title: U2OS ASH1L knockout cells transfected with ASH1L-CTD, no UV, biol rep1


title: U2OS ASH1L knockout cells transfected with empty vector, 3H, biol rep2

status: Public on Jun 08 2023

type: SRA

city: Zurich

first: Michelle

last: Yancoskie

address: Winterthurerstr. 260

department: Vetsuisse Faculty

country: Switzerland

institute: Institute of Veterinary Pharmacology and Toxicology, University of Zurich

description:
ASH1LCTD_ALKO_3h_Rep2.broadPeak.gz
ASH1LCTD_ALKO_3h_Rep2.bw

library_source: genomic

data_processing:
Raw reads were trimmed to remove reads shorter than 99 base pairs and crop reads exceeding 101 bp, or for paired-end top-up reads, to crop to 149-151 bp (TrimGalore v.0.6.5), then aligned (bwa mem v.0.7.17-r1188) to the human reference genome build GCA hg38 lacking chrY but including non-canonical contigs.
Alignments were filtered to exclude reads with mapping quality scores below 30 (bedtools v.2.29.2), PCR and optical duplicates (Picard MarkDuplicates, v.2.23.8), ENCODE-blacklisted regions, non-canonical contigs, and unmapped or secondary alignments (and for paired-end top-up reads, unpaired reads) (samtools v.1.7).
Filtered alignments (with single-end reads and paired-end top-up alignments pooled for H3K36me2) were used to call peaks (macs2 v.2.2.7.1) from treatment (IP) over pooled control (input control for H3K36me2, empty vector-transfected ASH1L knockout cells for ASH1L-CTD ChIP-seq) tagAlign files, with default parameters and cutoff p-value of 1e-2; broad peaks were called for both H3K36me2 and ASH1L-CTD ChIP-seq. Peaks were used to verify replicabiity with idr (v.2.0.4.2). For H3K36me32, only robust peaks (those shared across both biological duplicates) were retained in downsteam analyses. For ASH1L-CTD ChIP-seq, only the top quartile (when peaks were rank ordered by signal strength) of robust (shared across at least two of three biological triplicates) were used in downstream analyses.
Fold enrichment (bigWig) tracks were generated of IP signal over input control.
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak BED files

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Low glucose DMEM, 10% fetal calf serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Non-UV or 3h-post UV cells were crosslinked with 1% formaldehyde for 10 minutes. Quenching and lysis was followed by sonication (BioRuptor Plus) for 20 cycles (30 sec on/off).
To remove UV-induced DNA lesions with the potential to inhibit sequencing, samples were incubated with PreCR Repair mix (New England BioLabs, M0309) for 15 min at 37°C, then re-purified, quantified by Qubit (Invitrogen, Q33238) and sent to the Functional Genomics Center Zurich for final library preparation with the NEB Next Ultra Kit (New England BioLabs, E7645). Libraries were sequenced as 100 bp single-end reads on a NovaSeq 6000 (Illumina). Topped up reads for the H3K36me2 experiment were sequenced as 150 bp paired-end reads (NovaSeq 6000).

treatment_protocol: Cells grown to 80-90% confluency were left untreated (non-UV) or were UV-C irradiated at 20 J/m2 and left to recover for 3h.

tag: cell line

tag: genotype

value: ASH1L knockout

tag: treatment

value: 3h post UV

tag: chip antibody

value: anti-FLAG (Sigma, F1804)


title: U2OS wildtype cells, 3h post UV, biol rep2, input [paired-end]

description:
H3K36me2_WT_3h_Rep2.bw
H3K36me2_WT_3h_Rep2.broadPeak.gz

value: wildtype


title: U2OS wildtype cells, 3h post UV, biol rep2 [paired-end]

value: H3K36me2 (abcam, ab9049)


title: U2OS wildtype cells, 3h post UV, biol rep2, input [single]


title: U2OS wildtype cells, 3h post UV, biol rep1, input [single]

description:
H3K36me2_WT_3h_Rep1.bw
H3K36me2_WT_3h_Rep1.broadPeak.gz


title: U2OS ASH1L knockout cells transfected with ASH1L-CTD, 3H, biol rep2


title: U2OS wildtype cells, 3h post UV, biol rep1 [paired-end]


title: U2OS wildtype cells, 3h post UV, biol rep1, input [paired-end]


title: U2OS wildtype cells, 3h post UV, biol rep2 [single]


title: U2OS wildtype cells, no UV, biol rep2, input [single]

description:
H3K36me2_WT_noUV_Rep2.bw
H3K36me2_WT_noUV_Rep2.broadPeak.gz

value: no UV


title: U2OS wildtype cells, no UV, biol rep2 [paired-end]


title: U2OS wildtype cells, no UV, biol rep2, input [paired-end]


title: U2OS wildtype cells, no UV, biol rep1, input [paired-end]

description:
H3K36me2_WT_noUV_Rep1.bw
H3K36me2_WT_noUV_Rep1.broadPeak.gz


title: U2OS wildtype cells, no UV, biol rep1, input [single]


title: U2OS wildtype cells, 3h post UV, biol rep1 [single]


title: U2OS wildtype cells, no UV, biol rep2 [single]


title: U2OS ASH1L knockout cells transfected with ASH1L-CTD, no UV, biol rep2

description:
ASH1LCTD_ALKO_noUV_Rep2.broadPeak.gz
ASH1LCTD_ALKO_noUV_Rep2.bw


title: U2OS ASH1L knockout, no UV, biol rep2

data_processing:
Raw reads (FASTQ files) were processed based on the ENCODE ATAC-seq pipeline for paired-end reads. Adapters were trimmed (cutadapt v.1.9.1) and trimmed reads aligned (bowtie2 v.2.4.5) to the human reference genome build GCA hg38 excluding chromosome Y but including non-canonical contigs.
Alignments underwent further filtering steps (samtools v.1.7, bedtools v.2.29.2, Picard MarkDuplicates v.2.23.8) to exclude reads that were PCR or optical duplicates, were unmapped or non-primary alignments, failed platform and/or vendor quality checks, had mapping quality scores below 30, or that mapped to ENCODE blacklisted regions, non-canonical chromosomes or mitochondrial DNA.
Filtered alignments were used to generate signal tracks and to call peaks (macs2 v.2.2.7.1 with default parameters), which were used to verify replicability across biological replicates (idr v.2.0.4.2).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak BED files

extract_protocol:
DNA to be tagmented was processed according to the Omni-ATAC-seq protocol by Corces et al. 2017 (doi: 10.1038/nmeth.4396). 50k cells were pelleted, incubated in ATAC-seq lysis buffer, washed, and re-pelleted; nuclei were exposed to the transposition reaction using Tn5 pre-loaded with Illumina adapters.
Purified transposition reactions were PCR-amplified with custom ATAC-seq primers using the minimum number of PCR cycles determined from qPCR. The resulting libraries were purified and size selected with AMPure beads, analyzed on a TapeSttation to verify desired fragment size range, pooled at equimolar concentration, and submitted to the Functional Genomics Center Zurich to be sequenced as 50 bp paired-end reads on a NovaSeq 6000.

treatment_protocol: Cells grown to 80-90% confluency were left untreated (non-UV) or were UV-C irradiated at 20 J/m2 and left to recover for 3h. Cells were treated with DNAse to digest dead or damaged cells, and counted.


title: U2OS ASH1L knockout, 3h post UV, biol rep1


title: U2OS wildtype cells, no UV, biol rep1 [single]


title: U2OS ASH1L knockout, 3h post UV, biol rep2


title: U2OS wildtype cells, no UV, biol rep1 [paired-end]


title: U2OS ASH1L knockout cells, no UV, biol rep1


title: U2OS wildtype cells, 3h post UV, biol rep2


title: U2OS wildtype cells, no UV, biol rep2


title: U2OS wildtype cells, 3h post UV, biol rep1


title: BT549-SNHGIS

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

country: China

institute: Shantou University Medical College

description: mRNA profiling by RNA sequencing

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Seqtk.
Clean reads were compared with hg38.The analysis was performed by the Shanghai Biotechnology Corporation.
Assembly: hg38
Supplementary files format and content: Tab-delimited files include FPKM values

molecule: total RNA

growth_protocol: BT549-SNHGI5 and BT549-pcIP2 Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100U/ml penicillin,  and 100 µg/ml streptomycin at 37 °C in a humid environment with 5 % CO2

extract_protocol:
Total RNA was extracted using MJzol animal RNA Extraction Kit(MagBeads) (Cat#T102096)following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

tag: cell type

value: breast cancer cells

value: SNHG15 overexpression


title: BT549--pcIp2

description: mRNA profiling by RNA sequencing

value: vector control


title: scRNA-seq_pt17

city: Houston

first: Michael

last: Green

state: TX

address: 1515 Holcombe Blvd

department: Lymphoma/Myeloma

country: USA

institute: MD Anderson Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Transcript level counting with cell ranger v6.0.0
Assembly: hg38
Supplementary files format and content: gene expression matrix

source_name: Bone marrow

extract_protocol:
LymphoprepTM density gradient medium and SepMateTM tubes (STEMCELL Technologies Inc.) were used for isolation of mononuclear cells (MNCs) from bone marrow aspirate, according to the manufacturer’s instructions.
Libraries were generated using a 10x Genomics Chromium Controller instrument and Chromium Single-Cell 3′ V5.1 reagent kits (10x Genomics) according to manufacturer's protocol.

tag: tissue

value: Bone marrow

tag: disease state

value: Normal

value: No


title: scRNA-seq_pt18

description: 10x Genomics


title: scRNA-seq_pt20

description: 10x Genomics

value: rrLBCL

value: Chemo


title: scRNA-seq_pt22

description: 10x Genomics

value: CART


title: scRNA-seq_pt21

description: 10x Genomics


title: scRNA-seq_pt16

description: 10x Genomics


title: scRNA-seq_pt19

description: 10x Genomics


title: scRNA-seq_pt13

description: 10x Genomics


title: scRNA-seq_pt14

description: 10x Genomics


title: scRNA-seq_pt15

description: 10x Genomics


title: scRNA-seq_pt09

description: 10x Genomics


title: scRNA-seq_pt11

description: 10x Genomics


title: scRNA-seq_pt08

description: 10x Genomics


title: scRNA-seq_pt06

description: 10x Genomics


title: scRNA-seq_pt10

description: 10x Genomics


title: scRNA-seq_pt12

description: 10x Genomics


title: scRNA-seq_pt05

description: 10x Genomics


title: scRNA-seq_pt03

description: 10x Genomics


title: XPC U2OS XPC knockout cells, 3h post UV, biol rep2

data_processing:
Raw reads were trimmed to remove reads shorter than 99 base pairs and crop reads exceeding 101 bp (TrimGalore v.0.6.5), then aligned (bwa mem v.0.7.17-r1188) to the human reference genome build GCA hg38 lacking chrY but including non-canonical contigs.
Alignments were filtered to exclude reads with mapping quality scores below 30 (bedtools v.2.29.2), PCR and optical duplicates (Picard MarkDuplicates, v.2.23.8), ENCODE-blacklisted regions, non-canonical contigs, and unmapped or secondary alignments (samtools v.1.7).
Filtered alignments were used to call peaks (macs2 v.2.2.7.1) from treatment (IP) over pooled control (input control for H3K4me3, XPC knockout IPs for XPC ChIP-seq) tagAlign files, with default parameters and cutoff p-value of 1e-2; narrow peaks were called for H3K4me3 ChIP-seq and broad peaks called for XPC ChIP-seq. For XPC ChP-seq, peaks were only used to verify replicabiity with idr (v.2.0.4.2) due to the non-peaky nature of XPC binding. For H3K4me3, only robust peaks (those shared across a majority of biological replicates) were retained in downsteam analyses.
Fold enrichment (bigWig) tracks were generated of IP signal over input control (for H3K4me3), or over IP signal from XPC knockout cells (for XPC).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (for H3K4me3 ChIP-seq), broadPeak (for XPC ChIP-seq)

extract_protocol:
Non-UV or 1h- or 3h-post UV cells were crosslinked with 1% formaldehyde for 10 minutes. Quenching and lysis was followed by sonication (BioRuptor Plus) for 20 cycles (30 sec on/off).
To remove UV-induced DNA lesions with the potential to inhibit sequencing, samples were incubated with PreCR Repair mix (New England BioLabs, M0309) for 15 min at 37°C, then re-purified, quantified by Qubit (Invitrogen, Q33238) and sent to the Functional Genomics Center Zurich for final library preparation with the NEB Next Ultra Kit (New England BioLabs, E7645). Libraries were sequenced as 100 bp single-end reads on a NovaSeq 6000 (Illumina).

