title: Hippocampus_TDP43-KQ_Male_rep2

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

data_processing:
Raw reads were trimmed and filtered of adapter sequencing using cutadapt (Martin 2011), and filtered such that at least 90% of bases had a quality score of at least 20
Reads were then aligned to the reference mouse genome (mm10, RefSeq gene annotations) using STAR v2.5.2b (Dobin 2013), and transcript abundance was estimated using salmon (Patro 2017)
Differential expression between TDP43-KQ and TDP43-WT cortex and hippocampus was then detected using DESeq2 v1.34.0 (Love 2014) in R v4.1.0 using a design that corrects for both mouse sex and litter effects. These batch effects were also removed from the VST-normalized expression values using limma (Ritchie 2015)
Differential splicing analyses were performed on splice junctions extracted from genome-aligned BAM files using regtools and LeafCutter, where tests compared TDP43-KQ to TDP43-WT correcting for sex for each brain region. Results were then summarized and visualized using LeafViz
Assembly: mm10
Supplementary files format and content: VST normalized expression values from DESeq2, corrected by sex and batch

source_name: Hippocampus

growth_protocol: Mice were housed in ventilated microbarrier cages on racks providing HEPA filtered air supply to each cage. Animals were kept on a 12hr light-dark cycle with access to food and water ad libitum. All animal husbandry, experiments, and procedures were performed in strict compliance with animal protocols approved by the Institutional Animal Care and Use Committee (IACUC) of the University of North Carolina at Chapel Hill (#21.257).

extract_protocol:
Mouse brain tissue was isolated, flash frozen, and pulverized as described above. Approximately 20mg of pulverized brain tissue per sample was used to isolate RNA. 1mL of TRIzol (Invitrogen 15596018) was added to each nuclease-free eppendorf tube containing pulverized tissue, and cells were lysed via trituration with a P1000 pipette tip, followed by trituration with a 21G and then a 25G needle on a 1mL syringe. Samples were centrifuged at 4°C for 5min at 10,000rcf to remove tissue debris. The supernatant was removed and added to a new tube containing 200uL of chloroform, which were mixed by inversion and cooled on ice for 5min. Samples were centrifuged at 4°C for 15min at 10,000rcf, and the upper aqueous phase containing RNA was transferred into a new tube, followed by the addition of 100uL of isopropanol to precipitate RNA and overnight incubation at -20°C. The next day, samples were centrifuged at top speed (18,000rcf) for 20min at 4°C to pellet the RNA. The pellets were washed twice with 1mL of ice-cold 70% molecular biology grade ethanol and then air dried for 15min at RT. The RNA pellets were resuspended in 20uL of nuclease-free water. On-column DNAse digestion and RNA clean-up was then performed using the Qiagen RNeasy mini kit (Qiagen, Inc. 74106) per manufacturer’s instructions, followed by elution in nuclease-free water.
RNA concentration was assessed using Qubit® RNA BR Assay Kit (Q10210) and a Qubit® 3.0 Fluorometer. RNA integrity was assessed using an Agilent 4150 TapeStation system and associated RNA screen tape reagents (Agilent 5067-5576). Only samples with an estimated RNA integrity number (RIN) ≥7.0 were sent to the New York Genome Center (NYGC) for bulk total RNA sequencing. Upon receipt at NYGC, RNA samples were re-evaluated for quantification and integrity, using Ribogreen and Fragment Analyzer 5300, respectively. Total RNA libraries were prepped using Kapa Total library prep with Ribo-Erase, in accordance with manufacturer recommendations. Briefly, 500ng of total RNA was used for ribosomal depletion and fragmentation of total RNA. Depleted RNA underwent first and second strand cDNA synthesis. cDNA was then adenylated, ligated to Illumina sequencing adapters, and amplified by PCR (using 9 cycles). The cDNA libraries were quantified using Fragment Analyzer 5300 (Advanced Analytical) kit FA-NGS-HS (Agilent, catalog number DNF-474-1000) and Spectramax M2 (Molecular Devices) kit Picogreen (Life Technologies, catalog number P7589). Libraries were sequenced on an Illumina NovaSeq sequencer, using paired end sequencing (2 x 100 bp cycles) to a depth of >75M read pairs per sample.

treatment_protocol: Mice were anesthetized deeply with isoflurane and euthanized via rapid decapitation. The hippocampus and neocortex were dissected out of the brain on a cold surface using clean surgical tools, placed into cryo-safe nuclease-free microcentrifuge tubes, flash frozen in liquid nitrogen (LN2), and stored at –80C until processing. Frozen tissue was then pulverized in LN2-cooled stainless steel Cryo-Cups using cold stainless steel pestles and transferred into cold nuclease-free microcentrifuge tubes and immediately stored at –80C until use.

value: Hippocampus

value: Male

tag: replicate

tag: litter


title: Hippocampus_TDP43-KQ_Female_rep1

status: Public on Jan 09 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: Sex

value: Female


title: Hippocampus_TDP43-WT_Male_rep1


title: Hippocampus_TDP43-KQ_Female_rep2


title: Hippocampus_TDP43-KQ_Female_rep3


title: Hippocampus_TDP43-KQ_Male_rep1


title: A2058 8q-loss c2 rep 2

city: New Haven

first: Jason

last: Sheltzer

state: CT

address: 300 George Street

department: Surgery

institute: Yale University

description: Melanoma cell line with engineered loss of chr8q trisomy

data_processing:
Custom Novogene QC scripts
Novogene: Remove reads containing adapters
Novogene: Remove reads containing >10% undetermined bases (N)
Novogene: Remove reads with >=50% of bases with Qscore <= 5
Hisat2 (v2.0.5) alignment to hg38
featureCounts v1.5.0-p3 to count reads mapped to each gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

growth_protocol: Cells were plated and allowed to grow for 24 hours prior to extraction

extract_protocol:
Qiagen RNEeasy
In brief, mRNA was purified from total cellular RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis. Subsequently, libraries were prepared with end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Single cell derived clones with engineered chr losses were generated through a collection of ReDACT techniques

tag: cell line

tag: cell type

value: melanoma

tag: treatment

value: ReDACT-CO, targeting chr8q


title: A2058 8q-loss c1 rep 2


title: Cortex_TDP43-KQ_Male_rep3

source_name: Cortex

value: Cortex


title: Cortex_TDP43-KQ_Male_rep1


title: Hippocampus_TDP43-WT_Female_rep1


title: Cortex_TDP43-KQ_Male_rep2


title: Hippocampus_TDP43-WT_Female_rep3


title: Hippocampus_TDP43-WT_Female_rep2


title: Cortex_TDP43-WT_Male_rep1


title: Cortex_TDP43-KQ_Female_rep2


title: Cortex_TDP43-WT_Male_rep2


title: Cortex_TDP43-KQ_Female_rep3


title: SAS2

status: Public on Jan 01 2023

city: Chicago

first: Peter

last: Savage

state: IL

department: Pathology

institute: University of Chicago

description: CD4-Cre TCRβtg Tcra-/-

data_processing:
Raw reads were aligned to reference genome mm10 using the STAR aligner.
ENSEMBL genes were quantified using FeatureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text, unnormalized counts per gene

source_name: Pooled spleen and lymph nodes

extract_protocol:
RNA was isolated following a standard chloroform extraction and isopropanol precipitation protocol.
Strand-specific RNA-seq libraries were prepared using the TruSEQ mRNA RNA-seq library protocol (Illumina).

treatment_protocol: Cell populations of interest were FACS sorted into TRI Reagent (Sigma), frozen in dry ice, and stored at -80°C prior to use.

value: Pooled spleen and lymph nodes

tag: strain

value: CD4-Cre TCR{beta}tg Tcra-/-

value: Inoculum with retrovirally transduced bone marrow (SAS TCRα)

value: CD4+ T cells


title: SAS1

description: CD4-Cre TCRβtg Tcra-/-


title: Cortex_TDP43-WT_Female_rep3


title: Cortex_TDP43-KQ_Female_rep1


title: Cortex_TDP43-WT_Female_rep2


title: Cortex_TDP43-WT_Female_rep1


title: A2058 WT rep 4

description: Wildtype melanoma cell line, harboring gains of chr1q, 7p, and 8q

value: WT

value: Wildtype


title: SAS3

description: CD4-Cre TCRβtg Tcra-/-


title: SAS6

description: CD4-Cre TCRβtg Tcra-/-


title: ANT5

description: CD4-Cre TCRβtg Tcra-/-

value: Inoculum with retrovirally transduced bone marrow (ANT TCRα)


title: ANT4

description: CD4-Cre TCRβtg Tcra-/-


title: ANT3

description: CD4-Cre TCRβtg Tcra-/-


title: ANT1

description: CD4-Cre TCRβtg Tcra-/-


title: P54_L3

status: Public on Dec 07 2022

city: Bangkok-noi

first: Chandhanarat

last: Chandhanayingyong

state: Bangkok

address: 2 Wanglang road

department: Orthopaedic Surgery

country: Thailand

institute: Mahidol University

data_processing:
The sequencing was done by Vishuo Biomedical Ltd. Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
The original raw data from Illumina platform are transformed to Sequenced Reads, known as Raw Data or RAW Reads, by base calling. Raw data are recorded in a FASTQ file, which contains sequencing reads and corresponding sequencing quality.

source_name: Colorectal adenocarcinoma

extract_protocol:
RNA from fresh frozen tissue was harvested using RNeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
The library construction was conducted by Vishuo Biomedical Ltd. RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Colorectal adenocarcinoma

tag: time


title: P50_L3


title: P70_L3


title: P72_L3


title: P61_L3


title: P65_L3


title: P44_L3


title: P27_L3


title: P30_L3


title: P07_L3


title: P32_L3


title: P40_L3


title: P02_L3


title: TBi_RNA94

data_processing:
The sequencing was done by Novogene Co Ltd. From the RNA samples to the final data, each step, including sample test, library preparation, and sequencing, influences the quality of the data, and data quality directly impacts the analysis results. To guarantee the reliability of the data, quality control (QC) is performed at each step of the procedure.
The filtering process is as follows:  (1) Remove reads containing adapters.  (2) Remove reads containing N > 10% (N represents the base cannot be determined).  (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.    5'-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3'    3' Adapter:    5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3'
tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA from fresh frozen tissue was harvested using RNeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
The library construction was conducted by Novogene Co Ltd. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.


