title: MOLM-13 shDDX6 rep2

city: Badalona

first: Laureano

last: Tomás-Daza

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Raw reads were processed using HiCUP with default parameters
Captured reads were selected using hicup_capture function
Interactions were called using CHiCAGO R package with default parameters
Significant interactions were selected with a CHiCAGO score <= 5
Assembly: GRCh38.p13
Supplementary files format and content: ibed file format containing the coordinates of both end of the interactions together with the annotation, the number of reads and the CHiCAGO score

growth_protocol: MOLM-13 cells were maintained in RPMI 1640 supplemented with 20% fetal bovine serum (FBS), L-glutamine, and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
After fixating the cells, cell lysis and isolation of nuclei, chromatin was restriction-digested, followed by Klenow fill-in and ligation of DNA fragments.DNA ligation products were sheared by sonication, repaired, and immunoprecipitated.
DNA fragments were ligated to adapters, and the products were amplified by PCR.The amplified library was size-selected, enriched for promoter-containing ligation products, and amplied by PCR.

treatment_protocol: DDX6 knockdown was induced by transduction of cells with shRNA-expressing lentivirus.

value: AML

value: DDX6 knockdown


title: mESC, naive pluripotency, WT, rep1

status: Public on Aug 09 2024

type: SRA

city: San Francisco

first: Harold

last: Marin

state: CA

address: 555 Mission Bay Boulevard South

department: Smith Cardiovascular Institute

country: USA

institute: University of California San Francisco

description:
WT_naive_1
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed of the first T overhang using cutadapt (version 2.5) as suggested by Illumina.
Trimmed reads were mapped to the GENCODE primary assembly M30 release of the mouse genome (GRCm39) using STAR (version 2.7.10a): --runMode alignReads --readFilesCommand zcat --clip3pAdapterSeq CTGTCTCTTATA CTGTCTCTTATA --clip3pAdapterMMp 0.1 0.1 --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --twopassMode Basic. Bam files were indexed with SAMtools (version 1.10).
The subread featureCounts package (version 1.6.4) and GENCODE M30 primary annotation file was used to generate a read counts table for all conditions.
The subread featureCounts package was used for obtaining read counts on uniquely mapped transposable elements using a custom annotation file made by the Hammell lab.
For multimapping of RNA-seq reads, as recommended by the TEtranscripts authors, STAR parameters were changed from –outFilterMultimapNmax 1 to the following: –outFilterMultimapNmax 100 --winAnchorMultimapNmax 100. A read counts table was generated using the TEcount command from the TEtranscripts package (version 2.2.3) with the following parameters: --sortByPos --format BAM --mode multi. The GENCODE M30 primary annotation file was used for gene annotations and a custom annotation file from the Hammell lab for transposable elements were used to generate a read counts table.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes raw counts from uniquely-mapped reads in genes for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts from uniquely-mapped reads in transposable elements for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts from multi-mapped reads in genes and transposable elements for each sample.

molecule: total RNA

organism: Mus musculus

source_name: mESC

growth_protocol: Cells were cultured at 5% CO2 and 37°C. mESCs were grown in serum- and feeder-free 2i + LIF medium: N2B27 basal medium supplemented with the following compounds at a final concentration of 3 μM CHIR-99021 (Selleckchem S1263), 1 μM PD0325901 (Selleckchem S1036), 103 U/mL LIF (MilliporeSigma™ ESG1107), 55 μM β-mercaptoethanol (Gibco™ 21985023), and 1X PenStrep (GenClone 25-512). N2B27 medium was made by mixing equal parts of DMEM:F12 (GenClone 25-503) and Neurobasal medium (Gibco™ 21103049) then adding 1X N-2 (Gibco™ 17502001), 1X B-27 (Gibco™ 17504001) and 2 mM Glutamax (Gibco™ 35050061). mESCs were seeded at 2.11 x 104 cells/cm2 on dishes pre-coated with either Geltrex (Gibco™ A1413202) or Cultrex (Bio-Techne 3445-005-01). mESCs were replenished with fresh 2i + LIF medium after 24 hours then collected at 48 hours for RNAseq. EpiLCs were differentiated by seeding 2.11 x 104 cells/cm2 mESCs into either Geltrex or Cultrex coated dishes containing N2B27 media supplemented with 20 ng/mL FGF (Peprotech 100-18B) and 12 ng/mL Activin A (Peprotech 120-14E). EpiLCs were replenished with fresh differentiation medium after 24 hours then collected at 48 hours for RNAseq.

extract_protocol:
Total RNA was isolated from cells using the RNeasy Plus Mini Kit (QIAGEN 74136). RNA was treated with DNAse using the TURBO DNA-free kit (Invitrogen™ AM1907) prior to prepping libraries. RNA quality was assessed by electrophoresis on a 1% agarose gel and detecting 28S and 18S rRNA bands with ethidium bromide staining (0.6µg/mL).
Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina 20040525) was used following the manufacturer’s protocol to prep libraries with a starting RNA input of 500ng. Libraries were amplified using 11 cycles on the thermocycler. Each library was uniquely indexed with IDT for Illumina–DNA/RNA UD Indexes (Illumina 20026121), then pooled together in equimolar amounts. Library concentration was measured using the Qubit dsDNA HS assay kit (Invitrogen Q32851) and Qubit 4 fluorometer. Library size was assayed using the Agilent Bioanalyzer 2100 with the High sensitivity DNA kit.

tag: cell line

value: mESC

tag: cell type

tag: genotype

value: wildtype


title: 2-cell embryo - Dam-H3K9me3(CBX1) - CBABL6F1 homozygous (KIN7553_index10)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID processing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
DamID separating allelic data: For samples derived from hybrid mouse crosses, the DamID reads are aligned in paired-end mode to two reference genomes that have the maternal and paternal SNPs incorporated, respectively. Alignments for each read are then compared and reads are assigned to the parent for which the aligned showed the lowest edit distance and highest alignment score. In case of ties, reads were considered to be ambiguous. During read processing, UMIs are flattened across alleles. In other words, if the same UMI is found at the same GATC position between maternal, paternal and ambiguous alleles, only one count is maintained at the parental allele (in case of finding the UMI at for one parent and ambiguous) or the ambiguous allele (in case of finding the UMI at both parental alleles).
CELseq alignment: CELseq R2 reads are aligned using GRCm38 (v. 89) transcript models and hisat2 (v. 2.1.0) with the following parameters: : “--mp 2,0 --sp 4,0”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
CELseq separating allelic data: For samples derived from hybrid mouse crosses, the CELseq R2 reads are aligned to two reference genomes that have the maternal and paternal SNPs incorporated, respectively. Alignments for each read are then compared and reads are assigned to the parent for which the aligned showed the lowest edit distance and highest alignment score. In case of ties, reads were considered to be ambiguous. During read processing, UMIs are flattened across alleles. In other words, if the same UMI is found for the same gene between maternal, paternal and ambiguous alleles, only one count is maintained at the parental allele (in case of finding the UMI at for one parent and ambiguous) or the ambiguous allele (in case of finding the UMI at both parental alleles).
Assembly: mm10
Supplementary files format and content: CELseq count table: count table containing UMI-unique transcript counts per gene for all single-cell samples; DamID binary contact table: binary table indicating for each sample which of the 100-kb bins had signal above a threshold to indicate that it was in contact with the Dam-fusion protein. DamID count table: count table containing UMI-unique GATC counts per 10-kb/100-kb interval for all single-cell samples; DamID Contact Frequency track: The frequency of single-cell contacts for a particular bin over all cells of that condition (includes both scDamID and scDam&T-seq samples passing DamID thresholds); DamID combined single-cell track: The combined data of all single cells of that condition, normalized for depth and control (includes both scDamID and scDam&T-seq samples passing DamID thresholds); sample annotations: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. CELseq barcodes follow a 3-NNNNNNNN or 3-NNNN-3-NNNN format, where "N" positions indicate the barcode-specific sequence, the "3" indicates positions of a 3nt UMI sequence. DamID barcodes follow a 3-NNNN-3-NNNNGA or 3-NNNNNNGA format. All DamID barcodes end in "GA", complementing the genomic TC of the cleaved GATC motifs.
Library strategy: scDam&T-seq

molecule: genomic DNA

source_name: 2-cell embryo

growth_protocol: For the preimplantation embryos: WT mouse embryos were obtained from either B6CBAF1/JxB6CBAF1/J non-hybrid crosses or hybrid crosses between B6CBAF1/J females and CAST/EiJ males. For Eed maternal KO experiments embryos were obtained by mating Eedfl/fl C57BL/6J (control) with PWK/PhJ males or Eedfl/fl;Gdf9-Cre C57BL/6J (maternal KO) females with JF1/MsJ males. Mouse embryos were obtained from super-ovulated females by administering females with mare serum gonadotropin (PMSG) and human chorionic gonadotropin (HCG) via intraperitoneal injections. HCG was injected 2 days after PMSG and that same day females were mated with a male. The next day zygotes were collected, injected with the relevant Dam construct and cultured ex-vivo in M16 (Sigma, MR-016-D) or KSOM medium (Sigma, MR-106-D) until reaching the stage of collection. Ex-vivo culturing was carried out in an incubator at 37C with 5% CO2. For the mESC: F1 hybrid 129/Sv:Cast/Eij mouse embryonic stem cells (mESCs) were cultured on irradiated primary mouse embryonic fibroblasts (MEFs), in ES cell culture media CM+/+; G-MEM (Gibco) supplemented with 10% FBS (Hyclone, Sigma lot no), 1% Pen/Strep, 1x GlutaMAX (Gibco), 1x non-essential amino acids (Gibco), 1x sodium pyruvate (Gibco), 0.1mM β-mercaptoethanol (Sigma) and 10^3U/ml ESGROmLIF (EMD Millipore ESG1107). Cells were split every 3 days and medium was changed every other day.

