponential phase OD 0.27

value: WT

value: growth in MH


title: NUGC-3 Xenograft, PC14586, QDx6, 24h, bio rep 1

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma

value: NUGC-3 xenografted to Mus musculus

value: Day6, 24h


title: NL, 10dpl, rep 1

description: 10x Genomics

value: spinal cord

tag: experimental batch

tag: library batch

value: Wildtype

value: Nonlesion

value: Male


title: NUGC-3 Xenograft, PC14586, QDx6, 8h, bio rep 3

value: Day6, 8h


title: CBO-MOK20077P-A08, KO

description:
Library name: SIX3_PTC_A08_GT24-05565_GTATGTTC-TTCCTGTT_S187
KOLF2.2J derived knockout cell line, SIX3 PTC, differentiated to cortical brain organoid

value: iPSC

value: Cortical brain (dorsal forebrain patterning)


title: CBO-MOK20077P-C07, KO

description:
Library name: SIX3_PTC_C07_GT24-05566_ACGCACCT-CCTTCACC_S191
KOLF2.2J derived knockout cell line, SIX3 PTC, differentiated to cortical brain organoid

value: Termination codon


title: vchM_MH_replicate3

description: Vibrio cholerae N16961 hapR+

value: exponential phase OD 0.25

value: delta-vchM small colony


title: CBO-MOK20074P-A10, KO

description:
Library name: NR2F1_PTC_A10_GT24-06987_CAATTAAC-ATATCTCG_S193
KOLF2.2J derived knockout cell line, NR2F1 PTC, differentiated to cortical brain organoid

value: day 22


title: NUGC-3 Xenograft, PC14586, QDx6, 8h, bio rep 4


title: Les, 20dpl, rep 3

description: 10x Genomics

tag: sequencing batch

tag: disease state

value: Lesion


title: CBO-MOK20077P-A07, KO

description:
Library name: SIX3_PTC_A07_GT24-05564_CGCTATGT-GTGTCGGA_S180
KOLF2.2J derived knockout cell line, SIX3 PTC, differentiated to cortical brain organoid

tag: cell type

tag: editing strategy

value: day 8


title: Les, 10dpl, rep 1

description: 10x Genomics

value: Female


title: Les, 10dpl, rep 2

description: 10x Genomics


title: NUGC-3 Xenograft, PC14586, QDx6, 8h, bio rep 2

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma


title: NL, 5dpl, rep 1

description: 10x Genomics


title: WT_MH_replicate3

description: Vibrio cholerae N16961 hapR+

value: bacterial culture

value: exponential phase OD 0.28

value: WT

value: growth in MH


title: PrS-MOK20047_48_49-WT3, WT

description:
Library name: DLX4_5_6_WT_3_GT24-03498_CGGAACTG-TCGTAGTG_S14
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Not applicable

tag: altered gene_symbol

tag: altered locus

value: day 6

value: primitive syncytium


title: NUGC-3 Xenograft, PC14586, QDx6, 8h, bio rep 1

tag: tissue

value: NUGC-3 xenografted to Mus musculus

tag: time

value: Day6, 8h


title: vchM_MH_replicate2

description: Vibrio cholerae N16961 hapR+

value: exponential phase OD 0.25


title: NUGC-3 Xenograft, PC14586, QDx4, 24h, bio rep 4

value: Day4, 24h


title: PrS-MOK20047_48_49-WT2, WT

description:
Library name: DLX4_5_6_WT_2_GT24-03497_AGCTCGCT-GATTCTGC_S7
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

tag: model system

tag: parental cell_line


title: Les, 5dpl, rep2

description: 10x Genomics

value: spinal cord

value: Wildtype

value: Lesion

tag: Sex


title: vchM_MH_replicate1

description: Vibrio cholerae N16961 hapR+

value: delta-vchM small colony


title: vchM_TOB_replicate3

description: Vibrio cholerae N16961 hapR+

value: TOB 0,4 ug/ml


title: PrS-MOK20047_48_49-WT1, WT

description:
Library name: DLX4_5_6_WT_1_GT24-03496_GATCTATC-AGCCTCAT_S18
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: cell line


title: vchM_TOB_replicate2

description: Vibrio cholerae N16961 hapR+

value: bacterial culture

tag: genotype


title: Les, 5dpl, rep1

description: 10x Genomics

value: Female


title: PrS-MOK20049P-G04, KO

description:
Library name: DLX6_PTC_G04_GT24-03495_CATAATAC-CGTTAGAA_S6
KOLF2.2J derived knockout cell line, DLX6 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon


title: WT_MH_replicate1

description: Vibrio cholerae N16961 hapR+

value: exponential phase OD 0.26

value: WT

tag: treatment

value: growth in MH


title: NUGC-3 Xenograft, PC14586, QDx4, 24h, bio rep 3

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma

tag: model


title: formative ESC, double catalytic dead, rep2

city: New York

first: Tony

middle: T

last: Huang

state: NY

address: 450 East 29th St, Rm 807

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

description:
DCD_F2
DCD_F_out_sum_WCbinned.txt

data_processing:
Quality check of paired-end fastq files (FastQC)
Adaptor trimming (Trim Galore)
Alignment to hg19 (bowtie2)
Duplicate removal (Picard)
Split fragments mapped to each DNA strand with custom Python script
Convert each strand data to bedgraph in 1-kb bin sizes in a .txt file
Assembly: mm10
Supplementary files format and content: .txt files containing watson and crick strand reads binned to 1-kb of summed biological replicates
Library strategy: replication fork directionality and origin mapping

source_name: mESCs

extract_protocol:
EdU pulse-labeled Okazaki fragments were extracted from frozen and lysed cell pellets, isolated by ultracentrifugation on a 5-30% sucrose gradient, and purified by biotinylation-azide Click chemistry
Library was constructed with adapter ligation, PCR amplification, and purification with SPRI beads. Quality testing of DNA was performed using Qubit and TapeStation analyses.