title: TBi_RNA96


title: TBi_RNA93


title: TBi_RNA97


title: TBi_RNA99


title: TBi_RNA92


title: TBi_RNA89


title: TBi_RNA90


title: TBi_RNA98


title: TBi_RNA95


title: TBi_RNA87


title: TBi_RNA91


title: TBi_RNA86


title: TBi_RNA85


title: P20_L3


title: TBi_RNA80


title: TBi_RNA82


title: TBi_RNA78


title: TBi_RNA77


title: TBi_RNA83


title: TBi_RNA79


title: TBi_RNA81


title: TBi_RNA75


title: TBi_RNA73


title: TBi_RNA69


title: TBi_RNA67


title: TBi_RNA88


title: TBi_RNA68


title: TBi_RNA72


title: TBi_RNA65


title: TBi_RNA63


title: TBi_RNA66


title: TBi_RNA61


title: TBi_RNA59


title: TBi_RNA62


title: TBi_RNA64


title: TBi_RNA58


title: TBi_RNA57


title: TBi_RNA84


title: TBi_RNA55


title: TBi_RNA56


title: TBi_RNA54


title: TBi_RNA70


title: TBi_RNA74


title: TBi_RNA53


title: TBi_RNA52


title: TBi_RNA49


title: TBi_RNA47


title: TBi_RNA51


title: TBi_RNA46


title: TBi_RNA45


title: TBi_RNA60


title: TBi_RNA43


title: TBi_RNA40


title: TBi_RNA41


title: TBi_RNA38


title: TBi_RNA36


title: TBi_RNA35


title: TBi_RNA37


title: TBi_RNA39


title: TBi_RNA31


title: TBi_RNA3


title: TBi_RNA42


title: TBi_RNA33


title: TBi_RNA32


title: TBi_RNA30


title: TBi_RNA27


title: TBi_RNA28


title: TBi_RNA29


title: TBi_RNA48


title: TBi_RNA25


title: TBi_RNA26


title: TBi_RNA21


title: TBi_RNA22


title: TBi_RNA50


title: TBi_RNA20


title: TBi_RNA18


title: TBi_RNA19


title: TBi_RNA15


title: TBi_RNA17


title: TBi_RNA13


title: TBi_RNA14


title: TBi_RNA114


title: TBi_RNA111


title: TBi_RNA107


title: TBi_RNA109


title: TBi_RNA104


title: TBi_RNA102


title: TBi_RNA100


title: TBi_RNA105


title: TBi_RNA106


title: TBi_RNA09


title: TBi_RNA07


title: TBi_RNA108


title: TBi_RNA04


title: TBi_RNA05


title: TBi_RNA11


title: TBi_RNA02


title: TBi_RNA01


title: TBi_RNA103


title: C21_spleen_isotype [scRNA-seq]

status: Public on Nov 29 2022

first: Jun

last: Huang

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

description:
scRNA Sample 4
Single-cell RNA-seq
mRNA

data_processing:
scRNA-seq: The scRNA-seq reads were aligned to the mm10 reference genome and quantified using the cellranger count (10X Genomics, version 3.0.0). The filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: For both scATAC and scRNA-seq, the filtered matrix output folder from the 10X pipeline of each sample is provided as a tar archive.

source_name: P14 CD8+ T cells

extract_protocol:
By using fluorescence-activated cell sorting, CD8+ T cells were obtained from the spleens or lungs of chronic virus-infected mice and from the subcutaneous tumor tissues or metastatic lungs of tumor-engrafted mice. Then, the CD8+ T cells were performed with single-cell RNA-seq library construction.
For single-cell RNA-seq library construction, the libraries were prepared using Chromium Next GEM Single Cell 3’ reagent Kits (10x Genomics) according to the manufacturer’s instructions. Briefly, sorted CD8 T cells were suspended in DPBS containing 0.04% BSA and captured in droplets using a Chromium Single Cell Controller instrument (10x Genomics). After reverse transcription and cell barcoding in droplets, cDNA was purified and PCR amplified, followed by fragmentation, end-repair, double-size selection and PCR amplification with sample-indexing primers.

value: Spleen

value: P14 CD8+ T cells

value: Isotype

tag: disease state

value: Chronic viral infection


title: T21_subcutaneous_aPD-L1 [scRNA-seq]

description:
scRNA Sample 7
Single-cell RNA-seq
mRNA

value: Subcutaneous tumor (B16F10-GP model)

value: Subcutaneous tumor


title: T21_lung_aPD-L1 [scRNA-seq]

description:
scRNA Sample 5
Single-cell RNA-seq
mRNA

value: Lung (B16F10-GP metastasis model)

value: Lung metastasis


title: T21_subcutaneous_isotype [scRNA-seq]

description:
scRNA Sample 8
Single-cell RNA-seq
mRNA


title: C21_lung_isotype [scRNA-seq]

description:
scRNA Sample 2
Single-cell RNA-seq
mRNA

value: Lung


title: Jiang_CD4_HIVdelta6_HTO

status: Public on Dec 05 2022

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Hashtag oligo and gene expression was computed and cells were deconvoluted using alevin-fry using a ‘splici' reference genome constructed using the concatenated hg38 and HIV genomes and GENCODE v36 transcriptomes.
Hashtag oligo and gene expression data were then imported into R v4.1 using fishpond, and hashtag oligos were demultiplexed using Seurat HTODemux
Cells were filtered if they contained a significant contribution of mitochondrial transcript signal using miQC, and subsequently filtered to contain at least 2,000 UMIs and at least 1,000 detected genes per cell.
Gene expression data were then normalized using scTransform v2 and samples were integrated together to identify one joint collection of cell clusters using Seurat with Louvain-Jaccard clustering with multilevel refinement (resolution=0.25).
Differential expression between HA15 and control-treated cells was performed using Distinct using log2 CPM (p_adj.glb < 0.05), and significant pathway enrichment was identified using g:Profiler focusing on KEGG and REACTOME pathways (FDR < 0.05).
Assembly: hg38-HIVp379d6
Supplementary files format and content: alevin-fry output files for GEX and HTO: GEX_quants_mat_rows.txt.gz, GEX_quants_mat_cols.txt.gz, GEX_quants_mat.mtx.gz, HTO_quants_mat_rows.txt.gz, HTO_quants_mat_cols.txt.gz, HTO_quants_mat.mtx.gz
Supplementary files format and content: Seurat output files: ClusterIdents.txt, SCTnormalized.txt.gz, SampleIdents.txt
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: HTO

growth_protocol: Peripheral blood or leukapheresis samples were collected from HIV-positive individuals receiving suppressive ART. CD4+ T cells were isolated using the EasySep CD4+ T cells Enrichment Kit or a custom resting CD4+ T cells isolation kit (StemCell Technologies) as previously described (Jiang et al., 2019; Jiang et al., 2018; Jiang et al., 2017). The purified CD4+ T cells were plated at a density of 1x106 cells and treated with indicated compounds

extract_protocol:
Single cell RNA-seq was performed by the Advanced Analytics core at UNC. Briefly, the primary CD4+ T cells of HIV latency were treated with or without HA15 for 2 days. The single cell suspensions were prepared and loaded on a GemCode Single-Cell instrument (10X Genomics, Pleasanton, CA) to generate single-cell beads in emulsion. All 3 replicates of each condition were multiplexed using hashtag oligos (Biolegend).
Then, scRNA-seq libraries were prepared using GemCode Single Cell 3′ Gel bead and library kit (10X Genomics) and quantified by quantitative PCR (Kappa Biosystems, Wilmington, MA)
Libraries were sequenced on an Illumina NovaSeq 6000-SP (San Diego CA). Read lengths were 28 bp for read 1, 10 bp i7 index, 10 bp for i5 index and 90 bp read 2. The flowcell was run in XP mode over both lanes.

value: HA15 and control

value: Primary CD4+ T with latent HIV infection

tag: antibodies/tags

value: TotalSeq_A0251=NegControl_Rep1; TotalSeq_A0252=NegControl_Rep2; TotalSeq_A0253=NegControl_Rep3; TotalSeq_A0254=HA15_Rep1; TotalSeq_A0255=HA15_Rep2; TotalSeq_A0256=HA15_Rep3


title: C21_lung_aPD-L1 [scRNA-seq]

description:
scRNA Sample 1
Single-cell RNA-seq
mRNA


title: TBi_RNA08


title: GD9_4hr_Veh_Rep5

status: Public on Oct 19 2022

data_processing:
Reads were quality-ﬁltered by requiring at least 90% of bases to have a quality score greater than 20 using fastq_quality_ﬁlter in FASTX 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Adapter sequences were removed using cutadapt 1.12 (Martin, 2011)
Reads were then aligned to the mm9 reference genome using STAR 2.5.2b (Dobin et al., 2013)
Transcript abundance was measured using salmon (77), and differential expression tests were performed using DESeq2 1.22.2 and hidden batch effects were removed using sva and limma
Assembly: mm9
Supplementary files format and content: VST normalized expression values from DESeq2

molecule: polyA RNA

source_name: Whole embryo

growth_protocol: Male and female adult C57BL/6J mice (Stock #: 000664) were obtained from Jackson Laboratories (Bar Harbor, ME) and housed in standard polycarbonate cages with cob bedding, shelter, and nesting material. Males were housed singly and females were housed in groups of up to five mice per cage. Mice had ad libitum access to food (Prolab Isopro RMH 3000, LabDiet, St. Louis, MO) and water and were maintained on a 12:12 hr light/dark cycle. Mice were mated in 2 hr sessions and copulation was confirmed by presence of a vaginal plug. The beginning of the mating session when the plug was found was defined as E0.0. All experimental procedures were approved by the Animal Care and Use Committee at UNC-Chapel Hill in accordance with NIH Guidelines

extract_protocol:
Either 2 or 4 hr after the injection, dams were sacrificed via CO2 followed by cervical dislocation. Embryos were dissected from the placenta and stage-matched based on somite number (2 hr: 19-20 somites; 4 hr: 20-21 somites). A maximum of two embryos per litter were used to minimize litter effects. RNA from the rostroventral neural tube (RVNT) from each embryo was isolated using the RNeasy Plus Micro kit (Qiagen, Germantown, Maryland) as previously described (Boschen et al., 2020). RNA from a total of 6 embryos per condition and time point (24 total embryos) were submitted for RNA-seq.
Libraries for RNA sequencing (RNA-seq) were prepared using the SMARTr Ultra Low Input RNA (Clontech, Mountainview, CA) and Nextera XT DNA (Illumina, San Diego, CA) kits by the UNC High Throughput Sequencing Facility. Samples were pooled prior to sequencing, after RNA extraction and library preparation was complete. Six total pools (1 sample/group/pool) and 1 pool per lane were used. Paired-end (50bp) sequencing was performed on an Illumina HiSeq 4000.

treatment_protocol: Pregnant dams were administered a single dose of 2.9 g/kg ethanol (25% vol/vol; Pharmaco-Aaper, Brookfield, CT) in Lactated Ringer’s solution via i.p. injection on E9.0 to target neurulation. Blood alcohol concentrations ± standard error, collected from a separate cohort of dams (n = 6), were 366.8 ± 30.3 mg/dl 30 min after injection and 337.9 ± 18.8 mg/dl 2 hr after injection. Control mice were administered an equal volume of Lactated Ringer’s solution (1.5 ml/100 g body weight).