extract_protocol:
For the preimplantation embryos: At the time of collection, the zona pellucida was remove using Tyrode's acid (Sigma, T1788-100ML), embryos were washed in M2 medium (Sigma, MR-015-D) and dissociated into single cells by incubating in TryplE (Thermo Fisher, 12605010) for approximately 5 minutes and pipetting up an down with a mouth pipet. Embryos were dissociated one by one and the resulting single cells were placed in M2 medium. They were then transferred to a 384-well plate (one single cell per well) containing 5uL of mineral oil and 100nL of CELseq primer (scDam&T) or 100nL of DamID buffer (0.15% NP40 and 2mM dNTPs) using a mouth pipet. For the mESC: Cells were trypsinized and harvested in medium with 20 μg/mL Hoechst 34580 (Sigma 63493) per 1x10^6 cells for 45 minutes at 37°C. The cells were stained for live/dead gating with 1ug/ml propidium iodide and singlets were index sorted based on their Hoechst profile. One cell per well was sorted into 384-well plates (Biorad, HSP3801) using the BD FACS Jazz cell sorter. Wells contained 5 μL filtered mineral oil (Sigma) and 50nL of 0.5uM unique CELseq primer.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

treatment_protocol: For the mESC: Expression of the Dam-LMNB1 construct was suppressed by addition of 0.5mM indole-3-acetic acid (IAA; Sigma, I5148) during standard culturing. When plated for experiments the cells were passaged 2 times in feeder free conditions on plates coated with 0.1% gelatin in 60% BRL conditioned medium (40% CM+/+ medium and 60% of CM+/+ medium conditioned on Buffalo Rat Liver cells) at 1mM IAA for the final 24 hours before harvesting of the cells. For timed induction of the constructs the IAA is washed out at 6 hours before harvesting single cells for sorting.

tag: tissue

value: 2-cell embryo

tag: dam-fusion protein

value: CBX1 protein domain (3x)

tag: molecule subtypes

value: genomic DNA; mRNA


title: MOLM-13 shCTRL rep1

organism: Homo sapiens

value: WT

tag: treatment

value: shCTRL


title: MOLM-13 shDDX6 rep1


title: mESC - Dam-LMNB1 - 129S1xCAST hybrid (KIN6284_index01)

source_name: ESC

value: ESC

value: 129S1/SvImJ x CAST/Eij


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous & CBABL6F1xCAST hybrid (KIN6284_index04)

value: CBABL6F1; CBABL6F1 x CAST/EiJ


title: 2-cell embryo - Dam-LMNB1 - C57BL6xJF1 hybrid - WT & EEDmKO (KIN6284_index10)

value: C57BL/6J x JF1/Ms:WT & EED mKO


title: zygote & 2-cell embryo - Dam-LMNB1 - CBABL6F1xCAST hybrid (KIN7553_index09)

source_name: zygote; 2-cell embryo

value: zygote; 2-cell embryo

value: CBABL6F1 x CAST/EiJ


title: MOLM-13 shCTRL rep2


title: 8-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN4223_index08)

source_name: 8-cell embryo

value: 8-cell embryo


title: zygote & 8-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN4612_index02)

source_name: zygote; 8-cell embryo

value: zygote; 8-cell embryo


title: EpiLC, primed pluripotency, WT, rep3

description:
WT_epi_3
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt

source_name: EpiLC

value: EpiLC


title: mESC, naive pluripotency, WT, rep3

description:
WT_naive_3
RNAseq_epilc_counts_genes.txt
RNAseq_epilc_counts_TE_unique.txt
RNAseq_epilc_counts_genes_and_TE_multimapped.txt


title: 2-cell embryo - Dam-LMNB1 - C57BL6xJF1 hybrid - WT & EEDmKO (KIN6777_index12)


title: 8-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3845_index04)


title: zygote - Dam-LMNB1 - CBABL6F1 homozygous (KIN3934_index05)

source_name: zygote

value: zygote


title: zygote - Dam-LMNB1 - CBABL6F1 homozygous (KIN4951_index04)


title: 8-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3845_index03)


title: 8-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3620_index10)


title: 2-cell embryo - Dam-only - CBABL6F1 homozygous (KIN7167_index27)

value: untethered Dam


title: 2-cell embryo - Dam-H3K27me3(2E12) - CBABL6F1 homozygous (KIN3600_index21)

value: anti-H3K27me3 (2E12 mintbody)


title: 8-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3620_index09)


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3600_index20)

value: 2-cell embryo


title: Sample1

city: London

first: Tallulah

middle: Suzanne

last: Andrews

state: Ontario

address: 1151 Richmond St.

country: Canada

institute: University of Western Ontario

description: 10X Chromium 3' scRNAseq

library_source: transcriptomic single cell

data_processing:
reads were mapped to human and mouse genomes using STARsolo
Cells were filtered based on reads aligning to the human genome using for >500 genes/cell and >875 UMI/cell and < 10% mitochondrial expression resulting in 1746 unique cells detected based on human gene expression
Cells were filtered for significant mouse expression by exclusively reads aligning to mouse transcripts where > 1000 mouse genes were detected, and < 5% of mouse RNA was mitochondrial in origin.
The data was normalized using Seurat’s “LogNormalize” method. Data was scaled then PCA analysis was performed using the top 2,000 highly variable genes  (after excluding mitochondrial transcripts) followed by UMAP analysis on the top 10 principal components Clustering with Seurat’s Louvain method, resolution = 0. (human), or resolution = 0.8 (mouse)
Assembly: GRCh38 (human), GRCm39 (mouse)
Supplementary files format and content: Processed_Human_metadata.csv : final metadata with clusters, annotation, and UMAP coordinates
Supplementary files format and content: Processed_Mouse_metadata.csv : final metadata with clusters, annotation, and UMAP coordinates
Supplementary files format and content: hPSC_Macs_STARsolo_GRCh38_barcodes.tsv.gz : barcode label file for human filtered count matrix from STARsolo
Supplementary files format and content: hPSC_Macs_STARsolo_GRCh38_features.tsv.gz : gene label file for human filtered count matrix from STARsolo
Supplementary files format and content: hPSC_Macs_STARsolo_GRCh38_matrix.mtx.gz : count matrix for human filtered count matrix from STARsolo
Supplementary files format and content: hPSC_Macs_STARsolo_GRCm39_barcodes.tsv.gz : barcode label file for mouse filtered count matrix from STARsolo
Supplementary files format and content: hPSC_Macs_STARsolo_GRCm39_features.tsv.gz : gene label file for mouse filtered count matrix from STARsolo
Supplementary files format and content: hPSC_Macs_STARsolo_GRCm39_matrix.mtx.gz : count matrix for mouse filtered count matrix from STARsolo

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: Liver

extract_protocol:
Engrafted Prim-mac populations were generated from HES2-tdRFP hESCs. At 7 weeks following transplantation into NSG-LSEC mice, the NPC liver cell fractions from two mice were harvested, pooled and sorted (DAPI-RFP+CD45+) using FACS Aria Fusion (BD) at the UHN flow cytometry facility.
A single-cell RNAseq library was prepared at the Princess Margaret Genomics Center in Toronto ON, Canada using 10x Genomics reagents (3 prime, version 3 chemistry) following manufacture recommendations.

treatment_protocol: To generate hPSC-LSEC humanized NSG mice, cryopreserved day 8 VECs (>95% CD34+) were transplanted into adult NSG mice pre-conditioned with monocrotaline (MCT, Sigma-Aldrich) as previously described (Gage et al., 2020). Briefly, on the day of transplantation, the cells were thawed rapidly at 37°C, collected by centrifugation and resuspended in base media for transplantation. Prior to cell delivery (18-24h), adult male and female NSG mice (8–20 week-old) received a 150 mg/kg intraperitoneal injection of MCT, to induce hepatic endothelial damage and make the livers more receptive to the vascular grafts. At VEC transplantation, 1.5 × 106 cells in 40-50uL of base media were injected into the spleen. Following transplantation, mice were transitioned to enrofloxacin (Baytril) for 14 days and endothelial grafts were allowed to expand and mature for 7-8 weeks prior to macrophage transplantation. hPSC-derived Prim-macs (RFP+) were transplanted into NSG-LSEC mice pre-conditioned with 50 µL/mouse clodronate liposomes (CLOD, Liposoma, Cat#C-005-5ml) 2 days prior to transplant, to selectively deplete mouse macrophage populations, and sub-lethal irradiation (220cGy) 1 day prior to transplant. At macrophage transplantation, 2.5-3 × 106 cells in 40-50uL of complete diluted StemPro-34 media were injected into the spleen taking care to avoid injection in the electrocautery scar from the previous hPSC-VEC transplant. Following transplantation, mice were transitioned to enrofloxacin for 14 days and grafts were allowed to expand and mature for 8 days to 7 weeks prior to analysis. For all transplantations, we first optimized clodronate conditioning at increasing doses from 0 µL/mouse to 200 µL/mouse to determine that 50 µL/mouse functionally depleted mouse F4/80+ liver macrophage populations, 2 days following intraperitoneal injection, without inducing mortality, acute toxicity or formation of ascites or macroscopic necrotic liver damage over 14 days. Isoflurane-anesthetized mice received Tramadol and bupivacaine for pain management associated with laparotomy and intrasplenic injection of transplantable populations. After cell infusion over 15 s, local cauterization was applied to the splenic surface to control bleeding. Mice were transitioned to enrofloxacin for the remainder of the experiment.