value: mESCs


title: vchM_TOB_replicate1

description: Vibrio cholerae N16961 hapR+

tag: growth phase

value: exponential phase OD 0.25


title: PrS-MOK20049P-F03, KO

description:
Library name: DLX6_PTC_F03_GT24-03494_TGCGGCGT-TACCGAGG_S31
KOLF2.2J derived knockout cell line, DLX6 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: day 6

value: primitive syncytium


title: Naïve, rep 2

description: 10x Genomics

value: spinal cord

value: Naïve

tag: experimental batch

tag: library batch

value: Male


title: NUGC-3 Xenograft, PC14586, QDx4, 24h, bio rep 1

value: NUGC-3 xenografted to Mus musculus

value: Day4, 24h


title: WT_TOB_replicate3

description: Vibrio cholerae N16961 hapR+

value: bacterial culture

value: TOB 0,4 ug/ml


title: PrS-MOK20049P-D03, KO

description:
Library name: DLX6_PTC_D03_GT24-03493_CACGAGCG-TGGCAGAT_S27
KOLF2.2J derived knockout cell line, DLX6 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: Termination codon


title: formative ESC, double catalytic dead, rep1

description:
DCD_F1
DCD_F_out_sum_WCbinned.txt


title: formative ESC, double KO, rep2

description:
DKO_F2
DKO_F_out_sum_WCbinned.txt


title: NUGC-3 Xenograft, PC14586, QDx4, 8h, bio rep 4

value: Day4, 8h


title: WT_TOB_replicate2

description: Vibrio cholerae N16961 hapR+

value: WT


title: Les, 5dpl, rep3

description: 10x Genomics

tag: sequencing batch

value: Wildtype

tag: disease state

value: Lesion


title: PrS-MOK20048P-F03, KO

description:
Library name: DLX5_PTC_F03_GT24-03492_TGGTGGCA-TTACAGGA_S11
KOLF2.2J derived knockout cell line, DLX5 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: cell type

tag: editing strategy


title: NUGC-3 Xenograft, PC14586, QDx4, 24h, bio rep 2

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma


title: NUGC-3 Xenograft, PC14586, QDx4, 8h, bio rep 3


title: formative ESC, double KO, rep1

description:
DKO_F1
DKO_F_out_sum_WCbinned.txt

value: mESCs


title: PrS-MOK20048P-D03, KO

description:
Library name: DLX5_PTC_D03_GT24-03491_CAACAATG-CCGTGAAG_S32
KOLF2.2J derived knockout cell line, DLX5 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: altered gene_symbol

tag: altered locus

value: day 6

value: primitive syncytium


title: NUGC-3 Xenograft, PC14586, QDx4, 8h, bio rep 1

tag: tissue

tag: time


title: WT_TOB_replicate1

description: Vibrio cholerae N16961 hapR+

value: exponential phase OD 0.25


title: KPN tumoroid (bulk line KPN 18)

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
The quality of raw data was assessed using FastQC (v.0.11.9) and MultiQC (v.1.9) prior to processing the data.
The first 12 bases as well as low-quality bases (Phred score < 20) were trimmed from each sequence using Cutadapt (v1.18).
STAR (v.2.7.4.a) was applied to align sequences to the mouse genome (GRCm38) and to determine counts per gene.
Assembly: mm10
Supplementary files format and content: Excel file includes raw count data

source_name: small intestinal tumor

growth_protocol: Tumoroids and organoids were cultured in Matrigel (Corning, the Netherlands) and culture medium, composed of basal medium (ADF) with freshly added mouse EGF (50 ng/ml, 315-09, ThermoFisher, the Netherlands), R-spondin (20 vol% of in house produced conditioned medium) and Noggin (10 vol% of in house produced conditioned medium). ADF medium consists of advanced DMEM F/12, N2 (100x diluted) and B27 (50x diluted) supplements, 10 mM HEPES, 100 units/ml of penicillin, 100 μg/ml of streptomycin, 0,25 μg/ml Amphotericin B and 2 mM Glutamax (all Gibco, the Netherlands). To recombine target genes containing loxP sites in organoids in vitro, 1 µM 4-Hydroxytamoxifen (4-OHT, H7904, Sigma-Aldrich) was added to culture medium overnight and refreshed with plain culture medium the day after. Tumoroid and organoid cultures were maintained in humidified air containing 5% CO2 at 37°C.

extract_protocol:
The NucleoSpin RNA kit (740955, Bioké) was used to extract RNA according to manufacturer’s protocol. 250 ng RNA per sample was used.
RNA libraries for RNA seq were prepared with KAPA mRNA Hyperprep according to manufacturer's protocol.

value: small intestinal tumor

value: KPN


title: PrS-MOK20048P-A03, KO

description:
Library name: DLX5_PTC_A03_GT24-03490_GGTGAACC-TCCAACGC_S15
KOLF2.2J derived knockout cell line, DLX5 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: model system

tag: parental cell_line


title: KPN tumoroid (bulk line KPN 1g)

tag: cell line


title: NUGC-3 Xenograft, PC14586, QDx2, 24h, bio rep 4

tag: genotype

value: NUGC-3 xenografted to Mus musculus

value: Day2, 24h


title: formative ESC, control KO, rep2

description:
CKO_F2
CKO_F_out_sum_WCbinned.txt


title: naïve ESC, double catalytic dead, rep2

description:
DCD_N2
DCD_N_out_sum_WCbinned.txt


title: PrS-MOK20047P-B02, KO

description:
Library name: DLX4_PTC_B02_GT24-03489_AACAGGTT-CTTGGTAT_S23
KOLF2.2J derived knockout cell line, DLX4 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20047P-A02, KO

description:
Library name: DLX4_PTC_A02_GT24-03488_GCGCTCTA-GTCGGAGC_S36
KOLF2.2J derived knockout cell line, DLX4 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: NUGC-3 Xenograft, PC14586, QDx2, 24h, bio rep 3

tag: treatment


title: naïve ESC, double catalytic dead, rep1

description:
DCD_N1
DCD_N_out_sum_WCbinned.txt


title: PrS-MOK20047P-A01, KO

description:
Library name: DLX4_PTC_A01_GT24-03487_ATATCTCG-ACTAAGAT_S22
KOLF2.2J derived knockout cell line, DLX4 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: KPN tumoroid (bulk line KPN 1c)