tag: age

value: Veh

tag: time point


title: GD9_4hr_Veh_Rep2


title: GD9_4hr_Veh_Rep4


title: GD9_4hr_Veh_Rep1


title: GD9_4hr_EtOH_Rep6

value: EtOH


title: GD9_4hr_EtOH_Rep4


title: GD9_4hr_Veh_Rep6


title: GD9_2hr_EtOH_Rep5


title: GD9_4hr_EtOH_Rep1


title: Jiang_CD4_HIVdelta6_GEX

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

source_name: mRNA


title: GD9_2hr_EtOH_Rep6


title: GD9_4hr_EtOH_Rep5


title: Vd2 cells healthy

status: Public on Oct 24 2022

city: Duarte

first: Anastasia

middle: I

last: Kousa

state: CA

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

data_processing:
The cell-gene count matrix was constructed using the Sequence Quality Control (SEQC) package. Viable cells were identified on the basis of library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis.
Genome_build: GRCm38.p5 (mm10)
Supplementary_files_format_and_content: *_HTO.h5ad =  An h5ad file with hashtag annotation per cell index
Supplementary_files_format_and_content: *_fastqc.html = A quality control report which can spot problems that originate either in the sequencer or in the starting library material.
Supplementary_files_format_and_content: *_HTO_final-classification.tsv.gz = A hashtag classification file that tells you which cell is classified as which hashtag (tab-separated, gzipped)
Supplementary_files_format_and_content: *_HTO_final-matrix.tsv.gz = A gene expression matrix + hashtag classification file. A cell x gene matrix from scRNA-seq + one additional column that tells you which hashtag a given cell is classified as. (tab-separated, gzipped)
Supplementary_files_format_and_content: *_HTO_reads_barcodes.tsv.gz = A file containing the feature names, in this context our tags.
Supplementary_files_format_and_content: *_HTO_reads_features.tsv.gz = A file containing the cell barcodes.
Supplementary_files_format_and_content: *_HTO_reads_matrix.mtx.gz = A file containing the actual read count values
Supplementary_files_format_and_content: *_HTO_run_report.yaml = contains the parameters used for the run as well as some statistics
Supplementary_files_format_and_content: *_HTO_tag-list.csv = A comma-separated file with the hashtag list
Supplementary_files_format_and_content: *_HTO_umis_barcodes.tsv.gz =  A file containing the feature names, in this context our tags.
Supplementary_files_format_and_content: *_HTO_umis_features.tsv.gz = A file containing the cell barcodes.
Supplementary_files_format_and_content: *_HTO_umis_matrix.mtx.gz = A file containing the collapsed umi counts
Supplementary_files_format_and_content: *.h5 = A ReadArray object containing cell barcode, UMI, gene ID, genomic locus, and its status (e.g. uniquely mapped, barcode error, ...) for each read
Supplementary_files_format_and_content: *_Aligned.out.bam = A file containing reads aligned to genome
Supplementary_files_format_and_content: *_alignment_summary.txt = A text file containing alignment summary statistics
Supplementary_files_format_and_content: *_cb-correction.csv.gz = Cell-barcode correction file. This file is only needed for Velopipe (RNA Velocity pipeline for SEQC)
Supplementary_files_format_and_content: *_cell_filters.png = Visualization of cell filtering applied
Supplementary_files_format_and_content: *_de_gene_list.txt = List of differentially expressed genes in each cluster compared to rest (using MAST)
Supplementary_files_format_and_content: *_dense.csv = Filtered count matrix. Rows are cells and collumns are genes.
Supplementary_files_format_and_content: *_mini_summary.json = Key metrics in JSON format: Number of recovered cells, Number of reads, Percentage of reads uniquely mapped to genome, Sequencing saturation rate and etc.
Supplementary_files_format_and_content: *_mini_summary.pdf = SEQC alignment summary as a pdf
Supplementary_files_format_and_content: *_seqc_log.txt = A log file generated during a SEQC run
Supplementary_files_format_and_content: *_sparse_counts_barcodes.csv = Cell barcodes in numeric format.
Supplementary_files_format_and_content: *_sparse_counts_genes.csv = Gene names in the data
Supplementary_files_format_and_content: *_sparse_molecule_counts.mtx = Unfiltered molecule (UMI) count matrix in sparse matrix data format.
Supplementary_files_format_and_content: *_sparse_read_counts.mtx = Unfiltered read count matrix in sparse matrix data format
Supplementary_files_format_and_content: *_summary.tar.gz = Detailed information about alignments, filtering, etc. in gzipped tarball format
Supplementary_files_format_and_content: *_umi-correction.csv.gz = Cell-barcode correction file. This file is only needed for Velopipe (RNA Velocity pipeline for SEQC)
Supplementary_files_format_and_content: *_clean.h5ad = H5AD file with raw and normalized read counts and cell annotation (after bad quality cell filtering)

source_name: Healthy control subjects

extract_protocol:
PBMCs were collected into Becton Dickinson Vacutainer® CPTTM Cell Preparation Tubes with Sodium Citrate. Cells were frozen in liquid nitrogen in a freezing medium containing RPMI, 10% DMSO and 12.5% HSA. Between 0.3 and 10 x 106 PBMCs were stained in PBS with LIVE/DEAD Zombie UV Fixable dye (Biolegend) for 20 min at room temperature. Human Fc block (Miltenyi Biotec) was then added for 10 minutes at 4ºC, followed by a staining with MR1‐5‐OP‐RU APC and CD1d-PBS-57 BV421 or MR1‐Ac‐6‐FP and CD1d unloaded tetramer (acquired from NIH tetramer core facility) for 40 minutes at room temperature. The tetramer staining was followed by surface antibody staining for 15 minutes at room temperature. In each batch of samples (n per batch ranged from 23 to 30) we included one or more healthy control samples stained with loaded and unloaded tetramer and in most of the batches we included a pooled patient sample stained with the unloaded tetramer. PBMCs from healthy samples were isolated using density centrifugation with Ficoll Paque®. PBMC samples were stained for flow cytometry and purified populations of MAIT and Vd2 cells from 5 patients and 5 healthy controls were collected using FACS sorting.
The single-cell RNA-Seq of FACS-purifed cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1. In brief, purified cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Between 6,000 to 30,000 cells were targeted for each sample. Samples were multiplexed together on one lane of 10X Chromium following cell hashing protocol. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).
single cell RNA-seq

value: Vd2 cells


title: T21_lung_isotype [scRNA-seq]

description:
scRNA Sample 6
Single-cell RNA-seq
mRNA


title: GD9_2hr_Veh_Rep6


title: GD9_4hr_EtOH_Rep2


title: GD9_2hr_Veh_Rep5


title: GD9_2hr_EtOH_Rep3


title: C21_spleen_aPD-L1 [scRNA-seq]

description:
scRNA Sample 3
Single-cell RNA-seq
mRNA


title: GD9_2hr_EtOH_Rep4


title: GD9_2hr_EtOH_Rep1


title: GD9_2hr_Veh_Rep3


title: GD9_2hr_Veh_Rep4


title: GD9_2hr_Veh_Rep2


title: GD9_4hr_Veh_Rep3


title: GD9_2hr_Veh_Rep1


title: Visium, STEMI

status: Public on Oct 03 2022

city: La Jolla

first: Kevin

middle: R

last: King

address: 9500 Gilman Dr. MC 0412

department: Medicine and Bioengineering

institute: UC San Diego

description:
polyA RNA
V_Human_STEMI

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger software v3.0.2  or Space Ranger v1.2.2
Further processing was done with Seurat v4.1(cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Highly variable gene markers were identified using FindVariableFeatures from Seurat R package version 4.1
Assembly: GRCh38.p12.premrna2, mm10-1.2.0-premrna
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cardiac

extract_protocol:
Visium: Sections obtained from C57BL/6J (Jackson Laboratories) mice were imaged and processed for spatially resolved gene expression using the Visium Spatial Transcriptomics kit (10x Genomics). Samples were immediately snap-frozen in OCT using isopentane that was cooled in a liquid nitrogen bath. For cryosectioning, samples were equilibrated to −22 °C. 10 μm thick short axis sections were cut from the blocks onto Visium slides (10X Genomics) and processed according to the manufacturer’s protocol. Tissue permeabilization time was optimized at 30 minutes for infarcted mouse hearts. Hematoxylin and eosin (H&E) images generated during the Visium protocol were captured at 20x magnification on Nikon Eclipse Ti2-E widefield microscope and exported as tiled tiffs for analysis. Libraries were sequenced on the Illumina NovaSeq platform, and resulting data were processed using SpaceRanger (v.1.2.2, 10X Genomics)
Nuclei: Single nuclei were isolated from frozen tissue using a modified version of the protocol described (52). Mice hearts were weighed and minced before flash freezing with liquid nitrogen. Minced samples were resuspended in 0.5 ml nuclei lysis buffer (Millipore Sigma, Nuclei EZ prep, NUC101), 0.2 U/µl RNAse inhibitor (stock 40U/µl, Enzymatics Y9240L) and homogenized with a 2 ml dounce grinder for 10 strokes with A motor and at least 20 strokes with B motor (Sigma-Aldrich D8938). The lysates were resuspended with another 1 mL of nuclei lysis buffer and 2.5 minutes of incubation, and were filtered through 100 µm ,50 µm and 20 µm cell strainers (CellTrics filters 04-004-2318, 04-004-2317, 04-0042-2315). Then, they were centrifuged at 1000 x g for 5 min at 4°C to pellet nuclei. As Cui et al., 2020 described, the nuclear pellet was subsequently washed once in 6 mL of Sucrose buffer and centrifuged the cushioned suspension at 1,000 g for 10 min at 4°C to pellet nuclei. The pellet then was washed with 2ml of Nuclei Storage Buffer with 10 µg/ml 4′,6-diamidino-2-phenylindole (DAPI) and centrifuged at 1000 x g for 5 min at 4°C (5mg/ml, Invitrogen D1306). 200 µl of nuclei wash buffer (freshly 2% bovine serum albumin (BSA) in 1xPBS, 0.2 U/µl RNAse inhibitor and 1mM of EDTA) were added and nuclei were resuspended.  Fluorescence-activated cell sorting (FACS) were used to sort extracted nuclei. Nuclei was collected based on the separation between DAPIhigh and DAPIlow; After sorting using purity mode, DAPIhigh nuclei were pelleted at 1000 x g for 15 min at 4°C, resuspended in 2% BSA and trypan blue stained nuclei suspension were quality controlled and counted using hemocytometer (Hausser Scientific 3110V).    Single-nucleus RNA-seq was performed by microfluidic droplet-based encapsulation, barcoding, and library preparation, (10X Genomics). Paired end sequencing was performed on an Illumina Novaseq instrument. Low-level analysis, including demultiplexing, mapping to a reference transcriptome (mm10-1.2.0-premrna), and eliminating redundant UMIs, was performed with Cell Ranger 3.0.2 pipeline for 10X samples.
Single-nucleus RNA-seq was performed by microfluidic droplet-based encapsulation, barcoding, and library preparation, (10X Genomics). Paired end sequencing was performed on an Illumina Novaseq instrument. Low-level analysis, including demultiplexing, mapping to a reference transcriptome (mm10-1.2.0-premrna), and eliminating redundant UMIs, was performed with Cell Ranger 3.0.2 pipeline for 10X samples.