value: Liver

value: HES2-tdRFP hESC

value: Kupffer cells


title: WT.LPS

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

data_processing:
Bcl2fastq ver 2.0 was used for the base calling
Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation (Macosko et al; 2015), the reads were demultiplexed for the cell barcode and UMI. The genes mapped to mm9 whole genome using STAR genome aligner - with default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts

source_name: Brain

extract_protocol:
FACS‐sorted CD11b+CD45int cells were collected in pre‐cooled HBSS and 0.5% BSA and transferred directly for subsequent Drop‐seq analysis. The cells were stored on ice until the start of the Drop‐seq experiment (tissue harvest to running of Drop‐seq was < 1 h). Prior to cell loading on the Drop‐seq chips, the cell viability was verified and the concentration was adjusted to ~150 cells/μl. This was optimal based on Poissonian statistics to achieve single‐cell encapsulation within each droplet of ~800–900 pl droplet size. All samples analysed in this work had a cell viability > 95%
Single cell RNA seq using Dropseq - 3' bead based enrichment technique, using SMART synthesis (Macosko et al; 2015)

value: Brain

value: microglia

value: PARK7/DJ-1 wild type (WT)

value: LPS


title: zygote - Dam-LMNB1 & 2-cell embryo - Dam-H3K27me3mut(2E12mut) - CBABL6F1 homozygous (KIN2577_index44)

data_processing:
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID processing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
Assembly: mm10
Supplementary files format and content: DamID binary contact table: binary table indicating for each sample which of the 100-kb bins had signal above a threshold to indicate that it was in contact with the Dam-fusion protein. DamID count table: count table containing UMI-unique GATC counts per 10-kb/100-kb interval for all single-cell samples; sample annotations: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. DamID barcodes follow a 3-NNN-3-NNNGA or 3-NNNNNNGA format, where "N" positions indicate the barcode-specific sequence, the "3" indicates positions of a 3nt UMI sequence. All DamID barcodes end in "GA", complementing the genomic TC of the cleaved GATC motifs.

growth_protocol: WT mouse embryos were obtained from either B6CBAF1/JxB6CBAF1/J non-hybrid crosses or hybrid crosses between B6CBAF1/J females and CAST/EiJ males. For Eed maternal KO experiments embryos were obtained by mating Eedfl/fl C57BL/6J (control) with PWK/PhJ males or Eedfl/fl;Gdf9-Cre C57BL/6J (maternal KO) females with JF1/MsJ males. Mouse embryos were obtained from super-ovulated females by administering females with mare serum gonadotropin (PMSG) and human chorionic gonadotropin (HCG) via intraperitoneal injections. HCG was injected 2 days after PMSG and that same day females were mated with a male. The next day zygotes were collected, injected with the relevant Dam construct and cultured ex-vivo in M16 (Sigma, MR-016-D) or KSOM medium (Sigma, MR-106-D) until reaching the stage of collection. Ex-vivo culturing was carried out in an incubator at 37C with 5% CO2.

extract_protocol:
At the time of collection, the zona pellucida was remove using Tyrode's acid (Sigma, T1788-100ML), embryos were washed in M2 medium (Sigma, MR-015-D) and dissociated into single cells by incubating in TryplE (Thermo Fisher, 12605010) for approximately 5 minutes and pipetting up an down with a mouth pipet. Embryos were dissociated one by one and the resulting single cells were placed in M2 medium. They were then transferred to a 384-well plate (one single cell per well) containing 5uL of mineral oil and 100nL of CELseq primer (scDam&T) or 100nL of DamID buffer (0.15% NP40 and 2mM dNTPs) using a mouth pipet.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457, Supplementary Methods: scDamID2).

value: LMNB1; anti-H3K27me3mut (aspecific 2E12 mintbody)


title: KO.LPS

value: PARK7/DJ-1 knock-out (KO)


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3408_index22)

value: genomic DNA; mRNA


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN3408_index23)


title: 2-cell embryo - Dam-LMNB1 - C57BL6xJF1 hybrid - WT & EEDmKO (KIN7437_index09)

value: C57BL/6J x JF1/Ms:WT & EED mKO


title: 2-cell embryo - Dam-LMNB1 & Dam-only - CBABL6F1 homozygous (KIN2477_index04)

value: LMNB1; untethered Dam


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN2477_index02)


title: zygote - Dam-LMNB1 - CBABL6F1xCAST hybrid (KIN6777_index11)

value: CBABL6F1 x CAST/EiJ


title: 2-cell embryo - Dam-LMNB1 & Dam-only - CBABL6F1 homozygous (KIN2477_index03)


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN2477_index01)


title: 2-cell embryo - Dam-H3K27me3(2E12) - CBABL6F1 homozygous (KIN2577_index43)


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN1971_index04)


title: ICR, tumor, NP19_1

city: Birmingham

first: Fengyuan

last: Huang

state: AL

address: University Blvd

department: Genetics

institute: University of Alabama at Birmingh

data_processing:
Sequence reads were mapped to GRCh38 using STAR software (v2.6.1).
Read counts were calculated using HTSeq (v0.11.2) and normalized using Deseq2 (v3.14).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: rectum

extract_protocol:
RNA was extracted using the Allprep kit (Qiagen)
RNA libraries for RNA-seq were prepared using Illumina protocol.

value: rectum

value: Incomplete Response

tag: disease state

value: rectal cancer


title: ICR, tumor, NP17_3


title: 2-cell embryo - Dam-LMNB1 - CBABL6F1 homozygous (KIN1971_index03)

value: 2-cell embryo


title: CR, tumor, NP10_4


title: CR, tumor, NP10_3


title: CR, tumor, NP10_2


title: ICR, tumor, NP17_1


title: CR, tumor, NP10_1


title: CR, tumor, NP20

value: Complete Response


title: ICR, tumor, NP17_2


title: CR, tumor, NP05_1


title: ICR, tumor, NP14


title: CR, tumor, NP05_2


title: 2-cell embryo - Dam-H3K27me3mut(2E12mut) - CBABL6F1 homozygous (KIN2765_index44)

value: anti-H3K27me3mut (aspecific 2E12 mintbody)


title: CR, tumor, NP05_3


title: CR, tumor, NP02


title: CorpusLuteum_E2_S127_1

city: Miles City

first: Carolina

middle: Lucila

last: Gonzalez-Berrios

state: Montana

address: 243 Fort Keogh Road

institute: USDA-ARS

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S127

data_processing:
Sequence reads were trimmed by Zoetis.
Trimmed sequence reads were aligned for respective bovine genome assembly (E1: UMD 3.1 and E2: ARS-UCD 1.2) by Zoetis using CLC Genomics Workbench.
RNA-Seq data were exported to Excel Spreedsheets, organized (R package: dplyr and plyr) and filtered (R package: edgeR) to exclude samples with less than 10 mRNA raw counts.
Use of DESeq2 package in R controlled for potential false discovery using an adjusted p-value and the Benjamini-Hochberg method.
Assembly: Experiment 1: UMD 3.1; Experiment 2: ARS-UCD 1.2
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

organism: Bos taurus

extract_protocol:
RNA was extracted using TRIzol reagent following the manufacturer’s instructions. Remaining DNA was removed by treatment with Qiagen-RNase free DNase and -RNAeasy MinElute Cleanup Kit 50.
Total RNA from tissues were shipped to be processed by Zoetis Inc. (Kalamazoo, MI, USA) for  construction of cDNA libraries using Illumina’s TruSeq Stranded mRNA Library Prep Kit.
For experiment 1, there were 100 bp paired-end reads. For experiment 2, there were 75 bp single-end reads.

value: CorpusLuteum

tag: group

value: Normal

tag: time


title: CorpusLuteum_E2_S128_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S128

value: Non-Pregnant


title: CorpusLuteum_E2_S129_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S129


title: CorpusLuteum_E2_S125_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S125

value: Embryo Mortality


title: CorpusLuteum_E2_S123_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S123


title: CorpusLuteum_E2_S126_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S126


title: CorpusLuteum_E2_S124_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S124


title: CorpusLuteum_E2_S122_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S122


title: ICR, tumor, NP19_2


title: CorpusLuteum_E2_S120_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S120


title: CorpusLuteum_E2_S119_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S119


title: CorpusLuteum_E2_S121_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S121


title: CorpusLuteum_E2_S115_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S115


title: CorpusLuteum_E2_S118_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S118


title: CorpusLuteum_E2_S117_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S117


title: CorpusLuteum_E2_S114_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S114


title: CorpusLuteum_E2_S111_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S111


title: CorpusLuteum_E2_S113_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S113


title: PeripheralBloodMononuclearCells_E2_S107_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S107

value: PeripheralBloodMononuclearCells


title: CorpusLuteum_E2_S110_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S110


title: CorpusLuteum_E2_S109_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S109


title: CorpusLuteum_E2_S108_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S108


title: PeripheralBloodMononuclearCells_E2_S105_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S105


title: PeripheralBloodMononuclearCells_E2_S106_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S106


title: PeripheralBloodMononuclearCells_E2_S102_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S102


title: PeripheralBloodMononuclearCells_E2_S103_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S103


title: PeripheralBloodMononuclearCells_E2_S100_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S100


title: PeripheralBloodMononuclearCells_E2_S98_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S98


title: PeripheralBloodMononuclearCells_E2_S97_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S97


title: PeripheralBloodMononuclearCells_E2_S101_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S101


title: CorpusLuteum_E2_S116_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S116


title: PeripheralBloodMononuclearCells_E2_S93_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S93


title: PeripheralBloodMononuclearCells_E2_S94_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S94


title: PeripheralBloodMononuclearCells_E2_S90_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S90

value: EM


title: PeripheralBloodMononuclearCells_E2_S92_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S92


title: PeripheralBloodMononuclearCells_E2_S91_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S91


title: CorpusLuteum_E2_S112_1

description:
CorpusLuteum_E2_UCD1.2_RNA-seq_Counts
CorpusLuteum_E2_S112


title: PeripheralBloodMononuclearCells_E2_S89_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S89


title: PeripheralBloodMononuclearCells_E2_S87_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S87


title: Endometrium_E2_S85_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S85

value: Endometrium


title: PeripheralBloodMononuclearCells_E2_S88_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S88


title: PeripheralBloodMononuclearCells_E2_S104_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S104


title: PeripheralBloodMononuclearCells_E2_S86_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S86


title: Endometrium_E2_S82_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S82


title: Endometrium_E2_S80_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S80


title: Endometrium_E2_S84_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S84


title: PeripheralBloodMononuclearCells_E2_S99_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S99


title: Endometrium_E2_S81_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S81


title: Endometrium_E2_S83_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S83


title: Endometrium_E2_S79_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S79


title: Endometrium_E2_S77_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S77


title: Endometrium_E2_S78_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S78


title: PeripheralBloodMononuclearCells_E2_S96_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S96


title: Endometrium_E2_S76_1


title: Endometrium_E2_S74_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S74


title: Endometrium_E2_S72_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S72


title: Endometrium_E2_S75_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S75


