title: Recurrent_tumor_mix

address: 450 Brookline Ave, SM936

department: Cancer Biology

description:
Library name: Recurrent_tumor_mix
10X Genomics

data_processing:
For RNA-seq:Count data were generated using Thermo Fisher’s Torrent Suite 5.12.3 and the ampliSeqRNA analysis plugin (V5.12.0.1). Reference is  AmpliSeq_Mouse_Transcriptome_v1 and targeted region is AmpliSeq_Mouse_Transcriptome_V1_Designed.bed
For snRNA-seq: the filtered feature-barcode matrix files were imported into Scanpy (version 1.10.0) for quality control, analysis, and exploration. The Scrublet package (version 0.2.3) was used to eliminate doublets
Assembly: mouse mm10 / AmpliSeq_Mouse_Transcriptome_v1
Supplementary files format and content: table-delimited text files includes raw counts
Supplementary files format and content: table-delimited text files includes value files and matrix files

extract_protocol:
For RAN-seq:Total RNA was extracted using the RNeasy Plus Mini Kit. The first step involved synthesizing first-strand cDNA from  2 μg of total RNA using the iScript reverse transcription supermix. For snRNA-seq: Nuclei isolation was using low-retention microcentrifuge tubes (Fisher Scientific) to minimize nuclei loss throughout the procedure. Briefly, tissue samples were manually dissociated with fine spring scissors for 10 minutes, homogenized in TST solution, filtered through a 30-μm MACS SmartStrainer (Miltenyi Biotec), and pelleted by centrifugation at 500g for 10 minutes at 4ْC. The nuclei pellets were further then purified for single-nuclei enrichment and debris removal with Anti Nucleus MicroBeads (Miltenyi Biotec, #130-132-997) according to the manufacturer’s guidelines. The nuclei were resuspended in 100 μL of resuspension buffer (1X PBS + 1% BSA). Dual-fluorescent staining was performed using ViaStainTM AOPI Staining Solution (Nexcelom Bioscience, #CS2-0106). The quality and quantity of the nuclei were assessed using a Cellometer-K2 Fluorescent Cell Counter (Nexcelom Bioscience) in both brightfield, and the PE/Texas Red® channel with a bandpass filter 610/10 (nuclei stained fluorescent red). Although slightly compromised, the nuclei yield was high.
For RNA-seq: we used an Ion AmpliSeq Custom Panel containing 4,604 cancer- and immune-associated genes, designed by Thermo Fisher using Ion AmpliSeq Designer, as described previously 45. A total of 10 ng of RNA from each sample was used to prepare the cDNA library. The libraries were multiplexed, amplified using the Ion OneTouch 2 System, and sequenced on an Ion Torrent Proton System (Thermo Fisher). For snRNA-seq:For single-cell Gel Beads-in-Emulsion (GEM) generation, we utilized the Chromium X system (10X Genomics) droplet-based microfluidic technology, following the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) protocol. The standard 5′-10X Genomics workflow was applied to generate sequencing-ready libraries in all downstream steps.

value: uterine tumor

value: mouse tumor cell


title: pDC, WT, day12

status: Public on Feb 24 2026

type: SRA

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: pDC_Dot1l_WT
1_pDC_DOT1L_WT

library_source: transcriptomic

data_processing:
51-bp paired-end reads were aligned against the mouse reference genome (Ensembl build 38) using Tophat (version 2.1, bowtie version 1.1).
Tophat was supplied with a Gene Transfer File (GTF, Ensembl version 77) and was supplied with the following parameters: “prefilter-multihits –no-coverage-search – bowtie1 –library-type fr-firststrand”.
To count the number of reads per gene, a custom script which is based on the same ideas as HTSeq-count has been used.
A list of the total number of uniquely mapped reads for each gene that is present in the provided Gene Transfer Format (GTF) file was generated.
Assembly: mm10
Supplementary files format and content: Tab delineated text file with raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: pDC

extract_protocol:
Bone marrow was isolated from femur and tibia. pDC, DC1 and DC2 populations were sorted by FACS. Cells from 5 (WT or KO) mice were pooled per sample. Cells were resuspended in RLT supplemented with 2-mercapthoethanol. Total RNA was isolated with the RNAeasy mini kit (Qiagen).
cDNA libraries were generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) as per manufacturers protocol.

treatment_protocol: Mice received intraperitoneal injections of 4-hydroxytamoxifen (4-OHT), 75 mg/kg on three consecutive days. Mice were sacrificed ten days after the final injection (day 12).

tag: strain

tag: genotype

value: het; wt

tag: cell type

value: pDC

tag: treatment

tag: time

value: day 12


title: Adult, vastus lateralis, Adult 9, RNAseq

city: Cambridge

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

country: USA

institute: Harvard University

description: Library name: Adult_VastusLateralis_RNA_adult9

data_processing:
FastQC (v.0.11.5) was used to determine per base sequence quality, GC content, and adapter content to ensure that all FASTQ files met our standards.
Adapter sequences and low-quality bases below Q20 were removed using Trimmomatic (v.0.39.0).
To target more high-value portions of the transcriptome (i.e., mRNA), residual ribosomal RNA reads were removed using RiboDetector (v.0.3.1).
Reads were aligned to the mouse mm10 genome using STAR (v.2.7.11).
To evaluate the relationships between samples, Principal Component Analysis (PCA) was performed using the plotPCA function in R and Multidimensional Scaling analysis (MDS) was performed using PoiClaClu (v.1.0.2.1). One adult m. vastus intermedius sample (“A Vast Int 7/27/21 RNA”) was removed from downstream RNA-seq analysis due to clustering with E18.5 samples. Therefore, N = 5 for adult m. vastus intermedius and N = 47 RNA-seq samples total.
To perform a quantitative comparison of gene expression (relative read count), a raw read count matrix was generated from filtered RNA-seq data using the featureCounts function of Subread (v.2.0.6).
Genes differentially expressed between time points (i.e., adult and E18.5), muscles (i.e., m. soleus and all others), myofiber biases (i.e., fast and slow), and anatomical regions (i.e., calf and thigh) were identified using DESeq2 (v.1.44.0) with an FDR < 0.05.
Genes with < 5 read counts across all samples were removed, leaving 20,889 genes for analysis.
Filtered read counts were normalized by variance stabilized transformation with respect to library size.
Differentially expressed genes meeting the following threshold (|log2 fold change| > 0.6, adjusted p-value < 0.05) were considered significant.
Assembly: mm10
Supplementary files format and content: txt file; raw read count data (gene expression)
Supplementary files format and content: csv files; DESeq2 output (count count matrices of gene expression)

source_name: vastus lateralis

growth_protocol: All mouse procedures were performed in accordance with relevant guidelines, regulations and protocols approved by the University of Oregon and Harvard University Institutional Animal Care and Use Committees (IACUC) (protocol number 13-04-161-2). All mice were maintained in accordance with the Guide for the Care and Use of Laboratory Animals at the Harvard University Biological Research Infrastructure Mouse Facility (Capellini laboratory mouse room). Adult FVB/NJ mice were obtained at 3-4 months of age. Mice were free of disease or injury at the time of sample collection and were not previously involved in biological research. Male and female mice were used to establish timed matings.

extract_protocol:
At E18.5 pregnant females were euthanized to acquire embryos. Adult mice were exposed to CO2 at a constant rate for 5 minutes and secondary euthanasia was performed via cervical dislocation by a trained investigator. E18.5 embryos were collected from pregnant females, euthanized via decapitation, and anatomically sexed. To minimize the signal of X-chromosome silencing factors (e.g., Xist, Tsix), only muscle samples from male mice were used for ATAC-seq and RNA-seq analysis. Four hindlimb skeletal muscles were chosen for dissection based on previously described differences in slow myofiber content. The m. soleus and m. vastus intermedius represent slow-biased muscles, and the m. gastrocnemius and m. vastus lateralis represent fast-biased muscles. Muscle samples were collected from adult male (N = 6) and E18.5 (N = 6) mice and placed in TRIzol reagent (Invitrogen). Muscle samples were pulverized using an electric homogenizer and subjected to a phenol-chloroform reaction. Total RNA extraction and purification was performed using a Zymo Direct-zol RNA Microprep Kit following the manufacturer’s instructions. RNA was eluted using nuclease-free water and assessed for quantity and quality. Samples were quantified using a Qubit and nanoDrop to determine their 260/230 and 260/280 values. Aliquots of samples were run on a TapeStation to determine their RNA integrity number (RIN) scores. Only samples with a RIN score above 7.0 were retained for library preparation and processed for sequencing.
RNA-seq libraries were prepared by the Harvard Bauer Core Facility using the Kapa mRNA HyperPrep Kit and automated using a PerkinElmer Sciclone NGS Workstation. RNA was reverse transcribed into cDNA using random primers. Total RNA was quantified using a fluorimetric Quant-iT RiboGreen RNA Assay Kit and total RNA integrity was assessed using an Agilent BioAnalyzer 2100 RNA Nano Kit. All libraries were pooled and assessed for quality using qPCR. To obtain a minimum of 30 million reads per sample, all deep sequencing was performed using 2 x 100-bp PE reads on an Illumina NovaSeq6000 instrument. Demultiplexed sequencing results were analyzed following ENCODE RNA-seq guidelines (www.encodeproject.org/about/experiment-guidelines/).

tag: tissue

value: vastus lateralis

value: skeletal muscle

value: FVB/NJ

tag: developmental stage

value: Adult

tag: mouse

value: Adult 9

tag: Sex

value: male


title: Adult, gastrocnemius, Adult 9, RNAseq

description: Library name: Adult_Gastrocnemius_RNA_adult9

source_name: gastrocnemius

value: gastrocnemius


title: Primary_tumor_mix

city: Boston

first: Jean

last: Zhao

institute: Dana Farber Cancer Institute

description:
Library name: Primary_tumor_mix
10X Genomics

library_source: transcriptomic single cell

source_name: uterine tumor


title: Adult, gastrocnemius, Adult 8, RNAseq

description: Library name: Adult_Gastrocnemius_RNA_adult8

value: Adult 8


title: Adult, vastus intermedius, Adult 8, RNAseq

description: Library name: Adult_VastusIntermedius_RNA_adult8

source_name: vastus intermedius

value: vastus intermedius


title: Adult, soleus, Adult 9, RNAseq

description: Library name: Adult_Soleus_RNA_adult9

source_name: soleus

value: soleus


title: Adult, soleus, Adult 7, RNAseq

description: Library name: Adult_Soleus_RNA_adult7

value: Adult 7


title: Adult, vastus intermedius, Adult 6, RNAseq

description: Library name: Adult_VastusIntermedius_RNA_adult6

value: Adult 6


title: Adult, vastus lateralis, Adult 6, RNAseq

description: Library name: Adult_VastusLateralis_RNA_adult6


title: Adult, soleus, Adult 8, RNAseq

description: Library name: Adult_Soleus_RNA_adult8


title: Adult, gastrocnemius, Adult 7, RNAseq

description: Library name: Adult_Gastrocnemius_RNA_adult7


title: Adult, vastus intermedius, Adult 9, RNAseq

description: Library name: Adult_VastusIntermedius_RNA_adult9


title: Adult, vastus intermedius, Adult 7, RNAseq

description: Library name: Adult_VastusIntermedius_RNA_adult7


title: Adult, vastus intermedius, Adult 5, RNAseq

description: Library name: Adult_VastusIntermedius_RNA_adult5

value: Adult 5


title: DC1, IP, rep1

description:
Library name: DC1_IP_rep1
H3K79me2_rep1_DC1

library_source: genomic

data_processing:
51-bp paired-end reads were mapped to a hybrid genome made from concatenating the mouse mm10 genome (Ensembl GRCm38) with the yeast sacCer3 genome.
Mapping was performed using BWA-MEM (version 0.7.18-r1243) with the option ‘-M’ and filtered for a mapping quality of 10. Duplicate alignments were removed using MarkDuplicates from the Picard toolset (version 3.3.0) with the option ‘-REMOVE_DUPLICATES true’.
Paired-end reads were converted to fragments by reading in mapped, properly paired reads using the GenomicAlignments R/Bioconductor package (release 3.20). Peaks were called using MACS2 version 2.2.9.1 using samples pooled by treatment and pooled input samples as the ‘control’ argument using the options ‘-f BEDPE -g mm --keep-dup all --broad’. Peaks detected on yeast chromosomes were removed.
Genomic bigwig tracks were generated for both individual samples and samples pooled by treatment from fragments mapping to the mouse genome using a custom R script using the ‘coverage’ function from the GenomicRanges R/Bioconductor package. The track heights were multiplied by a factor ‘1x10e6 / number of yeast reads’ for values to represent ‘coverage per million yeast reads’ to allow quantitative comparisons. Signal values per peak were obtained by using the BigWigFile-method of the ‘summary’ function in the rtracklayer R/Bioconductor package.
For aggregate visualization of coverage data the tornadoplot R/GitHub package was used and TSS/exons were determined using the EnsDb.Mmusculus.v75 R/Bioconductor package. To calculate distances to the first internal exon, exons within a gene were first collapsed to disjoint ranges using the ‘reduce’ function from the GenomicRanges R/Bioconductor package. The distance was then taken as the number of basepairs between the 3’ end of the most 5’ exon and the 5’ end of the subsequent exon for genes that have at least 2 distinct exons.
Assembly: mm10, sacCer3
Supplementary files format and content: bigwig (per sample)
Supplementary files format and content: broadpeak (per cell type)
Supplementary files format and content: Excel workbook (normalized peak counts of all samples)