treatment_protocol: Cells grown to 80-90% confluency were UV-C irradiated at 20 J/m2, and left to recover for 1h or 3h.

value: XPC knockout

value: XPC (Invitrogen, PA5-97019)


title: scRNA-seq_pt02

description: 10x Genomics


title: U2OS wildtype cells, no UV, biol rep1


title: scRNA-seq_pt04

description: 10x Genomics


title: XPC U2OS ASH1L knockout cells, 3h post UV, biol rep3

value: ASH1L knockout


title: scRNA-seq_pt01

description: 10x Genomics


title: XPC U2OS XPC knockout cells, 3h post UV, biol rep1

value: 3h post UV


title: XPC U2OS ASH1L knockout cells, 3h post UV, biol rep2


title: XPC U2OS wildtype cells, 3h post UV, biol rep3


title: XPC U2OS wildtype cells, 3h post UV, biol rep2


title: XPC U2OS ASH1L knockout cells, 3h post UV, biol rep1


title: XPC U2OS XPC knockout cells, 1h post UV, biol rep1

value: 1h post UV


title: XPC U2OS ASH1L knockout cells, 1h post UV, biol rep3


title: XPC U2OS wildtype cells, 3h post UV, biol rep1

value: wildtype


title: scRNA-seq_pt07

description: 10x Genomics


title: XPC U2OS XPC knockout cells, 1h post UV, biol rep2


title: XPC U2OS ASH1L knockout cells, 1h post UV, biol rep2


title: XPC U2OS ASH1L knockout cells, 1h post UV, biol rep1


title: XPC U2OS wildtype cells, 1h post UV, biol rep2


title: XPC U2OS XPC knockout cells, no UV, biol rep2


title: XPC U2OS wildtype cells, 1h post UV, biol rep3


title: XPC U2OS wildtype cells, 1h post UV, biol rep1


title: XPC U2OS wildtype cells, no UV, biol rep2


title: XPC U2OS ASH1L knockout cells, no UV, biol rep1


title: H3K4me3 U2OS ASH1L knockout cells, 3h post UV, biol rep3, input


title: XPC U2OS wildtype cells, no UV, biol rep4


title: XPC U2OS wildtype cells, no UV, biol rep3


title: XPC U2OS XPC knockout cells, no UV, biol rep1


title: H3K4me3 U2OS ASH1L knockout cells, 3h post UV, biol rep1, input


title: H3K4me3 U2OS ASH1L knockout cells, 3h post UV, biol rep1

value: H3K4me3 (abcam, ab8580)


title: H3K4me3 U2OS ASH1L knockout cells, 1h post UV, biol rep3, input


title: XPC U2OS ASH1L knockout cells, no UV, biol rep3

value: no UV


title: XPC U2OS wildtype cells, no UV, biol rep1


title: H3K4me3 U2OS ASH1L knockout cells, 1h post UV, biol rep2


title: H3K4me3 U2OS ASH1L knockout cells, 3h post UV, biol rep3


title: H3K4me3 U2OS ASH1L knockout cells, 3h post UV, biol rep2, input


title: H3K4me3 U2OS ASH1L knockout cells, no UV, biol rep1, input


title: H3K4me3 U2OS ASH1L knockout cells, 1h post UV, biol rep3


title: H3K4me3 U2OS ASH1L knockout cells, 1h post UV, biol rep2, input


title: H3K4me3 U2OS wildtype cells, 3h post UV, biol rep3, input


title: H3K4me3 U2OS wildtype cells, 3h post UV, biol rep2, input


title: H3K4me3 U2OS wildtype cells, 3h post UV, biol rep1, input


title: H3K4me3 U2OS ASH1L knockout cells, no UV, biol rep3, input


title: H3K4me3 U2OS wildtype cells, 1h post UV, biol rep3, input


title: H3K4me3 U2OS ASH1L knockout cells, no UV, biol rep3


title: H3K4me3 U2OS wildtype cells, 1h post UV, biol rep3


title: H3K4me3 U2OS ASH1L knockout cells, no UV, biol rep1


title: H3K4me3 U2OS ASH1L knockout cells, 1h post UV, biol rep1


title: H3K4me3 U2OS ASH1L knockout cells, 1h post UV, biol rep1, input


title: XPC U2OS ASH1L knockout cells, no UV, biol rep2


title: H3K4me3 U2OS wildtype cells, no UV, biol rep3, input


title: H3K4me3 U2OS ASH1L knockout cells, no UV, biol rep2, input


title: H3K4me3 U2OS ASH1L knockout cells, no UV, biol rep2


title: H3K4me3 U2OS wildtype cells, no UV, biol rep1, input


title: H3K4me3 U2OS wildtype cells, no UV, biol rep2


title: H3K4me3 U2OS wildtype cells, no UV, biol rep1


title: H3K4me3 U2OS ASH1L knockout cells, 3h post UV, biol rep2


title: H3K4me3 U2OS wildtype cells, 1h post UV, biol rep2, input


title: H3K4me3 U2OS wildtype cells, 1h post UV, biol rep1, input


title: H3K4me3 U2OS wildtype cells, 3h post UV, biol rep3


title: H3K4me3 U2OS wildtype cells, 3h post UV, biol rep1


title: Control, periphery, rpechor (scATAC-seq)

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

library_source: genomic single cell

data_processing:
FASTQ files were generated from base calls with the bcl2fastq software (Illumina).
mtscATAC-seq reads were mapped to a modified GRCh38 reference genome that was generated by hard-masking nuclear regions that share homology with mitochondrial sequences, as described previously (39). Mapping and quantification were carried out by Cell Ranger ATAC (v2.0.0, 10X Genomics) using the ‘count’ function.
ATAC peaks for each sample were filtered using Signac (v1.4.0). Peaks with widths less than 20 or greater than 10000 were removed. Objects containing fragments for each sample were generated
Cells were filtered with the Signac (v1.4.0) subset function. Cells with fewer than 1000 peak region framents or greater than 75000 peak region framents were removed. Cells with less than 10x average mtDNA depth or greather than 1000x mtDNA depth were also removed. Mitochondrial DNA sequencing depth (mtDNA_depth) was calculated using mgatk.
Term frequency inverse document frequency (TF-IDF) normalization and partial singular value decomposition were performed on each library using  RunTFIDF() and RunSVD() (Signac) with default settings. Gene activities were computed using GeneActivity().
Integration anchors between datasets were identified using reciprocal LSI projection using  FindIntegrationAnchors() in Signac. Dimensions 2-30 from the CCA were used. LSI embeddings were integrated using IntegrateEmbeddings based on these anchors and using dimensions 1-30. A UMAP was generated using the integrated embeddings using RunUMAP(integrated_object, reduction = "integrated_lsi", dims = 2:30).
Cell identity was transferred from corresponding scRNAseq data of the same samples using TransferData() (Signac). Transfer anchors between RNA and ATAC data were identified using FindTransferAnchors with the following parameters:   reduction = 'cca', dims = 1:40.
Assembly: hg38
Supplementary files format and content: Processed gene activity data matrix files are provided in comma-delimited format for count (*_count.csv) and processed/normalized (*_normalized.csv) activity values. For processed/normalized files, log-normalized activity values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene activity values. For count files, raw gene activity level were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

source_name: RPE/choroid

extract_protocol:
Neural retina was dissected away from the underlying retinal pigment epithelium and choroid prior to tissue dissociation. Neural retina samples were dissociated with 20 units/mL of papain (Worthington Biochemical Corporation) with 0.0005% DNase I (Worthington Biochemical Corporation) on a shaker at 37˚C for 75 minutes. RPE/choroid samples were dissociated mechanically using razor blades into one-millimeter pieces then dissociated enzymatically using collagenase on a shaker at 37˚C for 60 minutes. Following dissociation, cells were cryopreserved in DMSO-based Recovery Cell Cryopreservation Media (Gibco). After overnight cooling at -80˚C, samples were transferred to liquid nitrogen (vapor phase) for long-term storage prior to encapsulation and library preparation.
Cells were prepared for mt-scATAC sequencing using the protocol described previously by Lareau, Ludwig et al. Briefly, cells were thawed as above and filtered through a 70µm cell strainer. Cells were then washed twice with dPBS-/- (Gibco). Cells were fixed with 1% formaldehyde (Sigma) in PBS-/- for 10 minutes at room temperature. Fixation was quenched with the addition of glycine (Research Products International) to a final concentration of 0.125M for 5 minutes at room temperature. Following fixation, cells were washed twice with ice-cold PBS-/-. Following the second wash, cells were resuspended in 100µL ice-cold Lysis Buffer (10 mM Tris-HCl pH 7.4 (Millipore-Sigma), 10 mM NaCl (Ambion/Invitrogen), 3 mM MgCl2 (Ambion/Invitrogen), 0.1% Nonidet-P40 substitute (Research Products International), 1% Fraction V BSA (Research Products International)) and incubated on ice for 2.5 minutes. Following incubation, 1mL of ice-cold Wash Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA) was added, and cells were pelleted at 500 x g for 5 minutes at 4˚C. Cells were resuspended in 10µL diluted Nuclei Buffer (10X Genomics) and counted using Trypan Blue (Gibco) with the Countess automated cell counter (Invitrogen). Based on these counts, cell suspensions were diluted in diluted Nuclei Buffer to a final target concentration of 6,000 cells per µL. Cells were then processed following the 10X Chromium Next GEM Single Cell ATAC Reagent Kit v1.1 User Guide (Rev. D) without modification. Final libraries were quantified using the Qubit dsDNA HS Assay Kit (Life Technologies) and diluted to 3ng/µL. Library quality was checked using the Bioanalyzer instrument (Agilent), wherein periodicity of fragment length was observed, consistent with high quality ATAC-seq library construction.