value: Cardiac

value: 45-year-old male

value: STEMI,LAD occlusion


title: GD9_4hr_EtOH_Rep3


title: Visium, Day7 MI biol rep 3

description:
polyA RNA
V_d7_3

value: WT

value: MI surgery


title: Visium, Day7 MI biol rep 2

description:
polyA RNA
V_d7_2


title: Visium, Day3 MI biol rep 1

description:
polyA RNA
V_d1_1


title: Visium, Day3 MI biol rep 3

description:
polyA RNA
V_d1_3


title: Visium, Day7 MI biol rep 1

description:
polyA RNA
V_d7_1


title: Visium, Day3 MI biol rep 2

description:
polyA RNA
V_d1_2


title: Visium, Day3 TAC, Day3 Needle pass biol rep 2

description:
polyA RNA
V_TAC_d3_Np_1


title: Visium Day 3 Sham biol rep 2, Day3 Needle pass biol rep 4

description:
polyA RNA
V_sham2_Np_3


title: Visium, Day 3 Sham biol rep 1, Day3 Needle pass biol rep 3

description:
polyA RNA
V_sham1_Np_2


title: Visium, 1HR 4HR Day3 Needle Pass, biol rep 1

description:
polyA RNA
V_1Hr_4Hr_d3_Np_4


title: Single nuclei, Day3 MI, biol rep 2

description:
nuclear RNA
snd3_2


title: Single nuclei, Day3 MI, biol rep 1

description:
nuclear RNA
snd3_1

value: I/R surgery


title: GD9_2hr_EtOH_Rep2


title: Single nuclei, Day7 MI, biol rep 2

description:
nuclear RNA
snD7 _2


title: Single nuclei, Day7 MI, biol rep 1

description:
nuclear RNA
snD7_1


title: Single nuclei, Day7 MI, biol rep 3

description:
nuclear RNA
snD7_3


title: Single nuclei, Day1 MI, biol rep 6

description:
nuclear RNA
snd1_6


title: Single nuclei, Day1 MI, biol rep 5

description:
nuclear RNA
snd1_5


title: Single nuclei, Day1 MI, biol rep 2

description:
nuclear RNA
snd1_2


title: Single nuclei, 4HR MI

description:
nuclear RNA
sn4hr


title: Single nuclei, Day1 MI, biol rep 1

description:
nuclear RNA
snd1_1


title: Single nuclei, Day1 MI, biol rep 4

description:
nuclear RNA
snd1_4


title: Single nuclei, Day1 MI, biol rep 3

description:
nuclear RNA
snd1_3


title: Single nuclei, 1HR MI, biol rep 2

description:
nuclear RNA
sn1hr_2


title: Single nuclei, 1HR MI, biol rep 1

description:
nuclear RNA
sn1hr_1


title: Single nuclei, Day0 MI, biol rep 3

description:
nuclear RNA
snd0_3


title: Visium, 4HR MI

description:
polyA RNA
V_4hr


title: Visium, 1HR MI

description:
polyA RNA
V_1hr


title: Single nuclei, Day3 MI, biol rep 3

description:
nuclear RNA
snd3_3


title: Single nuclei, Day0 MI, biol rep 1

description:
nuclear RNA
snd0_1


title: Single nuclei, Day0 MI, biol rep 2

description:
nuclear RNA
snd0_2


title: Visium, Day3 Isoproterenol

description:
polyA RNA
V_ISO_d3


title: PRO-seq, Rhesus LCL male, rmIFNa2, 1 hour, rep 1

status: Public on Oct 02 2022

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

data_processing:
Base calls and demultiplexing was done using Bcl2Fastq2 (v2.2.0).
Read quality and adapter trimming was done using BBMap (v38.05) bbduk with options ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=25 literal=AAAAAAAAAAAAAAAAAAAAAAA ref= The FASTA file containing common adapters found in https://github.com/Dowell-Lab/Nascent-Flow/blob/master/bin/adapters.fa.
Mapping was done usisng HISAT2 (v2.1.0) with options --very-sensitive --no-spliced-alignment.
SAM to BAM conversion was done using Samtools (v1.8).
Bidirectional loci were determined using Tfit and dREG as described in the Nextflow pipeline https://github.com/Dowell-Lab/Bidirectional-Flow. Tfit calls were obtained by first using the Tfit bidir module to call prelim regions. Added 3 kb-wide TSS regions to the prelim file and removed any part of the prelim regions that overlap with the TSS regions, cut the prelim regions that are > 10 kb down to equal size regions that have some overlap, coverage filtered to keep prelim regions having > 9 mapped reads. Finally, used the filtered/diced prelim regions on the Tfit model module to obtain Tfit calls. dREG calls were filtered as having FDR < 0.05, merged if within 20bp of each other, and having > 9 mapped reads.
Bigwigs were obtained using deepTools (v3.0.1) bamCoverage with options --binSize 1 --normalizeUsing RPKM --filterRNAstrand reverse (for pos file) or forward (for neg file) --scaleFactor 1 (for pos file) or -1 (for neg file).
Assembly: Homo sapiens datasets mapped to hg38, Macaca mulatta datasets mapped to rheMac10.
Supplementary files format and content: Files *.tfit.bed are 8-column BED files containing the interval of each detected bidirectional transcription locus. 1=Chr, 2=Start, 3=End, 4=Tfit Bidirectional Model Stats, 5-8= bedtools coverage interval report
Supplementary files format and content: Files *.dreg.bed are 7-column BED files containing the interval of each detected bidirectional transcription locus. 1=Chr, 2=Start, 3=End, 4-7= bedtools coverage interval report
Library strategy: PRO-seq

organism: Macaca mulatta

growth_protocol: The human and rhesus LCLs were cultured in RPMI-1640 media (Gibco 72400-047) using 15% FBS (Gibco 10437-028) and 100 units/mL Penicillin-Streptomycin (Gibco 15140-122) in vent-cap T-25 flasks (Corning 430639), and kept at a confluency between 400,000 cells/mL to 800,000 cells/mL during cell culture.

extract_protocol: PRO-seq datasets were prepared as described in Mahat 2016 (https://doi.org/10.1038/nprot.2016.086). Briefly, between 8 to 12 million nuclei per dataset were used for the PRO-seq transcription run-on using a mixture of rNTP and Biotin-11-CTP (PerkinElmer NEL542001EA). Total RNA was extracted using a phenol/chloroform precipitation. Isolated RNA was fragmented using base hydrolysis with NaOH. Biotinylated fragmented nascent transcripts were isolated using a first streptavidin Dynabeads M-280 (Invitrogen 11206D) pull down, and the VRA3 RNA adaptor was ligated at their 3’ end. A second streptavidin bead pull down was performed, followed by the enzymatic modifications of the RNA fragment 5’ ends with a pyrophosphohydrolase and a polynucleotide kinase, and the VRA5 RNA adaptor was ligated at their fixed 5’ ends. A third streptavidin bead pull down was performed, followed by the reverse transcription of the resulting adaptor-ligated libraries. The libraries were cleaned up with AMPure XP beads (Beckman Coulter A63881). Then, the libraries were amplified using 13 PCR cycles, and cleaned up again with another round of AMPure XP beads. The resulting library concentrations were measured with the Qubit dsDNA high sensitivity assay (Invitrogen Q32851), and their size distributions assessed using the Agilent High Sensitivity D1000 ScreenTape. PRO-seq datasets were sequenced using an Illumina NextSeq as single-end 75 bp long reads.

treatment_protocol: 48 hours prior to the IFN-α2 treatments, the cell cultures were switched to a similar media without antibiotics. To treat the LCLs with human IFN-α2, 10 ug of lyophilized purified protein obtained from Proteintech (Ref. HZ-1066 Lot. 0615-01) was resuspended in 100 uL of 0.1% BSA PBS, to yield a stock at 1.25x106 units/mL. The rhesus IFN-α2 was obtained from PBL Assay Science (Ref. 16105-1 Lot. 6987R) and already came resuspended in 0.1% BSA PBS at 4.03x106 units/mL. The LCLs were treated for 1 hour with either 100 units/mL of human IFN-α2, or with 100 units/mL of rhesus IFN-α2, or with an equal volume of 0.1% BSA PBS for the control untreated samples.

value: Male

value: Lymphoblastoid cell line

value: 1 hour


title: PRO-seq, Rhesus LCL female, rmIFNa2, 1 hour, rep 1

value: Female


title: PRO-seq, Rhesus LCL male, hsIFNa2, 1 hour, rep 1


title: PRO-seq, Rhesus LCL female, hsIFNa2, 1 hour, rep 1


title: PRO-seq, Rhesus LCL female, BSA, 1 hour, rep 1

value: BSA


title: OsEMF2b_Input

status: Public on Sep 28 2022

city: Wuhan

first: yue

last: li

address: Shizishan Street

country: China

institute: HUAZHONG Agriculture University

description: This Sample can be used as input for either the DJ_H3K27me3_ChIP or OsEMF2b_H3K27me3_ChIP samples.

library_source: genomic

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: bogWig file by deepTools bamCoverage

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: seedling

extract_protocol:
Rice tissues were crosslinked with 1% formaldehyde and quenched with 0.2 M glycine.
0.5 to 1g of the sample was ground into a fine powder in liquid nitrogen, the chromatin was fragmented into 200-600 bp by ultrasound processing using Bioruptor (Diagenode). The lysates were incubated at 4 °C for 1 to 6 h and rotated to form antibody-bead complexes. After reverse cross-linking of DNA and protein, ChIP-DNA was extracted using phenol: chloroform: isoamyl alcohol (P3803; Sigma-Aldrich). ChIP-DNA libraries were prepared by Illumina® (New England BioLabs, E7645) using the NEBNext® Ultra™ II DNA Library Preparation Kit. AMPure XP beads (Beckman, A63881) were used to select 250-650 bp library fragments.

tag: cultivar

value: Dongjin

value: seedling

tag: chip antibody


title: PRO-seq, Human LCL male, rmIFNa2, 1 hour, rep 1


title: PRO-seq, Human LCL male, hsIFNa2, 1 hour, rep 1


title: PRO-seq, Human LCL female, hsIFNa2, 1 hour, rep 1


title: PRO-seq, Human LCL female, rmIFNa2, 1 hour, rep 1


title: PRO-seq, Rhesus LCL male, BSA, 1 hour, rep 1


title: ST E3_aged

status: Public on Sep 04 2022

city: Lexington

first: Lance

middle: A

last: Johnson

state: KY

address: 760 Press Ave, HKRB 135

department: Physiology/Sanders-Brown Center on Aging

institute: University of Kentucky

description: 10x Genomics

data_processing:
Raw FASTQ data and H&E images were processed by the Space Ranger v1.3.0 (10X Genomics) pipeline. Illumina base call (BCL) files from the sequencing instrument were converted to FASTQ format for each sample using the mkfastq. Visium spatial expression libraries were analyzed with the count command. Image alignment to predefined spots was performed by the fiducial alignment grid of the tissue image to determine the orientation and position of the input image. Sequencing reads were aligned to the mm10 reference genome using STAR (v2.5.1b) aligner. Gene expression profiling in each spot was performed with UMI and 10X barcode information.
Assembly: GRCh38 and mm10 combined
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format fils, Tab-separated values files, and matrix files
Supplementary files format and content: Image files (.jpg, .png); json and csv files.
Library strategy: Spatial Transcriptome

source_name: Brain

extract_protocol:
The mirroring hemisphere (right) from brains processed for scRNAseq were immediately placed in OCT compound (Fisher HealthCare Tissue Plus O.C.T. Compound Clear 4585) and gently lowered into isopentane (Sigma Aldrich 2-Methylbutane M32631) in a beaker surrounded by dry ice (isopentane chilled to approximately -70°C). Brains were submerged for 60 seconds, placed on dry ice, wrapped in aluminum foil, and stored at -80°C until sectioning. Prepared brain hemispheres were cryosectioned to 10 μm thick coronal sections at approximately Bregma -2.00 mm. Serial 10 μm sections immediately rostral and caudal to the section mounted on the Visium Spatial Gene Expression slide (10X Genomics) were collected for immunohistochemistry. Optimal tissue permeabilization time was determined using the manufacturer’s optimization protocols (10X Genomics, Visium Spatial Tissue Optimization), and accordingly, experimental tissues were permeabilized for 18 min for Visium Spatial Gene Expression analysis. Prior to library preparation, tissue sections were methanol-fixed, stained with hematoxylin and eosin (H&E), and imaged on a Nikon NiU microscope with Fi3 color camera. Sections were then permeabilized and processed to obtain cDNA libraries, which were subsequently prepared according to the manufacturer’s protocol (https://support.10xgenomics.com/spatial-gene-expression/libraryprep).
Sample libraries were constructed using Next GEM automated 3’ reagents (10X Genomics, v3.1) following manufacturer’s suggested protocol (#CG000286 Rev B). Final library quantification and quality check was performed using BioAnalyzer (Agilent), and sequencing performed on a NovaSeq 6000 S4 flow cell, 150 bp Paired-End sequencing (Novogene).