molecule: genomic DNA

source_name: Isolated and sorted DC1

extract_protocol:
Bone marrow was isolated from femur and tibia. pDC, DC1 and DC2 populations (N=3 biological replicates) were sorted by FACS. Cells from 5 (WT or KO) mice were pooled per replicate. N=2 pools with the highest cell count for each cell type were fixed with 1% methanol free formaldehyde for 10 minutes & quenched with 125 mM glycine for 5 minutes. Quenced cells were lysed in 50 mM Tris-HCl pH8, 10 mM EDTA pH8, 1 % SDS + protease inhibitor cocktail, and sonicated for 3 minutes (30sec on, 30 sec off) on the Bioruptor PICO. Yeast chromatin was spiked in (1:1000) based on DNA concentration) prior to immunoprecipitation to allow for downstream normalization.
The library was prepped using the KAPA genomic DNA prep Hyper, purified and quantified using the Bioanalyzer DNA 7500.

tag: spike-in organism

value: Saccharomyces cerevisiae

value: Isolated and sorted DC1

tag: chip antibody

value: anti-H3K79me2 (04-835 Sigma), anti-HA-12CA5 (17 03 2019 NKI; in-house)


title: Adult, vastus lateralis, Adult 7, RNAseq

description: Library name: Adult_VastusLateralis_RNA_adult7


title: Adult, vastus lateralis, Adult 5, RNAseq

description: Library name: Adult_VastusLateralis_RNA_adult5


title: Adult, gastrocnemius, Adult 6, RNAseq

description: Library name: Adult_Gastrocnemius_RNA_adult6


title: Adult, soleus, Adult 5, RNAseq

description: Library name: Adult_Soleus_RNA_adult5


title: Adult, vastus intermedius, Adult 4, RNAseq

description: Library name: Adult_VastusIntermedius_RNA_adult4

value: Adult 4


title: Adult, gastrocnemius, Adult 4, RNAseq

description: Library name: Adult_Gastrocnemius_RNA_adult4


title: Adult, vastus lateralis, Adult 4, RNAseq

description: Library name: Adult_VastusLateralis_RNA_adult4

value: vastus lateralis


title: Adult, soleus, Adult 6, RNAseq

description: Library name: Adult_Soleus_RNA_adult6

value: skeletal muscle


title: Adult, gastrocnemius, Adult 5, RNAseq

description: Library name: Adult_Gastrocnemius_RNA_adult5

value: FVB/NJ


title: E18.5, vastus lateralis, Embryo 6, RNAseq

description: Library name: E18.5_VastusLateralis_RNA_embryo6

value: Embryo 6


title: Adult, soleus, Adult 4, RNAseq

description: Library name: Adult_Soleus_RNA_adult4

value: Adult


title: Adult, vastus lateralis, Adult 8, RNAseq

description: Library name: Adult_VastusLateralis_RNA_adult8

value: male


title: E18.5, gastrocnemius, Embryo 6, RNAseq

description: Library name: E18.5_Gastrocnemius_RNA_embryo6

value: gastrocnemius


title: E18.5, soleus, Embryo 6, RNAseq

description: Library name: E18.5_Soleus_RNA_embryo6


title: E18.5, vastus intermedius, Embryo 6, RNAseq

description: Library name: E18.5_VastusIntermedius_RNA_embryo6


title: E18.5, soleus, Embryo 5, RNAseq

description: Library name: E18.5_Soleus_RNA_embryo5

value: Embryo 5


title: E18.5, vastus lateralis, Embryo 5, RNAseq

description: Library name: E18.5_VastusLateralis_RNA_embryo5


title: E18.5, vastus intermedius, Embryo 5, RNAseq

description: Library name: E18.5_VastusIntermedius_RNA_embryo5

value: vastus intermedius


title: E18.5, gastrocnemius, Embryo 5, RNAseq

description: Library name: E18.5_Gastrocnemius_RNA_embryo5


title: E18.5, vastus intermedius, Embryo 4, RNAseq

description: Library name: E18.5_VastusIntermedius_RNA_embryo4

value: Embryo 4


title: E18.5, vastus lateralis, Embryo 4, RNAseq

description: Library name: E18.5_VastusLateralis_RNA_embryo4


title: E18.5, gastrocnemius, Embryo 4, RNAseq

description: Library name: E18.5_Gastrocnemius_RNA_embryo4


title: E18.5, gastrocnemius, Embryo 3, RNAseq

description: Library name: E18.5_Gastrocnemius_RNA_embryo3

value: Embryo 3


title: E18.5, soleus, Embryo 3, RNAseq

description: Library name: E18.5_Soleus_RNA_embryo3

value: soleus


title: E18.5, vastus intermedius, Embryo 3, RNAseq

description: Library name: E18.5_VastusIntermedius_RNA_embryo3


title: E18.5, vastus intermedius, Embryo 2, RNAseq

description: Library name: E18.5_VastusIntermedius_RNA_embryo2

value: Embryo 2


title: E18.5, vastus lateralis, Embryo 3, RNAseq

description: Library name: E18.5_VastusLateralis_RNA_embryo3


title: E18.5, soleus, Embryo 2, RNAseq

description: Library name: E18.5_Soleus_RNA_embryo2


title: E18.5, gastrocnemius, Embryo 2, RNAseq

description: Library name: E18.5_Gastrocnemius_RNA_embryo2


title: E18.5, vastus lateralis, Embryo 2, RNAseq

description: Library name: E18.5_VastusLateralis_RNA_embryo2


title: E18.5, soleus, Embryo 1, RNAseq

description: Library name: E18.5_Soleus_RNA_embryo1

value: Embryo 1


title: E18.5, soleus, Embryo 4, RNAseq

description: Library name: E18.5_Soleus_RNA_embryo4


title: E18.5, soleus, Litter 3, ATACseq

description: Library name: E18.5_Soleus_ATAC_Litter3

data_processing:
FastQC (v.0.11.5) was used to determine per base sequence quality, GC content, and adapter content to ensure that all FASTQ files met our standards.
Adapter sequences and low-quality bases below Q20 were removed using Trimmomatic (v.0.39.0).
Reads were aligned to the mouse mm10 genome using Bowtie2 (v.2.4.4).
To target more high-value portions of the genome, reads mapping to the mitochondrial genome were removed using SAMtools (v.1.14.0).
Duplicate reads were removed using Picard (http://broadinstitute.github.io/picard).
Filtered BAM files were assessed for read alignment enrichment (i.e., peaks) using MACS2 (v.2.1.1) and the callpeak parameters: -B -f BAMPE -g mm -p 0.05
Peaks of open chromatin reproducible across biological replicates were identified using an irreproducible discovery rate (IDR) threshold of < 0.05 (Li et al., 2011).
To reduce background noise and target peaks specific to muscle tissue, IDR peaks overlapping mm10 blacklist regions (Amemiya et al., 2019) and an IDR peak set generated from embryonic mouse brain tissue (Guo et al., 2017) were removed using BEDTools (v.2.25.0).
Assembly: mm10
Supplementary files format and content: bed format; contains the coordinates of the peaks called

extract_protocol:
At E18.5 pregnant females were euthanized to acquire embryos. Adult mice were exposed to CO2 at a constant rate for 5 minutes and secondary euthanasia was performed via cervical dislocation by a trained investigator. E18.5 embryos were collected from pregnant females, euthanized via decapitation, and anatomically sexed. To minimize the signal of X-chromosome silencing factors (e.g., Xist, Tsix), only muscle samples from male mice were used for ATAC-seq and RNA-seq analysis. Four hindlimb skeletal muscles were chosen for dissection based on previously described differences in slow myofiber content. The m. soleus and m. vastus intermedius represent slow-biased muscles, and the m. gastrocnemius and m. vastus lateralis represent fast-biased muscles. Muscle samples were collected from adult male (N = 3) and E18.5 (N = 3 pooled litters) mice. To ensure at least 50,000 cells per muscle for ATAC-seq analysis, each E18.5 biological replicate included pooled muscles (both left and right sides) from up to 5 male embryos belonging to the same litter. Each sample was subjected to a protocol that isolates muscle nuclei from undigested tissue (Young et al., 2022).
Cell counting was performed using trypan blue and a hemocytometer under an inverted microscope. Only samples having a death rate below 25% were subjected to an optimized ATAC-seq protocol (Corces et al., 2017). Briefly, muscle nuclei were lysed to extract DNA and treated with Tn5 transposase to tag transcriptionally accessible fragments of DNA not bound to histones (i.e., potential enhancers). Transposed DNA was purified using a Zymo DNA Clean and Concentrator Kit following the manufacturer’s instructions. Samples were then primer barcoded and PCR-amplified to generate ATAC-seq libraries. Libraries were treated for fragment size selection using the OMEGA Bead Purification Protocol and concentrations were determined using the KAPA Library Quantification Complete Kit. ATAC-seq library quality was assessed by the Harvard Bauer Core Facility using the Agilent Bioanalyzer 2100 DNA High Sensitivity Kit and the Agilent TapeStation 4200 (D1000 ScreenTape assay). All libraries were pooled and assessed for quality using qPCR and Illumina MiSeq Nano. Library pools were adjusted based on the Illumina MiSeq Nano results to optimize the distribution and final loading concentration. To obtain a minimum of 50 million reads per sample, all deep sequencing was performed using 2 x 100-bp PE reads on an Illumina NovaSeq 6000 instrument. Demultiplexed sequencing results were analyzed following ENCODE ATAC-seq guidelines (www.encodeproject.org/about/experiment-guidelines/).