tag: individual

value: control

value: RPE/choroid

tag: region

value: peripheral


title: H3K4me3 U2OS wildtype cells, 3h post UV, biol rep2


title: H3K4me3 U2OS wildtype cells, 1h post UV, biol rep2


title: Control, macula, rpechor (scATAC-seq)

value: macular


title: Control, periphery, RPE/choroid (scRNA-seq)

data_processing:
FASTQ files were generated from base calls with the bcl2fastq software (Illumina).
Reads were mapped to the pre-built GRCh38 reference with Cell Ranger v3.0.1 (10X Genomics) using the ‘count’ function.
Cells were filtered with the Seurat (v3.1) subset function. Cells with nUMIs less than 500 (to remove cells with poor read quality) or greater than 7000 (to remove cells likely to be doublets) were removed. RPE/choroid cells with greater than 65% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-"). RPE/choroid cells with greater than 40% of reads originating from ribosomal RNA genes were also removed. Retinal cells with greater than 40% of reads originating from mitochondrial genes or 20% of reads originating from ribosomal RNA genes were also removed.
For each of the eight libraries, reads were normalized with the Seurat (v3.1) NormalizeData function, and variable features were found with the following commands: my _object <- NormalizeData(my_object, normalization.method = "LogNormalize", scale.factor = 10000), my_object <- FindVariableFeatures(my_object, selection.method = “vst”, nfeatures = 2000)
Integration anchors from the first 25 dimensions of the canonical correlation analysis were used to integrate data with the following commands: retina.anchors <- FindIntegrationAnchors(object.list = my_object_list, dims=1:25), RETINA.combined <- IntegrateData(anchorset = retina.anchors, dims = 1:25)
Data scaling, principal component analysis, and clustering were performed with the following commands: RETINA.combined <- ScaleData(RETINA.combined, verbose = FALSE), RETINA.combined <- RunPCA(retina.combined, npcs = 30, verbose = FALSE), RETINA.combined <- RunUMAP(RETINA.combined, reduction = "pca", dims = 1:22), RETINA.combined <- FindNeighbors(RETINA.combined, reduction = "pca", dims = 1:23), RETINA.combined <- FindClusters(RETINA.combined, resolution = 0.5)
Assembly: GRCh38
Supplementary files format and content: Processed expression data matrix files are provided in comma-delimited format for count (*_count.csv) and processed/normalized (*_normalized.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

molecule: polyA RNA

extract_protocol:
Neural retina was dissected away from the underlying retinal pigment epithelium and choroid prior to tissue dissociation. Neural retina samples were dissociated with 20 units/mL of papain (Worthington Biochemical Corporation) with 0.0005% DNase I (Worthington Biochemical Corporation) on a shaker at 37˚C for 75 minutes. RPE/choroid samples were dissociated mechanically using razor blades into one-millimeter pieces then dissociated enzymatically using collagenase on a shaker at 37˚C for 60 minutes. Following dissociation, cells were cryopreserved in DMSO-based Recovery Cell Cryopreservation Media (Gibco). After overnight cooling at -80˚C, samples were transferred to liquid nitrogen (vapor phase) for long-term storage prior to encapsulation and library preparation.
Cryopreserved cells were rapidly thawed at 37 °C and resuspended in dPBS-/- (Gibco) with 0.04% non-acetylated bovine serum albumin (New England Biolabs). Cells were filtered through a 70µm filter and diluted to target 8,000 cells per run. Single cells were then partitioned and barcoded with the Chromium Controller instrument (10X Genomics) and Single Cell 3' Reagent (v3.1 chemistry) kit (10X Genomics) according to the manufacturer’s specifications with no modification (Rev C). Final libraries were quantified using the Qubit dsDNA HS Assay Kit (Life Technologies) and diluted to 3ng/µL in buffer EB (Qiagen). Library quality and concentration was confirmed using the Bioanalyzer High Sensitivity DNA Assay (Agilent) prior to sequencing.


title: Control, macula, retina (scATAC-seq)

source_name: neural retina

value: neural retina


title: MELAS, macula, rpechor (scATAC-seq)

value: MELAS patient

value: m.3243A/m.3243G (heteroplasmic)


title: Control, macula, neural retina (scRNA-seq)


title: MELAS, periphery, rpechor (scATAC-seq)


title: MELAS, macula, retina (scATAC-seq)


title: Control, macula, RPE/choroid (scRNA-seq)


title: Control, periphery, neural retina (scRNA-seq)


title: H3K4me3 U2OS wildtype cells, 1h post UV, biol rep1


title: MELAS, periphery, RPE/choroid (scRNA-seq)


title: MELAS, periphery, neural retina (scRNA-seq)


title: H3K4me3 U2OS wildtype cells, no UV, biol rep3


title: H3K4me3 U2OS wildtype cells, no UV, biol rep2, input


title: MELAS, macula, RPE/choroid (scRNA-seq)


title: MELAS, macula, neural retina (scRNA-seq)


title: Control, periphery, retina (scATAC-seq)


title: MELAS, periphery, retina (scATAC-seq)


title: PBMC_N_148_AT_F

type: genomic

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

description:
N_148
200722330104_R01C01

hyb_protocol: genomic DNA was bisulfite-converted using the EZ DNA Methylation kit (Zymo) then assayed by the Illumina Infinium MethylationEPIC BeadChip array that interrogates over 850,000 CpG methylation sites.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Dmrcate

label: Cy5 and Cy3

source_name: PBMC

label_protocol: A total of 50 ng of genomic DNA was used for genome-wide DNA methylation profiling at the Australian Research Genomics Facilities (ARGF, Melbourne) using Illumina’s Infinium MethylationEPIC (HM850K) platform.

extract_protocol: Genomic DNA was extracted from whole blood using Qiagen DNAeasy Blood and Tissue Kit (Qiagen) following the manufacturer’s instructions. DNA quality and concentration were checked using nanodrop and qubit instruments, respectively.

value: AT

tag: Sex

value: F


title: PBMC_N_147_AT_M

description:
N_147
200722330104_R04C01

value: M


title: PBMC_N_131_AT_F

description:
N_131
200722330104_R07C01


title: PBMC_N_050_AT_M

description:
N_050
200722330104_R08C01


title: PBMC_N_150_AT_M

description:
N_150
200722330104_R03C01


title: PBMC_N_149_AT_F

description:
N_149
200722330104_R02C01


title: PBMC_N_073_AT_M

description:
N_073
200722330104_R05C01


title: PBMC_N_053_AT_F

description:
N_053
200722330104_R06C01


title: PBMC_N_144_AT_F

description:
N_144
200722330093_R07C01


title: PBMC_N_142_AT_F

description:
N_142
200722330093_R06C01


title: PBMC_N_141_AT_M

description:
N_141
200722330093_R05C01


title: PBMC_N_138_AT_M

description:
N_138
200722330093_R04C01


title: PBMC_N_137_AT_M

description:
N_137
200722330093_R03C01


title: PBMC_N_136_AT_F

description:
N_136
200722330093_R02C01


title: PBMC_N_129_AT_M

description:
N_129
200722330091_R08C01


title: PBMC_N_130_AT_F

description:
N_130
200722330093_R01C01


title: PBMC_N_124_AT_F

description:
N_124
200722330091_R06C01


title: PBMC_N_120_AT_M

description:
N_120
200722330091_R04C01


title: PBMC_N_125_AT_M

description:
N_125
200722330091_R07C01


title: PBMC_N_123_AT_F

description:
N_123
200722330091_R05C01


title: PBMC_N_115_AT_M

description:
N_115
200722330091_R02C01


title: PBMC_N_112_AT_M

description:
N_112
200722330072_R08C01


title: PBMC_N_109_AT_M

description:
N_109
200722330072_R07C01


title: PBMC_N_107_AT_M

description:
N_107
200722330072_R06C01


title: PBMC_N_106_AT_M

description:
N_106
200722330072_R05C01


title: PBMC_N_117_AT_M

description:
N_117
200722330091_R03C01


title: PBMC_N_103_AT_F

description:
N_103
200722330072_R02C01


title: PBMC_N_088_AT_M

description:
N_088
200693480044_R07C01


title: PBMC_N_104_AT_F

description:
N_104
200722330072_R03C01


title: hESCs_differentiated_to_pancreatic_ductal_organoids [HUES8_4_WT_d20]

city: Ulm

first: Alexander

last: Kleger

address: Albert Einstein Allee 23

country: Germany

institute: Ulm University

description: ductal

hyb_protocol: DNA methylation was interrogated by the Infinium MethylationEPIC BeadChips (Illumina) following the manufacturer's guidelines.

scan_protocol: Samples were assessed using the Infinium MethylationEPIC BeadChip (Illumina) on a NextSeq550

data_processing: Raw IDAT files were imported into the R programming environment (v4.1.3) using the minfi package. Data was normalized using the preprocess Illumina function without background correction. The methylation level at each CpG was calculated as beta value. CpGs on the gonosomes were excluded in downstream analyses.

label: Cy3, Cy5

label_protocol: 250 ng of genomic DNA was bisulfite-converted using the EZ DNA methylation kit (ZymoResearch).

growth_protocol: Stem cells were cultivated on hESC-qualified Matrigel (Corning) coated plates in TeSR1 or TeSR Plus medium (STEMCELL technologies) at 5% CO2, 5% O2 and 37°C. Cells were passaged twice a week at a confluency of 80 to 100%.

extract_protocol: For DNA methylation analyses, cells were harvested at hESC, definite endoderm, pancreatic endoderm, pancreatic progenitor or pancreatic duct like organoid stage. For monolayer cultures, cells were washed with PBS and incubated with TrypLE Express for 3-7 min at 37°C before resuspending the cells in DMEM/F-12. PDLOs were harvested by incubation with collagenase dispase for 3h, followed by singularisation with Accutase for 30 min. Cells were once washed with PBS and pellets were frozen until DNA isolation was performed using the Animal Tissue Genomic DNA Purification Kit (Genaxxon).

treatment_protocol: To induce differentiation and to differentiate PPs into PDLOs, cells were cultivated for 2 weeks in matrigel, using a protocol published by our group (Breunig 2021).

value: WT

tag: day


title: PBMC_N_085_AT_M

description:
N_085
200693480044_R06C01


title: hESCs_differentiated_to_pancreatic_ductal_organoids [HUES8_1_WT_d27]

description: ductal


title: hESCs_differentiated_to_pancreatic_endoderm [HUES8_1_WT_d9]


title: PBMC_N_102_AT_M

description:
N_102
200722330072_R01C01


title: PBMC_N_058_AT_F

description:
N_058
200693480044_R01C01


title: hESCs_differentiated_to_pancreatic_ductal_organoids [HUES8_4_WT_d27]

description: ductal


title: PBMC_N_114_AT_M

description:
N_114
200722330091_R01C01


title: hESC_cells [HUES8_4_WT_d0]

description: hESC


title: hESC_cells [HUES8_3_WT_d0]

description: hESC


title: hESCs_differentiated_to_pancreatic_endoderm [HUES8_4_WT_d9]


title: PBMC_N_056_AT_M

description:
N_056
200727750033_R07C01


title: PBMC_N_055_AT_F

description:
N_055
200727750033_R06C01


title: PBMC_N_093_AT_F

description:
N_093
200693480044_R08C01


title: hESCs_differentiated_to_pancreatic_progenitor [HUES8_3_WT_d13]


title: PBMC_N_080_AT_F

description:
N_080
200693480044_R05C01


title: hESCs_differentiated_to_pancreatic_ductal_organoids [HUES8_5-Aza_d27]

description: ductal

source_name: PDLOs d27 + 5 µM 5-Aza

value: Aza


title: hESCs_differentiated_to_pancreatic_ductal_organoids [HUES8_3_WT_d20]

description: ductal


title: hESCs_differentiated_to_endoderm [HUES8_4_WT_d3]

description: endoderm


title: hESCs_differentiated_to_endoderm [HUES8_2_WT_d3]