title: PeripheralBloodMononuclearCells_E2_S95_1

description:
PeripheralBloodMononuclearCells_E2_UCD1.2_RNA-seq_Counts
PeripheralBloodMononuclearCells_E2_S95


title: Endometrium_E2_S68_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S68


title: Endometrium_E2_S73_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S73


title: Endometrium_E2_S67_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S67


title: Endometrium_E2_S65_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S65


title: Endometrium_E2_S70_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S70


title: Conceptus_E2_S62_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S62

value: Conceptus


title: Endometrium_E2_S66_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S66


title: Endometrium_E2_S71_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S71


title: Conceptus_E2_S61_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S61


title: Endometrium_E2_S64_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S64


title: Conceptus_E2_S57_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S57


title: Conceptus_E2_S54_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S54


title: Conceptus_E2_S55_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S55


title: Conceptus_E2_S60_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S60


title: Conceptus_E2_S63_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S63


title: Conceptus_E2_S51_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S51


title: Conceptus_E2_S52_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S52


title: Conceptus_E2_S53_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S53


title: Conceptus_E2_S59_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S59


title: Conceptus_E2_S56_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S56


title: Conceptus_E2_S50_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S50


title: Endometrium_E2_S69_1

description:
Endometrium_E2_UCD1.2_RNA-seq_Counts
Endometrium_E2_S69


title: PeripheralBloodMononuclearCells_E1_S47_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S47


title: Conceptus_E2_S49_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S49


title: PeripheralBloodMononuclearCells_E1_S45_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S45


title: PeripheralBloodMononuclearCells_E1_S43_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S43


title: PeripheralBloodMononuclearCells_E1_S44_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S44


title: PeripheralBloodMononuclearCells_E1_S42_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S42


title: PeripheralBloodMononuclearCells_E1_S46_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S46


title: PeripheralBloodMononuclearCells_E1_S41_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S41


title: PeripheralBloodMononuclearCells_E1_S48_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S48


title: Conceptus_E2_S58_1

description:
Conceptus_E2_UCD1.2_RNA-seq_Counts
Conceptus_E2_S58


title: PeripheralBloodMononuclearCells_E1_S38_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S38


title: PeripheralBloodMononuclearCells_E1_S39_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S39


title: PeripheralBloodMononuclearCells_E1_S36_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S36


title: PeripheralBloodMononuclearCells_E1_S37_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S37


title: PeripheralBloodMononuclearCells_E1_S35_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S35


title: Endometrium_E1_S29_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S29


title: Endometrium_E1_S31_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S31


title: Endometrium_E1_S32_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S32


title: Endometrium_E1_S30_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S30


title: Endometrium_E1_S20_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S20


title: Endometrium_E1_S27_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S27


title: Endometrium_E1_S33_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S33


title: Endometrium_E1_S24_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S24


title: Endometrium_E1_S25_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S25


title: PeripheralBloodMononuclearCells_E1_S34_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S34


title: Endometrium_E1_S26_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S26


title: Endometrium_E1_S28_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S28


title: Endometrium_E1_S21_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S21


title: Endometrium_E1_S17_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S17


title: Endometrium_E1_S19_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S19


title: Endometrium_E1_S16_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S16


title: Conceptus_E1_S9_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S9


title: Conceptus_E1_S10_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S10


title: Endometrium_E1_S14_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S14


title: Conceptus_E1_S8_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S8


title: Endometrium_E1_S13_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S13


title: PeripheralBloodMononuclearCells_E1_S40_1

description:
PeripheralBloodMononuclearCells_E1_UMD3.1_RNA-seq_Counts
PeripheralBloodMononuclearCells_E1_S40


title: Conceptus_E1_S12_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S12


title: Endometrium_E1_S15_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S15


title: Conceptus_E1_S11_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S11


title: Conceptus_E1_S7_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S7


title: Endometrium_E1_S22_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S22


title: Endometrium_E1_S23_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S23


title: Endometrium_E1_S18_1

description:
Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S18


title: Conceptus_E1_EM_S3_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S3


title: Conceptus_E1_EM_S2_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S2


title: Conceptus_E1_S1_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S1


title: MSC, day 1, hairpin inhibitor miR-199b-5p, sample 1

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

data_processing:
Kallisto was used for alignment free RNAseq processing. Tximport was used to import the RNAseq data into R for further processing
Differential gene expression was called using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of TPM values from Kallisto

source_name: mesenchymal stem cells

growth_protocol: Human bone marrow MSCs (from seven donors, 18–25 years of age) were isolated from human bone marrow mononuclear cells (Lonza Biosciences, Berkshire, U.K.) by adherence for more than 24 hours to tissue culture plastic. MSCs were monolayer cultured in mesenchymal stem cell growth medium (Lonza Biosciences) supplemented with 5 ng/ml fibroblast growth factor-2 (R&D Systems, Abingdon, U.K.). Cultures were maintained in a humid atmosphere of 5% CO2/95% air at 37°C. For differentiation to chondrocytes (chondrogenesis) MSCs were re-suspended in chondrogenic culture medium consisting of high-glucose DMEM containing 100 µg/ml sodium pyruvate, 10 ng/ml TGFβ3, 100 nM dexamethasone, 1× ITS-1 premix, 40 µg/ml proline and 25 µg/ml ascorbate-2-phosphate pipetted into 15ml falcon tubes and then centrifuged at 500 g for 5 min and cultured as above.

extract_protocol:
RNA was isolated using the mirVana miRNA Isolation Kit Phenol (Life Technologies) using a small disposable plastic pestle and an aliquot of Molecular Grinding Resin (G-Biosciences/Genotech), as per the manufacturers instructions.
RNA was quality assessed with the Agilent Technology 4200 TapeStation system using an RNA screentape assay (Agilent). cDNA libraries were generated using the Illumina TruSeq Stranded mRNA protocol, combinatorial dual index adapters were used to multiplex/pool libraries. Single-read sequencing, 76 cycles (75+1 cycle for index sequences), on an Illumina NextSeq500 instrument using a high-output 75 cycle kit.

treatment_protocol: For modulation of miR-199 levels in MSC, Dharmacon miRIDIAN mimics (C-300607) or miRIDIAN hairpin inhibitors (IH-300607) were transfected into 40%–50% confluent MSC using Dharmafect 1 lipid reagent (Horizon Discovery) at 100 nM final concentration. Analysis was performed in comparison with Dharmacon miRIDIAN miRNA mimic nontargeting Control #2 (CN-002000-01) or Dharmacon miRIDIAN miRNA hairpin inhibitor nontargeting Control #2 (IN-002005-01). For all experiments, cells were subject to a single transfection prior to induction of MSC differentiation.

value: mesenchymal stem cells

value: miR-199b-5p inhibited

tag: time point

value: day 1


title: MSC, day 1, hairpin inhibitor miR-199b-5p, sample 3


title: MSC, day 1, hairpin inhibitor miR-199b-5p, sample 2


title: MSC, day 1, hairpin control, sample 3

value: WT

value: hp-control


title: Conceptus_E1_S6_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S6


title: Conceptus_E1_EM_S4_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S4


title: MSC, day 1, hairpin inhibitor miR-199a-5p, sample 3

value: miR-199a-5p inhibited


title: Conceptus_E1_EM_S5_1

description:
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S5


title: MSC, day 1, hairpin inhibitor miR-199a-5p, sample 2


title: Tamoxifen, replicate 1, RNA-seq

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

description: miR-1 KO

data_processing:
Read sequences in fastq format were aligned to the mouse genome (mm10).
Assembly: mm10
Supplementary files format and content: Text document read counts.

source_name: gastrocnemius muscle

extract_protocol:
Gastrocnemius muscles were homogenized, and total RNA was isolated using a Zymo Direct-zol RNA Miniprep kit
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 ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: gastrocnemius muscle

value: HSA-MCM; miR-1-1f/f; miR-1-2f/f

value: Tamoxifen


title: Tamoxifen, replicate 4, RNA-seq

description: miR-1 KO


title: Vehicle, replicate 4, RNA-seq

description: WT

value: Vehicle


title: MSC, day 0, hairpin inhibitor miR-199b-5p, sample 1

value: day 0


title: MSC, day 1, hairpin control, sample 2


title: MSC, day 1, hairpin control, sample 1


title: Tamoxifen, replicate 2, RNA-seq

description: miR-1 KO


title: Tamoxifen, replicate 3, RNA-seq

description: miR-1 KO


title: MSC, day 0, hairpin inhibitor miR-199b-5p, sample 3


title: Vehicle, replicate 2, RNA-seq

description: WT


title: MSC, day 0, hairpin inhibitor miR-199b-5p, sample 2


title: Vehicle, replicate 3, RNA-seq

description: WT


title: MSC, day 0, hairpin inhibitor miR-199a-5p, sample 3


title: MSC, day 0, hairpin inhibitor miR-199a-5p, sample 2


title: Vehicle, replicate 1, RNA-seq

description: WT


title: MSC, day 0, hairpin inhibitor miR-199a-5p, sample 1


title: Sample2_VDJ

city: Canberra

first: Xin

last: Gao

state: ACT

address: 131 Garran Rd

department: Immunology

country: Australia

institute: The Australian National University

description: 10X Genomics

data_processing:
Cellranger software
Assembly: mm10
Supplementary files format and content: Default outputs from Cellranger
Library strategy: scVDJ-seq

source_name: Spleen

extract_protocol:
Splenocytes were incubated with antibody cocktail (including Hashtag antibodies), and Tfh cells were FACS-purified. After counting, Tfh cells were pooled, resuspend in sorting buffer (2% FBS in DPBS), and loaded onto the 10X Chromium.
Library construction was performed according to manufacturer's instruction (10X Genomics)

value: Spleen

value: Primary cell

value: Tfh (CD4+CD44+PD-1+CXCR5+)

tag: library type

value: VDJ


title: MSC, day 1, hairpin inhibitor miR-199a-5p, sample 1


title: MSC, day 0, hairpin control, sample 3


title: Sample2_Antibody_Capture

description: 10X Genomics

data_processing:
Cellranger software
Assembly: mm10
Supplementary files format and content: Default outputs from Cellranger
Library strategy: scADT-seq