value: Litter 3


title: E18.5, vastus lateralis, Litter 2, ATACseq

description: Library name: E18.5_VastusLateralis_ATAC_Litter2

value: Litter 2


title: E18.5, vastus intermedius, Litter 2, ATACseq

description: Library name: E18.5_VastusIntermedius_ATAC_Litter2


title: E18.5, gastrocnemius, Litter 3, ATACseq

description: Library name: E18.5_Gastrocnemius_ATAC_Litter3


title: E18.5, vastus lateralis, Litter 3, ATACseq

description: Library name: E18.5_VastusLateralis_ATAC_Litter3


title: E18.5, vastus intermedius, Litter 1, ATACseq

description: Library name: E18.5_VastusIntermedius_ATAC_Litter1

value: Litter 1


title: E18.5, gastrocnemius, Litter 2, ATACseq

description: Library name: E18.5_Gastrocnemius_ATAC_Litter2


title: E18.5, vastus intermedius, Litter 3, ATACseq

description: Library name: E18.5_VastusIntermedius_ATAC_Litter3


title: E18.5, vastus lateralis, Litter 1, ATACseq

description: Library name: E18.5_VastusLateralis_ATAC_Litter1

value: vastus lateralis


title: E18.5, soleus, Litter 2, ATACseq

description: Library name: E18.5_Soleus_ATAC_Litter2

value: skeletal muscle


title: E18.5, vastus intermedius, Embryo 1, RNAseq

description: Library name: E18.5_VastusIntermedius_RNA_embryo1

value: FVB/NJ


title: E18.5, gastrocnemius, Litter 1, ATACseq

description: Library name: E18.5_Gastrocnemius_ATAC_Litter1


title: E18.5, vastus lateralis, Embryo 1, RNAseq

description: Library name: E18.5_VastusLateralis_RNA_embryo1


title: Adult, vastus lateralis, Adult 3, ATACseq

description: Library name: Adult_VastusLateralis_ATAC_Adult3

value: Adult 3


title: Adult, vastus intermedius, Adult 3, ATACseq

description: Library name: Adult_VastusIntermedius_ATAC_Adult3

value: Adult


title: E18.5, soleus, Litter 1, ATACseq

description: Library name: E18.5_Soleus_ATAC_Litter1

value: male


title: Adult, soleus, Adult 3, ATACseq

description: Library name: Adult_Soleus_ATAC_Adult3


title: Adult, vastus intermedius, Adult 2, ATACseq

description: Library name: Adult_VastusIntermedius_ATAC_Adult2

value: Adult 2


title: Adult, gastrocnemius, Adult 3, ATACseq

description: Library name: Adult_Gastrocnemius_ATAC_Adult3

value: gastrocnemius


title: Adult, vastus lateralis, Adult 1, ATACseq

description: Library name: Adult_VastusLateralis_ATAC_Adult1

value: Adult 1


title: Adult, vastus lateralis, Adult 2, ATACseq

description: Library name: Adult_VastusLateralis_ATAC_Adult2


title: Adult, gastrocnemius, Adult 2, ATACseq

description: Library name: Adult_Gastrocnemius_ATAC_Adult2


title: Adult, vastus intermedius, Adult 1, ATACseq

description: Library name: Adult_VastusIntermedius_ATAC_Adult1

value: vastus intermedius


title: Adult, soleus, Adult 1, ATACseq

description: Library name: Adult_Soleus_ATAC_Adult1


title: Input-P7-MT-K27

city: Xiamen

first: Boxin

last: Zhang

address: 良渚实验室1369号

country: China

institute: 良渚实验室

data_processing:
The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
clean reads were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 (version 2.2.8).
Enriched peaks of H3K9me3 were identified by HOMER v4.10.1 with histone style (http://homer.ucsd.edu/homer).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: cortex

extract_protocol:
Approximately 1× 10^7 cells from cortex as above was fixed in 1% formaldehyde for 10 min at room temperature (RT), followed by quenching in 125 nM glycine for 5 min. Cell nuclei were collected and lysed in lysing buffer (50 mM HEPES/KOH pH 7.6, 1 mM EDTA, 140 nM NaCl, 10% v/v Glycerol, 0.5% NP-40, 0.25% v/v Triton X-100) supplemented with protease inhibitor. Nuclei were subjected to sonication to acquire DNA fragments of 200-350 bp. The sonicated chromatin was applied to immunoprecipitation by incubation with 1.5 μg H3K9me3 antibody (Abcam, #ab232324) or 3 μg H3K27ac antibody (Abcam, #ab4729) overnight at 4°C, followed with collection using 30 μl protein A/G plus agarose beads (Millipore). After elute and purify the chromatin, the ChIP-seq library was constructed using a KAPA HyperPrep Kits (Roche, 07962347001) according to the manufacturer’s instructions，and then run on the Illumina sequencer Hiseq-Xten PE150.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 7962347001)

value: cortex

value: input

value: mG-cKO


title: E18.5, gastrocnemius, Embryo 1, RNAseq

description: Library name: E18.5_Gastrocnemius_RNA_embryo1

value: Embryo 1


title: P7-MT-K27

value: H3K27ac antibody (abcam , #ab4729)


title: Adult, gastrocnemius, Adult 1, ATACseq

description: Library name: Adult_Gastrocnemius_ATAC_Adult1


title: Input-P7-WT-K27

value: Ctrl


title: Adult, soleus, Adult 2, ATACseq

description: Library name: Adult_Soleus_ATAC_Adult2

value: soleus


title: MG-p7-mt-H3K27ac-CHIP_FKDL210393761-1a


title: Input-P7-WT-K9


title: P7-WT-K9

value: H3K9me3 antibody (Abcam, #ab232324)


title: P7-WT-K27


title: P7-MT-K9


title: MG-p7-wt-input_FKDL210393758-1a


title: MG-p7-wt-H3K27ac-CHIP_FKDL210393759-1a


title: p7-mt-input_FKDL210363125-1a


title: p7-wt-H3K9me3-CHIP_FKDL210363124-1a


title: p7-wt-input_FKDL210393757-1a


title: MOF Degron mESC: Auxin-NascentRNA_TTSeq_Rep1

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Nascent IP RNA from auxin-treated MOF degron mESCs

data_processing:
TT-Seq: TT-Seq data analysis was performed as previously described. The data were processed through the snakePipes mRNA-seq pipeline (modified version of v.2.1.2), similar to RNA-seq analysis. Adapters and low-quality bases (<Q20) were removed using Cutadapt (v.2.8; https://github.com/marcelm/cutadapt). For all of the samples, reads were then mapped to the reference genome with STAR (v.2.7.4a). Then, reads per gene were counted using featureCounts (v.2.0.0). The gene-level counts obtained from featureCounts were then used for differential expression analysis using DESeq2 (v.1.26.0), similar to the RNA-seq analysis. For transcriptional rate calculations, read counts for all genes were obtained from each corresponding labeled and unlabelled TT-seq sample. To estimate the rates of RNA degradation and synthesis, we used a statistical model that was described previously.
ChIP-Seq: ChIP-Seq data was processed using the default parameters of SnakePipes v. 2.5.1 DNA-mapping and ChIP-Seq pipelines with "--trim --dedup --mapq 3 --properPairs" options.
Assembly: mm10
Supplementary files format and content: Tab-limited text files include raw counts for total and nascent RNA samples. Narrowpeak files were generated using default settings of MACS2.
Supplementary files format and content: bigwig files: Input-normalized log2 ChIP enrichment for MOF, spikein-normalized ChIP enrichment for H4-ac sites and sequencing depth normalized input samples.
Library strategy: TT-Seq

source_name: Embryo

growth_protocol: ESCs were cultured at 37°C and 5 % CO2 on 0.1% gelatin (Merck #G1393)-coated dishes and were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco #37966-021) supplemented with 15% heat- inactivated ES-cell specific fetal calf serum (FCS), 100 U/mL penicillin and 100 U/mL streptomycin (Gibco #15140-122), 1mM glutamine (GlutaMax, Gibco #35050061), 1mM sodium pyruvate (Gibco #11360-70), non-essential amino acids (NEAA, Gibco #11140050), ß-Mercaptoethanol (Gibco #31350-010), and in-house purified LIF.

extract_protocol:
ChIP-Seq: ESCs were crosslinked with 1 % Formaldehyde in 1X PBS for 10 minutes at RT followed by quenching with 125 mM Glycine at 4 °C. After washing the ESCs twice with PBS, ESCs were lysed in LB1 buffer (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10 % Glycerol, 0.5 % NP-40, 0.25 % Triton X-100) for 20 minutes at 4 °C. Then, samples were washed in LB2 buffer (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 5 minutes at 4 °C. Chromatin was extracted by incubation in LB3 buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1 % DoC-Na, 0.5 % Na-Sarcosinate, 1 % Triton X-100) for 10 minutes on ice followed by sonication for 12 minutes on a Covaris sonicator. The sonicated chromatin was spun down at 16,000g for 10 minutes at 4 °C and the supernatant was incubated with the appropriate antibody overnight at 4 °C. Antibody-bound chromatin fragments were collected by incubation with Protein A or G DynaBeads for 3 h at 4 °C. The beads were washed for 5 minutes at 4 °C with the following buffers: RIPA-150 (50 mM Tris- HCl, pH 8.0, 150 mM NaCl, 0.1 % SDS, 0.5 % DoC-Na, 1 % NP-40), RIPA-500 (50 mM Tris-HCl, pH 8.0, 500 mM NaCl, 0.1 % SDS, 1 % NP-40), Li-Buffer (50 mM Tris- HCl, pH 8.0, 250 mM LiCl, 0.5 % DoC-Na, 1 % NP-40), TE Buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA). After an additional wash with TE Buffer, beads were resuspended in 100 μL of elution buffer (50 mM Tris-HCl, pH 7.4, 1 % SDS, 1 mM EDTA) and crosslinks were reversed by incubation at 65 °C for at least 4 h. Proteins and RNA were degraded by further incubations with RNase A and Proteinase K, respectively. Resulting DNA was purified using ChIP DNA Clean and Concentrator kit (Zymo) according to the manufacturer's protocol.                                                                                Native Histone ChIP-Seq: 3 x 106 ESCs per replicate were harvested using accutase, washed once in 1X PBS and flash-frozen. The cell pellet was thawn on ice and resuspended in 150 μL of 1X PBS and mixed with 150 μL of 2X Lysis buffer (100 mM Tris-HCl, pH 8.0, 0.2 % Triton X-100, 0.1 % DOC-Na, 10 mM CaCl2, 10 mM Na-Butyrate) containing 0.9 μL of MNase. The cell lysate was incubated first for 20 minutes at 4 °C and then for 10 minutes at 37 °C. The MNase digestion was quenched by addition of 30 μL of 25 mM EGTA. Afterwards, the sample was immediately placed on ice and mixed ocassionally by inverting the tube for 2 minutes. The soluble chromatin was collected by spinning down the sample at 16000g for 5 minutes at 4 °C and mixed with the dilution buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% DOC-Na, 2.2% Triton X-100, 50 mM EDTA, 50 mM EGTA, 5 mM Na-Butyrate). 2 % of the soluble fraction was taken as input and the rest was incubated overnight with the histone PTM antibody at 4 °C. The next day, magnetic Protein A or G Dynabeads were washed in PBS thrice and 20 μl per sample were added to collect the antibody-chromatin conjugates. Then, they were washed in the following buffers, each for 5 minutes at 4 °C: Low salt buffer (0.1 % SDS, 1 % Triton X-100, 0.1 % DOC-Na, 20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 150 mM NaCl)[twice], high salt buffer (0.1 % SDS, 1 % Triton X-100, 0.1 % DOC-Na, 20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 360 mM NaCl), LiCl buffer (0.25 M LiCl, 1 % NP- 40, 1 % DOC-Na. 1 mM EDTA, 10 mM Tris-HCl, pH 8.0) [twice]. Finally, the samples were rinsed once in TE buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA) and resuspended in 100 μL of elution buffer (50 mM Tris-HCl, pH 7.4, 1 % SDS, 1 mM EDTA) and incubated first for 1 h at 55 °C with Proteinase K and then for 30 minutes at 37 °C with RNAse A. Resulting DNA was purified using ChIP DNA Clean and Concentrator kit according to manufacturer’s protocol.                                                                                TT-Seq: TT-Seq was performed as previously described with minor modifications 28: ESCs were treated with 500 μM 4-sU for 5 minutes under regular growth conditions and lysed using Trizol (Invitrogen) immediately afterwards. Total RNA was purified using chloroform and isopropanol precipitation and resuspended in TE buffer. 300 μg of total RNA for each sample was spiked with spike-in mix (appendix) and fragmented using Bioruptor Plus (30 seconds ON, 30 seconds OFF, 1 cycle, HIGH setting) and an aliquot was taken as Total RNA sample. The rest of the fragmented total RNA was biotinylated using Biotin-HPDP (Thermo Fisher) at room temperature for 2 hours. To remove excess Biotin-HPDP, RNA was precipitated using phenol:chloroform-isoamyl alcohol (Sigma) and ethanol and resuspended in ddH2O. Biotinylated RNA fragments were purified using μMACS streptavidin beads and μMACS columns (Miltenyi Biotec) according to the recommendations of the manufacturer. Labeled RNA was eluted twice using 100 mM DTT and purified using Oligo Clean and Concentrator Kit (Zymo Research). Both total and labeled RNA samples were treated with Turbo DNAse (Invitrogen) for 30 minutes at 37 °C and purified again Oligo Clean and Concentrator Kit (Zymo Research).
RNA libraries for total RNA and TT-Seq samples were prepared using Illumina Stranded Total RNA Prep Kit with RiboZero Plus. ChIP-Seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: PROTAC reagents were prepared in DMSO and diluted in cell culture medium to the indicated concentrations at 37°C. Auxin was dissolved in water and diluted in cell culture medium to 500 µM.