description: endoderm


title: PBMC_N_046_AT_F

description:
N_046
200727750033_R01C01


title: PBMC_N_031_AT_M

description:
N_031
200727750032_R06C01


title: PBMC_N_030_AT_F

description:
N_030
200727750032_R05C01


title: hESCs_differentiated_to_endoderm [HUES8_3_WT_d3]

description: endoderm


title: PBMC_N_017_AT_M

description:
N_017
200727750032_R03C01


title: PBMC_N_016_AT_M

description:
N_016
200727750032_R02C01


title: hESCs_differentiated_to_pancreatic_progenitor [HUES8_4_WT_d13]


title: PBMC_N_011_AT_F

description:
N_011
200727750031_R08C01


title: PBMC_N_063_AT_F

description:
N_063
200693480044_R02C01


title: hESC_cells [HUES8_1_WT_d0]

description: hESC


title: hESCs_differentiated_to_pancreatic_ductal_organoids [HUES8_Aza-ctrl_d27]

description: ductal

source_name: PDLOs d27 -5-Aza

value: Aza-Ctrl


title: hESCs_differentiated_to_pancreatic_progenitor [HUES8_1_WT_d13]


title: hESCs_differentiated_to_pancreatic_ductal_organoids [HUES8_1_WT_d20]

description: ductal


title: PBMC_N_005_AT_F

description:
N_005
200727750031_R04C01


title: PBMC_N_009_AT_F

description:
N_009
200727750031_R06C01


title: PBMC_N_057_AT_M

description:
N_057
200727750033_R08C01


title: PBMC_N_022_SP_F

description:
N_022
200693480019_R06C01

value: SP


title: PBMC_N_108_SP_F

description:
N_108
200693480019_R07C01


title: PBMC_N_105_AT_M

description:
N_105
200722330072_R04C01


title: hESCs_differentiated_to_pancreatic_ductal_organoids [HUES8_3_WT_d27]

description: ductal


title: hESCs_differentiated_to_pancreatic_endoderm [HUES8_3_WT_d9]