value: Brain

value: non-neuronal brain cells

value: Brain cells


title: PRO-seq, Human LCL female, BSA, 1 hour, rep 1


title: PRO-seq, Human LCL male, BSA, 1 hour, rep 1


title: Physio_comp_Rep2

status: Public on Sep 01 2022

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Adaptor sequences and low-quality reads were trimmed using Trim Galore (v0.6.0; Martin, 2011). Trimmed reads were aligned to the mm10 reference genome using STAR (v2.7.8; Dobin et al., 2013) with --quantMode GeneCounts.
Assembly: mm10
Supplementary files format and content: Connts per million (CPM) of each sample processed using edgeR (with low expressed genes removed)

source_name: CD8+ T cell

growth_protocol: In vitro-activated CD8+ T cells were generated by stimulating naïve CD8+ T cells (1e6 cells/mL) with plate-bound anti-CD3ε (clone 2C11) and anti-CD28 (clone 37.51) antibodies (eBioscience, San Diego, CA) and 50 U/mL IL2 (PeproTech, Rocky Hill, NJ) for 3 days.

extract_protocol:
Total RNA was isolated from the cells and following Dnase I treatment.
mRNA was captured using polyA, and stranded libraies were constructed.

treatment_protocol: Activated T cells were washed and re-cultured in IMDM or VIM medium containing 10% dialyzed FBS, with or without defined physiologic carbon sources (PCS) for 24 h prior to RNA extraction.

value: CD8+ T cell

value: wild type

value: VIM+PCS medium


title: Physio_comp_Rep3


title: ST E4_young

description: 10x Genomics


title: ST E3_FAD

description: 10x Genomics


title: Physio_Rep3

value: VIM medium


title: ST E4_FAD

description: 10x Genomics


title: Physio_comp_Rep1


title: Physio_Rep2


title: Regular_comp_Rep3

value: IMDM+PCS medium


title: Regular_comp_Rep2


title: Physio_Rep1


title: Regular_Rep3

value: IMDM medium


title: Regular_Rep2


title: ST E4_aged

description: 10x Genomics


title: SCH_2

status: Public on Aug 25 2022

city: Dalian

first: Man

last: Li

state: Liaoning Province

address: 467#, Zhongshan Road, Shahekou distinct

department: Department of Oncology

institute: The Second Hospital of Dalian Medical University

data_processing:
illimina  Casava 1.8 software used for basecalling
Raw data (raw reads) of fastq  format were firstly processed through in-house perl scripts. In this step, clean data  (clean reads) were obtained by removing reads containing adapter, reads containing N  base and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2  (v2.0.5) and paired-end clean reads were aligned to the reference genome using  Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a  database of splice junctions based on the gene model annotation file and thus a better  mapping result than other non-splice mapping tools
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Genome_build: Homo Sapiens(GRCh38/hg38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample

source_name: breast cancer cell

growth_protocol: MDA-MB-231 cells were sustained in RPMI-1640(Gibco, C11875500BT) supplemented with 10% fetal bovine serum (FBS, Biological Industries, 04-001-1ACS) and 100 units x ml-1 per penicillin/streptomycin (Hyclone, SC30010) at 5% CO2 and mesophilic temperature of 37 °C in an incubator.

extract_protocol:
Total RNA was isolated from cells using Trizol Reagent (Thermo Fisher, Massachusetts, USA) according to the manufacturer's in struction. RNA sequencing was carried out on Illumina HiSeq platform by Novogene Corporation (Beijing, China).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: MDA-MB-231 cells were cultured in the medium containing 100mg/l salvia chinensia benth or vehicle for 24 hours

value: breast cancer cell

value: salvia chinensis benth


title: SCH_3


title: vehicle_2

value: vehicle


title: PKO_Etop_1_RNAseq_etoposide, 100 micromolar, 6hrs_rep1

status: Public on Aug 20 2022

city: Albany

first: Morgan

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

data_processing:
kallisto v0.46.2
Human transcriptome (ENSEMBL Homo sapiens v104 release) was downloaded from http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
kallisto quant was using bootstrap mode (100 bootstraps) against the ENSEMBL v.104 Homo sapiens transcriptome index
Assembly: ENSEMBL Homo sapiens v104 transcriptome release
Supplementary files format and content: tab-separated value files containing standardized ENSMBL gene name, gene length, estimated tag counts, and transcripts per million (TPM) values
Supplementary files format and content: tab-separated value files containing differential gene expression data

source_name: colon

growth_protocol: Cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum at 37˚C and 5% carbon dioxide in a humidified, water-jacketed incubator.

extract_protocol:
Total RNA was extracted from the stated cell lines/genotypes/treatment conditions using Zymo Quick-RNA miniprep kits and eluted in RNAse-free water
PolyA-selected RNAseq libraries were constructed by GeneWiz/Azenta for sequencing on an Illumina HiSeq 2000.

treatment_protocol: Fresh media (McCoy's 5A with 10% fetal bovine serum) was added to cells which were then treated with either DMSO, Nutlin3A, etoposide, histidinol, or tunicamycin at the specified concentrations for 6 hrs before RNA was harvested

value: colon

value: colon carcinoma

value: etoposide, 100 micromolar, 6hrs


title: PKO_Tun_2_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep2

value: tunicamycin, 2 micromolar, 6hrs


title: PKO_His_3_RNAseq_histidinol, 2 millimolar, 6hrs_rep3

value: histidinol, 2 millimolar, 6hrs


title: Regular_comp_Rep1


title: PKO_His_1_RNAseq_histidinol, 2 millimolar, 6hrs_rep1


title: PKO_His_2_RNAseq_histidinol, 2 millimolar, 6hrs_rep2


title: PKO_Tun_1_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep1


title: vehicle_1


title: PKO_Etop_2_RNAseq_etoposide, 100 micromolar, 6hrs_rep2


title: PKO_DMSO_2_RNAseq_DMSO, 6hrs_rep2

value: DMSO, 6hrs


title: PKO_Etop_3_RNAseq_etoposide, 100 micromolar, 6hrs_rep3


title: WT_DMSO_1_RNAseq_DMSO, 6hrs_rep1


title: WT_Tun_3_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep3


title: PKO_Nut_2_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep2

value: Nutlin 3A, 5 micromolar, 6hrs


title: WT_Tun_2_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep2


title: WT_Tun_1_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep1


title: Regular_Rep1


title: PKO_Nut_1_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep1


title: PKO_DMSO_3_RNAseq_DMSO, 6hrs_rep3


title: WT_His_3_RNAseq_histidinol, 2 millimolar, 6hrs_rep3


title: SCH_1


title: ST E3_young

description: 10x Genomics

value: Brain

value: non-neuronal brain cells

value: Brain cells


title: vehicle_3

value: wild type


title: PKO_DMSO_1_RNAseq_DMSO, 6hrs_rep1


title: PKO_Tun_3_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep3


title: WT_His_2_RNAseq_histidinol, 2 millimolar, 6hrs_rep2


title: WT_Etop_3_RNAseq_etoposide, 100 micromolar, 6hrs_rep3


title: PKO_Nut_3_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep3


title: WT_Etop_1_RNAseq_etoposide, 100 micromolar, 6hrs_rep1


title: WT_DMSO_3_RNAseq_DMSO, 6hrs_rep3


title: WT_Nut_2_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep2


title: WT_Nut_3_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep3


title: WT_Etop_2_RNAseq_etoposide, 100 micromolar, 6hrs_rep2


title: WT_Nut_1_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep1


title: DRIP-seq

status: Public on Aug 16 2022

city: San Francisco

first: Bjoern

last: Schwer

institute: University of California, San Francisco

data_processing:
Library strategy: DRIP-seq
DRIP-seq read files in fastq format were adapter trimmed before mapping (TrimGalore 0.6.6 with default settings).
DRIP-seq analysis was performed as in Sanz et al., 2016 using a Hidden Markov Model-based peak calling algorithm for identification of DRIP-seq peaks.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: NSPC_DRIP.bw: Reads per kb per million (RPKM)-normalized bigWig tracks generated from BAM files containing uniquely mapped reads.
Supplementary_files_format_and_content: NSPC_input.bw: Reads per kb per million (RPKM)-normalized bigWig tracks generated from BAM files containing uniquely mapped reads.
Supplementary_files_format_and_content: NSPC_DRIP_peaks.bed: DRIP-seq peaks identified by Hidden Markov Model-based peak calling algorithm in BED format.

source_name: Neural stem/progenitor cells

growth_protocol: NSPCs were isolated from frontal brains of postnatal day seven mice and cultured as in Wei et al., 2016. All experiments were authorized by the Institutional Animal Care and Use Committee and Institutional Biosafety Committee at the University of California, San Francisco and performed in accordance with relevant guidelines and regulations.

extract_protocol:
Genomic DNA for DRIP was isolated and digested as in Stork et al., 2016 and Ginno et al., 2012. RNase A treatment prior to DRIP was performed as in Stork et al., 2016. Digested DNA was phenol/chloroform-extracted, precipitated, washed and resuspended. For each DRIP reaction, 4.4 ug DNA were incubated with 10 ug S9.6 antibody for 16 h at 4 C, followed by incubation with magnetic protein G beads for 2 h at 4 C. Samples were washed for 3 x 10 min with 140 mM NaCl, 0.05% (w/v) Triton X-100, 10 mM NaPO4, pH 7.0, at room temperature and eluted in 10 mM EDTA, 0.5% (w/v) SDS, 50 mM Tris-Cl, pH 8.0 containing Proteinase K for 45 min at 55 C. DNA was phenol/chloroform-extracted and precipitated as described above.
Per biological replicate, three repeat DRIP reactions were first analyzed separately by DRIP-qPCR to verify the DRIP procedure as in Sanz et al., 2019. Three DRIP reactions per biological replicate were then pooled for preparation of each DRIP-seq library. Input and DRIP DNA was sonicated to a size of ~300–700 bp and DRIP-seq library preparation was performed using NEB E6050 for end repair, NEB M0212 for A-tailing, and NEB E7335 for adapter ligation. 12 cycles of PCR were performed for library amplification and libraries were cleaned and size selected (Ampure XP beads).