title: KPN tumoroid (single cell clonal derived line (KPN 1c E12) biol rep 3


title: NUGC-3 Xenograft, PC14586, QDx2, 24h, bio rep 2

tag: model


title: KPN tumoroid (bulk line KPN 1b)


title: naïve ESC, double KO, rep2

description:
DKO_N2
DKO_N_out_sum_WCbinned.txt


title: naïve ESC, double KO, rep1

description:
DKO_N1
DKO_N_out_sum_WCbinned.txt


title: PrS-MOK20023_60_52-WT3, WT

description:
Library name: MBLN2_3_TWIST2_WT_3_GT24-03510_CAATTAAC-ATATCTCG_S19
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Not applicable


title: KPN tumoroid (single cell clonal derived line (KPN 1c E12) biol rep 2


title: naïve ESC, control KO, rep2

description:
CKO_N2
CKO_N_out_sum_WCbinned.txt


title: NUGC-3 Xenograft, PC14586, QDx2, 8h, bio rep 4

value: Day2, 8h


title: NUGC-3 Xenograft, PC14586, QDx2, 24h, bio rep 1


title: NUGC-3 Xenograft, PC14586, QDx4, 8h, bio rep 2


title: PrS-MOK20023_60_52-WT2, WT

description:
Library name: MBLN2_3_TWIST2_WT_2_GT24-03509_GTCTACAC-ACCTTGGC_S21
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC


title: PrS-MOK20023_60_52-WT1, WT

description:
Library name: MBLN2_3_TWIST2_WT_1_GT24-03508_ACTCGTGT-GTTCCAAT_S17
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: formative ESC, control KO, rep1

description:
CKO_F1
CKO_F_out_sum_WCbinned.txt


title: KPN tumoroid (single cell clonal derived line (KPN 1c E12) biol rep 1


title: PrS-MOK20052P-H09, KO

description:
Library name: TWIST2_PTC_H09_GT24-03507_ATTGTGAA-GCAATGCA_S20
KOLF2.2J derived knockout cell line, TWIST2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon


title: KPN tumoroid (single cell clonal derived line KPN 1b E4) biol rep 3


title: Cre_input_DMSO, adiocytes

city: Singapore

first: Jia

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
Sequencing reads were trimmed using Cutadapt, then mapped to the mouse genome (mm10) with STAR. BigWig files were generated using Bedtools and the bedGraphToBigWig tool from UCSC.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: adipocytes

extract_protocol:
Cells were harvested with cell scraper and transferred to an Eppendorf tube. Cell lysate was further homogenized by passage through a 25G syringe needle 10 times. The lysate was sonicated with a cup horn (Q700, QSONICA) for 3 cycles (30s ON/OFF, 50 Amp) to break the nuclei (microscopic examination) and to shred the RNA. Supernatant was collected by centrifugation at 13,000 RPM at 4oC.
The immunoprecipitated RNA was quantified with the Qubit RNA HS assay kit (Thermo Scientific) before rRNA Removal with NEBNext® rRNA Depletion Kit v2. The entire rRNA-depleted RNA was used for sequencing library construction.

treatment_protocol: we isolate stromal vascular fraction (SVF) cells from HuRflox/flox animals and employ adenoviral Cre 6h before induction of differentiation to delete HuR, followed by adipocyte differentiation

value: adipocytes

value: HuR flox/flox

value: Adeno-Cre HuR

tag: condition

value: DMSO


title: naïve ESC, control KO, rep1

description:
CKO_N1
CKO_N_out_sum_WCbinned.txt


title: NUGC-3 Xenograft, PC14586, QDx2, 8h, bio rep 3

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma


title: KPN tumoroid (single cell clonal derived line KPN 1b E4) biol rep 2


title: NUGC-3 Xenograft, PC14586, QDx2, 8h, bio rep 1


title: KPN tumoroid (single cell clonal derived line KPN 1b E4) biol rep 1


title: PrS-MOK20052P-A09, KO

description:
Library name: TWIST2_PTC_A09_GT24-03505_CCTTCACC-GGAGCGTC_S13
KOLF2.2J derived knockout cell line, TWIST2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: featureCounts.csv genesCounts.csv genesRawCounts.csv genesTPM.csv stats.csv txCounts.csv txRawCounts.csv txTPM.csv

value: day 6


title: Cre_IP_DMSO, adiocytes


title: PrS-MOK20052P-D09, KO

description:
Library name: TWIST2_PTC_D09_GT24-03506_GCCACAGG-ATGGCATG_S24
KOLF2.2J derived knockout cell line, TWIST2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: primitive syncytium


title: NUGC-3 Xenograft, PC14586, QDx1, 24h, bio rep 4

value: Day1, 24h


title: Control_input_DMSO, adiocytes


title: KPN organoid (bulk line 28.1.g) biol rep 2

source_name: small intestine

value: small intestine


title: Control_IP_DMSO, adiocytes


title: PrS-MOK20060P-F05, KO

description:
Library name: MBLN3_PTC_F05_GT24-03503_GTGTCGGA-GCGCAAGC_S10
KOLF2.2J derived knockout cell line, MBNL3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: KPN organoid (bulk line 28.1.g) biol rep 1

value: KPN


title: PrS-MOK20060P-E06, KO

description:
Library name: MBLN3_PTC_E06_GT24-03504_TTCCTGTT-AAGATACT_S35
KOLF2.2J derived knockout cell line, MBNL3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: NUGC-3 Xenograft, PC14586, QDx1, 24h, bio rep 3

value: NUGC-3 xenografted to Mus musculus


title: NUGC-3 Xenograft, PC14586, QDx1, 24h, bio rep 2


title: Cre_input_insulin, adiocytes

value: insulin


title: PrS-MOK20060P-C06, KO

description:
Library name: MBLN3_PTC_C06_GT24-03502_ACACTAAG-ATATGGAT_S26
KOLF2.2J derived knockout cell line, MBNL3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: NUGC-3 Xenograft, PC14586, QDx1, 24h, bio rep 1


title: PrS-MOK20023P-F11, KO

description:
Library name: MBLN2_PTC_F11_GT24-03501_CCATTCGA-CGGACAAC_S5
KOLF2.2J derived knockout cell line, MBNL2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Control_input_insulin, adiocytes