value: Embryo

tag: cell line

value: WT26 mESC

value: Mouse embryonic stem cells

value: 500 µM Auxin (3 h)


title: p7-mt-H3K9me3-CHIP_FKDL210363126-1a


title: MOF Degron mESC: Control-NascentRNA_TTSeq_Rep2

description: Nascent IP RNA from control MOF degron mESCs

value: Water


title: MOF Degron mESC: Auxin-NascentRNA_TTSeq_Rep2


title: MOF Degron mESC: Control-NascentRNA_TTSeq_Rep3


title: Input-P7-MT-K9


title: MG-p7-mt-input_FKDL210393760-1a


title: MOF Degron mESC: Auxin-TotalRNA_TTSeq_Rep1

description: Input total RNA for IP from auxin-treated MOF degron mESCs


title: MOF Degron mESC: Control-NascentRNA_TTSeq_Rep1


title: MOF Degron mESC: Auxin-TotalRNA_TTSeq_Rep3


title: MOF Degron mESC: Control-TotalRNA_TTSeq_Rep2

description: Input total RNA for IP from control MOF degron mESCs


title: BRD2 Degron mESC: dBET6-NascentRNA_TTSeq_Rep3

description: Nascent IP RNA from dBET6-treated BRD2 degron mESCs

value: 100 nM dBET6


title: MOF Degron mESC: Auxin-NascentRNA_TTSeq_Rep3


title: BRD2 Degron mESC: dBET6-NascentRNA_TTSeq_Rep1


title: MOF Degron mESC: Control-TotalRNA_TTSeq_Rep3


title: BRD2 Degron mESC: dBET6-NascentRNA_TTSeq_Rep2


title: MOF Degron mESC: Control-TotalRNA_TTSeq_Rep1


title: BRD2 Degron mESC: ZXH-3-26-NascentRNA_TTSeq_Rep2

description: Nascent IP RNA from ZXH-3-26-treated BRD2 degron mESCs


title: BRD2 Degron mESC: ZXH-3-26-Auxin-NascentRNA_TTSeq_Rep2

description: Nascent IP RNA from BRD2 degron mESCs treated with ZXH-3-26 and auxin


title: BRD2 Degron mESC: ZXH-3-26-NascentRNA_TTSeq_Rep1


title: BRD2 Degron mESC: DMSO-NascentRNA_TTSeq_Rep2

description: Nascent IP RNA from DMSO-control BRD2 degron mESCs

value: DMSO


title: BRD2 Degron mESC: ZXH-3-26-Auxin-NascentRNA_TTSeq_Rep1


title: BRD2 Degron mESC: ZXH-3-26-NascentRNA_TTSeq_Rep3


title: BRD2 Degron mESC: dBET6-TotalRNA_TTSeq_Rep3

description: Input total RNA for IP from dBET6-treated BRD2 degron mESCs


title: BRD2 Degron mESC: ZXH-3-26-Auxin-NascentRNA_TTSeq_Rep3


title: BRD2 Degron mESC: dBET6-TotalRNA_TTSeq_Rep2


title: MOF Degron mESC: Auxin-TotalRNA_TTSeq_Rep2


title: BRD2 Degron mESC: DMSO-NascentRNA_TTSeq_Rep3


title: BRD2 Degron mESC: ZXH-3-26-Auxin-TotalRNA_TTSeq_Rep3

description: Input total RNA for IP from BRD2 degron mESCs treated with ZXH-3-26 and auxin


title: BRD2 Degron mESC: ZXH-3-26-Auxin-TotalRNA_TTSeq_Rep1


title: BRD2 Degron mESC: DMSO-NascentRNA_TTSeq_Rep1


title: BRD2 Degron mESC: ZXH-3-26-TotalRNA_TTSeq_Rep2

description: Input total RNA for IP from ZXH-3-26-treated BRD2 degron mESCs


title: BRD2 Degron mESC: ZXH-3-26-TotalRNA_TTSeq_Rep1


title: BRD2 Degron mESC: dBET6-TotalRNA_TTSeq_Rep1


title: BRD2 Degron mESC: DMSO-TotalRNA_TTSeq_Rep2

description: Input total RNA for IP from DMSO-control BRD2 degron mESCs


title: BRD2 Degron mESC: DMSO-TotalRNA_TTSeq_Rep3


title: BRD2 Degron mESC: ZXH-3-26-Auxin-TotalRNA_TTSeq_Rep2


title: BRD2 Degron mESC: DMSO-TotalRNA_TTSeq_Rep1


title: BRD2 Degron mESC: ZXH-3-26-TotalRNA_TTSeq_Rep3


title: MOF Degron mESCs: Auxin_IP_for_BRD3-ChIP_Rep2

description: ChIP DNA sample for BRD3 ChIP-Seq in MOF degron mESCs.

data_processing:
TT-Seq: TT-Seq data analysis was performed as previously described. The data were processed through the snakePipes mRNA-seq pipeline (modified version of v.2.1.2), similar to RNA-seq analysis. Adapters and low-quality bases (<Q20) were removed using Cutadapt (v.2.8; https://github.com/marcelm/cutadapt). For all of the samples, reads were then mapped to the reference genome with STAR (v.2.7.4a). Then, reads per gene were counted using featureCounts (v.2.0.0). The gene-level counts obtained from featureCounts were then used for differential expression analysis using DESeq2 (v.1.26.0), similar to the RNA-seq analysis. For transcriptional rate calculations, read counts for all genes were obtained from each corresponding labeled and unlabelled TT-seq sample. To estimate the rates of RNA degradation and synthesis, we used a statistical model that was described previously.
ChIP-Seq: ChIP-Seq data was processed using the default parameters of SnakePipes v. 2.5.1 DNA-mapping and ChIP-Seq pipelines with "--trim --dedup --mapq 3 --properPairs" options.
Assembly: mm10
Supplementary files format and content: Tab-limited text files include raw counts for total and nascent RNA samples. Narrowpeak files were generated using default settings of MACS2.
Supplementary files format and content: bigwig files: Input-normalized log2 ChIP enrichment for MOF, spikein-normalized ChIP enrichment for H4-ac sites and sequencing depth normalized input samples.


title: MOF Degron mESCs: Control_IP_for_BRD3-ChIP_Rep3


title: MOF Degron mESCs: Control_IP_for_BRD3-ChIP_Rep2


title: MOF Degron mESCs: Control_IP_for_BRD3-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_BRD3-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_BRD3-ChIP_Rep3


title: MOF Degron mESCs: Auxin_Input_for_BRD3-ChIP_Rep3

description: Input DNA sample for BRD3 ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Control_Input_for_BRD3-ChIP_Rep3


title: MOF Degron mESCs: Control_Input_for_BRD3-ChIP_Rep2


title: MOF Degron mESCs: Auxin_IP_for_TAF1-ChIP_Rep3

description: ChIP DNA sample for TAF1 ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Control_Input_for_BRD3-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_TAF1-ChIP_Rep1


title: MOF Degron mESCs: Control_IP_for_TAF1-ChIP_Rep1


title: MOF Degron mESCs: Control_IP_for_TAF1-ChIP_Rep3


title: MOF Degron mESCs: Control_IP_for_TAF1-ChIP_Rep2


title: MOF Degron mESCs: Auxin_Input_for_BRD3-ChIP_Rep2


title: MOF Degron mESCs: Auxin_IP_for_BRD2-ChIP_Rep2

description: ChIP DNA sample for BRD2 ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Control_IP_for_BRD2-ChIP_Rep3


title: MOF Degron mESCs: Control_IP_for_BRD4-ChIP_Rep1

description: ChIP DNA sample for BRD4 ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Auxin_IP_for_TAF1-ChIP_Rep2


title: MOF Degron mESCs: Auxin_IP_for_BRD2-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_BRD2-ChIP_Rep3


title: MOF Degron mESCs: Control_IP_for_BRD2-ChIP_Rep2


title: MOF Degron mESCs: Auxin_Input_for_BRD-ChIP_Rep3

description: Input DNA sample for BRD ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Auxin_Input_for_BRD3-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_BRD4-ChIP_Rep3


title: MOF Degron mESCs: Auxin_IP_for_BRD4-ChIP_Rep2


title: MOF Degron mESCs: Auxin_IP_for_BRD4-ChIP_Rep1


title: MOF Degron mESCs: Control_IP_for_BRD4-ChIP_Rep2


title: MOF Degron mESCs: Control_IP_for_BRD4-ChIP_Rep3


title: MOF Degron mESCs: Control_Input_for_BRD-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_H4K16ac-ChIP_Rep3

description: ChIP DNA sample for H4K16ac ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Control_Input_for_BRD-ChIP_Rep3


title: MOF Degron mESCs: Auxin_IP_for_H4K16ac-ChIP_Rep2


title: MOF Degron mESCs: Control_Input_for_BRD-ChIP_Rep2


title: MOF Degron mESCs: Control_IP_for_BRD2-ChIP_Rep1


title: MOF Degron mESCs: Auxin_Input_for_BRD-ChIP_Rep2


title: MOF Degron mESCs: Auxin_Input_for_BRD-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_H4K16ac-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_H4K12ac-ChIP_Rep3

description: ChIP DNA sample for H4K12ac ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Auxin_IP_for_H4K12ac-ChIP_Rep2


title: MOF Degron mESCs: Auxin_IP_for_H4K12ac-ChIP_Rep1


title: MOF Degron mESCs: Control_IP_for_H4K16ac-ChIP_Rep3


title: MOF Degron mESCs: Control_IP_for_H4K12ac-ChIP_Rep3


title: MOF Degron mESCs: Control_IP_for_H4K16ac-ChIP_Rep1


title: MOF Degron mESCs: Control_IP_for_H4K8ac-ChIP_Rep3

description: ChIP DNA sample for H4K8ac ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Auxin_IP_for_H4K8ac-ChIP_Rep3


title: MOF Degron mESCs: Auxin_IP_for_H4K8ac-ChIP_Rep2


title: MOF Degron mESCs: Control_IP_for_H4K12ac-ChIP_Rep1


title: MOF Degron mESCs: Control_IP_for_H4K16ac-ChIP_Rep2


title: MOF Degron mESCs: Control_IP_for_H4K8ac-ChIP_Rep2


title: MOF Degron mESCs: Control_IP_for_H4K8ac-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_H4K8ac-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_H4K5ac-ChIP_Rep1

description: ChIP DNA sample for H4K5ac ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Auxin_IP_for_H4K5ac-ChIP_Rep2


title: MOF Degron mESCs: Auxin_IP_for_H4K5ac-ChIP_Rep3


title: MOF Degron mESCs: Control_IP_for_H4K5ac-ChIP_Rep1


title: MOF Degron mESCs: Auxin_Input_for_H4ac-ChIP_Rep3

description: Input DNA sample for H4ac native histone ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Control_IP_for_H4K5ac-ChIP_Rep3


title: MOF Degron mESCs: Control_IP_for_H4K12ac-ChIP_Rep2


title: MOF Degron mESCs: Control_IP_for_H4K5ac-ChIP_Rep2


title: MOF Degron mESCs: Auxin_Input_for_H4ac-ChIP_Rep1


title: MOF Degron mESCs: Auxin_IP_for_V5-ChIP_Rep2

description: ChIP DNA sample for V5 ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Control_IP_for_V5-ChIP_Rep1


title: MOF Degron mESCs: Control_IP_for_V5-ChIP_Rep2


title: MOF Degron mESCs: Control_Input_for_H4ac-ChIP_Rep3


title: MOF Degron mESCs: Auxin_IP_for_V5-ChIP_Rep1


title: MOF Degron mESCs: Auxin_Input_for_V5-ChIP_Rep1

description: Input DNA sample for V5 ChIP-Seq in MOF degron mESCs.


title: MOF Degron mESCs: Control_Input_for_V5-ChIP_Rep2


title: MOF Degron mESCs: Control_Input_for_H4ac-ChIP_Rep2


title: MOF Degron mESCs: Auxin_Input_for_V5-ChIP_Rep2


title: MOF Degron mESCs: Control_Input_for_V5-ChIP_Rep1


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, complexed JetPEI:CREST phospho-mimetic, rep5

city: Irvine

first: Kousha

last: Changizi

state: CA

address: 4038 Donald Bren Hall

department: Computer Science

institute: University of California, Irvine

data_processing:
Reads aligned to mm10 assembly and RefSeq genes using TopHat release 2.1.1
Gene expression results (FPKM) obtained using Cufflinks release 2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Samples

source_name: dorsal hippocampus hemisphere

growth_protocol: mice were single-housed and received OLM behavior or handling only (homecage)

extract_protocol:
RNA was extracted using the RNAeasy Qiagen kit.
A RNA integrity number was measured for each sample with the Qubit RNA HS assay kit, and only samples with a RIN ≥ 7.0 were included for submission to Novogene for cDNA synthesis, amplification, library construction, and sequencing using the Illumina NovaSeq and HiSeq platforms with paired-end 150bp (PE150) sequencing.