title: PBMC_N_150_SP_M

description:
N_150
200693480019_R01C01


title: PBMC_N_048_AT_M

description:
N_048
200727750033_R03C01


title: PBMC_N_054_AT_F

description:
N_054
200727750033_R05C01


title: PBMC_N_047_AT_M

description:
N_047
200727750033_R02C01


title: PBMC_N_148_SP_F

description:
N_148
200693480006_R07C01


title: PBMC_N_037_AT_M

description:
N_037
200727750032_R08C01


title: PBMC_N_142_SP_F

description:
N_142
200693480006_R04C01


title: PBMC_N_141_SP_M

description:
N_141
200693480006_R03C01


title: PBMC_N_138_SP_M

description:
N_138
200693480006_R02C01


title: PBMC_N_034_AT_M

description:
N_034
200727750032_R07C01


title: PBMC_N_023_AT_F

description:
N_023
200727750032_R04C01


title: PBMC_N_129_SP_M

description:
N_129
200720130006_R06C01


title: PBMC_N_130_SP_F

description:
N_130
200720130006_R07C01


title: PBMC_N_065_AT_M

description:
N_065
200693480044_R03C01


title: PBMC_N_013_AT_F

description:
N_013
200727750032_R01C01


title: PBMC_N_010_AT_M

description:
N_010
200727750031_R07C01


title: PBMC_N_124_SP_F

description:
N_124
200720130006_R04C01


title: PBMC_N_113_SP_F

description:
N_113
200727750031_R01C01


title: PBMC_N_111_SP_M

description:
N_111
200693480019_R08C01


title: PBMC_N_004_SP_M

description:
N_004
200693480019_R05C01


title: PBMC_N_002_AT_F

description:
N_002
200727750031_R03C01


title: PBMC_N_132_SP_F

description:
N_132
200693480019_R03C01


title: PBMC_N_003_SP_F

description:
N_003
200693480019_R04C01


title: PBMC_N_001_AT_M

description:
N_001
200727750031_R02C01


title: PBMC_N_131_SP_F

description:
N_131
200693480019_R02C01


title: PBMC_N_008_AT_M

description:
N_008
200727750031_R05C01


title: PBMC_N_149_SP_F

description:
N_149
200693480006_R08C01


title: PBMC_N_116_SP_M

description:
N_116
200693480004_R08C01


title: PBMC_N_112_SP_M

description:
N_112
200693480004_R05C01


title: PBMC_N_137_SP_M

description:
N_137
200693480006_R01C01


title: PBMC_N_144_SP_F

description:
N_144
200693480006_R05C01


title: PBMC_N_109_SP_M

description:
N_109
200693480004_R04C01


title: PBMC_N_106_SP_M

description:
N_106
200693480004_R02C01


title: PBMC_N_107_SP_M

description:
N_107
200693480004_R03C01


title: PBMC_N_136_SP_F

description:
N_136
200720130006_R08C01


title: PBMC_N_125_SP_M

description:
N_125
200720130006_R05C01


title: PBMC_N_104_SP_F

description:
N_104
200722330090_R08C01


title: PBMC_N_123_SP_F

description:
N_123
200720130006_R03C01


title: PBMC_N_102_SP_M

description:
N_102
200722330090_R06C01


title: PBMC_N_120_SP_M

description:
N_120
200720130006_R02C01


title: PBMC_N_117_SP_M

description:
N_117
200720130006_R01C01


title: PBMC_N_115_SP_M

description:
N_115
200693480004_R07C01


title: PBMC_N_105_SP_M

description:
N_105
200693480004_R01C01


title: PBMC_N_079_SP_F

description:
N_079
200722330090_R01C01


title: PBMC_N_065_SP_M

description:
N_065
200722330064_R08C01


title: PBMC_N_093_SP_F

description:
N_093
200722330090_R05C01


title: PBMC_N_114_SP_M

description:
N_114
200693480004_R06C01


title: PBMC_N_103_SP_F

description:
N_103
200722330090_R07C01


title: PBMC_N_079_AT_F

description:
N_079
200693480044_R04C01


title: PBMC_N_054_SP_F

description:
N_054
200722330064_R02C01


title: PBMC_N_052_SP_F

description:
N_052
200722330064_R01C01


title: PBMC_N_085_SP_M

description:
N_085
200722330090_R03C01


title: PBMC_N_080_SP_F

description:
N_080
200722330090_R02C01


title: PBMC_N_037_SP_M

description:
N_037
200722330063_R05C01


title: PBMC_N_063_SP_F

description:
N_063
200722330064_R07C01


title: PBMC_N_058_SP_F

description:
N_058
200722330064_R06C01


title: PBMC_N_056_SP_M

description:
N_056
200722330064_R04C01


title: PBMC_N_031_SP_M

description:
N_031
200722330063_R03C01


title: PBMC_N_055_SP_F

description:
N_055
200722330064_R03C01


title: PBMC_N_048_SP_M

description:
N_048
200722330063_R08C01


title: PBMC_N_057_SP_M

description:
N_057
200722330064_R05C01


title: PBMC_N_016_SP_M

description:
N_016
200722330062_R07C01


title: PBMC_N_047_SP_M

description:
N_047
200722330063_R07C01


title: PBMC_N_034_SP_M

description:
N_034
200722330063_R04C01


title: PBMC_N_046_SP_F

description:
N_046
200722330063_R06C01


title: PBMC_N_023_SP_F

description:
N_023
200722330063_R01C01


title: PBMC_N_030_SP_F

description:
N_030
200722330063_R02C01


title: PBMC_N_002_SP_F

description:
N_002
200727750044_R08C01


title: PBMC_N_001_SP_M

description:
N_001
200727750044_R07C01


title: PBMC_N_088_SP_M

description:
N_088
200722330090_R04C01


title: PBMC_N_008_SP_M

description:
N_008
200722330062_R02C01


title: PBMC_N_073_BI_M

description:
N_073
200727750044_R05C01

value: BI


title: PBMC_N_017_SP_M

description:
N_017
200722330062_R08C01


title: PBMC_N_053_BI_F

description:
N_053
200727750044_R06C01


title: PBMC_N_147_BI_M

description:
N_147
200727750044_R04C01


title: PBMC_N_013_SP_F

description:
N_013
200722330062_R06C01


title: PBMC_N_052_AT_F

description:
N_052
200727750033_R04C01


title: PBMC_N_149_BI_F

description:
N_149
200727750044_R02C01


title: PBMC_N_010_SP_M

description:
N_010
200722330062_R04C01


title: PBMC_N_150_BI_M

description:
N_150
200727750044_R03C01


title: PBMC_N_011_SP_F

description:
N_011
200722330062_R05C01


title: PBMC_N_144_BI_F

description:
N_144
200739040029_R07C01


title: PBMC_N_148_BI_F

description:
N_148
200727750044_R01C01


title: PBMC_N_005_SP_F

description:
N_005
200722330062_R01C01


title: PBMC_N_142_BI_F

description:
N_142
200739040029_R06C01


title: PBMC_N_138_BI_M

description:
N_138
200739040029_R04C01


title: PBMC_N_141_BI_M

description:
N_141
200739040029_R05C01


title: PBMC_N_129_BI_M

description:
N_129
200739040028_R08C01


title: PBMC_N_137_BI_M

description:
N_137
200739040029_R03C01


title: PBMC_N_136_BI_F

description:
N_136
200739040029_R02C01


title: PBMC_N_130_BI_F

description:
N_130
200739040029_R01C01


title: PBMC_N_125_BI_M

description:
N_125
200739040028_R07C01


title: PBMC_N_123_BI_F

description:
N_123
200739040028_R05C01


title: PBMC_N_124_BI_F

description:
N_124
200739040028_R06C01


title: PBMC_N_120_BI_M

description:
N_120
200739040028_R04C01


title: PBMC_N_117_BI_M

description:
N_117
200739040028_R03C01


title: PBMC_N_114_BI_M

description:
N_114
200727750024_R08C01


title: PBMC_N_009_SP_F

description:
N_009
200722330062_R03C01


title: PBMC_N_116_BI_M

description:
N_116
200739040028_R02C01


title: PBMC_N_112_BI_M

description:
N_112
200727750024_R07C01


title: PBMC_N_115_BI_M

description:
N_115
200739040028_R01C01


title: PBMC_N_109_BI_M

description:
N_109
200727750024_R06C01


title: PBMC_N_107_BI_M

description:
N_107
200727750024_R05C01


title: PBMC_N_106_BI_M

description:
N_106
200727750024_R04C01


title: PBMC_N_105_BI_M

description:
N_105
200727750024_R03C01


title: PBMC_N_102_BI_M

description:
N_102
200727750023_R08C01


title: PBMC_N_103_BI_F

description:
N_103
200727750024_R01C01


title: PBMC_N_104_BI_F

description:
N_104
200727750024_R02C01


title: PBMC_N_093_BI_F

description:
N_093
200727750023_R07C01


title: PBMC_N_085_BI_M

description:
N_085
200727750023_R05C01


title: PBMC_N_065_BI_M

description:
N_065
200727750023_R02C01


title: PBMC_N_079_BI_F

description:
N_079
200727750023_R03C01


title: PBMC_N_080_BI_F

description:
N_080
200727750023_R04C01


title: PBMC_N_088_BI_M

description:
N_088
200727750023_R06C01


title: PBMC_N_063_BI_F

description:
N_063
200727750023_R01C01


title: PBMC_N_057_BI_M

description:
N_057
200727750022_R07C01


title: PBMC_N_058_BI_F

description:
N_058
200727750022_R08C01


title: PBMC_N_054_BI_F

description:
N_054
200727750022_R04C01


title: PBMC_N_056_BI_M

description:
N_056
200727750022_R06C01


title: PBMC_N_047_BI_M

description:
N_047
200727750022_R01C01


title: PBMC_N_052_BI_F

description:
N_052
200727750022_R03C01


title: PBMC_N_031_BI_M

description:
N_031
200739040015_R05C01


title: PBMC_N_037_BI_M

description:
N_037
200739040015_R07C01


title: PBMC_N_030_BI_F

description:
N_030
200739040015_R04C01


title: PBMC_N_034_BI_M

description:
N_034
200739040015_R06C01


title: PBMC_N_016_BI_M

description:
N_016
200739040015_R01C01


title: PBMC_N_011_BI_F

description:
N_011
200739040008_R07C01


title: PBMC_N_023_BI_F

description:
N_023
200739040015_R03C01


title: PBMC_N_010_BI_M

description:
N_010
200739040008_R06C01


title: PBMC_N_008_BI_M

description:
N_008
200739040008_R04C01


title: PBMC_N_002_BI_F

description:
N_002
200739040008_R02C01


title: PBMC_N_005_BI_F

description:
N_005
200739040008_R03C01


title: PBMC_N_001_BI_M

description:
N_001
200739040008_R01C01


title: PBMC_N_009_BI_F

description:
N_009
200739040008_R05C01


title: PBMC_N_048_BI_M

description:
N_048
200727750022_R02C01


title: PBMC_N_055_BI_F

description:
N_055
200727750022_R05C01


title: PBMC_N_046_BI_F

description:
N_046
200739040015_R08C01


title: 2-AA2-FM

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Rstudio
The reads count of gene was computed by RSEM v1.2.28 with default settings except choosing STAR 2.7.1a aligner for reads mapping.
The reference transcripts were generated using hg38 as reference genome and GENCODE v22 as gene annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count, TPM and FPKM values for each gene

growth_protocol: MCF7 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Equal amount of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Cells were treated with 100nM fulvestrant for 24hrs.
Cells were starved in charcoal-stripped serum containing medium for 72hrs and then stimulated with DMSO or 10nM estradiol for 8hrs.

value: ER+ breast cancer cell line

value: sgNT

value: DMSO

tag: time


title: 1-AA10-FM


title: 2-AA10-E2

value: 10nM Estrogen stimulated


title: 2-AA10-EDM

value: Estrogen depleted


title: 2-AA2-E2


title: 1-AA2-FM


title: 1-AA10-E2


title: 1-AA2-E2


title: PBMC_N_017_BI_M

description:
N_017
200739040015_R02C01


title: PBMC_N_013_BI_F

description:
N_013
200739040008_R08C01


title: 2-AA5-E2+


title: 2-AA8-E2+


title: 437_2-AA2-E2+


title: 2-AA8-E2-


title: 2-AA5-E2-


title: 437_2-AA2-E2-


title: 1-AA8-E2+


title: 1-AA5-E2+


title: 437_1-AA2-E2+


title: 1-AA8-E2-


title: 1-AA5-E2-


title: 2-AA8-Ful

value: 100nM Fulvestrant


title: 2-AA2-EDM


title: 437_1-AA2-E2-


title: 2-AA10-FM


title: 2-AA5-Ful


title: 1-AA2-EDM


title: 649_2-AA2-Ful


title: 1-AA10-EDM


title: 2-AA8-DMSO


title: 649_1-AA2-DMSO


title: 1-AA5-Ful


title: 1-AA5-DMSO


title: 649_2-AA2-DMSO


title: 1-AA8-Ful


title: 1-AA8-DMSO


title: 2-AC2-E2+


title: 2-AC1-E2+

value: EV


title: 2-AC2-E2-


title: 2-AC1-E2-


title: 1-AC2-E2+


title: 1-AC1-E2+


title: 1-AC1-E2-


title: 1-AC2-E2-


title: 2-AC2-Ful


title: 2-AC1-DMSO


title: 1-AC2-Ful


title: 1-AC1-Ful


title: 1-AC2-DMSO


title: 2-AC2-DMSO


title: 1-AC1-DMSO


title: 2-AA3-E2+


title: 2-AA4-E2+


title: 2-AA5-DMSO


title: 2-AA2-E2+


title: 2-AA2-E2-


title: 1-AA2-E2+


title: 2-AA3-E2-


title: 1-AA2-E2-


title: 2-AA4-E2-


title: 1-AA4-E2-


title: 2-AA4-Ful


title: 649_1-AA2-Ful


title: 1-AA3-E2+


title: 2-AA3-Ful


title: 2-AA4-DMSO


title: 2-AA3-DMSO


title: 1-AA4-Ful


title: 2-AC1-Ful


title: 1-AA2-Ful


title: 1-AA3-Ful


title: 1-AA4-DMSO


title: 1-AA3-DMSO


title: 1-AA4-E2+


title: T47D, anti-IMP1 antibody

description:
LncRNA profiling by RNA sequencing
T47Dshiyanzu

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Fastx.
Clean reads were compared with hg19.The analysis was performed by the Shanghai Biotechnology Corporation.
Assembly: hg19
Supplementary files format and content: Tab-delimited files include FPKM values

growth_protocol: T47D Cells were cultured in  DMEM supplemented with 10% fetal bovine serum, 100U/ml penicillin,  and 100 µg/ml streptomycin at 37 °C in a humid environment with 5 % CO2

extract_protocol:
the co-precipitated RNAs were extracted  with TRIzol reagent following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared according to Illumina's protocol.

treatment_protocol: Cell lysates were prepared from cultured T47D cells and then incubated with protein A beads coated with anti-IMP1 antibody or normal IgG control at 4°C for 4 h in the presence of RNasin (200 U/mL) and protease inhibitors. After incubation, the supernatant was removed by a short centrifugation and the beads were washed three times in ice-cold lysis buffer. Immunoprecipitates were verified by western blotting using the anti-IMP1 antibody.

value: breast cancer cells

value: anti-IMP1 antibody


title: tsk-4_H3K27me3_rep2

city: Beijing

first: Danhua

last: Jiang

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
and filtered for duplicated reads using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard)
H2A.W, H3K9me2 or H3K27me3 peaks in WT were called using MACS2 version 2.1.2 with default parameters
Genes or TEs were assigned to the peaks when the genic regions overlapped with the peak regions for at least one base pair
For data visualization, data from two biological replicates were merged and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp
Average ChIP-seq profiles were plotted using deepTools utility plotProfile
Assembly: TAIR10
Supplementary files format and content: *.bw, normlized ChIP-seq coverage files

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: 7-day old seedlings

extract_protocol:
Mononucleosomes from 7-day old seedlings prepared by MNase digestion were immunoprecipitated with anti-H2A.W (Yelagandula et al., 2014), anti-H3K9me2 (Abcam, ab1220) or anti-H3K27me3 (Millipore, 07-449) antibody.
Immunoprecipitated DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction. Prepared libraries were sequenced on a NovaSeq 6000 platform and paired-end 150bp reads were generated

value: seedlings

tag: age

value: 7-day old


title: tsk-4;lhp1-3_H3K27me3_rep1


title: T47D, IgG control

description:
LncRNA profiling by RNA sequencing
T47Dduizhaozu

value: IgG control


title: tsk-4_H3K27me3_rep1


title: 1-AA3-E2-


title: lhp1-3_H3K27me3_rep2


title: lhp1-3_H3K27me3_rep1


title: Col_H3K27me3_rep2

value: wildtype


title: tsk-4;lhp1-3_input_rep2

value: input


title: tsk-4;lhp1-3_input_rep1


title: lhp1-3_input_rep2


title: Col_H3K27me3_rep1


title: tsk-4_input_rep2


title: lhp1-3_input_rep1


title: Col_input_rep2


title: Col_input_rep1


title: 2-AA2-DMSO


title: tsk-4_RNA_rep3

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10
Reads per gene were counted by HTseq version 0.11.2
Differential gene expression analysis was performed using DESeq2 version 1.26.0
Genes were considered as differentially expressed in RNA-seq if they exhibited a more than two-fold change in expression and had a P adjust value < 0.05
Gene ontology analysis was performed with DAVID (https://david.ncifcrf.gov/)
Assembly: TAIR10
Supplementary files format and content: *.txt, TPM values for all samples

extract_protocol:
7-day old seedlings were collected and total RNA was extracted with Minibest plant RNA extraction kit (Takara, 9769)
Sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB, 7530L) according to the manufacturer’s instruction

tag: ecotype

value: Col


title: Col_RNA_rep3


title: Col_RNA_rep2


title: tsk-4_RNA_rep1


title: 1-AA2-DMSO


title: tsk-4;lhp1-3_H3K27me3_rep2


title: Col_RNA_rep1


title: Col_MNase_rep1

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
ow quality reads were filtered with fastp version 0.20.1 (Chen et al., 2018). Reads were mapped to the Arabidopsis (TAIR10) genome with Botiew2 version 2.4.2
and were filtered for duplicated reads by using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard)
For data visualization, data from two biological replicates were merged and bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and the MNase parameter
Average MNase-seq profiles were generated using deepTools utility plotProfile
Assembly: TAIR10
Supplementary files format and content: *.bw, normlized MNase-seq coverage files

extract_protocol:
For MNase-seq analysis, 7-day old seedlings were fixed with 1% formaldehyde. After nuclei extraction, mononucleosomes were generated with micrococcal nuclease (MNase) (NEB, M0247S) digestion as previously described
The mononucleosomal DNA were subjected to library preparation with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607-02) according to the manufacturer’s instruction

value: MNase


title: Col_MNase_rep2


title: tsk-4_MNase_rep1


title: tsk-4_input_rep1


title: tsk-4_BS-seq_rep3

description:
tsk-4 7-day old seedlings
tsk-4_BS-seq.CGmap.gz

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with BS-Seeker2 version 2.1.8 using default parameters
Duplicated reads were filtered with Picard version 2.24.0 MarkDuplicates
CG, CHG, and CHH methylation levels were calculated with CGmaptools (version 0.1.2)
Assembly: For data visualization, data from three biological replicates were merged and methylation data were visualized with ggplot2 in R
Supplementary files format and content: TAIR10
Supplementary files format and content: .gz, DNA methylation level

extract_protocol:
Genomic DNA was extracted from 7-day old seedlings with Quick-DNA Plant/Seed Miniprep Kit (ZYMO, D6020)
200ng fragmented genomic DNA (200bp-500bp) was used for library preparation with VAHTS universal Pro DNA library prep kit for Illumina (Vazyme, ND608). NEBNext Multiplex Oligos for Illumina (NEB, E7535) were used for adapter ligation


title: Col_BS-seq_rep3

description:
Col 7-day old seedlings
Col_BS-seq.CGmap.gz


title: tsk-4_BS-seq_rep1


title: Col_BS-seq_rep2


title: Col_H2A.W_rep2


title: Col_H2A.W_rep1


title: 2-AA2-Ful


title: tsk-4_H3K9me2_rep2


title: Col_H3K9me2_rep1


title: tsk-4_H2A.W_rep2


title: tsk-4_H3K9me2_rep1


title: tsk-4_RNA_rep2


title: Col_H3K9me2_rep2


title: tsk-4_H2A.W_rep1


title: atm1-1_Sucrose_5DO_Rep1

city: Ames

first: Natalie

middle: M

last: Clark

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

data_processing:
Adapters trimmed using bbduk
Reads aligned to TAIR10 genome using STAR
Read counts per gene obtained using htseq-count (all_counts.csv)
TMM-normalized gene expression calculated using edgeR (all_tmm.csv)
Assembly: TAIR10
Supplementary files format and content: Comma separated value (.csv) file of read counts per gene for each sample
Supplementary files format and content: Comma separated value (.csv) file of TMM-normalized expression values per gene for each sample

source_name: seedling

growth_protocol: Seeds were surfaced sterilized using 50% bleach and 0.01% Triton X-100 for 10 min and then washed five times with sterile water. Seeds were then imbibed in sterile water for 2 days at 4 °C. The growth conditions used for experiments were 12-h white light/12-h dark, at 22°C. The light intensity was 45 μmol m−1 s−1 except otherwise stated.