title: KPN organoid (bulk line 20.5.a) biol rep 1


title: Cre_IP_insulin, adiocytes


title: NUGC-3 Xenograft, PC14586, QDx2, 8h, bio rep 2


title: NUGC-3 Xenograft, PC14586, QDx1, 16h, bio rep 4

value: Day1, 16h


title: Neuron, BB, CaMKII inh, replicate 3

city: Piscataway

first: Brian

last: Daniels

address: 604 Allison Road

department: Cell Biology and Neuroscience

institute: Rutgers, The State University of New Jersey

data_processing:
Raw data quality was evaluated by FastQC.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
the gene hit counts table was used for downstream differential expression analysis via DESeq2. The Wald test was used to generate p-values and log2 fold changes.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes unique gene hit counts for each sample

source_name: Primary cerebral cortical neurons

growth_protocol: Primary cerebral cortical neurons were derived from E15 embryonic brains and was processed using a Neural Tissue Dissociation Kit-T. Neurons were seeded onto multi-well plates that had been pre-coated with 50μg/mL Poly-D-Lysine. Cultures were sustained in Neurobasal-Plus Medium, enhanced with B-27-Plus supplement.

extract_protocol:
Total RNA from mouse brain was harvested using Zymo Direct-zol RNA Miniprep kit following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: Neurons were treated with B/B or vehicle solution in the presence of KN93, 666-15, or control solution for 24 hours prior to harvest.

value: Primary cerebral cortical neurons

value: Ripk3-2xFV-fl_fl Nestin-Cre+

value: KN93, B/B


title: PrS-MOK20023P-B09, KO

description:
Library name: MBLN2_PTC_B09_GT24-03499_TAAGGTCA-CTACGACA_S9
KOLF2.2J derived knockout cell line, MBNL2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: Termination codon


title: NUGC-3 Xenograft, PC14586, QDx1, 16h, bio rep 3


title: Control_IP_insulin, adiocytes

value: adipocytes

value: HuR flox/flox


title: PrS-MOK20023P-C12, KO

description:
Library name: MBLN2_PTC_C12_GT24-03500_TTGCCTAG-TAAGTGGT_S30
KOLF2.2J derived knockout cell line, MBNL2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Neuron, BB, CaMKII inh, replicate 2


title: 18M Vehicle NL rep3

first: Phillip

middle: Steven

last: Gross

state: District Of Columbia

data_processing:
Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de- multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification. After investigating the quality of the raw data, sequence reads were trimmed to remove adapter sequences. The trimmed reads were mapped to the mouse reference genome GRCm38 available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Assembly: GRCm38
Supplementary files format and content: excel table. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.

source_name: Spinal Cord

extract_protocol:
To identify the lesion, 500 ul of 1% neutral red dye in PBS was injected intraperitoneally 2h prior to cardiac perfusion with ice-cold RNA-ase free 1X PBS. Spinal cords were flash frozen in isopentane and embedded in OCT on dry ice. Spinal cords were extracted and lesion and distant contralateral non-lesion tissue were microdissected out and flash frozen on dry ice. RNA was isolated using the Direct-zol RNA Miniprep Kits (Zymo Research #R2050) and sent to Azenta Life Sciences (South Plainfield, NJ, USA) for RNA quality check, library preparation, sequencing and analysis.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Lesions were induced by injection of 1% LPC between the T11-12 vertebrae into the ventral white watter columns of the spinal cord. INK-ATTAC mice were treated twice a week intraperitoneally with AP20187 (2 mg/kg, MedchemExpress B/B homodimerizer, #HY-13992) or with vehicle (10% DMSO, 40% peg400, 5% tween 80, 45% saline) at equal volumes (10ul/g bodyweight) from day of lesion until final timepoint.

value: Spinal Cord

value: 18 months

value: INK-ATTAC

value: Vehicle


title: NUGC-3 Xenograft, PC14586, QDx1, 16h, bio rep 1

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma


title: Neuron, BB, CREB inh, replicate 3


title: PrS-MOK20043_50_51-WT2, WT

description:
Library name: HEY1_HOPX_MAFF_WT_2_GT24-03521_TCATCCTT-AGCTCGCT_S16
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Not applicable

value: day 6

value: primitive syncytium


title: Neuron, BB, CaMKII inh, replicate 1


title: 18M Vehicle NL rep2


title: NUGC-3 Xenograft, PC14586, QDx1, 16h, bio rep 2

value: NUGC-3 xenografted to Mus musculus

value: Day1, 16h


title: KPN organoid (bulk line 20.5.a) biol rep 2

value: small intestine

value: KPN


title: 18M Vehicle NL rep1


title: NUGC-3 Xenograft, PC14586, QDx1, 8h, bio rep 3

value: Day1, 8h


title: Neuron, BB, CREB inh, replicate 2

value: Primary cerebral cortical neurons

value: Ripk3-2xFV-fl_fl Nestin-Cre+


title: PrS-MOK20043_50_51-WT1, WT

description:
Library name: HEY1_HOPX_MAFF_WT_1_GT24-03520_CTGCTTCC-GATCTATC_S34
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC


title: 3M Vehicle NL rep3

value: Spinal Cord

value: 3 months


title: Neuron, BB, CREB inh, replicate 1


title: NUGC-3 Xenograft, PC14586, QDx1, 8h, bio rep 2


title: 3M Vehicle NL rep2

value: INK-ATTAC


title: NUGC-3 Xenograft, PC14586, QDx1, 8h, bio rep 1


title: PrS-MOK20051P-D07, KO

description:
Library name: MAFF_PTC_D07_GT24-03518_AACTGTAG-TGCGGCGT_S25
KOLF2.2J derived knockout cell line, MAFF PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon

value: MAFF


title: 3M Vehicle NL rep1

value: Vehicle


title: Neuron, CaMKII inh, replicate 2

value: KN93, Ethanol


title: PrS-MOK20051P-C07, KO

description:
Library name: MAFF_PTC_C07_GT24-03517_GTGAATAT-GAATGAGA_S29
KOLF2.2J derived knockout cell line, MAFF PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: day 6