value: ADT


title: MSC, day 0, hairpin control, sample 1


title: Unfertilized Ovule biological rep 1

city: Irapuato

first: Charles

middle: Stewart

last: Gillmor

state: Guanajuato

address: Libramiento Norte Carretera Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: CINVESTAV

description:
ov.CC.BR1
processed data file:
total.reads.tsv

data_processing:
Diploid genome and annotations were generated using the variants called with freebayes v1.0.0 (Garrison and Marth, 2012) from raw Tsu-1 sequencing data (Warthmann et al., 2008), TAIR10 assembly and Araport 11 annotation. Variants were filtered to have a minimum phred quality of 20 and a maximum of 0.05 normalized likelihood of being heterozygous
Reads were aligned agains generated diploid genome using STAR V 2.7.0d (Dobin et al., 2013) with parameters: --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 0 --alignIntronMax 900 --alignMatesGapMax 900, for allele-specific expression. For total expression, with parameters: --alignIntronMax 900 --alignMatesGapMax 900 --twopassMode Basic
Reads aligned to variants inside annotated genes were counted using featurecounts V 1.6.0 (Liao et al., 2014) with flags: -p -O –fraction, for allele-specific expression. For total expression with flags: -p -M -O –fraction.
Differential expression analysis was performed using the likelihood ratio test impremented in edgeR (Robinson et al., 2010) on the counts for each accession; the normalization factors and library sizes were calculated using the total variant counts per gene (adding counts for each parent)
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab-delimited file containing either total read count per gene; or estimated maternal fraction and BH-adjusted P values, calculated by edgeR, and reads aligned to variants added across technical and biological replicates.

organism: Arabidopsis thaliana

source_name: Ovule

extract_protocol:
Embryos were manually isolated as in Xiang et al., 2011. Embryos were washed by moving them away form the maternal tissues to a corner of the petri dish and then pipetted along with <5uL intro another petri dish containing 50 mL of the isolating solution.
RNA was extracted using the RNAqueous-Micro kit (Ambion, Catalog# 1927). The mRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750). Illumina mRNA-seq libraries were prepared using the TruSeq RNA kit (Ver 1, rev A).

value: Ovule

tag: Stage

value: Unfertilized

tag: female parent strain

tag: male parent strain


title: Unfertilized Ovule biological rep 2

description:
ov.CC.BR2
processed data file:
total.reads.tsv


title: Sample2_Transcriptomes

description: 10X Genomics

data_processing:
Cellranger software
Assembly: mm10
Supplementary files format and content: Default outputs from Cellranger

value: GEX


title: TRMT1L, TRMT1L gRNA, rep 3, AlkB-treated

city: Santa Cruz

first: Todd

last: Lowe

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

data_processing:
Sequencing adaptors were trimmed from raw reads using cutadapt, v1.18 with the following parameters -m 15 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC. A 7-nt UMI was then removed from the 5' end of reads using umi_tools followed by trimming of 1-nt from the 3'end of reads using cutadapt -u -1. Read counts were generated for small RNA types using tRAX (Holmes et al. biorxiv). Briefly, trimmed reads were mapped to the mature tRNAs of GRCh38/hg38 human genome assembly obtained from GtRNAdb (Lowe and Chan 2016) and the reference genome sequence using Bowtie2 in very-sensitive mode with the following parameters to allow for a maximum of 100 alignments per read: --very-sensitive --ignore-quals --np 5 -k 100. Mapped reads were filtered to retain only the “best mapping” alignments. Raw read counts of tRNAs and other small RNA types were computed using tRNA annotations from GtRNAdb, and annotations from  GENCODE M23 and miRBase v22 (Koomara et al. 2014). Raw read counts were then normalized using DESeq2.
Assembly: Homo Sapiens GRCh38/hg38
Supplementary files format and content: Processed data files include a tab-separated file generated using tRAX (Holmes et al., bioRxiv) that includes the raw, and DESeq2 normalized, coverage and nucleotide frequency values for each Sprinzl base in all detected cytosolic tRNAs.
Library strategy: OTTR-seq

extract_protocol:
RNA was extracted using TRIzol LS reagent (Invitrogen). RNAs were diluted into formamide load buffer, heated to 95°C for 3 minutes, and fractionated on a 10% polyacrylamide, Tris-Borate-EDTA (TBE) gel containing 7M urea. Sybr Gold nucleic acid staining (Invitrogen) was conducted to identify the RNA pattern. For primer extension analysis, 1.5 μg of total RNA was pre-annealed with 5’-32P-labeled oligonucleotide and 5x hybridization buffer (250 mM Tris, pH 8.5, and 300 mM NaCl) in a total volume of 7 μl. The mixture was heated at 95°C for 3 min followed by slow cooling to 42°C. An equal amount of extension mix consisting of avian myeloblastosis virus reverse transcriptase (Promega), 5x AMV buffer and 40 μM dNTPs was added. The mixture was then incubated at 42°C for 1 hour and loaded on 15% 7M urea denaturing polyacrylamide gel. Gels were exposed on a phosphor screen (GE Healthcare) and scanned on a Bio-Rad personal molecular imager followed by analysis using NIH ImageJ software. Primer extension oligonucleotide sequences were previously described (Dewe et al., 2017).
RNA 3’ de-phosphorylation was carried out as previously described (Huppertz et al., 2014) using 500 ng of total RNA from each sample. Briefly, samples were treated with T4 Polynucleotide Kinase (T4PNK; New England Biolabs) in a modified 5x reaction buffer (350 mM Tris-HCl, pH 6.5, 50 mM MgCl2, 5mM dithiothreitol) under low pH conditions in the absence of ATP for 30 mins. AlkB treatment was performed as previously described (Cozen et al. Nat Methods. 2015). OTTR-seq libraries were generated as previously described (Upton et al. 2021). Briefly, total PNK-treated RNA was 3’ tailed using mutant BoMoC RT in buffer containing only ddATP for 90 minutes at 30 ̊C, with the addition of ddGTP for another 30 minutes at 30 ̊C. This was then heat-inactivated at 65 ̊C for 5 minutes, and unincorporated ddATP/ddGTP was hydrolyzed by incubation in 5 mM MgCl2 and 0.5 units of shrimp alkaline phosphatase (rSAP) at 37 ̊C for 15 minutes. 5 mM EGTA was added and incubated at 65 ̊C for 5 minutes to stop this reaction. Reverse transcription was then performed at 37 ̊C for 30 minutes, followed by heat inactivation at 70 ̊C for 5 minutes. The remaining RNA and RNA/DNA hybrids were then degraded using 1 unit of RNase A at 50 ̊C for 10 minutes. cDNA was then cleaned up using a MinElute Reaction CleanUp Kit (Qiagen). To reduce adaptor dimers, cDNA was run on a 9% UREA page gel, and the size range of interest was cut out and eluted into gel extraction buffer (300mM NaCl, 10mM Tris; pH 8.0, 1mM EDTA, 0.25% SDS) and concentrated using EtOH precipitation. Size-selected cDNA was then PCR amplified for 12 cycles using Q5 High-fidelity polymerase (NEB #M0491S). Amplified libraries were then run on a 6% TBE gel, and the size range of interest was extracted to reduce adaptor dimers further. Gel slices were eluted into gel extraction buffer (300mM NaCl, 10mM Tris; pH 8.0, 1mM EDTA) followed by concentration using EtOH precipitation. Final libraries were pooled and sequenced on an Illumina NextSeq 500 150-cycle high-output kit.

treatment_protocol: CRISPR editing was performed using plasmid pX333 (Andrea Ventura, Addgene plasmid # 64073) (Maddalo et al, 2014). The oligonucleotide DNA sequences encoding single guide RNA (sgRNA) targeting TRMT1 and TRMT1L were cloned into px333 using BsmB1 and BbsI (Supplemental Table 3). Plasmids were transfected into human 293T embryonic cells using calcium phosphate transfection. Individual clones were by single-cell depositing into 96-well plates. The presence of CRISPR-induced deletion in either TRMT1 or TRMT1L was detected by PCR amplification and confirmed by Sanger sequencing of PCR products amplified from genomic DNA using primers TRMT1 gPCR F2 and TRMT1 gPCR R6 (Supplemental Table 3).

value: Human embryonic kidney

value: TRMT1L knockout

value: CRISPR gRNA


title: TRMT1L, TRMT1L gRNA, rep 2, AlkB-treated


title: TRMT1L, TRMT1L gRNA, rep 1, AlkB-treated


title: TRMT1, TRMT1 gRNA, rep 3, AlkB-treated

value: TRMT1 knockout


title: Mature Tsu1xCol0 biological rep 1

description:
ma.TC.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv

source_name: Embryo

value: embryo

value: Mature


title: TRMT1, TRMT1 gRNA, rep 2, AlkB-treated


title: Sample1_Antibody_Capture

description: 10X Genomics


title: Sample1_VDJ

description: 10X Genomics


title: Sample1_Transcriptomes

description: 10X Genomics


title: Mature Col0xTsu1 biological rep 2

description:
ma.CT.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv


title: SCR, scramble gRNA, rep 2, AlkB-treated

value: WT


title: TRMT1, TRMT1 gRNA, rep 1, AlkB-treated


title: SCR, scramble gRNA, rep 1, AlkB-treated


title: Mature Col0xTsu1 biological rep 1

description:
ma.CT.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv


title: TRMT1L, TRMT1L gRNA, rep 3


title: TRMT1L, TRMT1L gRNA, rep 2


title: LG1233-OVA_sgUhrf1_2  (biol rep 2)

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

description: RNA

data_processing:
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads with default parameter. Only bases with quality ≥20 and only reads that were ≥20nt after trimming were kept for further analysis.
Reads were mapped to mouse genome reference combining the GRCm38.  STAR software was used to align reads to reference genome. Reads were kept for subsequent analysis if they mapped to a single genomic location. Reads with mappiing quality <20 were excluded. Gene counts were measured using the featureCounts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited and gziped text file, including raw gene counts for each sample

source_name: Tumor

growth_protocol: One million sgNT or sgUhrf1 LG1233-OVA cells were subcutaneously injected into female C57BL/6 mice. Tumor tissues were collected on day 27.