treatment_protocol:
CREST phospho-null or -mutant complexed with the JetPEI in vivo transfection reagent and delivered bilaterally into the adult dorsal hippocampus 3days prior to mice receiving training
dorsal hippocampus was rapidly dissected and snap-frozen at 1hr after the end of OLM training period

value: dorsal hippocampus hemisphere

value: brain

value: wt

value: 3min sub-threshold

value: CREST phospho-mimetic


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, complexed JetPEI:CREST phospho-mimetic, rep2


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, complexed JetPEI:CREST phospho-mimetic, rep6


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, complexed JetPEI:CREST phospho-mimetic, rep1


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, complexed JetPEI:CREST phospho-mimetic, rep4


title: MOF Degron mESCs: Auxin_Input_for_H4ac-ChIP_Rep2


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, complexed JetPEI:CREST phospho-mimetic, rep3


title: MOF Degron mESCs: Control_Input_for_H4ac-ChIP_Rep1


title: dorsal hippocampus, 1hr after 10min threshold training, complexed JetPEI:CREST phospho-null, rep6

value: 10min Threshold

value: CREST phospho-null


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, vehicle, rep1

value: Vehicle


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, vehicle, rep5


title: dorsal hippocampus, 1hr after 10min threshold training, complexed JetPEI:CREST phospho-null, rep2


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, vehicle, rep3


title: dorsal hippocampus, 1hr after 10min threshold training, complexed JetPEI:CREST phospho-null, rep4


title: dorsal hippocampus, 1hr after 10min threshold training, complexed JetPEI:CREST phospho-null, rep5


title: dorsal hippocampus, 1hr after 10min threshold training, complexed JetPEI:CREST phospho-null, rep3


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, vehicle, rep6


title: dorsal hippocampus, 1hr after 10min threshold training, vehicle, rep5


title: dorsal hippocampus, 1hr after 10min threshold training, complexed JetPEI:CREST phospho-null, rep1


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, vehicle, rep2


title: dorsal hippocampus, 1hr after 10min threshold training, vehicle, rep4


title: dorsal hippocampus, 1hr after 3min sub-threshold OLM training, vehicle, rep4


title: dorsal hippocampus, homecage, vehicle, rep5

value: Homecage


title: dorsal hippocampus, 1hr after 10min threshold training, vehicle, rep6


title: dorsal hippocampus, 1hr after 10min threshold training, vehicle, rep2


title: dorsal hippocampus, 1hr after 10min threshold training, vehicle, rep1


title: dorsal hippocampus, 1hr after 10min threshold training, vehicle, rep3


title: dorsal hippocampus, homecage, vehicle, rep2


title: dorsal hippocampus, homecage, vehicle, rep3


title: dorsal hippocampus, homecage, vehicle, rep1


title: ChIL_Par_2

city: Kobe

first: Hirohisa

last: Kyogoku

state: Hyogo

address: 1-1, Rokkodai-chou

department: Agricultural Science

country: Japan

institute: Kobe university

data_processing:
ChIL-seq: fastq files were aligned to mouse reference genome GRCm38 using the bowtie2 with the options '-q -N 1 -L 25 -p 16 --no-mixed --no-discordant'.
ChIL-seq: PCR duplicates were removed using Picard and uniquely mapped reads were extracted with samtools using the "XS:" flag.
ChiL-seq: number of reads in each 100-bp bin were counted using deepTools.
mouse reference genome GRCm38
a tab-delimited text file including CPM normalized count values in each 100-bp bin for each sample

source_name: 1-cell embryos

extract_protocol:
BDF1(C57BL/6×DBA2) ×JF1/Ms zygotes were selected 10 h after fertilization (late G2 or PN5 stage) and the second polar body was removed using a micromanipulator. Zygotes were fixed with 1% PFA for 30 min after removal of the second polar body. After permeabilization with 1% Triton X-100 for 10 min, zygotes were blocked with Blocking One-P (Nacalai Tesque) for 20 min. Zygotes were incubated with mouse anti-histone H3K4me3 antibody (1:200, Cosmo Bio, MABI0004-100) for 8-10 h at 4°C. We observed the immunofluorescence signals of the probes under a microscope to selectively collect 1PN biparental zygotes and not parthenotes.
ChIL-seq libraries were prepared as previously described 45 with some modifications, including a change in the SDS concentration from 0.2% to 0.05%.

tag: methods

tag: embryo type

value: Parthenote

tag: embryo type in silico


title: ChIL_P1PN_1

value: BDF1(C57BL/6xDBA2) xJF1/Ms


title: ChIL_1PN_1


title: dorsal hippocampus, homecage, vehicle, rep4


title: ChIL_Par_1


title: ChIL_P1PN_2


title: Len_6

description:
Library name: Len_6
Ion Torrent

value: uterine tumor

value: mouse tumor cell


title: Len_7

description:
Library name: Len_7
Ion Torrent


title: ChIL_2PN_1


title: dorsal hippocampus, homecage, vehicle, rep6


title: ChIL_2PN_2


title: ChIL_1PN_2


title: Len_5

description:
Library name: Len_5
Ion Torrent


title: Len_3

description:
Library name: Len_3
Ion Torrent


title: Len_4

description:
Library name: Len_4
Ion Torrent


title: Len_2

description:
Library name: Len_2
Ion Torrent


title: Con_5

description:
Library name: Con_5
Ion Torrent


title: Con_4

description:
Library name: Con_4
Ion Torrent


title: Con_3

description:
Library name: Con_3
Ion Torrent


title: Con_2

description:
Library name: Con_2
Ion Torrent


title: Len_1

description:
Library name: Len_1
Ion Torrent


title: Con_1

description:
Library name: Con_1
Ion Torrent


title: Recurrent_tumor_9

description:
Library name: Recurrent_tumor_9
Ion Torrent


title: Con_6

description:
Library name: Con_6
Ion Torrent


title: Recurrent_tumor_2

description:
Library name: Recurrent_tumor_2
Ion Torrent


title: Recurrent_tumor_4

description:
Library name: Recurrent_tumor_4
Ion Torrent


title: Recurrent_tumor_5

description:
Library name: Recurrent_tumor_5
Ion Torrent


title: Recurrent_tumor_8

description:
Library name: Recurrent_tumor_8
Ion Torrent


title: Recurrent_tumor_3

description:
Library name: Recurrent_tumor_3
Ion Torrent


title: Recurrent_tumor_1

description:
Library name: Recurrent_tumor_1
Ion Torrent


title: Primary_tumor_3

description:
Library name: Primary_tumor_3
Ion Torrent


title: Recurrent_tumor_6

description:
Library name: Recurrent_tumor_6
Ion Torrent


title: Primary_tumor_2

description:
Library name: Primary_tumor_2
Ion Torrent


title: WT_Test_Jak2_Host_2_LSK

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

description: Library name: WT_Test_Jak2_Host_2

data_processing:
For RNA sequencing, reads were sequenced using NovaSeq X Plus platform and alligned to mm10 using STAR and gene counts identified using subread:feature count.
Assembly: mm10
Supplementary files format and content: reads are aligned to mm10

source_name: HSPC (LSK)

extract_protocol:
For RNA sequencing, 7000 HSPC cells were sorted using a MoFlo cell sorter. RNA was extracted using NucleoSpin RNA plus XS (Takara:740990.50)
RNA libraries for RNAseq was prepared using Takara Clonetech SMARTer mRNA library kit following manufacturers protocol.

value: HSPC (LSK)

value: Vav-Cre


title: WT_Test_Jak2_Host_4_LSK

description: Library name: WT_Test_Jak2_Host_4


title: Tet2_Test_Jak2_Host_4_LSK

description: Library name: Tet2_Test_Jak2_Host_4


title: Primary_tumor_1

description:
Library name: Primary_tumor_1
Ion Torrent


title: Tet2_Test_Jak2_Host_2_LSK

description: Library name: Tet2_Test_Jak2_Host_2


title: Tet2_Test_Jak2_Host_3_LSK

description: Library name: Tet2_Test_Jak2_Host_3


title: WT_Test_Jak2_Host_1_LSK

description: Library name: WT_Test_Jak2_Host_1


title: Tet2_Test_Jak2_Host_1_LSK

description: Library name: Tet2_Test_Jak2_Host_1


title: Recurrent_tumor_7

description:
Library name: Recurrent_tumor_7
Ion Torrent


title: WT_Test_Jak2_Host_3_LSK

description: Library name: WT_Test_Jak2_Host_3


title: Tet2_Test_WT_Host_4_LSK

description: Library name: Tet2_Test_WT_Host_4


title: WT_Test_WT_Host_4_LSK

description: Library name: WT_Test_WT_Host_4


title: WT_Test_WT_Host_3_LSK

description: Library name: WT_Test_WT_Host_3


title: Tet2_Test_WT_Host_3_LSK

description: Library name: Tet2_Test_WT_Host_3


title: WT_Test_WT_Host_2_LSK

description: Library name: WT_Test_WT_Host_2


title: WT_Test_WT_Host_1_LSK

description: Library name: WT_Test_WT_Host_1


title: Tet2_Test_WT_Host_2_LSK

description: Library name: Tet2_Test_WT_Host_2


title: CD45+ cells, olaparib

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

description:
Library name: WN_UVA_2
PE150

data_processing:
Once the FASTQ files for each sample were generated, data analysis was initiated. scRNA-seq reads were processed using the Cell Ranger software (10x Genomics) with default parameters, and each sample was analyzed individually. Briefly, N nucleotides (nt) from Read1 and Read2 were aligned to the reference genome using STAR. Barcodes and unique molecular identifiers (UMIs) were filtered and corrected. PCR duplicates were identified based on barcode, UMI, and gene ID, and only confidently mapped, non-duplicate reads with valid barcodes and UMIs were retained for the generation of the gene-barcode matrix. The filtered gene expression matrices containing only high-confidence cellular barcodes were produced during this processing step. Subsequent quality control and downstream analyses were performed using the Seurat R package.
Assembly: Mouse mm10
Supplementary files format and content: Normalized gene expression.matrix

source_name: breast tumor

extract_protocol:
Tumor tissues collected from mice treated with vehicle, olaparib alone, or the combination of olaparib and IRG1-IN-1 were enzymatically dissociated into single-cell suspensions using a collagenase/hyaluronidase-based digestion buffer. CD45 positive immune cells were then enriched using a CD45 positive selection kit (18945, StemCell Technologies). For each treatment group, single-cell suspensions from four individual tumors were pooled by centrifugation and resuspended in CryoStor CS10 (100-1061, StemCell Technologies) for preservation. Single-cell RNA sequencing was performed by Novogene using the 10x Genomics platform.
To ensure high-quality sequencing data, a rigorous library construction and quality control strategy is implemented. The process begins with library preparation, during which multiple quality control steps are performed to monitor and ensure library integrity. Specifically, Qubit 2.0 is used for preliminary quantification of library concentration, Agilent 2100 is employed to assess insert size distribution, and qPCR is conducted to accurately measure the effective concentration of the library. Only libraries that pass all QC steps are pooled according to their effective concentrations and anticipated data output, and subsequently subjected to high-throughput sequencing on an Illumina platform.

value: breast tumor

value: CD45+ cells from BP tumor

value: BP is Mouse breast cancer cell

value: Olalarib


title: Colonic Organoids, Butyrate, Day 3

city: New York

first: Chia-Wei

last: Cheng

state: NY

address: 650 West 168th Street, Rm 1110

institute: Columbia University Irving Medical Center

description:
Library name: CC059
Sample ID in Gene Counts.csv: CC059

data_processing:
Libraries were sequenced using Element AVITI at Columbia Genome Center.Samples were multiplexed in each lane, yielding  targeted number of paired-end 75bp reads reads for each sample.
Bases2fastq version 1.7.0.1196148384 was used for converting BCL to fastq format, coupled with adaptor trimming. Gene-level expression counts were generated by a pseudoalignment to a kallisto index created from transcriptomes (Mouse:GRCm38.p6) using kallisto (0.44.0)
Assembly: GRCm38.p6
Supplementary files format and content: csv file for Gene-level expression counts: Gene Counts.csv

source_name: Colon

growth_protocol: Organoids were established from WT male jmouse aged 24 weeks  with approval from IACUC/ animal welfare and ethics committee of Columbia University (#AC-AABI4557). We have complied with all relevant ethical regulations for animal use. Mice were sacrificed by euthanasia with carbon dioxide asphyxiation, and death was ensured by cervical dislocation. Organoids were maintained in complete crypt culture medium: crypt media consisted of Advanced DMEM (supplemented with 1% Glutamax and 1% Penicillin-Streptomycin along with the following components (Table S1): 40ng/ml Recombinant EGF, 200ng/ml Recombinant Noggin, and 500ng/ml Recombinant R-spondin, 1x B27 supplement, 1x N2 supplement, 3μM CHIR99021, and 10μM Y-27632 dihydrochloride monohydrate.Prganoids were maintained for upto five passages in a humidified incubator with 5% CO2 at 37°C, with routine passaging by mechanical dissociation every 7-10 days.