title: NUGC-3 Xenograft, vehicle, 2QDx1, 48h, bio rep 4

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma

value: Vehicle (2QDx1)


title: 18M AP 20dpl rep3

value: 18 months

value: AP


title: PrS-MOK20043_50_51-WT3, WT

description:
Library name: HEY1_HOPX_MAFF_WT_3_GT24-03522_AGGTTATA-CGGAACTG_S12
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Not applicable

value: primitive syncytium


title: NUGC-3 Xenograft, vehicle, 2QDx1, 48h, bio rep 3

value: NUGC-3 xenografted to Mus musculus


title: Neuron, CaMKII inh, replicate 1

value: Primary cerebral cortical neurons

value: Ripk3-2xFV-fl_fl Nestin-Cre+


title: PrS-MOK20050P-G05, KO

description:
Library name: HOPX_PTC_G05_GT24-03516_ACAGGCGC-AGGCAGAG_S28
KOLF2.2J derived knockout cell line, HOPX PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: HOPX


title: 18M AP 20dpl rep1

value: Spinal Cord

value: INK-ATTAC


title: NUGC-3 Xenograft, vehicle, 2QDx1, 48h, bio rep 2


title: NUGC-3 Xenograft, PC14586, QDx1, 8h, bio rep 4

value: Day1, 8h


title: PrS-MOK20050P-B06, KO

description:
Library name: HOPX_PTC_B06_GT24-03515_CATAGAGT-TGGTGGCA_S4
KOLF2.2J derived knockout cell line, HOPX PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon


title: Neuron, CREB inh, replicate 2

value: 666-15, Ethanol


title: PrS-MOK20050P-A06, KO

description:
Library name: HOPX_PTC_A06_GT24-03514_TGCGAGAC-CAACAATG_S8
KOLF2.2J derived knockout cell line, HOPX PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: day 6


title: Neuron, CREB inh, replicate 3


title: NUGC-3 Xenograft, vehicle, 2QDx1, 48h, bio rep 1

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma


title: PrS-MOK20051P-H07, KO

description:
Library name: MAFF_PTC_H07_GT24-03519_GGTCACGA-CATAATAC_S2
KOLF2.2J derived knockout cell line, MAFF PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: MAFF


title: PrS-MOK20043P-A08, KO

description:
Library name: HEY1_PTC_A08_GT24-03513_GACGTCTT-GGTGAACC_S1
KOLF2.2J derived knockout cell line, HEY1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: 18M Vehicle 20dpl rep2

value: 18 months

value: Vehicle


title: Neuron, BB, replicate 3

value: DMSO, B/B


title: Neuron, CREB inh, replicate 1


title: NUGC-3 Xenograft, vehicle, 2QDx1, 24h, bio rep 4

value: NUGC-3 xenografted to Mus musculus

value: Vehicle (2QDx1)


title: 18M Vehicle 20dpl rep3


title: Neuron, CaMKII inh, replicate 3

value: Primary cerebral cortical neurons

value: Ripk3-2xFV-fl_fl Nestin-Cre+

value: KN93, Ethanol


title: NUGC-3 Xenograft, vehicle, 2QDx1, 24h, bio rep 3


title: PrS-MOK20043P-A06, KO

description:
Library name: HEY1_PTC_A06_GT24-03512_AGTACTCC-AACAGGTT_S3
KOLF2.2J derived knockout cell line, HEY1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: primitive syncytium


title: 18M Vehicle 20dpl rep1

value: Spinal Cord

value: INK-ATTAC


title: PrS-MOK20043P-A03, KO

description:
Library name: HEY1_PTC_A03_GT24-03511_TGGCCGGT-GCGCTCTA_S33
KOLF2.2J derived knockout cell line, HEY1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon


title: Neuron, BB, replicate 2


title: NUGC-3 Xenograft, vehicle, 2QDx1, 24h, bio rep 2


title: 3M AP 20dpl rep3

value: 3 months

value: AP


title: PrS--MOK20036_41_42-WT3, WT

description:
Library name: WT_PITX1_LMO2_ZBTB7C_3_GT23-14994_ATATCTCG-ACTAAGAT_S45_L001
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: csv files including raw and normalised counts

value: Not applicable

value: day 6


title: 18M AP 20dpl rep2

value: 18 months


title: 3M AP 20dpl rep2


title: Neuron, control, replicate 3

value: DMSO, Ethanol


title: NUGC-3 Xenograft, vehicle, 2QDx1, 24h, bio rep 1

value: Xenografted tumor

value: Xenografted gastric adenocarcinoma


title: PrS--MOK20036_41_42-WT2, WT

description:
Library name: WT_PITX1_LMO2_ZBTB7C_2_GT23-14993_ACCTTGGC-ATGAGGCC_S36_L001
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: NUGC-3 Xenograft, vehicle, 2QDx1, 7h, bio rep 4

value: NUGC-3 xenografted to Mus musculus

value: Vehicle (2QDx1)


title: NUGC-3 Xenograft, vehicle, 2QDx1, 7h, bio rep 3


title: 3M AP 20dpl rep1


title: Neuron, control, replicate 2

value: Primary cerebral cortical neurons

value: Ripk3-2xFV-fl_fl Nestin-Cre+


title: PrS--MOK20036_41_42-WT1, WT

description:
Library name: WT_PITX1_LMO2_ZBTB7C_1_GT23-14992_GTTCCAAT-GCAGAATT_S41_L001
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC


title: 3M Vehicle 20dpl rep3

value: Vehicle


title: PrS-MOK20042P-B10, KO

description:
Library name: ZBTB7C_PTC_B10_GT23-14991_GCAATGCA-AACGTTCC_S44_L001
KOLF2.2J derived knockout cell line, ZBTB7C PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: primitive syncytium


title: PrS-MOK20042P-A11, KO

description:
Library name: ZBTB7C_PTC_A11_GT23-14990_ATGGCATG-GGTACCTT_S35_L001
KOLF2.2J derived knockout cell line, ZBTB7C PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: 3M Vehicle 20dpl rep1

value: Spinal Cord

value: INK-ATTAC


title: NUGC-3 Xenograft, vehicle, 2QDx1, 7h, bio rep 2


title: NUGC-3 Xenograft, vehicle, 2QDx1, 7h, bio rep 1


title: 3M Vehicle 20dpl rep2

value: 3 months


title: SC_Multiplex_CMO_Rep_2

city: MADRID

first: Ignacio

last: Heras-Murillo

state: MADRID

address: c/Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description: CMO reads from multiplexed samples from 4 conditions (replicate 2): Naïve: Day 5 MC38 tumor i.d.; PBS: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth); Anti-PD1: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with anti-PD1 on days 3 and 8); cDC1-vaccine: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with cDC1 vaccination on days 3 and 8).