extract_protocol:
Total RNA was extrated using a kit from ZYMO RESEARCH (Direct-zol RNA miniprep, cat. No. R2052) according to the manufacturer’s instructions and dissolved in RNase-free water.
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 ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were sequenced using an Illumina NovaSeq machine and paired-end reads were generated.

treatment_protocol: CRISPR/Cas9 technology was used to generate Uhrf1 knockout stable cell lines.

value: Tumor

value: murine lung cancer

value: Uhrf1 Knockout

value: Knockout


title: Bent Tsu1xCol0 biological rep 1

description:
be.TC.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv

value: Bent


title: TRMT1L, TRMT1L gRNA, rep 1


title: TRMT1, TRMT1 gRNA, rep 3


title: LG1233-OVA_sgUhrf1_3  (biol rep 3)

description: RNA


title: Mature Tsu1xCol0 biological rep 2

description:
ma.TC.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv


title: Bent Tsu1xCol0 biological rep 2

description:
be.TC.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv


title: LG1233-OVA_sgUhrf1_1  (biol rep 1)

description: RNA


title: TRMT1, TRMT1 gRNA, rep 1


title: TRMT1, TRMT1 gRNA, rep 2


title: Bent Col0xTsu1 biological rep 2

description:
be.CT.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv


title: MSC, day 0, hairpin control, sample 2

value: mesenchymal stem cells

value: hp-control

value: day 0


title: LG1233-OVA_sgNT_3  (biol rep 3)

description: RNA

value: Control


title: SCR, scramble gRNA, rep 3, AlkB-treated


title: SCR, scramble gRNA, rep 3


title: LG1233-OVA_sgNT_2  (biol rep 2)

description: RNA


title: SCR, scramble gRNA, rep 2


title: Torpedo Tsu1xCol0 biological rep 2

description:
to.TC.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv

value: Torpedo


title: Bent Col0xTsu1 biological rep 1

description:
Be.CT.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv


title: Torpedo Tsu1xCol0 biological rep 1

description:
to.TC.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv


title: SCR, scramble gRNA, rep 1

value: Human embryonic kidney


title: Microglia, invitro, infected, rep3

city: Hannover

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

country: Germany

institute: Twincore, Centre for Experimental and Clinical Infection Research

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control of the sequenced raw FASTQ-files was performed with FastQC software (version 0.11.9) and mapped to Ensembl mouse genome reference version GRCm38 (mm10) using STAR (version 2.5.4b). Gene abundance was also determined by FeatureCounts. Differential expression analysis was performed using DESeq2 package in R environment (version 1.26.0).
Assembly: mm10
Supplementary files format and content: Matrix table with raw counts for every gene and there corresponding Ensembl ID

growth_protocol: Brains from newborn mice were dissected at day 3 post birth, meninges and blood vessels were removed using a stereomicroscope. Next, the brains were minced and digested with 0.1% trypsin and 0.25% DNAse, single cell suspensions were seeded in pre-coated poly-L-lysine flasks in DMEM with 1% penicillin/streptomycin supplemented with 10% FCS. Medium was changed on day 1 and 5. After 10 days of mixed glial culture, microglia were harvested by shaking the flasks (125 rpm) for 40 min at 37°C. Microglial cells were re-plated at a density of 2.0 x 105 cells per well in 24 well plates.

extract_protocol:
RNA from “input” and RiboTag-IP fractions was extracted using Qiagen RNeasy Mini Kit following manufactures instruction. For cultured microglia, RNA was isolated using Direct-zol RNA Miniprep Plus Kit. RNA quality and concentrations were accessed using Bioanalyzer RNA kit and samples with RIN value >8.0 were selected for further processing.
RNA libraries for RNA-seq were prepared using NEBNext Low input RNA library Prep Kit for Illumina (NEB, E6420) following manufacturer's protocols.

treatment_protocol: Culture microglia were inoculated at a MOI of 0.5 of VSV diluted in DMEM medium for 1 hr at 37°C in 5% CO2. At 8 hr post infection, supernatant was removed and the adhering cells for RNA analyses were then harvested and lysed by TRIzol.

value: Brain

value: Microglia

value: Wild type

value: infected

tag: sample type

value: invitro


title: Torpedo Col0xTsu1 biological rep 2

description:
to.CT.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv

value: embryo


title: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L & ASXL1del lentiviral vectors rep3

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: SA+Ctrl

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using bowtie2 aligner (v2.2.8)
Dupicate reads were removed using picard (v2.2.4)
Bigwig files were generated using macs (v2.1.0) bamCoverage function with --skipNonCoveredRegions  --binSize=1  --normalizeUsing RPKM options
Assembly: hg38
Supplementary files format and content: bigwig file for each sample

source_name: hematopoietic

extract_protocol:
Qiagen DNeasy Blood & Tissue Kit
Illumina Tagment DNA TDE1 Enzyme and Buffer Kit

value: hematopoietic

value: Human iPSC N-2.12-D1-1

value: HSPC


title: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L & ASXL1del followed by NRAS G12D lentiviral vector rep1

description: SA+R

value: SRSF2P95L, ASXL1del1900-1922, NRASG12D


title: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L & ASXL1del followed by NRAS G12D lentiviral vector rep3

description: SA+R


title: Microglia, invitro, infected, rep2


title: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L & ASXL1del lentiviral vectors rep2

description: SA+Ctrl


title: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L & ASXL1del lentiviral vectors rep1

description: SA+Ctrl


title: Microglia, invitro, infected, rep1


title: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D followed by SRSF2 P95L & ASXL1del lentiviral vectors rep3

description: R+SA

value: NRAS G12D, SRSF2P95L, ASXL1del1900-1922


title: Microglia, invitro, mock, rep3

value: mock


title: Torpedo Col0xTsu1 biological rep 1

description:
to.CT.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv


title: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D followed by SRSF2 P95L & ASXL1del lentiviral vectors rep2

description: R+SA


title: Heart Tsu1xCol0 biological rep 2

description:
he.TC.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv

value: Heart


title: Heart Tsu1xCol0 biological rep 1

description:
he.TC.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv


title: Heart Col0xTsu1 biological rep 2

description:
he.CT.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv


title: Microglia, invitro, mock, rep2


title: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D followed by SRSF2 P95L & ASXL1del lentiviral vectors rep1

description: R+SA


title: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L & ASXL1del followed by NRAS G12D lentiviral vector rep2

description: SA+R


title: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D lentiviral vector rep3

description: R+Ctrl

value: NRAS G12D


title: P28 cortical microglia Nanopore Sequencing rep3

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

description:
Methylation_5mC_sites_cov9.bed.gz
Methylation_5hmC_sites_cov9.bed.gz
DMS_Astrocyte_Microglia_5mC_cov9.bed.gz
DMS_Neuron_Microglia_5mC_cov9.bed.gz
DMS_Astrocyte_Microglia_5hmC_cov9.bed.gz
DMS_Neuron_Microglia_5hmC_cov9.bed.gz

data_processing:
The raw signal stored in fast5 files were converted to nucleotide sequence, which were mapped to the mouse reference genome mm10 with the tool megalodon (v 2.4.2). Quality control was performed using the tool, pycoQC (v2.5.2) with the sequencing summary file generated by Megalodon.
Methylated CpG sites were distinguished based on the electronic signal difference and mapping result with the model provided by Remora (v0.1.2). The final output provides the position and quantitative methylation level of each cytosine site for both 5mc and 5hmc modification.
Only CpG sites with average coverage greater than 3 and identified in at least two libraries were used for the following analysis. Methylated sites were defined as CpG sites with methylation levels over 10%. DMSs and DMRs among neurons, astrocytes and microglia were identified with the R package DSS (v2.44.0) with smoothing = T setting.
Only sites with methylation level difference greater than 10% and FDR less than 0.01 were considered as DMSs.
Assembly: mm10

source_name: cortex

extract_protocol:
High molecular weight (HMW) DNA was extracted from isolated cells using the Monarch HMW DNA extraction kit (New England Biolabs, #T3050L) following the manufacturer’s instructions.
The HMW DNA was sheared to 20kb with g-TUBE (Covaris #520079). Library preparation was following Nanopore protocols to attach sequencing adapters to the DNA ends with Ligation Sequencing Kit (Oxford Nanopore Technologies, #SQK-LSK110). One flow cell was applied for each library to ensure an optimal sequencing depth of around 20x coverage at each cytosine and sequenced on PromethION (Steger Hall sequencing core, Virginia Tech).

value: cortex

value: microglia

value: WT

tag: developmental stage


title: P28 cortical microglia Nanopore Sequencing rep2


title: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D lentiviral vector rep2

description: R+Ctrl

tag: cell line


title: LG1233-OVA_sgNT_1  (biol rep 1)

description: RNA

value: Tumor

tag: cell type

value: murine lung cancer

value: Control


title: Microglia, invitro, mock, rep1

value: Brain

value: Microglia

tag: genotype

value: Wild type


title: P28 cortical microglia Nanopore Sequencing rep1

tag: tissue


title: P28 cortical astrocytes Nanopore Sequencing rep3

description:
Methylation_5mC_sites_cov9.bed.gz
Methylation_5hmC_sites_cov9.bed.gz
DMS_Astrocyte_Neuron_5mC_cov9.bed.gz
DMS_Astrocyte_Microglia_5mC_cov9.bed.gz
DMS_Astrocyte_Neuron_5hmC_cov9.bed.gz
DMS_Astrocyte_Microglia_5hmC_cov9.bed.gz

value: astrocyte


title: Microglia, IP, infected, rep3

value: infected

value: IP


title: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D lentiviral vector rep1

description: R+Ctrl

value: hematopoietic

value: Human iPSC N-2.12-D1-1

value: HSPC


title: Heart Col0xTsu1 biological rep 1

description:
he.CT.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv

value: embryo

value: Heart


title: Globular Tsu1xCol0 biological rep 2

description:
gl.TC.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv

value: Globular


title: P28 cortical astrocytes Nanopore Sequencing rep2

value: cortex


title: Globular Tsu1xCol0 biological rep 1

description:
gl.TC.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv


title: GMP_rep3

description:
GMP
salmon_gene_counts_cmp_gmp.csv
salmon_gene_counts_normalized_cmp_gmp.csv