extract_protocol:
Total RNA was extracted from 5-day old plants in three biological replicates using Trizol reagent followed by column clean up using a Zymo Direct-zol RNA purification kit. RNA quality was measured using a Bioanalyzer at the Iowa State University DNA facilty.
QuantSeq libraries were constructed at the Iowa State University DNA facility using a Lexogen 3’ mRNA-Seq FWD kit. 50bp single-end reads were generated using a NovaSeq6000

treatment_protocol: Imbibed seeds were plated on half strength Murashige and Skoog (MS) medium (MSP01 Caisson) plates solidified with 0.8% Agar (80-100 Mesh Agar BP2641-1 from Fisher scientific) and supplemented without (mock)/with 15mM glucose or 15mM sucrose.

value: seedling

tag: replicate

value: Sucrose


title: atm1-1_Sucrose_5DO_Rep2


title: atm1-1_Sucrose_5DO_Rep3


title: atm1-1_Glucose_5DO_Rep3

value: Glucose


title: tsk-4_MNase_rep2


title: atm1-1_Glucose_5DO_Rep1


title: atm1-1_Glucose_5DO_Rep2


title: Col_BS-seq_rep1


title: atm1-1_Mock_5DO_Rep3

value: Mock


title: atm1-1_Mock_5DO_Rep2


title: atm1-1_Mock_5DO_Rep1


title: Col-0_Sucrose_5DO_Rep3


title: Col-0_Sucrose_5DO_Rep1


title: tsk-4_BS-seq_rep2


title: Col-0_Glucose_5DO_Rep2


title: Col-0_Glucose_5DO_Rep3


title: Col-0_Mock_5DO_Rep2


title: Col-0_Glucose_5DO_Rep1


title: Col-0_Mock_5DO_Rep3


title: HeLa_ZBTB2-myc_myc_biol_rep_3

city: Kyoto

first: Christalle

middle: CT

last: Chow

state: Kyoto

address: Sakyo Ward, Yoshidakonoecho

department: Graduate School of Biostudies

country: Japan

institute: Kyoto University

data_processing:
Data processing was performed by Active Motif. 75-nt sequences reads were mapped to the genome using the BWA algorithm with default settings. Only reads that passed Illumina's purity filter, aligned with < 2 mismatches, and map uniquely to the genome were used in subsequent analysis. Duplicate reads were removed.
To create ChIP-Seq coverage plots, 5'-ends of the aligned reads (tags) were extended at their 3'-end to 150-200 bp. To identify the density of the extended tags, the genome was divided into 32-nt bins and the number of fragments in each bin was determined. The histogram of fragment densities was stored in a bigWig File.
Peak calling was performed with MACS
Normalization was performed by reducing by random sampling the tag number of all samples within a comparison group to the number of tags present in the smallest sample.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: HeLa

growth_protocol: DMEM, 10% fetal bovine serum, 1X penicillin/streptomyic. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cell samples for ChIP-Seq were prepared according to Active Motif’s Epigenetic Services ChIP Cell Fixation protocol and then snap-frozen and sent to Active Motif for processing and analysis.
Library construction was performed by Active Motif

treatment_protocol: Cells were seeded and transfected with EGFP-myc or ZBTB2-myc overexpression vectors. 16 hours after transfection, cells were moved into a RUSKINN INVIVO2 500 Hypoxic Work Station set at < 0.1% O2, 5% CO2, and 4% H2, and 90.9% N2 gas and cultured for 24 hours.

value: HeLa

value: Human cervical adenocarcinoma

value: myc (Active Motif, #91203)

value: Hypoxia (0.1% O2)


title: HeLa_ZBTB2-myc_myc_biol_rep_2


title: HeLa_EGFP-myc_myc_biol_rep_1


title: HeLa_EGFP-myc_myc_biol_rep_2


title: Col-0_Mock_5DO_Rep1


title: HeLa_EGFP-myc_myc_biol_rep_3


title: CXCR5pos_CD11Cpos biol rep 4

city: Cambridge

first: Vinay

middle: S

last: Mahajan

state: MA

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

description:
CXCR5pos_CD11Cpos_827543
mRNA

data_processing:
bcl2fastq
rsem
Ebseq
Assembly: hg38
Supplementary files format and content: trim_full_ebseq.counts.matrix.results.normalized_data_matrix.txt: Tab-delimited text file includes counts for each sample.

source_name: Blood

extract_protocol:
Qiagen RNeasy micro kit.
SmartSeq2

value: Blood

tag: diagnosis

value: IgG4-related disease


title: CXCR5pos_CD11Cpos biol rep 2

description:
CXCR5pos_CD11Cpos_716681
mRNA


title: CXCR5pos_CD11Cpos biol rep 1

description:
CXCR5pos_CD11Cpos_301487
mRNA


title: HeLa_ZBTB2-myc_myc_biol_rep_1


title: CXCR5pos_CD11Cneg biol rep 4

description:
CXCR5pos_CD11Cneg_827543
mRNA


title: HeLa_Pooled_Inputs


title: CXCR5pos_CD11Cpos biol rep 3

description:
CXCR5pos_CD11Cpos_719814
mRNA


title: CXCR5pos_CD11Cneg biol rep 1

description:
CXCR5pos_CD11Cneg_301487
mRNA


title: CXCR5pos_CD11Cneg biol rep 3

description:
CXCR5pos_CD11Cneg_719814
mRNA


title: CXCR5neg_CD11Cneg biol rep 4

description:
CXCR5neg_CD11Cneg_827543
mRNA


title: CXCR5pos_CD11Cneg biol rep 2

description:
CXCR5pos_CD11Cneg_716681
mRNA


title: CXCR5neg_CD11Cpos biol rep 2

description:
CXCR5neg_CD11Cpos_716681
mRNA


title: CXCR5neg_CD11Cpos biol rep 1

description:
CXCR5neg_CD11Cpos_301487
mRNA


title: CXCR5neg_CD11Cneg biol rep 3

description:
CXCR5neg_CD11Cneg_719814
mRNA


title: Col-0_Sucrose_5DO_Rep2


title: CXCR5neg_CD11Cneg biol rep 2

description:
CXCR5neg_CD11Cneg_716681
mRNA


title: LNCAP-LCMT1-MED1

city: Philadelphia

first: Irfan

last: Asangani

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Illumina bcl2fastq for demultiplexing to generate fastq files
fastq files were aligned to hg19 reference genome using STAR aligner (2.7.3a) with default parameters or bowtie2 with â€œ--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700â€
samtools (v1.9) was used to convert SAM to BAM and filter out duplicates and reads q<30
bamCoverage was used to convert Bam to bigwig using â€œ--normalizeUsing CPMâ€
Assembly: hg19
Supplementary files format and content: bigWig files containing signal of each sample to be displayed on genome browser of preference

source_name: Derived from LNCAP

growth_protocol: MDVR cell lines were grown in the medium supplemented with Enzalutamide.

extract_protocol:
Diagenode ChIP Seq kit was used to ChIP the transcription factor/co-factor associated DNA for the construction of sequencing libraries.
Libraries were prepared for sequencing using standard NEBNext Ultra II FS DNA Library Prep Kit for Illumina  protocols.

treatment_protocol: ARD-69 or DT-061 treatments were done at a concentration of 100 nM and 10 uM for a time point of 12 and 24 hours respectivily.

value: LNCAP parental over-expressing LCMT1

value: MED1 (Bethyl, abA300-793A)


title: CXCR5neg_CD11Cneg biol rep 1

description:
CXCR5neg_CD11Cneg_301487
mRNA


title: LNCAP-LCMT1-AR

value: AR (Millipore, 06-680-EMD)


title: LNCAP-LACZ-AR

value: LNCAP parental over-expressing LACZ


title: LNCAP-LACZ-MED1


title: LNCAP_INPUT_CTRL

source_name: ATCC

value: LNCAP parental


title: LNCAP-EnzaR_DMSO_MED1

value: LNCAP-Enzalutamide resistant

value: DMSO


title: RB39050

city: Moncton

first: Eric

middle: P

last: Allain

state: New Brunswick

address: 330 University ave

department: Medical Genetics

country: Canada

institute: Vitalité Health Network

data_processing:
Raw reads from sRNAseq were processed with the Torrent Suite Software (v5.4.0), which runs the Torrent Mapping Alignment Program (TMAP).
Fastq's adapters removal and quality trimming with  TrimGalore (v 0.6.5).
Alignment was performed using STAR (version 2.7.0f) to the human genome GRCh38 version
Reads Counts performed using Derfinder (version 1.18.9) in R(v3.4.1)
Counts normalized with TMM  and differential expression analysis was performed using the Bioconductor package edgeR (v3.18.1)
Assembly: Human genome GRCh38
Supplementary files format and content: Raw reads counts in a csv (or tsv) format

source_name: Peptide affinity captured plasma extracellular RNA

extract_protocol:
miRVana miRNA isolation kit
CleanTag Small RNA library prep kit

tag: condition

value: PDAC


title: LNCAP-EnzaR_DT061_MED1

tag: cell line


title: PG1626 analysis - mutant iron deplete 3

city: Richmond

first: Janina

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

description:
Wt + DP vs Mut + DP, Mut Vs Mut + DP
77-KO+DP-3_TGTGAA

data_processing:
Base calls were done using CLC Genomic Workbench
Reads were aligned to the genome of Porphyromonas gingivalis 33277 using Genomic Workbench
Reads per gene were determined using Genomic Workbench
Statistical analysis was done using Genomic Workbench
Supplementary_files_format_and_content: (WT - BHI vs PG1626 KO - BHI)
Supplementary_files_format_and_content: (WT - BHI + DP vs PG1626 KO - BHI + DP)
Supplementary_files_format_and_content: (WT - BHI + DP vs WT - BHI)
Supplementary_files_format_and_content: (PG1626 KO - BHI +DP vs PG1626 KO - BHI)

organism: Porphyromonas gingivalis ATCC 33277

source_name: Bacterial cell

growth_protocol: Samples of wildtype P. gingivalis  ATCC33277 V3176 and V3177 PG1626 mutant were grown in an overnight culture of BHI media. The overnight cultures served to inoculate cultures of BHI media starting at an OD660 of approximately 0.05. Cultures were grown with and without dipyridyl to mid-log phase, centrifuged, and stored at -20 °C.

extract_protocol:
RNA isolation was carried out using the RNeasy mini-kit (Qiagen) following manufacturers protocol. Residual DNA was removed using the DNA-free DNase kit (Ambion) following manufacturers protocol.
For RNA-seq library generation, the Ovation complete Prokaryotic RNA-Seq DR multiplex kit (Nugen) was used. The library was generated following the manufacturers protocol and fragment sizes from sonication during library generation was confirmed using a bioanalyzer (Agilent Technologies). Libraries were sequenced by VCU nucleic acid sequencing core using Miseq Illumina sequencing.