data_processing:
Single-cell RNA-sequencing data were processed using the Cell Ranger (v6.1.2) default parameters and the mm10 (GRCm38.p6) mouse genome reference provided by 10x Genomics.
Results from RNA quantification were imported into R (v4.1.2) and analyzed using Seurat (v4.2.1). Cells were filtered to retain those with <10% mitochondrial RNA content, more than 300 genes and with a number of unique molecular identifiers (UMIs) comprised between 500 and 50,000. Then, the remaining cells were demultiplexed using the cellhashR R package (v1.0.2) using htodemux, bff_cluster, gmm_demux, multiseq and dropletutils methods. The consensus classification was finally used for further analyses. In addition, contamination of cells not expressing CD3 or CD90 were excluded, resulting in a total of 15,253 analyzed cells.
Counts were normalized for library size using Seurat’s default normalization parameters. RNA count was used as a source of unwanted variation and regressed using Seurat’s built-in regression model.
Assembly: mm10 (GRCm38.p6) mouse genome
Supplementary files format and content: Matrix.mtx files contain the raw read counts per gene per cell. A file is provided for every biological replicate.
Supplementary files format and content: Features.tsv files contain information of the detected genes. A file is provided for every biological replicate.
Supplementary files format and content: Barcodes.tsv files contain cell barcodes. A file is provided for every biological replicate.

source_name: TILs, d5 i.d. MC38 Rep 2, CMO multiplex; 1. tumor-naïve mice; 2. neoadjuvant PBS treatment, rechallenge; 3. neoadjuvant anti-PD1 treatment, rechallenge; 4. neoadjuvant cDC1-vaccine treatment, rechallenge.

growth_protocol: 12 to 14 weeks-old mice house at the Spanish National Centre for Cardiovascular Disease (CNIC)

extract_protocol:
At day 5 upon tumor rechallenge, mice were euthanized and tumors disected. Tumors were minced and incubated for 30 min in HBSS shacking at 37 °C with 0.5 mg/ml Collagenase IV  and 50 μg/ml DNAseI, squeezed through a 70 μm cell strainer and re-filtered through a 40 μm cell strainer. Cells from each biological replicate (6 per experimental group) were pooled in equal cell numbers in n=2 per experimental condition and independently labelled using Cell Multiplexing Oligos (CMOs), following the manufacturer’s protocol. Cells were then antibody-stained and DAPI-CD45+CD3+CD90+ cells that were CD8+ or CD4+ were FACS sorted and equal numbers of cells per replicate were mixed.
The mixed cell suspension was processed using the 10x Genomics 3′ v2 kit, as specified by the manufacturer’s instructions

treatment_protocol: Naïve: mice were inoculated with 1.5x10^6 MC38 cells intradermally (i.d.) in the right flank. PBS: mice were inoculated with 0.5x10^6 MC38 cells i.d. in the right flank, treated with PBS at days 3 and 8 of tumor growht and tumor resected at day 10. 30 days thereafter, mice were inoculated with 1.5x10^6 MC38 cells intradermally (i.d.) in the right flank. anti-PD1: mice were inoculated with 0.5x10^6 MC38 cells i.d. in the right flank, treated with anti-PD1 (100 µg, intraperitoneally) at days 3 and 8 of tumor growht and tumor resected at day 10. 30 days thereafter, mice were inoculated with 1.5x10^6 MC38 cells intradermally (i.d.) in the right flank. cDC1: mice were inoculated with 0.5x10^6 MC38 cells i.d. in the right flank, treated i.d.  with 10^6 splenic cDC1s activated ex vivo with CpG ODN 1826 and pulsed with MC38 tumor cell lysate at days 3 and 8 of tumor growht and tumor resected at day 10. 30 days thereafter, mice were inoculated with 1.5x10^6 MC38 cells intradermally (i.d.) in the right flank.

value: Tumor

value: CD4+ and CD8+ T cells (CD45+,CD90+,CD3+)

value: 4 multiplexed conditions:Naïve:Day 5 MC38 tumor i.d.; PBS:Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth); Anti-PD1:Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with anti-PD1 on days 3 and 8); cDC1-vaccine:Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with cDC1 vaccination on days 3 and 8)


title: SC_Multiplex_GEX_Rep_2

description: Gene expression reads from multiplexed samples from 4 conditions (replicate 2): Naïve: Day 5 MC38 tumor i.d.; PBS: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth); Anti-PD1: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with anti-PD1 on days 3 and 8); cDC1-vaccine: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with cDC1 vaccination on days 3 and 8).

source_name: TILs, d5 i.d. MC38 Rep 2, GEX multiplex; 1. tumor-naïve mice; 2. neoadjuvant PBS treatment, rechallenge; 3. neoadjuvant anti-PD1 treatment, rechallenge; 4. neoadjuvant cDC1-vaccine treatment, rechallenge


title: SC_Multiplex_CMO_Rep_1

description: CMO reads from multiplexed samples from 4 conditions (replicate 1): Naïve: Day 5 MC38 tumor i.d.; PBS: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth); Anti-PD1: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with anti-PD1 on days 3 and 8); cDC1-vaccine: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with cDC1 vaccination on days 3 and 8).

source_name: TILs, d5 i.d. MC38 Rep 1, CMO multiplex; 1. tumor-naïve mice; 2. neoadjuvant PBS treatment, rechallenge; 3. neoadjuvant anti-PD1 treatment, rechallenge; 4. neoadjuvant cDC1-vaccine treatment, rechallenge.