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Sample normalization was carried out using the median-ratio normalization method from DESeq2 R package (v1.30.1)
Assembly: hg38
Supplementary files format and content: comma-delimited csv file includes raw counts for each sample
Supplementary files format and content: comma-delimited csv file includes normalized counts for each sample

source_name: Immunophenotypic GMPs sorted from CB CD34+ cells transduced with NRASG12D followed by SRSF2 P95L and ASXL1del lentiviral vectors rep3

extract_protocol:
RNAeasy kit (Qiagen)
PerkinElmer:NOVA-5138-08 NEXTflex Rapid Directional RNA-Seq Kit

value: Primary CB cells

value: GMP

value: SRSF2P95L, ASXL1del1900-1922, NRASG12D


title: Microglia, IP, infected, rep2


title: Microglia, IP, infected, rep1


title: GMP_rep2

source_name: Immunophenotypic GMPs sorted from CB CD34+ cells transduced with NRASG12D followed by SRSF2 P95L and ASXL1del lentiviral vectors rep2


title: P28 cortical astrocytes Nanopore Sequencing rep1

value: WT


title: Globular Col0xTsu1 biological rep 2

description:
gl.CT.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv


title: GMP_rep1

source_name: Immunophenotypic GMPs sorted from CB CD34+ cells transduced with NRASG12D followed by SRSF2 P95L and ASXL1del lentiviral vectors rep1


title: P28 cortical neurons Nanopore Sequencing rep3

description:
Methylation_5mC_sites_cov9.bed.gz
Methylation_5hmC_sites_cov9.bed.gz
DMS_Astrocyte_Neuron_5mC_cov9.bed.gz
DMS_Neuron_Microglia_5mC_cov9.bed.gz
DMS_Astrocyte_Neuron_5hmC_cov9.bed.gz
DMS_Neuron_Microglia_5hmC_cov9.bed.gz

value: neuron


title: Microglia, IP, mock, rep3

value: Brain

value: Microglia

value: mock


title: Globular Col0xTsu1 biological rep 1

description:
gl.CT.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv
Two technical replicates were produced for this sample. These technical replicates represent independent library preparations from the same RNA extraction. One technical replicates was sequenced with single-end sequencing and one was sequenced with paired-end sequencing.


title: Octant Tsu1xCol0 biological rep 2

description:
oc.TC.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv

value: Octant


title: Microglia, IP, mock, rep2

value: Wild type

value: IP


title: CMP_rep3

description:
CMP
salmon_gene_counts_cmp_gmp.csv
salmon_gene_counts_normalized_cmp_gmp.csv

source_name: Immunophenotypic CMPs sorted from CB CD34+ cells transduced with NRASG12D followed by SRSF2 P95L and ASXL1del lentiviral vectors rep3

value: hematopoietic

value: CMP


title: Microglia, IP, mock, rep1


title: P28 cortical neurons Nanopore Sequencing rep2


title: P28 cortical neurons Nanopore Sequencing rep1


title: CMP_rep1

source_name: Immunophenotypic CMPs sorted from CB CD34+ cells transduced with NRASG12D followed by SRSF2 P95L and ASXL1del lentiviral vectors rep1


title: Microglia, input, infected, rep3

value: infected

value: input


title: SA+R3

description:
SA+R
salmon_gene_counts_ras_early_late.csv
salmon_gene_counts_normalized_ras_early_late.csv

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L and ASXL1del followed by NRAS G12D lentiviral vectors rep3

value: Human iPSC N-2.12-D1-1

value: HSPC


title: Octant Col0xTsu1 biological rep 2

description:
oc.CT.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv

value: embryo


title: Microglia, input, infected, rep2


title: KLR_2

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

data_processing:
Reads were aligned to the mm10 genome with salmon v1.10.0, and differential gene expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: txImport_processed.txt: raw and tpm counts of gene/sample

growth_protocol: Spleens from 4 mice bearing KP.SIY flank tumors were harvested 14 days after tumor inoculation.

extract_protocol:
CXCR3+CX3CR1+ and CXCR3+CX3CR1- SIY-reactive CD8+ T cells were FACS-sorted directly into TRIzol reagent and RNA was isolated using a TRIzol-cholorform extraction.
The RNA-containing aqueous layer was collected and purified using the RNeasy MinElute Cleanup Kit (QIAGEN) following manufacturer’s instructions and submitted to the KI Genomics Core / MIT BioMicro Center for RNA library preparation (Clonetech ZapR) and sequencing (Illumina NextSeq500).

treatment_protocol: CD8+ T cells were isolated and enriched using the Miltenyi CD8+ T cell isolation kit and prepared for FACs as described above.

value: Spleen

value: CD8+ T cell


title: Microglia, input, infected, rep1


title: Octant Col0xTsu1 biological rep 1

description:
oc.CT.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv


title: KLR_3


title: INT_4

value: Intermediate


title: SA+R1

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L and ASXL1del followed by NRAS G12D lentiviral vectors rep1

value: SRSF2P95L, ASXL1del1900-1922, NRASG12D


title: Zygote Tsu1xCol0 biological rep 1

description:
zy.TC.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv

value: zygote


title: SA+R2

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L and ASXL1del followed by NRAS G12D lentiviral vectors rep2


title: Microglia, input, mock, rep3

source_name: Brain

value: Brain

value: Microglia


title: SA+Ctrl3

description:
SA+Ctrl
salmon_gene_counts_ras_early_late.csv
salmon_gene_counts_normalized_ras_early_late.csv

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L and ASXL1del lentiviral vectors rep3


title: KLR_1


title: INT_3


title: Zygote Tsu1xCol0 biological rep 2

description:
zy.TC.BR2
processed data file:
total.reads.tsv
parental.contributions.tsv


title: CMP_rep2

source_name: Immunophenotypic CMPs sorted from CB CD34+ cells transduced with NRASG12D followed by SRSF2 P95L and ASXL1del lentiviral vectors rep2

value: Primary CB cells


title: Zygote Col0xTsu1 biological rep 1

description:
zy.CT.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv
Three technical replicates were produced for this sample. These technical replicates represent independent library preparations from the same RNA extraction. Two technical replicates were sequenced with single-end sequencing and one was sequenced with paired-end sequencing.


title: Octant Tsu1xCol0 biological rep 1

description:
oc.TC.BR1
processed data file:
total.reads.tsv
parental.contributions.tsv

value: Octant


title: SA+Ctrl2

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L and ASXL1del lentiviral vectors rep2


title: SA+Ctrl1

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with SRSF2 P95L and ASXL1del lentiviral vectors rep1


title: INT_2

source_name: Spleen


title: Microglia, input, mock, rep1

value: Wild type

value: mock


title: INT_1


title: R+SA3

description:
R+SA
salmon_gene_counts_ras_early_late.csv
salmon_gene_counts_normalized_ras_early_late.csv

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D followed by SRSF2 P95L and ASXL1del lentiviral vectors rep3

value: hematopoietic

value: NRAS G12D, SRSF2P95L, ASXL1del1900-1922


title: F4/80 pos HSCs rep3

city: Madison

last: GAO

state: WI

address: 1111 Highland Ave

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

description: Pos 7

data_processing:
Reads were aligned and mapped to the mouse genome using the program HISAT2 v.2.0.5. Fragments Per Kilobase of transcript sequence per Millions base pairs sequence (FPKM) was calculated to adjust for sequencing depth and gene length on raw counts
Assembly: Mus Musculus(GRCm39/mm39)
Supplementary files format and content: Xin Gao F480 PositivevsNegative_deg (xls format) contains normalised read counts, read counts and all statistical results by DESeq2 R package

source_name: bone marrow

extract_protocol:
Total RNA from 2000 to 5000 sorted HSCs was extracted using the RNAeasy Plus Micro kit (Qiagen), and assessed for integrity and quantity using an Aligent 2100 Bioanalyzer (Agilent Technologies).
SmarterStranded V4 Library Prep

value: bone marrow

value: F4/80 positive

value: HSC

value: WT


title: F4/80 pos HSCs rep2

description: Pos 5


title: F4/80 pos HSCs rep1

description: Pos 4


title: R+SA2

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D followed by SRSF2 P95L and ASXL1del lentiviral vectors rep2

value: Human iPSC N-2.12-D1-1

value: HSPC


title: R+SA1

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D followed by SRSF2 P95L and ASXL1del lentiviral vectors rep1


title: F4/80 neg HSCs rep3

description: Neg 7

value: F4/80 negative


title: F4/80 neg HSCs rep2

description: Neg 5


title: Microglia, input, mock, rep2

value: input


title: F4/80 neg HSCs rep1

description: Neg 4


title: p300_ChIP_LPS2h_Rep2

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description:
BMDM_ChIP_p300_AllTFmerged.txt
BMDM_ChIP_p300_ATACmerged.txt

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
For p300, SREBP and LXR ChIP-seq experiments peaks were called with HOMER for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Only peaks with > 16 normalized tags (normalized to total tags of 1e7) were kept. Overlapping peak sets were determined using mergePeaks command. The pooled tag directory from two replicates was used for track visualization. To annotate p300 signal in ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 200 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential p300 signal > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For H3K27ac analysis: To annotate H3K27ac signal around ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 1000 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal or chromatin accessibility with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For p65 and ATAC-Seq analysis of data from GSE79423 and GSE109965 respectively: Relevant raw FASTQ files were mapped to mm10 genome with Bowtie2 with default parameters (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010). For p65 peaks were called with HOMER findPeaks for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Peak files across various timepoints for vehicle and KLA treated timepoints were merged using HOMER mergePeaks. Merged peaks were annotated for H3K27ac and p300 signal as indicated. For ATAC-Seq, mm10 mapped, IDR defined peaks from GSE109965, for both vehicle and KLA treatment conditions, were used. Peaks were merged using HOMER mergePeaks, then merged peak file was used for further analysis as indicated in text.
To identify motifs enriched in peak regions over the background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. The background sequences were either from random genome sequences or from peaks from the comparing condition indicated in the main text and in the figure legends.
Assembly: mm10
Supplementary files format and content: Processed files include peak text files (ChIP-Seq, ATAC, and H3K27Ac peak or region data, using default HOMER parameters). Peak or region files BMDM_ChIP_p300_AllTFmerged.txt and BMDM_ChIP_H3K27Ac_AllTFmerged.txt are summed transcription factor peak files annotated with normalized tag counts from either p300 or H3K27Ac ChIP-seq data as indicated. Peak files BMDM_ChIP_p300_ATACmerged.txt and BMDM_ChIP_H3K27Ac_ATACmerged.txt are summed ATAC-Seq peak files annotated with normalized tag counts from either p300 or H3K27Ac ChIP-seq data. Peak annotation, with p300 and H3K27Ac tag directories, was done using HOMER annotatePeaks command, with option -size 200 or -size 1000, respectively. All genomic coordinates are relative to mm10 mouse assembly.