value: Primary neural stem/progenitor cells

value: postnatal day 7

tag: drip antibody


title: WT_DMSO_2_RNAseq_DMSO, 6hrs_rep2


title: CD69negDP_WT_HIC_rep1

status: Public on Aug 15 2022

city: London

first: Ya

last: Guo

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
in situ Hi-C
CD69negDPWTR1R2R3R4_merged.hic

data_processing:
Basecalls performed using CASAVA-1.82 or CASAVA-1.84
Hi-C Sequenced data (100 bp paired-end) were mapped using the bowtie 2 (version 2.3.2) and then processed by the HiC-Pro (version 2.7.8) with default settings. After converting using the script, HiC-Pro hicpro2juicebox.sh, valid chromatin contacts were normalized and .hic files were created by the Juicer Pre (Juicer tools version 0.7.5).
ChIP-seq raw reads (50 bp single-end) were mapped using the bowtie (version 1.0.0). After alignment and duplicates removal, peaks were identified using MACS2 (version 2.1.0).
Assembly: mm9
Supplementary files format and content: .hic files were created by the Juicer Pre (Juicer tools version 0.7.5)
Supplementary files format and content: Peak files were generated using MACS2 (version 2.1.0)

source_name: primary CD69-CD4+CD8+ cells

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature and then the reaction was quenched with 125 mM glycine at room temperature for 5 minutes. [Hi-C] Chromatin was digested with 100 units of MboI overnight at 37 °C while shaking at 900 rpm. After overnight incubation, 100 units of MboI were added for the second-round digestion for 2-4 hours. The DNA polymerase I, large (Klenow) fragment, was used to fill in MboI-digested fragment overhangs in the presence of biotin-labelled dATP. Fragment ends were then ligated with 4000 units of T4 DNA ligase by incubating at room temperature for 4-6 h with rotation at 12 rpm. After ligation, cell nuclei were collected by centrifugation, and chromatin was reverse crosslinked overnight at 65 °C. RNase A was used to remove RNA after decrosslinking. Genomic DNA was isolated and precipitated by sodium acetate-ethanol precipitation, and then purified DNA was sheared for 8 min using a sonicator (Bioruptor) with high power setting, and 30 seconds on and 30 seconds off per minute. DNA fragments in the range of 300–500 bp were then selected using the AMPure XP beads (Beckmann Coulter). [ChIP-seq] Cell nuclei were isolated using a RIPA lysis buffer (10mM Tris pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 0.1% SDS, 0.15M NaCl, 1X Roche protease inhibitors). Following isolation of cell nuclei, genomic DNA was sonicated in a high-salt RIPA buffer (10mM Tris pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1% SDS, 0.8M NaCl, 1X Roche protease inhibitors) for 30 minutes on a sonicator (Bioruptor) with high power setting, and 30 seconds on and 30 seconds off per minute. Immunoprecipitation was performed in a RIPA buffer (10mM Tris pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 0.1% SDS, 0.15M NaCl, 1X Roche protease inhibitors), and then antibody-antigen complex was precipitated using Dynabead Protein G (Thermo Fisher). Protein was digested using Proteinase K, and then DNA-protein complex was reverse crosslinked overnight at 65 °C. RNase A was added to remove RNA after decrosslinking.
[Hi-C] After biotin-labelled DNA fragments were captured on Dynabeads MyOne Streptavidin T1 (Thermo Fisher), fragment ends were repaired in a mixture of enzymes containing T4 polynucleotide kinase, T4 DNA polymerase I and DNA polymerase I, large (Klenow) fragment, and then NEBNext adaptors for Illumina sequencing were ligated to the dA-tailed fragment ends. After the USER enzyme digestion, NEBNext oligos for Illumina sequencing were used for PCR for library preparation. A PCR titration was firstly carried out to determine the lowest number of PCR cycles (8-10 cycles in this work). Final Hi-C sequencing libraries were quantified and checked for size distribution using Bioanalyzer (Agilent Technologies), and then sequenced on an HiSeq 2500 sequencer (Illumina). [ChIP-seq] ChIP-seq library preparation were carried out using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB) according to the manufacturer’s protocol.

value: thymus


title: CD69negDP_WT_HIC_rep2


title: CD69negDP_WT_HIC_rep3


title: CD69negDP_WT_HIC_rep4


title: WT_His_1_RNAseq_histidinol, 2 millimolar, 6hrs_rep1


title: rrp6l1-2 stress replicate 3

status: Public on Jul 15 2022

city: Taipei City

first: Paul

last: Verslues

address: No.128, Sec.2, Academia Rd., Nangang Dist.

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: seedlings grown for seven days under unstressed control conditions, transferred to low water potential (-0.7 Mpa) for 96 h before sample collection

data_processing:
Illumina CASAVA-Bcl2fastq version 1.8.4 for basecalling and demultiplexing
RNAseq reads were mapped to the TAIR10 genome using Bowtie2 and BLAT with default parameters
RPKM values were computed using Rackj (http://rackj.sourceforge.net/)
expression comparisons were performed using DESeq2
Genome_build: TAIR10 (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
Supplementary_files_format_and_content: comma-separate text files made by DESeq2

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: seeds plated on agar plates containing half strength Murashige-Skoog media with 2 mM MES buffer (pH 5.7) and stratified for 3 days at 4ᵒC.  Plates were then positioned vertically in a rack and and kept under continuous light (80-100 micromol photons m-2sec-1 ) at 23ᵒC in a controlled environment chamber.  Note that no sugar was added to any of the growth media used.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plant Mini Kit according to the manufacturer’s protocol.  RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and run on 2% agarose gel with post-run staining.
TruSeq Stranded Total RNA Library Prep Kit; input 3 ug total RNA, poly-A RNA were purified by oligo-dT beads; USER digest treatment was done to the adaptor ligation product; final library was amplified by 10 cycles of PCR using KAPA HiFi Mastermix. Library concentrations were normalized using KAPA Library Quantification Kit for Illumina.

treatment_protocol: After seven days of growth, seedlings of control condition (-0.25 MPa) continue grow until day elevent and seven days old stress treated seedlings were transfered to agar plates infused with polyethylene glycol 8000 (PEG) to impose low water potential (-0.7MPa) stress.  All samples were collected 96 h after transfer (control and stress treatments).

value: stress -0.7MPa

value: rrp6l1-2 T-DNA Salk_027601

value: whole seedling


title: ahl10-1 stress replicate 2


title: ahl10-1 control replicate 3

description: seedlings grown for elevent days under unstressed control conditions

value: unstressed control -0.25MPa


title: WT control replicate 3

value: wild type Col-0


title: ahl10-1 stress replicate 3


title: WT control replicate 2


title: rrp6l1-2 stress replicate 2


title: rrp6l1-2 control replicate 3


title: rrp6l1-2 control replicate 2


title: WT stress replicate 3


title: WT stress replicate 2


title: rrp6l1-2 stress replicate 1


title: ahl10-1 control replicate 2


title: rrp6l1-2 control replicate 1


title: ahl10-1 control replicate 1


title: ahl10-1 stress replicate 1


title: WT stress replicate 1


title: WT control replicate 1


title: SYOI, PCGF1 knockout, SS18-SSX2

status: Public on Jun 30 2022

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh

data_processing:
Paired-end reads were aligned to the newly released human genome build T2T-CHM13 and E.coli K12, MG1655 reference genome using Bowtie 2 (with options for T2T-CHM13: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 and for K12 --end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700).
To internally calibrate our CUT&RUN experiments, we used the exogenous60  E.coli genome to quantitatively compare the genomic profiles as previously described. We first calculated the percentage of spike-in reads in total reads that align uniquely (Nx). We then normalized the samples using a scaling factor so that E. coli spike-in signal is set to be equal across all samples. We used the sample displaying to smallest percentage of E.coli reads (Nmin) to downscale all the other conditions using the same constant to calculate our scaling factor: Scaling factor for sample x = 𝑁𝑚𝑖𝑛/𝑁𝑥.
Genome coverage files were generated using bamCoverage with 50bp bins, no normalisation and scaled (--scaleFactor).
Assembly: T2T
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: SYO-I

growth_protocol: DMEM, 10% fetal bovine serum and cultured at 37C at 5% CO2.

extract_protocol:
Chromatin profiles of endogenous SS18-SSX1/2, H2AK119ub1 in human synovial sarcoma cells and HA occupancy in osteosarcoma or synovial sarcoma cells expressing MSCV-HA-eGFP-SS18-PGK-Puro, MSCV-HA-eGFP-SS18-SSX1-PGK-Puro and MSCV-HA-eGFP- SSX-C-PGK-Puro was assayed using CUTANA ChIC/CUT&RUN Kit (EpiCypher, 14-1048)following manufacturer’s protocol. Briefly, 1 million cells (HS-SY-II, SYO-I or KHOS-240S)were harvested per sample and bound to activated Concanavalin A magnetic beads. Beads werethen incubated at 4 ̊C overnight with 1:50 dilution of antibodies per sample. Chromatin digestion was performed for 2 hours at 4 ̊C. Digestion is then stopped by chelating Ca++ ionsin a buffer containing E.coli DNA for Spike-in. DNA Fragments are then released in solution after a 10 min incubation at 37 ̊C on a ThermoMixer at 500 rpm. DNA Fragments were then purified using CUTANA DNA Purification Kit (EpiCypher).
DNA fragments obtained after CUT&RUN were quantified using Qubit dsDNA HS Assay Kit (Invitrogen). 5ng of DNA was used for libraries preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S), SPRIselect beads (Beckman Coulter, #B23317) and NEBNext Multiplex Oligos for Illumina (NEB, Set 1 #E7335S, Set 2 #E7500S). ChIP libraries were done following NEB’s guidelines (NEB, E7645S), CUT&RUN libraries were done following CUTANA ChIC/CUT&RUN Kit (EpiCypher, 14-1048) adapted protocol CUT&RUN libraries were sequenced as 75 bp Paired-End reads on Illumina NextSeq 550 platform Mid-Output.

value: SYO-I

value: Human synovial sarcoma cells

value: SS18-SSX2, Cas9, sgPCGF1


title: SYOI, PCGF1 knockout, H2Aub1


title: SYOI, IgG

value: IgG


title: SYOI, Control, SS18-SSX2

value: SS18-SSX2, Cas9


title: SYOI, Control, H2Aub1


title: HSSY, IgG

source_name: HS-SY-II

value: HS-SY-II


title: HSSY, Control, H2Aub1

value: HA-SS18-SSX1, Cas9


title: HSSY, PCGF1 knockout, HA (SS18-SSX1)

value: HA

value: HA-SS18-SSX1, Cas9, sgPCGF1


title: HSSY, PCGF1 knockout, H2Aub1


title: HSSY, Control, HA (SS18-SSX1)


title: Treat-stbl-2

status: Public on Jun 18 2022

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

data_processing:
For alignment and quantification of intron retention we used iREAD on STAR aligned bam files.
Supplementary_files_format_and_content: junction_reads  fpkm

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
After 24h RNA was extracted using RNATri (Bio&Sell) followed by DNaseI digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment with rCD1 or DMSO (rCD1 solvent) for 24 h

value: doubly-engineered cells with an N-terminal FKBP-tagged CRISPR knockin PRPF38A and stably expressing a lamin A-ECFP-SNAP fusion protein  (stbl)

tag: agent


title: DMSO-stbl-3

value: DMSO


title: Treat-stbl-1


title: Treat-ctr-2

value: control cells (ctr) with an N-terminal FKBP-tagged CRISPR knockin PRPF38A


title: Treat-ctr-3


title: DMSO-stbl-1


title: RNA-Seq ERY537SClone1_E2

status: Public on Jun 17 2022

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Sequencing reads were aligned to hg19 build of the human genome using HISAT2
SAMtools was used to convert SAM files to BAM files
Read counts were normalized and analyzed for differential expression via the DESeq2 package in R
Genes were defined by the University of California Santa Cruz (UCSC) Known Genes and reads that mapped to known genes were assigned with featureCounts
Assembly: hg19
Supplementary files format and content: Gene counts (raw) in a text file

source_name: Ishikawa ER-Y537S Clone 1

growth_protocol: Ishikawa ESR1 LBD mutant cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. At least 5 days prior to inductions, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific), since phenol-red is estrogenic, with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
Following inductions cells were washed with PBS and harvested with buffer RLT plus (Qiagen) containing 1% beta-mercaptoethanol (Sigma-Aldrich). Cells were passed through a 21-gauge needle and syringe (Sigma-Aldrich) to lyse genomic DNA before RNA was extracted and purified using a Quick RNA Mini Prep kit (Zymo Research).
Using the KAPA Stranded mRNA-Seq kit (KAPA Biosystems), poly(A) selected libraries were created with 500 ng of input RNA per sample.