extract_protocol:
Organoids were isolated from Matrigel domes by manual dissociation and incubation with TrypLE Dissociation reagent. Cells were lysed using the QIAzol Lysis reagent (Qiagen).
Poly-A pulldown was employed to enrich mRNAs from total RNA samples prior to library construction using Illumina TruSeq chemistry. The final PCR step has been modified using the KAPA HiFi HotStart Ready Mix.

treatment_protocol: 100mM stock solution of sodium butyrate dissolved in PBS was diluted to 2mM final treatment concentration in complete crypt media and used to treat organoid samples.

value: Colon

value: Organoid

value: WT

value: Butyrate 72h


title: Colonic Organoids, Butyrate, Day 2

description:
Library name: CC055
Sample ID in Gene Counts.csv: CC055

value: Butyrate, 48h


title: CD45+ cells, vehicle

description:
Library name: WN_UVA_1
PE150

value: Vehicle


title: Colonic Organoids, Untreated, Day 2

description:
Library name: CC054
Sample ID in Gene Counts.csv: CC054

value: Untreated


title: Colonic Organoids, Untreated, Day 3

description:
Library name: CC058
Sample ID in Gene Counts.csv: CC058


title: J2PN_21

data_processing:
RNA-seq: fastq files were aligned to mouse reference genome GRCm38 using the Hisat2 v2.0.5
RNA-seq: BAM files resulting from the alignments were summarized to genes using the featureCounts v2.0.0 with the parameters ' -p -O --fraction’
mouse reference genome GRCm38
tab-delimited text files include raw counts values for each sample

source_name: a single two cell embryo

extract_protocol:
C57BL/6 × JF1/Ms zygotes were selected 10 h after fertilization (late G2 or PN5 stage) and the second polar body was removed using a micromanipulator. Two-cell embryos were corrected 34 h after fertilization. Single 2-cell embryo were lysed using cell lysis buffer  [cantained in SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio)] in 0.2 mL single tube.
libraries were prepared with SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio) and Nextera XT DNA Library Preparation Kit (illumina).

value: RNA-seq


title: J2PN_19


title: J2PN_22


title: CD45+ cells, olaparib+IRG1-IN-1

description:
Library name: WN_UVA_3
PE150


title: Circular RNA_Rnasek KO_biological rep1

type: RNA

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

description: Circular RNA_Rnasek KO_biological rep1

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: The signals were scanned using the Agilent Scanner G2505C

data_processing: Quantification was processed and normalized based on quantiles by using Agilent Feature Extraction software (v.11.0.1.1). Mouse data were analyzed using the Significance Analysis of Microarrays (SAM) method implemented in the R package samr (v3.0), enabling sensitive detection of differential signals

source_name: MEFs

label_protocol: The enriched circular RNAs were amplified and transcribed into Cy3 labeled cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (QIAGEN)

growth_protocol: MEFs were isolated from day 12.5 to 13.5 embryos and cultured in a 100 mm cell culture dish containing DMEM (SH30243.01, Hyclone, Logan, USA), 10% FBS (12483-020, Gibco, Waltham, MA, USA), and 1% penicillin-streptomycin solution (SV30010, HyClone, Logan, USA) at 37°C in 5% CO2 condition.

extract_protocol: Total cell RNAs were purified TRIzol by manufacturer's recommendations.

treatment_protocol: For generating RNasek deficient MEFs, Rnasek fl/fl (control) MEFs and UBC-CreERT2; Rnasek fl/fl MEFs were treated with 4-hydroxy-tamoxifen (4-OHT) for four consecutive days at a concentration of 2 μM dissolved in 100% EtOH.

value: MEFs


title: J2PN_18


title: J2PN_20

value: Low quality


title: B2PN_43

value: C57BL/6 xJF1/Ms


title: B2PN_40


title: B2PN_42


title: Circular RNA_Rnasek KO_biological rep2

description: Circular RNA_Rnasek KO_biological rep2


title: Circular RNA_Control_biological rep2

description: Circular RNA_Control_biological rep2


title: B2PN_41


title: Circular RNA_Control_biological rep1

description: Circular RNA_Control_biological rep1


title: J2PN_17


title: J1PN_7

value: Parthenote


title: B2PN_38


title: B2PN_39


title: B1PN_21


title: B2PN_37


title: B2PN_32


title: B1PN_20


title: B2PN_35


title: B2PN_36


title: P_7


title: Tet2_Test_WT_Host_1_LSK

description: Library name: Tet2_Test_WT_Host_1

value: HSPC (LSK)

value: Vav-Cre


title: B2PN_30


title: B2PN_34


title: B2PN_31


title: B1PN_22


title: B2PN_33


title: P_5


title: P_3


title: P_9


title: P_4


title: P_32


title: P_6


title: P_8


title: P_29


title: P_28


title: P_31


title: JE590,GIT+,KD-

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

description: Library name: JE590,GIT+,KD-

data_processing:
Raw paired‑end RNA‑seq reads were aligned to the Ensembl reference genome using STAR (v2.7.3a) with the following parameters : --quantMode GeneCounts  --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --readFilesCommand gunzip -c . This to enable gene‑level quantification (GeneCounts), sorting of output BAM files by genomic coordinates, retention of unmapped reads, on‑the‑fly decompression of gzipped FASTQ files and standard SAM attributes. Alignment was performed using 19 threads ( --runThreadN 19).
Assembly: GRCh38
Supplementary files format and content: counts.xlsx: col_1 = ensembl gene id, col_2 = gene symbol (Homo_sapiens.GRCh38.99.gtf), other cols are raw count for each sample as generated by STAR

organism: Homo sapiens

source_name: Liver

extract_protocol:
Total RNAs from mouse bone marrow-sorted hCD45+ pellets and liver pieces were extracted using the QIAGEN AllPrep DNA/RNA Mini kit (Qiagen, Hilden, Germany) according to manufacturer instructions. RNA purity and integrity were monitored using Clariostar (BMG Labtech, Champigny sur Marne, France) and Agilent Fragment Analyzer Automated CE system (Agilent technologies, Les Ulis, France) with the DNF-471 RNA (15NT) standard sensitivity kit. Only RNA with no sign of contamination nor marked degradation were considered good quality and used for further analysis.
For RNA-seq, mRNA libraries were generated following the manufacturer recommendations (mRNA hyper prep from ROCHE). Bar-coded libraries were pooled and sequenced on the Novaseq6000 200 cycles Illumina sequencer, with a sequencing depth corresponding to a minimum of 40 million of 2x100bp paired-end reads per sample after demultiplexing

value: Liver

value: whole liver extract (murin cells + human MOLM14)

value: FLT3-ITD, MLLr

value: GIT+,KD-

tag: batch


title: P_24


title: P_26


title: JE590,GIT-,KD-

description: Library name: JE590,GIT-,KD-

value: GIT-,KD-


title: P_23


title: P_22


title: P_2


title: JE590,GIT+,KD+

description: Library name: JE590,GIT+,KD+

value: GIT+,KD+


title: JE558,GIT+,KD+

description: Library name: JE558,GIT+,KD+

source_name: Bone marrow

value: Bone marrow

value: purified human MOLM14 cells


title: P_27


title: JE590,GIT-,KD+

description: Library name: JE590,GIT-,KD+

value: GIT-,KD+


title: P_30


title: P_21


title: JE558,GIT-,KD+

description: Library name: JE558,GIT-,KD+


title: JE558,GIT+,KD-

description: Library name: JE558,GIT+,KD-


title: JE558,GIT-,KD-

description: Library name: JE558,GIT-,KD-


title: Neuron D10 3μM Uridine Rep 3

city: Dallas

first: Samuel

middle: Kent

last: McBrayer

state: Texas

address: 6000 Harry Hines Boulevard, NL11.110K

department: Children's Research Institute

institute: UT Southwestern Medical Center

description: Library name: Neuron_D10-3μM_Uridine_3

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.  Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values. Functional enrichment, when available, is performed using gene set enrichment analysis with gseapy v0.12 using the MSigDB Hallmark gene set.
Assembly: hg38
Supplementary files format and content: xlsx file contains raw reads for each sample
Supplementary files format and content: xlsx file contains CPM values for each sample

source_name: Neuron

growth_protocol: HNF cells were cultured in DMEM (Thermo Fisher 11995-065) supplemented with fetal bovine serum (FBS, 10%, GeminiBio 100-106) and penicillin/streptomycin (100 U/mL and 100 μg/mL, respectively, Thermo Fisher 15140148) in 5% CO2 and at ambient oxygen at 37°C. HNF-derived NPCs were cultured in DMEM / F12 (1:1) (Thermo Fisher 11320033) supplemented with sodium pyruvate (1 mM, Thermo Fisher 11360070), B27 supplement minus vitamin A (1×, Thermo Fisher 12587010), N2 supplement (1×, Thermo Fisher 17502048), laminin (1 µg/mL, Thermo Fisher OB1415-01), and bFGF (20 ng/mL, GoldBio 1140-02). NPC-derived neurons were cultured in DMEM / F12 (1:1) (Thermo Fisher 11320033) supplemented with sodium pyruvate (1 mM, Thermo Fisher 11360070), B27 supplement minus vitamin A (1×, Thermo Fisher 12587010), N2 supplement (1×, Thermo Fisher 17502048), laminin (1 µg/mL, Thermo Fisher OB1415-01), and FBS (10%, GeminiBio 100-106). All cells were routinely evaluated for mycoplasma contamination and confirmed to be negative.

extract_protocol:
RNA was prepared from cells using the RNeasy Plus Mini Kit (QIAGEN 74136) according to the manufacturer’s instructions.
Libraries were prepared by Plasmidsaurus via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

value: Neuron

value: NPC-derived neuron


title: P_1

value: RNA-seq


title: Plasma, NRS 6, sample 22

city: Gimcheon

first: Yeongdon

last: Ju

state: Gyeongsangbuk-do

address: 214, Daehak-ro, Gimcheon-si

department: Department of Biomedical Laboratory Science

institute: Gimcheon University

description: Library name: Patient 22

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
TMM+CPM normalization was performed by EdgeR.
Assembly: hsa
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Plasma