source_name: Bone Marrow Derived Macrophages

growth_protocol: Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

extract_protocol:
For H3K27ac ChIP-seq, culture media was removed and plates were washed once with PBS and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For p300, LXR and SREBP ChIP-seq, cells were crosslinked with 3mM DSG (ProteoChem) in PBS for 30 minutes at room temperature, and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then pelleted at 700 X G for 5 minutes at 4°C. Crosslinked cells were stored at –80°C until ready for ChIP-seq library preparation. Fixed cells were thawed on ice, resuspended in either ice-cold LB3 (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail, 1mM Na-Butyrate, for H3K27ac ChIP) or ice-cold RIPA-NR lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% Na-Deoxycholate, 0.1% SDS, 1% NP-40, 1x protease inhibitors, for p300, LXR, and SREBP ChIP). Frozen crosslinked nuclei were resuspended in wash buffer (10mM HEPES/KOH pH7.9, 85mM KCl, 1mM EDTA, 0.2% IGEPAL CA-630, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) for 5minutes on ice. Cells were spun down and then resuspended in RIPA-NR lysis buffer. Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles (samples in LB3) or 18 cycles (samples in RIPA-NR buffer) with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The LB3 lysate was diluted 1.1-fold with ice-cold 10% Triton X-100 after sonication. One percent of the lysate was kept as ChIP input. For each immunoprecipitation, aliquots of diluted lysate equivalent to 500,000 cells (for H3K27ac ChIP) or 1-2 million cells  (for p300, SREBP ChIP), 20 µl of Dynabeads Protein A (for rabbit polyclonal antibodies) or Dynabeads protein A/G (for p300, LXR, and SREBP ChIP) bound to specific antibodies for H3K27ac (2 μg, Active Motif, 39133), p300 (2 μg, Millipore, cat# 05-257,Diagenode, cat# C15200211), LXR (Santa Cruz Biotechnology: sc-1000X, sc- 133221X, sc-271064X) , and SREBP (2 μg, Santa Cruz Biotechnology: sc-8984X, Thermo Fisher Scientific: PA1-337, R&D Systems: AF7119) were combined and rotated overnight at 4°C. For H3K27ac ChIP, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA) and twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20). For p300, LXR and SREBP ChIP, beads were washed three times with RIPA-NR buffer (20 mM Tris-HCl/pH7.5, 150 mM NaCl, 0.1% SDS, 1% NP-40, 0.4 % Na-Deoxycholate, 1 mM EDTA, 0.5mM EGTA, 0.5mM DTT), six times with RIPA-LiCl buffer (10 mM Tris-HCl/pH 7.5, 250 mM LiCl, 1% NP-40, 0.7% Na-Deoxycholate, 1 mM EDTA), three times with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), and one time with IDTE (10mM Tris-HCl pH 8.0, 0.1mM EDTA). Bead complexes were resuspended in 25 μl TT (10 mM Tris/HCl pH 8.0, 0.05% Tween-20, 1x protease inhibitor cocktail) and sequencing libraries were prepared on-bead as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit with reaction volumes reduced by half, essentially as previously described (Heinz et al., 2018). Libraries were eluted and crosslinks reversed by adding to the 46.5 μl NEB reaction 20 μl water, 4 μl 10% SDS, 4.5 μl 5M NaCl, 3 μl 0.5 M EDTA, and 1 μl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 65C for 30 minutes to overnight in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries cleaned by adding 2 μl SpeedBeads 3 EDAC in 61 μl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 μl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 25 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 50 μl reaction volume using NEBNext Ultra II PCR master mix and 0.5 μM each Solexa 1GA and Solexa 1GB primers. Libraries were cleaned up with SpeedBeads as above using 36.5 μl 20% PEG 8000/1.5 M NaCl and 2 μl SpeedBeads. After ethanol washing and drying, PCR amplified libraries were eluted from the SpeedBeads using 20 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween- 20. Next, libraries were size selected 250-500 bp using gel extraction using 10% TBE acrylamide gels. Libraries were single-end sequenced using either a HiSeq 4000 or a NextSeq 500 to a depth of 10-20 million reads.

treatment_protocol: The following day after replating BMDMs, fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with or without 100 µg/ml 3'SL , with 10 ng/ml of LPS for 1 – 24 hours as indicated. For LXR and SREBP experiments cells were treated with 1uM GW3965.

value: Bone Marrow Derived Macrophages

value: LPS 2h


title: R+Ctrl2

description:
R+Ctrl
salmon_gene_counts_ras_early_late.csv
salmon_gene_counts_normalized_ras_early_late.csv

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D lentiviral vector rep2

value: NRAS G12D


title: p300_ChIP_PBS6_Rep2

value: PBS


title: p300_ChIP_3SL_LPS6h_Rep2

value: 3'SL_LPS 6h


title: p300_ChIP_PBS2_Rep2


title: mESC, naive pluripotency, QKO, rep4

city: San Francisco

first: Harold

last: Marin

address: 555 Mission Bay Boulevard South

institute: University of California San Francisco

description:
QKO_4
RNAseq_shLBR_counts_genes.txt
RNAseq_shLBR_counts_TE_unique.txt
RNAseq_shLBR_counts_genes_and_TE_multimapped.txt

data_processing:
Reads were mapped to the GENCODE primary assembly M30 release of the mouse genome (GRCm39) using STAR (version 2.7.10a): --runMode alignReads --readFilesCommand zcat --clip3pAdapterSeq CTGTCTCTTATA CTGTCTCTTATA --clip3pAdapterMMp 0.1 0.1 --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --twopassMode Basic. Bam files were indexed with SAMtools (version 1.10).
The subread featureCounts package (version 1.6.4) and GENCODE M30 primary annotation file was used to generate a read counts table for all conditions.
The subread featureCounts package was used for obtaining read counts on uniquely mapped transposable elements using a custom annotation file made by the Hammell lab.
For multimapping of RNA-seq reads, as recommended by the TEtranscripts authors, STAR parameters were changed from –outFilterMultimapNmax 1 to the following: –outFilterMultimapNmax 100 --winAnchorMultimapNmax 100. A read counts table was generated using the TEcount command from the TEtranscripts package (version 2.2.3) with the following parameters: --sortByPos --format BAM --mode multi. The GENCODE M30 primary annotation file was used for gene annotations and a custom annotation file from the Hammell lab for transposable elements were used to generate a read counts table.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes raw counts from uniquely-mapped reads in genes for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts from uniquely-mapped reads in transposable elements for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts from multi-mapped reads in genes and transposable elements for each sample.

source_name: mESC

growth_protocol: Cells were cultured at 5% CO2 and 37°C. mESCs were grown in serum- and feeder-free 2i + LIF medium: N2B27 basal medium supplemented with the following compounds at a final concentration of 3 μM CHIR-99021 (Selleckchem S1263), 1 μM PD0325901 (Selleckchem S1036), 103 U/mL LIF (MilliporeSigma™ ESG1107), 55 μM β-mercaptoethanol (Gibco™ 21985023), and 1X PenStrep (GenClone 25-512). N2B27 medium was made by mixing equal parts of DMEM:F12 (GenClone 25-503) and Neurobasal medium (Gibco™ 21103049) then adding 1X N-2 (Gibco™ 17502001), 1X B-27 (Gibco™ 17504001) and 2 mM Glutamax (Gibco™ 35050061). mESCs were seeded at 4.21 x 104 cells/cm2 on dishes pre-coated with 0.1% gelatin (MilliporeSigma ES-006-B).

extract_protocol:
Total RNA was isolated from cells using the RNeasy Plus Mini Kit (QIAGEN 74136). RNA was treated with DNAse using the TURBO DNA-free kit (Invitrogen™ AM1907) prior to prepping libraries. RNA quality was assessed by electrophoresis on a 1% agarose gel and detecting 28S and 18S rRNA bands with ethidium bromide staining (0.6µg/mL).
A version of the Tecan Genomics’ Universal Plus mRNA prep kit (Tecan Genomics 0520B-A01) was modified for rRNA depletion by replacing the mRNA isolation in the first segment of the protocol with ribo depletion using FastSelect rRNA (Qiagen 334387) as follows: 200ng of total RNA in 10µL of water was mixed with 10µL of Universal Plus 2X Fragmentation Buffer and 1µL FastSelect. The solutions were fragmented and ribo depleted simultaneously per the FastSelect protocol. 20µL of the resulting fragmented/ribo depleted RNA were prepped per the Universal Plus protocol starting with First Strand Synthesis. The Universal Plus Unique Dual Index Set B was used, and the samples were quality checked using a MiniSeq benchtop sequencer (Illumina).

treatment_protocol: Treated cells got doxycycline at a final concentration of 1µg/mL. Cells were replenished with fresh 2i + LIF medium every day. WT, TKO and QKO mESCs were collected after 2 days. For day 4 doxycycline timepoints, mESCs were split at day 2, keeping the same seeding density.

value: mESC

value: Lamins_and LBR_quadruple_knockout

value: Untreated, Lamins and LBR quadruple knockout mESC


title: R+Ctrl1

source_name: iPSC-derived CD34+/CD45+ sorted cells transduced with NRASG12D lentiviral vector rep1

value: hematopoietic


title: p300_ChIP_3SL_LPS2h_Rep2

value: 3'SL_LPS 2h