treatment_protocol: Dipyridyl (Fe Chelator) - 150uM

tag: growth phase

value: logarithmic phase of growth

tag: dp treatment

value: iron deplete

tag: strain


title: CXCR5neg_CD11Cpos biol rep 3

description:
CXCR5neg_CD11Cpos_827543
mRNA

tag: cell type


title: LNCAP-EnzaR_ARD69_MED1

tag: treatment

tag: chip antibody


title: LNCAP-EnzaR_ARD69_AR


title: RB38750


title: PG1626 analysis - mutant iron deplete 4

description:
Wt + DP vs Mut + DP, Mut Vs Mut + DP
77+DP-KO-4_TGTTGC


title: RB39005


title: RB38749


title: PG1626 analysis - mutant iron deplete 1

description:
Wt + DP vs Mut + DP, Mut Vs Mut + DP
77-KO+DP_TTCAGC


title: RB38731


title: PG1626 analysis - mutant iron replete 3

description:
Wt vs Mut KO, Mut Vs Mut + DP
77-KO-3_GTGTTA

value: iron replete


title: PG1626 analysis - mutant iron deplete 2

description:
Wt + DP vs Mut + DP, Mut Vs Mut + DP
77-KO+DP-2_TTCGCT


title: PG1626 analysis - mutant iron replete 4

description:
Wt vs Mut KO, Mut Vs Mut + DP
77-KO-4_GTGGCC


title: RB38688


title: RB38644


title: RB38620


title: PG1626 analysis - wild type iron deplete 4

description:
Wt vs Wt + DP, Wt + DP vs Mut + DP
77+DP-4_CACCTC


title: PG1626 analysis - mutant iron replete 2

description:
Wt vs Mut KO, Mut Vs Mut + DP
77-KO-2_GGATGT


title: PG1626 analysis - mutant iron replete 1

description:
Wt vs Mut KO, Mut Vs Mut + DP
77-KO_GGACCC


title: RB38502


title: LNCAP-EnzaR_DT061_AR


title: PG1626 analysis - wild type iron deplete 3

description:
Wt vs Wt + DP, Wt + DP vs Mut + DP
77+DP-3_CACACA


title: RB38378


title: RB34422


title: PG1626 analysis - wild type iron deplete 2

description:
Wt vs Wt + DP, Wt + DP vs Mut + DP
77+DP-2_CCTCGG


title: LNCAP-EnzaR_DMSO_AR


title: PG1626 analysis - wild type iron deplete 1

description:
Wt vs Wt + DP, Wt + DP vs Mut + DP
77+DP_CCTTCA


title: ACRI506


title: ACRI491


title: ACRI456


title: PG1626 analysis - wild type iron replete 2

description:
Wt vs Mut KO, Wt vs Wt + DP
77-2_AAGACG


title: PG1626 analysis - wild type iron replete 4

description:
Wt vs Mut KO, Wt vs Wt + DP
77-4_ACAAAC


title: ACRI455


title: PG1626 analysis - wild type iron replete 3

description:
Wt vs Mut KO, Wt vs Wt + DP
77-3_ACACGA


title: aRBC_RNAPolIISer5P_Rep2

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

data_processing:
ChIP-seq reads were mapped to the GRCg6a genome using Bowtie2 (v2.3.5). Mapped reads were normalized using the S2R+ spike-in and duplicates were removed to generate BAM files using Samtools (v1.9).
Peaks were called with MACS2 (v2.2.7.1) with a significance level of 0.001 and the peaks conserved between two biological replicates were used for analysis
Assembly: GRCg6a
Supplementary files format and content: NarrowPeak file with the peaks obtained per biological replicate with MACS2 using p val <0.001.

organism: Gallus gallus

source_name: Primary red blood cells from adult hens (28-38 weeks old)

growth_protocol: HD3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO) supplemented with 10% fetal bovine serum (Biowest), 2% chicken serum and penicillin/streptomycin (Invitrogen).

extract_protocol:
Cells were fixed with formaldehyde 1% and sonicated. RNA Pol II Ser5-P immunoprecipitation was carried out using AB5131.
Libraries were constructed using the NEBnext Mutiplex Oligos primer set kit.

tag: genotype

value: WT


title: ACRI480


title: PG1626 analysis - wild type iron replete 1

description:
Wt vs Mut KO, Wt vs Wt + DP
77_AAGGGA


title: eRBC_RNAPolIISer5P_Rep2

source_name: Primary embryonic red blood cells (Embryonic day 10)


title: ACRI75

value: Non-affected individual


title: eRBC_RNAPolIISer5P_Rep1

value: Primary embryonic red blood cells (Embryonic day 10)


title: Erythroblasts_RNAPolIISer5P_Rep2

source_name: HD3 Cell line

value: HD3 Cell line

value: Chicken erythroblasts


title: ACRI69


title: ACRI35


title: ACRI355


title: Erythroblasts_RNAPolIISer5P_Rep1


title: ACRI347


title: ACRI345


title: ACRI300


title: ACRI331


title: ACRI311


title: PANC-1, GEMIN5, rep3

city: Guangzhou

first: Rui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Reads were mapped to the hg38 human genome by Bowtie2 followed by removing adapters and removing low-quality reads by fastp
CLIP-seq peaks were identified using Piranha
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
IGV was used to visualize the binding sites of GEMIN5.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: After treatment with 4-thiouridine (200 µM) for 14 h, PANC-1 cells were subjected to UV crosslinking and lysed on ice.

extract_protocol:
After end repair using T4 PNK (NEB), the bead-antibody-RNA complexes were treated with proteinase K, and the bound RNA was purified by acidic phenol/chloroform extraction and ethanol precipitation.
For PAR-CLIP sequencing, the purified RNAs were utilized for library construction using the NEBNext small RNA library prep kit (E7330S) and sequenced on an Illumina HiSeq4000

treatment_protocol: Cell lysate was then sonicated, digested with DNase I and RNase I for 15 min at 37 °C and incubated with Dynabeads protein A/G (Millipore) conjugated with anti-GEMIN5 antibody overnight at 4 °C.

value: PDAC cells

tag: rip antibody


title: ACRI247


title: aRBC_RNAPolIISer5P_Rep1

value: Primary red blood cells from adult hens (28-38 weeks old)


title: WT_4C_rep3

first: Fengling

last: Chen

state: Beijing

address: 30 Shuangqing Rd.

institute: Tsinghua University

description:
WT_4C_rep3
Obox_RNASeq_FPKM.xlsx

data_processing:
ATAC-Seq and Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
RNA-seq reads were trimmed by Trim Galore v0.6.6 then mapped to mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat from UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: Bigwig for Stacc-seq and ATAC-Seq signals
Supplementary files format and content: gene expression FPKM table for RNA-seq data

organism: Mus musculus

source_name: 4-cell mouse embryos

growth_protocol: 2i ESCs were cultured on 0.1% gelatin pre-coated dishes in DMEM medium (Gibco, 11995-065) containing leukemia-inhibiting factor (LIF) (Millipore, ESG1107), 15% fetal bovine serum (FBS; Hyclone, SH30396.03), GlutaMAX (Gibco, 35050-061), penicillin/ streptomycin (Millipore, TMS-AB2-C), nucleosides (Millipore, ES-008-D), non-essential amino acids (Gibco, 25-025-CIR), and β-mercaptoethanol (Gibco, 21985- 023). Naïve mESCs (2i) mESCs were cultured on feeder-free dishes coated with 0.1% gelatin in the N2B27 medium supplemented with 1 μM PD035901, 3 μM Chir99021, and 1 × 103 units/mL LIF. The cells were passaged 1:10-1:20.

extract_protocol:
For embryos, the zona pellucida was gently removed by treatment with Tyrode’s solution (Sigma, T1844). Then the embryos were lysed in lysis buffer containing RNase inhibitor. 2i ESCs were lysed in lysis buffer containing RNase inhibitor. The following steps followed the Smart-seq2 protocol as previously described (Picelli et al., 2014). For whole genome sequence, the tail tip DNA were extracted with isopropanol precipitation method.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing. For stacc-seq, the library was prepared following the protocol as descripted before (Liu et al., 2020). For ATAC-seq,  the library was prepared following the protocol as descripted before (Buenrostro et al., 2013; Wu ET AL., 2016).
The Smart-seq2, WGS (Picelli et al., 2014) and stacc-seq (Liu et al., 2020) library strategies were followed the protocols described.

treatment_protocol: siRNAs (25 uM for each) were injected into FGOs for maternal Obox KD and zygotes for zygotic Obox KD. For stacc-seq, Obox mRNA was injected into zygotes.

tag: tissue

value: 4-cell mouse embryos

value: wild type


title: mzKO_4C_rep1

description:
mzKO_4C_rep1
Obox_RNASeq_FPKM.xlsx

source_name: mouse embryos collected at control 4-cell stage

value: Obox mzKO


title: PANC-1, GEMIN5, rep2


title: WT_4C_rep2

description:
WT_4C_rep2
Obox_RNASeq_FPKM.xlsx


title: ACRI176


title: WT_4C_rep1

description:
WT_4C_rep1
Obox_RNASeq_FPKM.xlsx


title: mzKO_4C_rep2

description:
mzKO_4C_rep2
Obox_RNASeq_FPKM.xlsx

value: mouse embryos collected at control 4-cell stage


title: ACRI74


title: ACRI169


title: PANC-1, GEMIN5, rep1


title: tumor-3

city: Chefoo Yantai Shandong China

first: Zhang

last: Ke

address: No. 20 Yuhuangding East Road, Zhifu District

institute: Yantai Yuhuangding Hospital

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. 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 ploy-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.11.2 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. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz. The CIRCexplorer program (v2.3.8) was used to identify both the circularizing junction and the spliced sequence of circRNAs. All circRNA candidates with junction reads less than 2 were discarded. The remaining circRNA candidates were considered bonafide circRNAs.
DESeq2 (v2) was applied for the detection of differentially expressed mRNAs between tumor and non-tumor samples, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM/TPM values for each sample

source_name: Human thyroid tissue

extract_protocol:
The normal tissues was 2cm adjacent to the carcinoma. Cancer tissues was confirmed by postoperative pathology as papillary thyroid carcinoma. The patients' cancer tissues and normal paracancer tissues were collected and stored in the refrigerator at -80℃ for long-term storage for high-throughput sequencing.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Human thyroid tissue

value: cancer tissues


title: tumor-2


title: mzKO_4C_rep3

description:
mzKO_4C_rep3
Obox_RNASeq_FPKM.xlsx


title: GP muscle from cKO mouse 1, 5 months of age [snRNA-seq]

city: Dallas

first: kenian

last: chen

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: GP muscle

extract_protocol: Single nucleus RNA-seq libraries were generated using Single Cell 30 Reagent Kits v2 (10xGenomics) according to the manufacturer’s protocol. Briefly, cells, reagents (10xGenomics, PN-120237), gel beads (10xGenomics, 220104), and partitioning oil (10xGenomics, 220088) were loaded into the Chromium Single Cell A Chip (10xGenomics, 2000019), targeting 2000$5000 nuclei to be recovered per channel. Chip was loaded to the Chromium Controller (10xGenomics) to generate Gel Bead-In-Emulsions (GEMs). After reverse tran- scription using GEM-RT incubation protocol, GEMs were broken with recovery reagent (10xGenomics, 220016), cDNA was purified with DynaBeads MyOne Silane beads (Thermo Scientific, 37002D), amplified with PCR for 14 cycles, and further purified with SPRI- select reagent (Beckman Coulter, B23318). Quality control of recovered PCR product was performed on a Tapestation (Agilent) with D5000 high sensitivity screentapes (Agilent, 5067-5592), and cDNA yield was measured by Qubit DNA high sensitivity assay (Invitro- gen, Q32854). After fragmentation, end-repair, A-tailing and size selection purification, cDNA was ligated with adaptor and subse- quently purified with SPRIselect reagents. Libraries were amplified using PCR with sample indexes from Chromium i7 Multiplex kit (10xGenomics, PN-120262), for a total of $14 sample index cycles, as estimated from original cDNA yield using Qubit assay. Final PCR products were subjected to double-sided size selection with SPRIselect reagents. Library quality control was performed on the Agilent Tapestation with D1000 screentapes (Agilent, 5067-5582), and library yield was quantified by Qubit DNA high sensitivity assay.