treatment_protocol: Media was changed 1 day prior to estradiol (E2) inductions and cells were treated with either DMSO (vehicle) or 10 nM E2 for 8 hours.

value: Ishikawa ER-Y537S Clone 1

value: endometrioid adenocarcinoma

value: ESR1 mutant

value: 8 hr 10 nM E2


title: RNA-Seq ERY537SClone2_E2

source_name: Ishikawa ER-Y537S Clone 2

value: Ishikawa ER-Y537S Clone 2


title: RNA-Seq ERY537SClone2_DMSO

value: 8 hr 0.1% DMSO


title: DMSO-stbl-2


title: DMSO-ctr-2


title: RNA-Seq ERY537SClone1_DMSO


title: ChIP-Seq ERY537SClone1_DMSO

data_processing:
Reads were aligned to hg19 using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2
SAMtools was used to sort and convert SAM files to BAM files
Peaks with a P-value cutoff of 1 x 10-10 and an mfold parameter between 15 and 100 were called by Model Based Analysis of ChIP-seq-2 (MACS2)
DESeq was used to normalize read counts and perform differential analysis at individual ER or CDK9 bound sites
genome build/assembly hg19
processed data files format and content: Bedgraph files
processed data files format and content: narrowPeak files from MACS2

growth_protocol: Ishikawa cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. At least 5 days prior to inductions, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific), since phenol-red is estrogenic, with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
For FLAG ChIPs (flag tagged ESR1), fixation was performed by treating cells with 1% formaldehyde for 10 minutes at room temperature. For CDK9 ChIPs, a double fixation was performed by treating cells with 2 mM disuccinimidyl glutarate (Thermo Scientific) for 20 minutes at room temperature followed by fixation with 1% formaldehyde for 10 minutes at room temperature. For both fixation methods, the cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via cell scraping in Farnham lysis buffer supplemented with protease inhibitors.
Chromatin immunoprecipitation was performed as previously described (Reddy et al. Genome Research 2009) with an Anti-FLAG (Sigma-Aldrich M2) antibody that recognizes a FLAG tag on ESR1 or an Anti-CDK9 (Abcam ab239364) that recognizes CDK9.

treatment_protocol: Media was changed 1 day prior to estradiol (E2) inductions and cells were treated with either DMSO (vehicle) or 10 nM E2 for 1 hour.

value: 1 hr 0.1% DMSO


title: ChIP-Seq ERY537SClone2_E2

value: 1 hr 10 nM E2


title: DMSO-ctr-1


title: ChIP-Seq ERY537SClone1_E2


title: DMSO-ctr-3


title: Treat-ctr-1


title: ATAC-Seq ERY537SClone2_E2

data_processing:
ATAC-seq reads were aligned to hg19 using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2
Sam files were converted to bam files and sorted with Samtools
ATAC-seq peaks were called using MACS2 with an adjusted P-value cutoff of <0.05
FeatureCounts was used to quantify reads that aligned to all ATAC-seq peaks called in any sample
Reads were normalized and analyzed for differential enrichment using the DESeq2 package for R
Assembly: hg19
Supplementary files format and content: Bedgraph files

growth_protocol: Ishikawa ESR1 LBD mutant and wildtype cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. At least 5 days prior to inductions, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific), since phenol-red is estrogenic, with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
After treatments, cells were trypsinized and isolated by centrifugation.
ATAC-seq was performed as originally described in Buenrostro et al. 2013


title: ATAC-Seq ERWTClone1_E2

source_name: Ishikawa ER-WT Clone 1

value: Ishikawa ER-WT Clone 1

value: ESR1 wildtype


title: ATAC-Seq ERY537SClone2_DMSO


title: ATAC-Seq ERWTClone2_E2

source_name: Ishikawa ER-WT Clone 2

value: Ishikawa ER-WT Clone 2


title: Treat-stbl-3


title: regenerating heart

city: ATLANTA

first: Jinhu

last: Wang

state: Georgia

address: 101 WOODRUFF CIRCLE WMB 2304

institute: Emory University

data_processing:
All processing was performed in 10X Genomics CellRanger v3.1.0 using default parameters
The 'count' function was used to align Fastq files to Danio_rerio.GRCz11 and to obtain the gene expression matrices
Genome_build: Danio_rerio_GRCz11
Supplementary_files_format_and_content: Cell Ranger outputs a .mtx file with the feature-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cell Ranger. The matrix is in market exchange format while the row (gene or feature) and columns (cell barcodes) are provided as TSV files. File formats are documented in the Cell Ranger software manual.

organism: Danio rerio

source_name: Heart

extract_protocol:
Hearts were dissected from adult zebrafish, and digested with Liberase TM. Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Single cells were processed through the 10X chromium controller. Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using 3' Gene Expression v3.1 Library kit
Chromium Next GEM Single Cell 3' v3.1 stadard protocol

treatment_protocol: To ablate cardiomyocytes, tcf21:nucEGFP;Z-CAT fish were treated for 12 hours in 1 μM 4-hydroxytamoxifen (4-HT) in fish water.

value: Heart

value: Facs-sorted GFP+ epicardial cells

tag: transgenic reporters

value: treated with 4-HT


title: ATAC-Seq ERY537SClone1_E2


title: RAW38C3

status: Public on May 31 2022

data_processing: For alignment and quantification of gene.tpm files we used the Whippet-quant function of Whippet v0.11. This aligns and quantifies in one step

growth_protocol: Raw264.7. cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin (Invitrogen).

extract_protocol:
After 12h RNA was extracted using RNATri (Bio&Sell) followed by DNaseI digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For temperature experiments, cells were seeded and allowed to adhere at 37°C. The cells were subsequently shifted to incubators set to 34°C, 37°C,  or 38°C


title: S2 Schneider cells — Input DNA rep2

status: Public on Jun 10 2022

city: Moscow

first: Marina

middle: Yu.

last: Mazina

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq reads were aligned to dm6 genome by bowtie2 v2.4.5 (usegalaxy.eu online tools). Aligned BAM files for replicate 1 and replicate 2 (for Combgap, Zeste, Psq ChIP-Seqs and Inputs) were merged by Merge BAM Files (Galaxy Version 1.2.0).
Bam files were filtered to MAPQ>5
BigWig files were generated using bamCoverage 3.5.1.0.0 with scores representing number of reads normalized by the size of the library. Final bigwig files were obtained using bigwigcompare 3.3.2.0.0 as ratio of ChIP signal to Input. Scores represent number of reads normalized by the size of the library.
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: bigwig

organism: Drosophila melanogaster

source_name: S2 Schneider cells

growth_protocol: Drosophila Schneider line 2 (S2-modencode) cells were maintained at 25°C in the Schneider’s insect medium (Sigma) containing 10% FBS (HyClone).

extract_protocol:
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine (crosslinking in Drosophila tissues was performed by 0,7% formaldehyde). After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 300-1000 bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

value: Primary culture of late stage (20-24 hours old) Drosophila melanogaster embryos

value: untreated


title: uninjured heart

tag: tissue


title: ATAC-Seq ERY537SClone1_DMSO

tag: genotype


title: ChIP-Seq ERY537SClone2_DMSO


title: RAW38C2


title: RAW34C2


title: RAW38C1


title: RAW37C3


title: RAW34C3


title: RAW37C4


title: RAW34C1


title: RAW37C1


title: RAW37C2


title: Cortex_18month_Chd8_HET_Untreated_Male_b4-17_RNA_Rep1

status: Public on Apr 01 2022

city: Boston

first: Jeremy

last: Simon

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description:
Cortex_18month_Chd8_HET_b4-17_Rep1
Jimenez_Chd8_18month_RNAseq_VST.xlsx

data_processing:
Reads were filtered for a quality score of 20 or more in at least 90% of all bases using fastq_quality_filter in the FASTX toolkit 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Sequencing adapters were trimmed using cutadapt 1.12 {Martin, 2011 #224}
Reads were then aligned to the mm10 reference genome using STAR 2.5.2b {Dobin, 2013 #37}
Transcript abundance was then estimated using salmon, and differential expression was detected using DESeq2 using a model that corrected for batch and/or sex/litter effects and a threshold of adjusted p-value < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression provided as VST-normalized values from DESeq2

source_name: Cerebral cortex

growth_protocol: All data presented in this study are from mice obtained by breeding Chd8V986*/+ male mice {Jiménez, 2020 #182} with C57BL/6J wild-type (WT) females. This breeding scheme was used because pup survival was reduced when raised by Chd8V986*/+ females {Jiménez, 2020 #182}. Upon confirmation of a vaginal plug, embryonic day 0 (E0), females were fed the first dose of oil control or DM (3 mg/kg) (ChemService, N-11579) mixed into peanut butter (Skippy, Hormel Foods), and were then fed DM or oil every 3 days up until weaning at postnatal day (PND) 22, to replicate work by Richardson et al {Richardson, 2015 #72}. To rigorously control for litter effects {Jiménez, 2021 #227}, only one animal of each sex and genotype were used per litter. Mice were raised in a facility with a 12:12-light:dark cycle with ad libitum access to food (Teklad 2020X, Envigo, Huntingdon, UK) and water. Animal protocols in this study were approved by the Institutional Animal Care and Use Committee at the University of North Carolina at Chapel Hill.

extract_protocol:
The brains were removed, and the cerebral cortex (one hemisphere) was dissected and stored at −80°C until RNA extraction. Samples were processed in 4 batches, including meticulous planning to ensure that equal numbers of each genotype and time point were centrifuged together, to minimize batch effects associated with any part of processing, handling, RNA isolation, or RNA-sequencing library preparation. To lyse the samples, 350 μl of Qiagen RLT Plus buffer (with 20 μL DTT per mL buffer) per 20 mg tissue was added. A hand-held motorized homogenizer was used to immediately homogenize the samples. The lysate (350 μL) was processed through a RNeasy Plus Mini Kit for RNA extraction following the manufacturer protocol (Qiagen, 74136). RNA concentration was measured using Qubit RNA Broad-Range Assay and stored at −80°C (Thermo Fisher Scientific, Q10211).
PolyA RNA-stranded libraries were prepared (TruSeq mRNA stranded, Illumina) and sequencing was performed at the New York Genome Center (NYGC). Sequencing was conducted on an Illumina NovaSeq with stranded paired-end 100 bp reads

treatment_protocol: WT and Chd8V986*/+ mice exposed to vehicle control or DM from E0 to PND 22 were sacrificed at PND 5 or at 12 months of age by decapitation. A separate cohort of unexposed WT and Chd8V986*/+ mice were sacrificed at 18 months of age by decapitation.