title: PrS-MOK20041P-F08, KO

first: MorPhiC

description:
Library name: LMO2_PTC_F08_GT23-14988_AAGATACT-ATGTAAGT_S40_L001
KOLF2.2J derived knockout cell line, LMO2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon

value: day 6


title: BMDM, Bmal1-KO, Vehicle control, rep6

city: Oxford

first: Laura

last: Bailey

address: Radcliffe Department of Medicine

department: Oxford Centre for Diabetes, Endocrinology and Metabolism

institute: University of Oxford

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. Index of the reference genome (mm10) was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: mm10
Supplementary files format and content: gene_couint.txt = Tab-delimited file with read-count for each sample with annotation of each gene

source_name: Bone-marrow derived macrophage

growth_protocol: Tibiae and femurae dissected from C57BL/6 mice, and the single-cell suspension from bone marrow was cultured on non-tissue culture treated dishes with complete DMEM, 20% FBS, MCSF for 7 days.

extract_protocol:
Cells were lysed in Trizol reagent and RNA extracted using chloroform, followed by Zymo RNA Clean & Concentrator.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Cells were treated with one of the four conditions for 6 hours before lysis for RNA extraction.

value: Bone-marrow derived macrophage

tag: strain

value: LysM-Cre;Bmal1 flox/flox

value: DMSO (vehicle control),


title: Neuron, BB, replicate 1

value: DMSO, B/B


title: PrS-MOK20042P-A09, KO

city: Hinxton

last: Consortium

address: Wellcome Genome Campus

institute: EMBL-EBI

description:
Library name: ZBTB7C_PTC_A09_GT23-14989_GGAGCGTC-GCACGGAC_S43_L001
KOLF2.2J derived knockout cell line, ZBTB7C PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: SJSA-1 cells, PC14586, 16h, bio rep 2

growth_protocol: Cells were maintained in RPMI-1640 (for NUGC-3, NUGC-3 KO, and SJSA-1) or DMEM/F12, 1:1 mixture (for T3M-4) supplemented with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted immediately from the cells after treatments for 5 or 16 h as indicated and purified by using QIAcube (Qiagen) with DNase I digestion, following the manufacturer's protocols.
After rRNA depletion by using Fastselect HMR kit (Qiagen), strand-specific RNA sequencing libraries were prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB), following manufacturers’ instructions.

treatment_protocol: Cells were treated on the second day after seeding, with either DMSO or PC14586 (5 µM) for 5 h or 16 h as indicated.

value: Osteosarcoma

value: TP53 WT


title: PrS-MOK20041P-F07, KO

description:
Library name: LMO2_PTC_F07_GT23-14987_GCGCAAGC-CGGCGTGA_S37_L001
KOLF2.2J derived knockout cell line, LMO2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC


title: SJSA-1 cells, PC14586, 16h, bio rep 1


title: BMDM, Bmal1-KO, CCM, rep6

value: 100uM CCM/DMSO


title: SJSA-1 cells, PC14586, 16h, bio rep 3


title: BMDM, Bmal1-KO, LPS + CCM, rep6

value: 100nM LPS/100uM CCM


title: MLL34dKO_Form3_lS

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

data_processing:
library strategy: BioRepli-seq
Bowtie2 mapping to mm10
BamtoBed
Bin into 50kb genome bins
Calculate RT
Quantile normalization
Bedgraph to bigwig
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Mouse ESCs were seeded and next day differentiated to formative state by removal of Lif+2i and growth for ~63h. Naive controls were grown in parallel in the presence of Lif+2i.

extract_protocol: NEBNext Ultra II (on-bead custom protocol)

tag: culture conditions

value: Formative

value: mESC cell line

tag: treatment time


title: PrS-MOK20041P-A06, KO

description:
Library name: LMO2_PTC_A06_GT23-14986_ATATGGAT-TAATACAG_S39_L001
KOLF2.2J derived knockout cell line, LMO2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

extract_protocol:
mRNA was captured using magnetic oligo-dT beads according to KAPA mRNA HyperPrep Kit
KAPA mRNA HyperPrep Kit Illumina NovaSeq X

value: primitive syncytium


title: Neuron, control, replicate 1

value: Primary cerebral cortical neurons

value: Ripk3-2xFV-fl_fl Nestin-Cre+

value: DMSO, Ethanol


title: SJSA-1 cells, DMSO, 16h, bio rep 3

value: DMSO Control


title: SC_Multiplex_GEX_Rep_1

description: Gene expression reads from multiplexed samples from 4 conditions (replicate 1): Naïve: Day 5 MC38 tumor i.d.; PBS: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth); Anti-PD1: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with anti-PD1 on days 3 and 8); cDC1-vaccine: Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with cDC1 vaccination on days 3 and 8).

source_name: TILs, d5 i.d. MC38 Rep 1, GEX multiplex, groups 1. tumor-naïve mice; 2. neoadjuvant PBS treatment, rechallenge; 3. neoadjuvant anti-PD1 treatment, rechallenge; 4. neoadjuvant cDC1-vaccine treatment, rechallenge

value: Tumor

value: CD4+ and CD8+ T cells (CD45+,CD90+,CD3+)

value: 4 multiplexed conditions:Naïve:Day 5 MC38 tumor i.d.; PBS:Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth); Anti-PD1:Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with anti-PD1 on days 3 and 8); cDC1-vaccine:Day 5 MC38 tumor rechallenge i.d. (35 days upon resection of primary tumor at day 10 of growth that was treated with cDC1 vaccination on days 3 and 8)


title: BMDM, Bmal1-KO, LPS, rep6

value: Bone-marrow derived macrophage

value: LysM-Cre;Bmal1 flox/flox

value: 100nM LPS/DMSO


title: SJSA-1 cells, DMSO, 16h, bio rep 2

value: Osteosarcoma

value: TP53 WT


title: MLL34dKO_Form3_eS


title: PrS-MOK20036P-C03, KO

description:
Library name: PITX1_PTC_C03_GT23-14985_CGGACAAC-AATCCGGA_S38_L001
KOLF2.2J derived knockout cell line, PITX1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: Termination codon