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

value: Plasma

value: gastrointestinal cancer


title: P_19

value: Parthenote


title: Plasma, NRS 6, sample 20

description: Library name: Patient 20


title: Neuron D10 3μM Uridine Rep 1

description: Library name: Neuron_D10-3μM_Uridine_1


title: Plasma, NRS 8, sample 19

description: Library name: Patient 19


title: Neuron D10 3μM Uridine Rep 2

description: Library name: Neuron_D10-3μM_Uridine_2


title: P_18


title: Neuron D10 0μM Uridine Rep 3

description: Library name: Neuron_D10-0μM_Uridine_3


title: Plasma, NRS 6, sample 21

description: Library name: Patient 21


title: Plasma, NRS 5, sample 17

description: Library name: Patient 17


title: P_20


title: P_17


title: Plasma, NRS 7, sample 16

description: Library name: Patient 16


title: Neuron D10 0μM Uridine Rep 2

description: Library name: Neuron_D10-0μM_Uridine_2


title: Plasma, NRS 5, sample 14

description: Library name: Patient 14


title: Plasma, NRS 4, sample 15

description: Library name: Patient 15


title: Neuron Rep 3

description: Library name: Neuron_3


title: Plasma, NRS 6, sample 18

description: Library name: Patient 18


title: P_15


title: Neuron D10 0μM Uridine Rep 1

description: Library name: Neuron_D10-0μM_Uridine_1


title: Plasma, NRS 6, sample 12

description: Library name: Patient 12


title: Plasma, NRS 5, sample 11

description: Library name: Patient 11


title: P_16


title: Plasma, NRS 6, sample 13

description: Library name: Patient 13


title: Neuron Rep 1

description: Library name: Neuron_1


title: Plasma, NRS 0, sample 7

description: Library name: Patient 7


title: Plasma, NRS 0, sample 8

description: Library name: Patient 8


title: P_11


title: P_14


title: Plasma, NRS 0, sample 4

description: Library name: Patient 4


title: c2NPC Rep 2

description: Library name: NPC_2

source_name: NPC

value: NPC

value: HNF-derived neural progenitor cell


title: P_13


title: Plasma, NRS 2, sample 6

description: Library name: Patient 6


title: Plasma, NRS 2, sample 5

description: Library name: Patient 5


title: P_12


title: Neuron Rep 2

description: Library name: Neuron_2


title: Plasma, NRS 3, sample 10

description: Library name: Patient 10


title: CPSF6 siRNA 3

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

description: Library name: Sample 6

data_processing:
Raw reads were trimed using fastp
Trimed reads were aligned to the reference genome using bowtie2
PCR duplicates were removed using umi tools
Samtools were used to sort, convert and index alignment files
Deeptools were used to generate bigwig files
Assembly: GRCh38
Supplementary files format and content: bigwig files

source_name: Cardiac fibroblast

extract_protocol:
RNA was extracted from right ventricular control, failing samples and  human cardiac fibroblast treated with  control and CPSF6 siRNA
PAC-seq as described in Routh et al, 2017

value: Cardiac fibroblast

value: CPSF6 siRNA


title: HNF Rep 3

description: Library name: HNF_3

source_name: HNF

value: HNF

value: Primary fibroblast


title: Plasma, NRS 3, sample 3

description: Library name: Patient 3


title: c2NPC Rep 1

description: Library name: NPC_1


title: CPSF6 siRNA 2

description: Library name: Sample 5


title: Plasma, NRS 0, sample 1

description: Library name: Patient 1


title: c2NPC Rep 3

description: Library name: NPC_3


title: CPSF6 siRNA 1

description: Library name: Sample 4


title: P_10


title: J2PN_9


title: HNF Rep 2

description: Library name: HNF_2


title: J2PN_7


title: Control siRNA 3

description: Library name: Sample 3

value: Control siRNA


title: Control siRNA 2

description: Library name: Sample 2


title: Plasma, NRS 3, sample 9

description: Library name: Patient 9


title: J2PN_8


title: Plasma, NRS 1, sample 2

description: Library name: Patient 2


title: HNF Rep 1

description: Library name: HNF_1


title: J2PN_6


title: Control siRNA 1

description: Library name: Sample 1


title: J2PN_5


title: Right ventricular failure 3

description: Library name: Sample 7

source_name: heart

extract_protocol:
RNA was extracted from right ventricular control and failing samples.
PAC-seq as described in Routh et al, 2017

value: heart

tag: sample group

value: Right ventricular failure


title: ME_ERK

city: HangZhou

first: WeiKang

last: Meng

state: ZheJiang

address: A4 Floor, Teaching Building, School of Medicine, Zijingang Campus, Zhejiang University

institute: ZheJiangUniversity

description:
Library name: sample 2
The raw data are being made available for controlled in dbGap

data_processing:
ChIP-seq data were processed using the nf-core/chipseq pipeline (v1.1.0).
Raw FASTQ files were quality-checked using FastQC (v0.11.8), and adaptor trimming was performed using TrimGalore (v0.5.0).
High-quality reads were aligned to the human reference genome (Ensembl GRCh38.99) using BWA (v0.7.17).
High-quality reads were aligned to the human reference genome (Ensembl GRCh38.99) using BWA (v0.7.17).
Peak calling was performed using MACS2 (v2.1.2), and narrow peaks with q-value < 0.05 were retained as final peaks.
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigWig files representing normalized genome-wide ERK1/2 binding signals and BED files containing called peak regions.

growth_protocol: hESCs were maintained in mTeSR medium in a humidified incubator at 37°C with 5% CO₂ and induced toward mesendoderm (ME) differentiation under defined conditions.

extract_protocol:
Cells were crosslinked with formaldehyde, chromatin was fragmented by sonication, and immunoprecipitation was performed using an ERK1/2 antibody. Input chromatin was processed in parallel without immunoprecipitation. DNA was purified for sequencing.
ChIP-seq libraries were prepared using standard Illumina library preparation protocols and sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: Cells were cultured under ME differentiation conditions prior to chromatin immunoprecipitation.

value: human embryo stem cell

value: WT

value: ME differentiation


title: Right ventricular failure 2

description: Library name: Sample 6


title: input_ERK

description:
Library name: sample 1
The raw data are being made available for controlled in dbGap


title: J2PN_4

tag: strain


title: Right ventricular control 2

description: Library name: Sample 2

value: Right ventricular control


title: J2PN_3

value: RNA-seq


title: Right ventricular control 1

description: Library name: Sample 1


title: J2PN_2


title: KO, 1G10, 5548

city: Omaha

first: Justin

last: Rudd

address: 2500 California Plaza

institute: Creighton University

description: Library name: 23_S22

data_processing:
Analysis of bulk RNA-seq data was performed in PartekFlow. Adapter-trimmed reads were aligned to hg38 using STAR (Dobin et al., 2013) and quantified to ‘hg38-Ensembl Transcripts release 105’ using PartekE/M. Gene counts were normalized by median ratio, and normalized counts were used for differential expression analysis using DESeq2 (Love et al., 2014).
Assembly: hg38
Supplementary files format and content: Text file includes normalized counts for each sample

molecule: polyA RNA

source_name: xenograft tumor

growth_protocol: For subcutaneous xenografts of hFWE WT or KO cells, 1*106 SCC13 cells were resuspended in 100µl of cold 1:1 sterile PBS:Matrigel (Corning 356237) and subsequently injected into the subcutaneous space on the dorsal flank of a NOD-Prkdcem26Cd52Il2rgem26Cd22/NjuCrl (NCG) mouse (Charles River 572). Tumors were harvested at 26d post injection for transcriptomic analysis.

extract_protocol:
At necropsy, tumors were weighed before partitioning for RNA isolation or histological processing. RNA was isolated from flash frozen samples using Qiagen RNeasy Mini Kit (Qiagen 74104).
For preparation of sequencing libraries, 500ng of RNA isolated from flash frozen tumors was used with the NEBNext Ultra II Directional RNA Library Prep kit for Illumina along with NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturers instructions. Library quality and quantity were assessed using RNA ScreenTape Assay (Agilent) and Agilent 4200 TapeStation System following the manufacturers protocol. 3 nM equimolar pooled libraries were sequence on the Illumina NextSeq 2000 system (Illumina) using NextSeq 1000/2000 P2 Reagent Cartridge 100 cycles and P2 Flow Cell (Illumina).

value: xenograft tumor

value: Cutaneous Squamous Cell Carcinoma

tag: genotype

value: hFWE KO


title: Right ventricular failure 4

description: Library name: Sample 8


title: KO, 1G10, 5549

description: Library name: 24_S23

tag: cell type


title: Right ventricular control 4

description: Library name: Sample 4


title: Immortalized endometrial stromal cells transfected with vitamin D receptor siRNA3

city: Durham

first: MyeongJin

last: Yi

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Library name: siVDR_THESC3

data_processing:
Reads were trimmed of adapter sequences using Trim Galore with default settings except for specifying Illumina adapter sequences and paired-end validation.
Assembly: hg38 genome
Supplementary files format and content: merged files contain merged peaks in bed format for each condition
Supplementary files format and content: bigwig files contain non-normalized bed files for each sample.

source_name: T-HESC

growth_protocol: The cells were cultured and distributed into a 6-well plate in DMEM/F12 containing 10% v/v fetal bovine serum, 100 units/mL penicillin, and 100 ug/mL streptomycin.

extract_protocol:
The cells were lysed with Greenleaf lysis buffer (10 mM Tris-Cl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, and ddH2O up to final volume)
The lysed cells were tagmented by Tn5 transposase, amplified using PCR, and purified by AMPure XP beads.

treatment_protocol: The cells were transfected with each siRNA in OPTI-MEM containing 2% v/v charcoal-stripped fetal bovine serum.

value: T-HESC

value: Endometrial Stromal Cells

value: VDR knockdown


title: Right ventricular failure 1

description: Library name: Sample 5


title: KO, 1G10, 5547

description: Library name: 22_S21


title: J2PN_1


title: Immortalized endometrial stromal cells transfected with vitamin D receptor siRNA2

description: Library name: siVDR_THESC2


title: KO, 1G10, 5546

description: Library name: 21_S20


title: Immortalized endometrial stromal cells transfected with vitamin D receptor siRNA1

description: Library name: siVDR_THESC1


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA3

description: Library name: siNT_THESC3

value: Non-target control


title: J2PN_16


title: KO, 2B8, 5544

description: Library name: 19_S18


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA2

description: Library name: siNT_THESC2


title: J2PN_15


title: Right ventricular control 3

description: Library name: Sample 3


title: Immortalized endometrial stromal cells transfected with pooled non-targeting siRNA1

description: Library name: siNT_THESC1


title: KO, 2B8, 5545

description: Library name: 20_S19


title: DB21_P-SF3B1_T235_DMSO_REP1

city: Pamplona

first: Igor

last: Ruiz de los Mozos

state: Nyp

address: C. del Sadar s/n

department: Department of Personalized Medicine

country: Spain

institute: NASERTIC

description:
Library name: DB21_P-SF3B1_T235_DMSO_REP1
P-SF3B1_T235_DMS
P-SF3B1_T235_DMSO_1_3_4_GROUP_chr.bed.gz
P-SF3B1_T235_DMSO_1_3_4_GROUP_chr_norm.bigWig

data_processing:
iCLIP sequencing data, including total, P-Thr211- and P-Thr235 SF3B1 samples, were analyzed on the flow.bio platform (https://app.flow.bio/ ) using the nf-core/clipseq pipeline (West, C. et al. 2023) (v1.0; https://github.com/nf-core/clipseq/tree/1.0.0 ).
Initial processing involved removing experimental barcodes (iCount version 2.0.0, de-multiplex function https://github.com/tomazc/iCount ),  followed by read alignment with STAR (Dobin, A. et al. 2013) against the human reference genome (hg38, GRCh38.p13 primary assembly, GENCODE version 39), allowing up to two mismatches. Unique molecular identifiers (UMIs) were applied to identify and eliminate PCR duplicates.
Cross-linking events were determined by identifying the nucleotide immediately preceding each uniquely mapped sequencing read.
Genome-wide coverage tracks for combined iCLIP replicates were generated using deepTools (Ramirez, F. et al. 2014) , normalized by sequencing depth and total read count, and binned per nucleotide.
Assembly: GRCh38.p13 primary assembly, GENCODE version 39
Supplementary files format and content: iCLIP individual sample crosslink site (bed.gz)
Supplementary files format and content: iCLIP individual sample crosslink site normalized by sequencing depth and total read count, and binned per nucleotide (bigWig)
Supplementary files format and content: iCLIP group merge sample crosslink site (bed.gz)
Supplementary files format and content: iCLIP group merge crosslink site normalized by sequencing depth and total read count, and binned per nucleotide (bigWig)

growth_protocol: Human colorectal HCT116 cell line was maintained in DMEM/high glucose media supplemented with L-glutamine, sodium pyruvate and 5% FBS at 37°C and 5% CO2.

extract_protocol:
Described in detail in library construction protocol
iCLIP was performed as previously described (Huppertz et al., 2014) with only minor modifications described below. Each cell pellet (originally from one 150 cm2 plate) was lysed in 1 ml of lysis buffer and the lysate was homogenized by passing three-times through an insulin syringe. Lysate was treated with 4 U/ml Turbo DNase (Thermo Fisher, AM2238), 12 U/ml RNase I (Thermo Fisher, AM2295) shaking at 1100 rpm and 37°C for 3 min. Clarified extracts (21000g for 30 min) were incubated for 2 h with appropriate antibody pre-bound to 50 µl of protein G Dynabeads. After series of stringent washes, adenylated L3 RNA adapter was ligated to the 3’end of crosslinked RNAs. Proteins and crosslinked RNAs were resolved by SDS-PAGE (NuPAGE 4-12% Bis-Tris Protein Gel, Thermo Fisher Scientific, NP0322) and transferred to nitrocellulose membrane. The region of the membrane containing the radioactively labeled crosslinked protein–RNA complexes was excised, RNA was isolated and reverse transcribed to cDNA. cDNA was fractionated using urea denaturing gel electrophoresis and three fractions running between 70-85 nt (L-low), 85-120 nt (M-medium) and 120-200 nt (H-high) were isolated. Each fraction was independently circularized by single-stranded DNA ligase, annealed to an oligonucleotide complementary to the restriction site and cut between the two adapter regions by BamHI. After final PCR amplification using P3 and P5 Solexa primers all three fractions were pooled together in ratio 1:5:5 (L:M:H). Multiplexed libraries were sequenced as 75 bp single-end reads on Illumina sequencer (HiSeq 2500 or NextSeq 500)

treatment_protocol: The OTS964 inhibitor was purchased from MedChem Express (HY-12467) and diluted in DMSO. HCT116 cells were plated onto 150 cm2 plates to reach 75 % confluency at the day of teatment. Next day cells were treated with solvent (DMSO) or 50 nM OTS964 for 1 h. The cells were than crosslinked by UV-C (254 nm, 200 mJ/cm2).