value: Untreated

tag: Sex

value: Male

tag: litter

tag: dissection

value: Jess

tag: batch


title: Cortex_18month_Chd8_WT_Untreated_Male_b4-20_RNA_Rep4

description:
Cortex_18month_Chd8_WT_b4-20_Rep3
Jimenez_Chd8_18month_RNAseq_VST.xlsx

tag: treatment


title: Cortex_18month_Chd8_HET_Untreated_Male_b4-22_RNA_Rep6

description:
Cortex_18month_Chd8_HET_b4-22_Rep6
Jimenez_Chd8_18month_RNAseq_VST.xlsx


title: Cortex_18month_Chd8_WT_Untreated_Male_b4-16_RNA_Rep6

description:
Cortex_18month_Chd8_WT_b4-16_Rep6
Jimenez_Chd8_18month_RNAseq_VST.xlsx


title: Cortex_18month_Chd8_WT_Untreated_Male_b4-14_RNA_Rep4

description:
Cortex_18month_Chd8_WT_b4-14_Rep4
Jimenez_Chd8_18month_RNAseq_VST.xlsx


title: Cortex_18month_Chd8_HET_Untreated_Male_b4-21_RNA_Rep5

description:
Cortex_18month_Chd8_HET_b4-21_Rep5
Jimenez_Chd8_18month_RNAseq_VST.xlsx


title: Cortex_18month_Chd8_HET_Untreated_Male_b4-13_Rep3

description:
Cortex_18month_Chd8_HET_b4-13_Rep3
Jimenez_Chd8_18month_RNAseq_VST.xlsx


title: Cortex_18month_Chd8_HET_Untreated_Male_b4-18_RNA_Rep2

description:
Cortex_18month_Chd8_HET_b4-18_Rep2
Jimenez_Chd8_18month_RNAseq_VST.xlsx


title: Cortex_18month_Chd8_WT_Untreated_Male_b4-15_RNA_Rep5

description:
Cortex_18month_Chd8_WT_b4-15_Rep5
Jimenez_Chd8_18month_RNAseq_VST.xlsx


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b4-8_RNA_Rep8

description: Jimenez_Chd8_DM_PND5_12month_RNAseq_VST.xlsx

value: Q


title: Cortex_18month_Chd8_WT_Untreated_Male_b4-12_RNA_Rep2

description:
Cortex_18month_Chd8_WT_b4-12_Rep2
Jimenez_Chd8_18month_RNAseq_VST.xlsx


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b4-9_RNA_Rep9

value: U


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b4-5_RNA_Rep10

value: V


title: Cortex_1year_Chd8_HET_Oil_control_Male_b4-7_RNA_Rep9

value: T


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b4-10_RNA_Rep10


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b4-3_RNA_Rep8


title: Cortex_18month_Chd8_WT_Untreated_Male_b4-11_RNA_Rep1

description:
Cortex_18month_Chd8_WT_b4-11_Rep1
Jimenez_Chd8_18month_RNAseq_VST.xlsx


title: Cortex_1year_Chd8_HET_Oil_control_Male_b4-6_RNA_Rep8

value: S


title: Cortex_1year_Chd8_WT_Oil_control_Male_b4-2_RNA_Rep9


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b4-4_RNA_Rep9


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b3-24_RNA_Rep7

value: P


title: Cortex_1year_Chd8_WT_Oil_control_Male_b4-1_RNA_Rep8


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b3-23_RNA_Rep6

value: M


title: Cortex_1year_Chd8_HET_Oil_control_Male_b3-20_RNA_Rep6

value: N


title: Cortex_1year_Chd8_HET_Oil_control_Male_b3-21_RNA_Rep7

value: R


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b3-22_RNA_Rep5

value: L


title: Cortex_1year_Chd8_HET_Oil_control_Male_b3-19_RNA_Rep5

value: K


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b3-17_RNA_Rep6


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b3-18_RNA_Rep7


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b3-16_RNA_Rep5


title: Cortex_1year_Chd8_WT_Oil_control_Male_b3-14_RNA_Rep6


title: Cortex_1year_Chd8_WT_Oil_control_Male_b3-15_RNA_Rep7


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Female_b3-12_RNA_Rep5

value: Female


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Male_b3-11_RNA_Rep5


title: Cortex_1year_Chd8_WT_Oil_control_Male_b3-13_RNA_Rep5


title: Cortex_P5_Chd8_HET_Oil_control_Male_b3-9_RNA_Rep5

value: D

value: Eric


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Female_b3-8_RNA_Rep5


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Male_b3-6_RNA_Rep6


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Male_b3-5_RNA_Rep5

value: A


title: Cortex_P5_Chd8_WT_Oil_control_Male_b3-2_RNA_Rep6

value: Male


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b2-24_RNA_Rep4

value: J

value: Jess


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b2-23_RNA_Rep3

value: G


title: Cortex_P5_Chd8_WT_Oil_control_Female_b3-4_RNA_Rep6


title: Cortex_P5_Chd8_WT_Oil_control_Female_b3-3_RNA_Rep5


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b2-19_RNA_Rep3


title: Cortex_1year_Chd8_WT_Oil_control_Male_b2-18_RNA_Rep4

value: I


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b2-20_RNA_Rep4


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Male_b2-14_RNA_Rep4


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Female_b2-16_RNA_Rep4


title: Cortex_1year_Chd8_WT_Oil_control_Male_b2-17_RNA_Rep3

value: H


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Female_b2-15_RNA_Rep3


title: Cortex_P5_Chd8_HET_Oil_control_Female_b3-10_RNA_Rep5


title: Cortex_P5_Chd8_HET_Oil_control_Female_b2-12_RNA_Rep4

value: O


title: Cortex_P5_Chd8_HET_Oil_control_Male_b2-9_RNA_Rep3

value: F


title: Cortex_P5_Chd8_HET_Oil_control_Female_b2-11_RNA_Rep3


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Female_b2-8_RNA_Rep4


title: Cortex_1year_Chd8_HET_Oil_control_Male_b2-22_RNA_Rep4


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Male_b2-13_RNA_Rep3

value: P


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Male_b2-6_RNA_Rep4


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Male_b2-5_RNA_Rep3


title: Cortex_P5_Chd8_WT_Oil_control_Female_b2-3_RNA_Rep3


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Female_b2-7_RNA_Rep3


title: Cortex_P5_Chd8_WT_Oil_control_Male_b3-1_RNA_Rep5


title: Cortex_P5_Chd8_WT_Oil_control_Female_b2-4_RNA_Rep4


title: Cortex_P5_Chd8_WT_Oil_control_Male_b2-2_RNA_Rep4


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b1-24_RNA_Rep2


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Male_b3-7_RNA_Rep7


title: Cortex_1year_Chd8_HET_Oil_deltamethrin_Male_b1-23_RNA_Rep1


title: Cortex_1year_Chd8_HET_Oil_control_Male_b1-22_RNA_Rep2

value: E


title: Cortex_1year_Chd8_HET_Oil_control_Male_b1-21_RNA_Rep1


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b1-19_RNA_Rep1


title: Cortex_1year_Chd8_WT_Oil_control_Male_b1-18_RNA_Rep2


title: Cortex_P5_Chd8_HET_Oil_control_Male_b2-10_RNA_Rep4


title: Cortex_P5_Chd8_WT_Oil_control_Male_b2-1_RNA_Rep3


title: Cortex_1year_Chd8_HET_Oil_control_Male_b2-21_RNA_Rep3


title: Cortex_1year_Chd8_WT_Oil_control_Male_b1-17_RNA_Rep1


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Female_b1-16_RNA_Rep2

value: Q


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Female_b1-15_RNA_Rep1

value: B


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Male_b1-14_RNA_Rep2


title: Cortex_P5_Chd8_HET_Oil_deltamethrin_Male_b1-13_RNA_Rep1


title: Cortex_P5_Chd8_HET_Oil_control_Female_b1-12_RNA_Rep2


title: Cortex_1year_Chd8_WT_Oil_deltamethrin_Male_b1-20_RNA_Rep2


title: Cortex_P5_Chd8_HET_Oil_control_Male_b1-9_RNA_Rep1

value: C


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Female_b1-8_RNA_Rep2

value: Female


title: Cortex_P5_Chd8_HET_Oil_control_Female_b1-11_RNA_Rep1


title: Cortex_P5_Chd8_HET_Oil_control_Male_b1-10_RNA_Rep2


title: Cortex_P5_Chd8_WT_Oil_control_Female_b1-3_RNA_Rep1


title: Cortex_P5_Chd8_WT_Oil_control_Female_b1-4_RNA_Rep2


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Female_b1-7_RNA_Rep1


title: Cortex_P5_Chd8_WT_Oil_deltamethrin_Male_b1-5_RNA_Rep1


title: Blastocyst derived extracellular vesicles replicate 2

status: Public on Mar 10 2022

city: Merelbeke

first: Krishna Chaitanya

last: Pavani

state: Gent

address: Salisburylaan 133, Merelbeke, Belgium

country: Belgium

institute: Ghent Univeristy

data_processing:
Quality and adapter trimming with cutadapt 2.0, cutadapt -j 20 --max-n 0 -a TGGAATTCTCGGGTGCCAAGG -m 15 -o <trimmed.fastq.gz> <in.fastq.gz>
Run mirPro, mirpro -i <trimmed.fastq.gz> -m <path_to_mirbase_v22.1/mature.fa> -p <path_to_mirbase_v22.1/hairpin.fa> -a null -s bta --novel 1 -g <Bos_taurus.ARS-UCD1.2.dna.toplevel.fa> --index <Bos_taurus.ARS-UCD1.2.dna.toplevel.idx> --other <other_species> <path_to_out/results> -t 20
Genome_build: Bos_taurus.ARS-UCD1.2 release 95 Ensembl
Supplementary_files_format_and_content: normalized_counts_deseq2.txt; first columns are the miRNA as obtained from mirPro, the remaining columns are normalized counts with DESeq2's default method

organism: Bos taurus

source_name: Bovine embryos conditioned media

growth_protocol: Routine in vitro methods were used for bovine embryo production, as described previously by (Wydooghe, et al. 2014), during the embryo culture the persumed zygote were cultured individually in 20-µL droplets. covered with Paraffin oil (SAGE oil for tissue culture, ART-4008-5P, Cooper Surgical Company), at 38 °C in 5% CO2, 5% O2, and 90% N2.

extract_protocol:
Firstly, Evs were isolated by qEV single size exclusion column (IZON Science, Cat. Number: qEV single ser. Y1000588) from blastocyst and non-blastocyst groups. Further on, 600 µL (× 6 replicates (3 blastocyst and 3 non-blastocyst) of the concentrated EV pellet from each group was used for total RNA extraction, using the Plasma/Serum Circulating & Exosomal RNA Purification Mini Kit (Norgen Biotek, Cat. 51000) according to the manufacturer's protocol. The quality and concentration of the RNA samples were examined using an RNA 6000 Pico Chip (Agilent Technologies) and a Quant-iT RiboGreen RNA Assay kit (Life Technologies), respectively.
Small RNA library preparation was performed with the Tailormix v2 kit

treatment_protocol: At 8 dpi, the developmental competence of each embryo was assessed, enabling a division of individually cultured embryos into two subgroups: 1) embryos that were not able to reach the blastocyst stage (non-blastocysts) and 2) blastocysts. CM of individually cultured blastocysts or non-blastocysts were pooled into two groups, both containing a total of nine replicates, used for extracellular vesicles isolation followed by total RNA isolation.

tag: cell type

value: Blastocyst

tag: media collection

value: 8 days post insemination


title: Cortex_P5_Chd8_WT_Oil_control_Male_b1-1_RNA_Rep1

value: Eric


title: Blastocyst derived extracellular vesicles replicate 3


title: Blastocyst derived extracellular vesicles replicate 1


title: Non-blastocyst derived extracellular vesicles replicate 2

value: NB

value: Non-blastocyst


title: Non-blastocyst derived extracellular vesicles replicate 3


title: Non-blastocyst derived extracellular vesicles replicate 1

description: Removed due to not meeting QC metrics