value: day 6


title: BMDM, Bmal1-KO, Vehicle control, rep5

value: DMSO (vehicle control),


title: MLL34dKO_Form2_lS

value: Formative

value: mESC cell line


title: PrS-MOK20036P-B03, KO

description:
Library name: PITX1_PTC_B03_GT23-14984_TAAGTGGT-GGCTTAAG_S42_L001
KOLF2.2J derived knockout cell line, PITX1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: primitive syncytium


title: BMDM, Bmal1-KO, LPS + CCM, rep5

value: 100nM LPS/100uM CCM


title: NUGC-3 KO cells, PC14586, 16h, bio rep 3

source_name: NUGC-3 KO

value: NUGC-3 KO

value: Gastric adenocarcinoma

value: TP53 KO


title: PrS-MOK20020-WT3, WT

description:
Library name: OVOL1_WT_3_GT23-14421_GATTCTGC-CTCTCGTC_S27_L002
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: BMDM, Bmal1-KO, LPS, rep5


title: MLL34dKO_Form1_lS


title: MLL34dKO_Form2_eS


title: NUGC-3 KO cells, PC14586, 16h, bio rep 2


title: PrS-MOK20020-WT2, WT

description:
Library name: OVOL1_WT_2_GT23-14420_AGCCTCAT-TCTCTACT_S19_L002
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: MLL34dKO_Form1_eS


title: BMDM, Bmal1-KO, CCM, rep5

value: 100uM CCM/DMSO


title: NUGC-3 KO cells, DMSO, 16h, bio rep 3

value: DMSO Control


title: BMDM, Wild-type, LPS + CCM, rep3

value: Bone-marrow derived macrophage

value: Bmal1 flox/flox


title: NUGC-3 KO cells, PC14586, 16h, bio rep 1


title: BMDM, Wild-type, Vehicle control, rep3


title: MLL3KO_Form3_lS


title: BMDM, Wild-type, CCM, rep3


title: PrS-MOK20020P-C10, KO

description:
Library name: OVOL1_PTC_C10_GT23-14418_TACCGAGG-AGTTCAGG_S28_L002
KOLF22 deleted OVOL1 by insertion of premature termination codon (PTC) derived primitive syncytium


title: PrS-MOK20020P-B03, KO

description:
Library name: OVOL1_PTC_B03_GT23-14417_AATGCCTC-TGGATCGA_S24_L002
KOLF22 deleted OVOL1 by insertion of premature termination codon (PTC) derived primitive syncytium


title: NUGC-3 KO cells, DMSO, 16h, bio rep 2


title: MLL3KO_Form2_lS


title: MLL3KO_Form2_eS


title: PrS-MOK20020P-A02, KO

description:
Library name: OVOL1_PTC_A02_GT23-14416_GGCATTCT-CAAGCTAG_S26_L002
KOLF2.2J differentiated to cortical brain organoid


title: SJSA-1 cells, DMSO, 16h, bio rep 1

value: Osteosarcoma


title: PrS-MOK20036P-A01, KO

description:
Library name: PITX1_PTC_A01_GT23-14983_CTACGACA-TTGGACTC_S34_L001
KOLF2.2J derived knockout cell line, PITX1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: BMDM, Bmal1-KO, Vehicle control, rep4

value: LysM-Cre;Bmal1 flox/flox


title: NUGC-3 KO cells, DMSO, 16h, bio rep 1


title: T3M-4 cells, PC14586, 16h, bio rep 2

value: Pancreatic ductal adenocarcinoma


title: CBO-MOK20005P-C10, KO

description:
Library name: TBR1_PTC_C10-_GT23-15127_TACCGAGG-AGTTCAGG_S165_L003
KOLF2.2J derived knockout cell line, TBR1 PTC, differentiated to cortical brain organoid

value: iPSC

value: Termination codon

value: Cortical brain (dorsal forebrain patterning)


title: MLL34dKO_Naive3_lS

value: Naive


title: BMDM, Bmal1-KO, LPS + CCM, rep4


title: T3M-4 cells, PC14586, 16h, bio rep 1


title: BMDM, Bmal1-KO, CCM, rep4


title: MLL3KO_Form1_eS

value: Formative

value: mESC cell line


title: CBO-MOK20005P-B03, KO

description:
Library name: TBR1_PTC_B03-_GT23-15126_AATGCCTC-TGGATCGA_S151_L003
KOLF2.2J derived knockout cell line, TBR1 PTC, differentiated to cortical brain organoid

value: day 6


title: PrS-MOK20020-WT1, WT

description:
Library name: OVOL1_WT_1_GT23-14419_CGTTAGAA-GACCTGAA_S14_L002
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: primitive syncytium


title: MLL3KO_Form3_eS


title: BMDM, Wild-type, LPS, rep3

value: 100nM LPS/DMSO


title: T3M-4 cells, DMSO, 16h, bio rep 3


title: MLL34dKO_Naive3_eS

description: MLL34dKO.naive.merged.bw AND MLL34dKO.eS.n.merged.bw


title: BMDM, Bmal1-KO, LPS, rep4


title: CBO-MOK20005P-A01, KO

description:
Library name: TBR1_PTC_A01-_GT23-15124_GGCATTCT-CAAGCTAG_S147_L003
KOLF2.2J derived knockout cell line, TBR1 PTC, differentiated to cortical brain organoid


title: T3M-4 cells, DMSO, 16h, bio rep 2


title: MLL34dKO_Naive2_lS


title: T3M-4 cells, DMSO, 16h, bio rep 1


title: MLL34dKO_Naive2_eS


title: NUGC-3 cells, PC14586, 16h, bio rep 3

value: Gastric adenocarcinoma


title: BMDM, Bmal1-KO, LPS + CCM, rep3

value: 100nM LPS/100uM CCM


title: MLL3KO_Form1_lS


title: MLL34dKO_Naive1_lS


title: CBO-MOK20005-WT2, WT

description:
Library name: TBR1_WT2-_GT23-15129_CGTTAGAA-GACCTGAA_S167_L003
KOLF2.2J differentiated to cortical brain organoid


title: T3M-4 cells, PC14586, 16h, bio rep 3


title: CBO-MOK20001-WT2, WT

description:
Library name: DMRTA1_WT_2_GT24-02322_TGGCCGGT-GCGCTCTA_S207_L005
KOLF2.2J differentiated to cortical brain organoid