tag: treatment

value: DMSO

value: biol. rep 1


title: J2PN_14


title: DB21_P-SF3B1_T211_OTS964_REP2

description:
Library name: DB21_P-SF3B1_T211_OTS964_REP2
P-SF3B1_T211_OTS964
DB21_P-SF3B1_T211_OTS964_GROUP.bed.gz
DB21_P-SF3B1_T211_OTS964_GROUP_norm.bigWig

value: biol. rep 2


title: KO, 2B8, 5543

description: Library name: 18_S17


title: J2PN_13


title: DB21_P-SF3B1_T211_OTS964_REP1

description:
Library name: DB21_P-SF3B1_T211_OTS964_REP1
P-SF3B1_T211_OTS964
DB21_P-SF3B1_T211_OTS964_GROUP.bed.gz
DB21_P-SF3B1_T211_OTS964_GROUP_norm.bigWig


title: DB21_P-SF3B1_T211_DMSO_REP2

description:
Library name: DB21_P-SF3B1_T211_DMSO_REP2
P-SF3B1_T211_DMSO
DB21_P-SF3B1_T211_DMSO_GROUP.bed.gz
DB21_P-SF3B1_T211_DMSO_GROUP_norm.bigWig


title: KO, 2B8, 5542

description: Library name: 17_S16


title: KO, 2F7, 5540

description: Library name: 15_S15


title: DB21_P-SF3B1_T211_DMSO_REP1

description:
Library name: DB21_P-SF3B1_T211_DMSO_REP1
P-SF3B1_T211_DMSO
DB21_P-SF3B1_T211_DMSO_GROUP.bed.gz
DB21_P-SF3B1_T211_DMSO_GROUP_norm.bigWig


title: B lymhocyte, Control, line1, G4C2 probe

city: Baltimore

first: Mingming

last: Liu

state: MD

address: 615 N. Wolfe Street

department: BMB, BSPH

institute: Johns Hopkins University

description: Library name: B_CTRL1_G4C2

data_processing:
Raw sequencing reads were processed with TrimGalore v.0.6.7 and quality of the raw sequencing reads was assessed using FastQC v.0.11.9
The trimmed reads were aligned to the human genome (hg19) using Bowtie v.2.3.5.1
Peaks were identified using the MACS2 v.2.1.1 software and filtered using a q-value cutoff of 0.01
BigWig files were generated using deepTools.
Assembly: hg19
Supplementary files format and content: BigWig files for each sample
Library strategy: ChIRP-seq

source_name: B lymphocyte

extract_protocol:
Cells were fixed with 1% glutaraldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator (Diagenode) until the chromatin DNA was 100–500 bp in size.
ChIRP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit complemented with  NEBNext Multiplex Oligos for Illumina by following the manufacturer's manual. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: B lymphocyte

value: Control


title: J2PN_12


title: DB21_P-SF3B1_T235_OTS964_REP1

description:
Library name: DB21_P-SF3B1_T235_OTS964_REP1
P-SF3B1_T235_OTS964
DB23_P-SF3B1_T235_OTS964_1_3_4_GROUP_chr.bed.gz
DB23_P-SF3B1_T235_OTS964_1_3_4_GROUP_chr_norm.bigWig


title: B lymhocyte, Control, line1, Input

description: Library name: B_CTRL1_Input


title: KO, 2F7, 5539

description: Library name: 14_S14


title: B lymhocyte, Control, line1, Antisense probe

description: Library name: B_CTRL1_AS


title: J2PN_11


title: B lymhocyte, C9-ALS, line1, Input

description: Library name: B_C9ALS1_Input


title: KO, 2F7, 5538

description: Library name: 13_S13


title: B lymhocyte, Control, line1, Sense probe

description: Library name: B_CTRL1_S


title: B lymhocyte, C9-ALS, line1, Sense probe

description: Library name: B_C9ALS1_S


title: J1PN_6


title: B lymhocyte, C9-ALS, line1, Antisense probe

description: Library name: B_C9ALS1_AS


title: WT, 6C10, 5536

description: Library name: 11_S11

value: hFWE WT


title: HEK293T, EMX1, 200928, Rep1

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

institute: Tsinghua University

data_processing:
ATAC-seq read adaptors were trimmed utilizing cutadapt (version 3.4, Martin 2011 ). Subsequently, reads were aligned to reference genome hg38 for human or mm10 for mouse using bowtie2 (version 2.4.4, Langmead 2009 ) with parameters "-X2000 –mm -t -q -N1 -L 25 --no-mixed --no-discordant". After alignment, reads were subjected to filtering through samtools (version 1.13, Danecek 2021) to exclude unmapped reads, unmapped mates, non-primary alignments, reads failing platform/vendor quality assessments, and duplicates (SAM flag 1804).
Following a standard samtools sort and fixmate operation, PCR duplicates were removed. This was accomplished using a combination of picard (version 2.20.4 sourced from http://broadinstitute.github.io/picard/), MarkDuplicates (employing standard parameters) and samtools view (with parameters "-F1804 -f2").
Regions rich in repetitive sequences and those challenging to alignment were masked in alignment with the encode blacklist ( Amemiya 2019 ). For estimating the accessibility coverage, each bam file read was extended by 250bp both upstream and downstream from its 5' end, accommodating the 4/5bp adjustment due to the Tn5 transposition.
Assembly: GRCh38
Supplementary files format and content: bigWig

growth_protocol: HEK293T cells were maintained in Dulbecco's Modified Eagle Medium (DMEM; Gibco, C11995500BT) supplemented with 10% Fetal Bovine Serum (FBS; NEWZERUM, FBS-CE500), penicillin/streptomycin (Gibco, 10378016). K562 cells were cultured in RPMI 1640  (Gibco, 72400047) supplemented with 10% FBS (FBS; NEWZERUM, FBS-CE500), penicillin/streptomycin (Gibco, 10378016).Mouse ESC were cultured on mouse embryonic fibroblast (MEF) and maintained in KnockOut DMEM (Gibco, 10829018) supplemented with 15% FBS (Gibco, 1009914), penicillin/streptomycin (Gibco, 10378016), sodium pyruvate (Gibco, 11360070), β-mercaptoethanol (ThermoFisher, 21985023), GlutaMAX (Gibco, 35050061), non-essential amino acids (NEAA; GIBCO, 11140050),  PD0325901 (Selleck, S1036), CHIR99021 (Selleck, S2924) and leukemia inhibitory factor (Milipore, ESG1107).All cells were cultured in a 5% CO2 humidified atmosphere at 37°C. Cells were passaged with 0.25% Trypsin-EDTA (Gibco, 25200072) at a 1:3 split and maintained in 10-cm tissue culture dishes.

extract_protocol:
The Dynabeads™ M-280 sheep anti-Rabbit IgG (Invitrogen, 11201D) was diluted at 1:10 in 1× PBS (Invitrogen, AM9624) to prepare 50 µL solution at room temperature. The mixture was placed on DynaMag™-96 Side Skirted (Invitrogen, 12027) for 3 minutes, and the supernatant was carefully pipetted off. 1 µL of Nesprin1 antibody (abcam, ab192234) and 1× PBS was added to a volume of 50 µL, and it was rotated at room temperature for 30 minutes. The tube was then transferred onto the magnetic strand for 3 minutes, the supernatant was pipetted off, and the beads were resuspended in 5µL of 1× PBS. This washing step with 1× PBS was repeated. The beads were subsequently resuspended with 250 µL (10µL per sample) of cell lysis buffer, which containing 10 mM HEPES (Gibco, 15630106), 2.5 mM MgCl2 (Invitrogen, AM9530G), 10 mM KCl (Sigma, P9333), 1mM DTT (ThermoFisher, 707265ML), 0.5% Triton™ X-100 (Sigma, 93443), 2 U Recombinant RNase Inhibitor (Takara, 2313A).500 GFP-positive cells were sorted into each well of a 96-well plate containing 10 µL lysis buffer by flow cytometer (BD Influx, 14005297) . The plate was centrifuged at 700 g for 1 minute, and then incubated at  4°C and 300 rpm for 30 minutes. After placing the plate on DynaMag™-96 Side Skirted for 3 minutes, the supernatant was carefully transferred to another plate for RNA-seq. The tagmentation mix containing TTE MIX (Vazyme, TD501), 5× TTBL (Vazyme, TD501), 0.3× PBS, 0.1%  Tween-20 (Sigma, P9416), 0.1% IGEPAL-630 (sigma, 13021), 10% DMF(Sigma, D4551) and 0.01% Digitonin (Promega, G9441), was prepared before this transfer. 5 µL tagmentation mix was used to resuspend the nuclei by vortexing for 1 s. Then, the nuclei were incubated at a prewarmed 37°C for 30 minutes. 5 µL of stop mix (1% SDS (Invitrogen, AM9822), 100 mM EDTA (Invitrogen, AM9260G) 0.4 µg/µl Proteinase K (NEB, P8107S, 0.2 µg/µl Carrier RNA (Applied Biosystems™, 4382878)) was then added and incubated at 55°C for 30 minutes. After that, 22 µL of VAHTS DNA Clean Beads (Vazyme, N411-02) was added, and the mixture was left at room temperature for 10 minutes. It was subsequently washed with 80% Ethanol (Sigma, E7023) twice.
The DNA fragment was eluted in 10 µL UltraPure DNase/RNase-Free Watre（Invitrogen, 10977015）, and 12.5 µL 2× KAPA HIFI ready mix (Roche, KK2602) and 1.25 µL 25 µM barcode primer were added for PCR amplification. The PCR program was set as follow: 72°C for 5 minutes, 98°C for 3 minutes, followed by 15 cycles of 98°C for 20 s, 63°C for 30 s, and 72°C  for 3 minutes, and then hold at 4°C until further use.RNA was purified by 2.2× VAHTS RNA Clean Beads (Vazyme, N412-03) from the supernatant and reverse transcribed using the SMART-seq2 protocol (Picelli S, 2014). The RNA-seq library construction was done using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501), following the manufacturer's manual.

treatment_protocol: For human HEK293T and mouse NIH/3T3 cells, a cell density of between 50 - 80% confluence was maintained on the day of transfection.For each well in a 24-well plate, 50 µL Opti-MEM I Reduced-Serum Medium (Gibco, 31985062)was pipetted into a sterile microcentrifuge tube.To this medium, 1.0 µL (0.5 µg/µL) of plasmid DNA was added and mixed thoroughly by gentle pipetting. Subsequently, 3 ug of PEI (Polysciences, 24765-1) was introduced to the diluted DNA mixture. The mixture was incubated at room temperature for 30 minutes before being transferred to individual wells.For mESC, 2 μg of plasmid was added to 50 μL Opti-MEM I and mixed well. Then, 4 μl of P3000 reagent (Invitrogen, L3000001) was added and mixed well. In another tube, 3 µL of Lipo3000 reagent (Invitrogen, L3000001) was combined with 50 μL Opti-MEM I and mixed well. The contents of the two tubes were combined in a single tube and mixed thoroughly. After a 15-minute incubation at room temperature, mESCs were resuspended and diluted to a concentration of 1E+6 cells/mL. 1 ml of this cell suspension was added to each well, followed by the addition of the previously prepared transfection reagent to the corresponding well. Gentle mixing was performed, and the plate was placed in a cell incubator at 37°C with 5% CO2 and saturated humidity.

value: embryonic kidney cell

value: WT

value: transfected with PX458 plasmid


title: B lymhocyte, C9-ALS, line1, G4C2 probe

description: Library name: B_C9ALS1_G4C2


title: J1PN_5

value: RNA-seq