treatment_protocol: 3 Control and 3 cKO GP muscles from were pooled together by experimental condition and muscles were pooled in cold phosphate-buffered saline (PBS) with 0.2 U/μl RNase inhibitor. PBS was removed and muscles were minced in 1 ml cold lysis buffer (10 mM Tris-HCl pH7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% NonidetTM P40 in Nuclease-Free Water) with scissors. After 2 min, 4 ml of cold lysis buffer were added and muscles were lysed for 3 min at +4 °C. Nine milliliter of cold wash buffer (PBS, BSA 2% and 0.2 U/μl RNase inhibitor from Roche) was added and the lysate was dounced with 10 strokes of loose pestle avoiding too much pressure and air bubbles. The homogenate was filtered with 70 and 40 μm cell strainers. Nuclei were pelleted by centrifugation for 5 min at 500 × g at +4 °C. Nuclei were washed to remove ambient RNAs in 1 ml of cold wash buffer, transferred in a 1.5 ml Eppendorf tube and centrifuged 5 min at 500 × g at +4 °C. The pellet was resuspended in 250 μl of wash buffer and stained during 15 min in the dark at +4 °C with DAPI (10 μg/ml). Then the nuclei were washed with 1 ml of wash buffer, centrifuged 5 min at 500 × g at +4 °C, resus- pended in 300 μl of wash buffer and filtered with 30 μm cell strainers. Nuclei were then FACS sorted to exclude debris with a BD FACSAria III and the BD FACSDIVA software. More than 200,000 nuclei were collected in a tube con- taining 200 μl of wash buffer.

value: GP muscle

tag: strain background

value: HSACreERT2;Net39 fl/fl cKO B6C3F1

value: 5 month mouse age

value: cKO

value: 3 months post-tamoxifen induced deletion


title: GP muscle from cKO mouse 3, 5 months of age

data_processing:
FastQC tool (version 0.11.8) for quality control of RNA-seq raw fastq data to evaluate low quality or adaptor portion of the reads for trimming. We then trimmed the reads using Trimmomatic (Version 0.39) and aligned to mm10 reference genome using HiSAT2 (Version 2.1.0) with default settings. Raw count matrix was generated using featureCounts (Version 1.6.2) with bam files as input.
Assembly: mm10
Supplementary files format and content: Raw count matrix

source_name: HSACreERT2;Net39 fl/fl

extract_protocol: RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep Library Prep Kit following manufacturer's protocols.

treatment_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.

value: HSACreERT2;Net39 fl/fl

value: 5 month;3 months post-tamoxifen


title: GP muscle from control mouse 1, 5 months of age [snRNA-seq]

description: 10x Genomics

value: Net39 fl/fl control B6C3F1

value: Control (Cre-)

value: 3 months post-tamoxifen


title: Polr2a_E13Ctx_2

city: Shanghai

first: XIAOSU

last: LI

state: Shanghai

address: 131 Dongan Road

institute: Fudan University

data_processing:
Illumina’s Genome Analyzer Sequencing Control Software and Pipeline Analysis Software
adapter trimming and filter low quality reads with trim_galore
alignment with subRead
remove PCR duplications and fileter low map quality reads with samtools and sambanba
Deeptools convert bam to bigwig
Assembly: mm39
Supplementary files format and content: bigwig
Library strategy: cut&tag

source_name: forebrain cortex

extract_protocol:
cut&tag, ChIP, ATAC
nucleo were treated with Tn5 at 37 for 30 min, DNA fragment was isolated using Qiagene mini-elut, Nextera XT DNA Library Preparation
ATAC-seq of P1 hGFAP-GFP FASC isolated cells, cut&tag of Polr2a, H3K4me3 and H3K27me3

value: forebrain cortex

value: mix

tag: antibody


title: Polr2a_E13Ctx_1


title: hGFAP_P1_B2

data_processing:
Illumina’s Genome Analyzer Sequencing Control Software and Pipeline Analysis Software
adapter trimming and filter low quality reads with trim_galore
alignment with subRead
remove PCR duplications and fileter low map quality reads with samtools and sambanba
Deeptools convert bam to bigwig
Assembly: mm39
Supplementary files format and content: bigwig

value: hGFAP-GFP


title: Polr2a_E15.5


title: hGFAP_P1_A2


title: GP muscle from cKO mouse 2, 5 months of age

tag: age


title: tumor-1


title: nomal-4

value: normal paracancer tissues


title: H3K4me3_E13Ctx_2


title: GP muscle from cKO mouse 1, 5 months of age


title: nomal-3


title: H3K4me3_E13Ctx_1


title: tumor-4


title: GP muscle from control mouse 3, 5 months of age

source_name: Net39 fl/fl

value: Net39 fl/fl


title: nomal-1

value: Human thyroid tissue


title: Gli3_E12Ctx_1


title: Bcl11a_E15Ctx_2


title: nomal-2


title: Bcl11a_E15Ctx_1


title: GP muscle from control mouse 2, 5 months of age


title: wt_d_LP7_S52455

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.5a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.12 package DESeq2 1.30.0, running under R 4.0.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: sorted macrophages

extract_protocol:
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 4000 instrument using 50 bp single-read chemistry.

value: duodenum

value: Tsc2fl/fl Lyz2+/+

tag: Sex

value: male


title: GP muscle from control mouse 1, 5 months of age

value: GP muscle


title: C2C12, INPUT 2

data_processing:
Basecalls were performed using bcl2fastq v2.17
After quality control using FastQC tool, reads were aligned to mm10 reference genome using bowtie2 (Version 2.3.2) with default settings. Picard (Version 2.10.3) was then used to remove duplicated reads. To increase sequencing depth for peak calling, replicates were merged for each condition. The LaminB1 DamID published dataset was analyzed (6). To identify large domains of Net39 and/or LaminB1 associated regions, Enriched domain detector (EDD, version 1.1.19) was used with bin size set to 10kb and output the log-ration between ChIP and control for genome browser visualization. To calculate the correlation between Net39-Ty1 and Lamin B1, log-ratio from EDD of 10kb bins was used.
Assembly: GRCm38 - mm10
Supplementary files format and content: bw

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2. Cells were differentiated in DMEM, 2% horse serum, 1x penicillin/streptomycin.

extract_protocol: ChIP-Seq libraries were generated using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645L) according to the manufacturer’s protocol.

treatment_protocol: Cells were fixed with 2% formaldehyde for 30 minutes. After quenching and cell lysis, chromatin was sheared on a Bioruptor Pico (Diagenode) for 20 cycles (30 sec on/ 30 sec off for each cycle) at 4°C in sonication buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.25% sarkosyl, 1 mM DTT, 1x cOmplete Protease Inhibitor Cocktail (Roche), and 200 μM PMSF, pH 8.0).

value: muscle


title: wt_d_LP6_S52453


title: Tumor_1314-2

city: Boston

first: Yingtian

last: Xie

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

data_processing:
Burrows-Wheeler Aligner (BWA) to map sequencing reads to the reference genome
MACS2 for peakcalling
DESeq2 was applied to identify the differentially accessible regions
Assembly: mm9
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: mouse small cell lung cancer (SCLC) tumor

extract_protocol:
Cells was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 150-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

value: mouse small cell lung cancer tumor cells


title: C2C12, TY1, DIAGENODE 2

value: TY1 (DIAGENODE, C15200054)


title: C2C12, INPUT 1


title: wt_d_LP4_S52435

value: female


title: wt_d_EC7_S52437

source_name: sorted epithelial cells

value: EpCam+, CD45-


title: wt_d_EC6_S52451


title: Tumor_1314-1

value: mouse small cell lung cancer (SCLC) tumor


title: C2C12, TY1, DIAGENODE 1


title: Tumor_1274


title: wt_d_EC2_S52447


title: GFP-46

city: Gainesville

first: Terence

middle: E.

last: Ryan

state: Florida

address: 1864 Stadium Rd

department: Applied Physiology and Kinesiology

institute: University of Florida

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences
Assembly: Mus musculus GRCm38 reference genome

source_name: gastrocnemius muscle

extract_protocol: Total RNA extracted using Zymo Research DirectZol RNA miniprep kit

treatment_protocol: Intramuscular injection of AAV9 encoding either a GFP (green fluorescent protein) of CAAHR (constitutively active AHR - aryl hydrocarbon receptor) driven by the ACTA1/human skeletal actin (HSA) promoter

value: gastrocnemius muscle


title: cre_d_LP9_S52459

value: Tsc2fl/fl Lyz2cre/+


title: GFP-43


title: Tumor_1270-1


title: Tumor_1270-2


title: GFP-42


title: Tumor_1125


title: cre_d_LP8_S52457


title: CAAHR-36


title: cre_d_LP10_S52445


title: Tumor_1117.


title: Tumor_713


title: cre_d_LP5_S52436


title: CAAHR-34


title: CAAHR-31


title: Tumor_672-2


title: Tumor_1116


title: Tumor_1198


title: cre_d_EC9_S52441


title: Tumor_168


title: MG_Cort_CON_p50

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.6.1, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.24.0 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: mouse- GRCm38.84
Supplementary files format and content: tab-delimited text containing DESeq2 normalized counts

source_name: mixed gastrocnemius

extract_protocol:
Mice were euthanized using CO2 and cervical dislocation. Tissues were collected, flash-frozen in liquid nitrogen, and stored at -80C until processed. Tissues were powdered and 20-25mg was used for RNA isolation using an Rneasy kit using the manufacturers protocol for skeletal muscle tissue.
Lexogen Quant-Seq; indexed and pooled samples, 50bp forward read

treatment_protocol: Male C57BL6J mice were provided with vehicle (1% EtOH) or corticosterone (cort; 100ug/ml) within their drinking water for two weeks.  A subset of animals treated with either vehicle or cort were provided with the ATGL inhibitor, atglistatin (571mg/kg) milled into their food (Teklad 8640), in order to reduce lipolysis.

value: mixed gastrocnemius

value: Cort CON

tag: disease state

value: Diabetic (Db)

tag: glucose (fed)

tag: insulin


title: Cont, Adipose, ATACseq, Rep2

city: Loma Linda

first: Isaac

middle: Jacob

last: Kremsky

state: CA

address: 11175 Campus St., Chan Shun Pavilion, Room A1022

department: Basic Sciences

institute: Loma Linda University

data_processing:
Raw fastq files were trimmed using trim_galore.
Trimmed fastq files were then mapped using bowtie2 version 2.3.5.1, with the flag “-X 2000” to allow for DNA fragments up to 2 kb. Reads that did not map uniquely to one location were removed, and then reads were sorted, and PCR duplicates were removed with samtools markdup.
Peaks were called with macs2 callpeak version 2.2.7.1.
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: Adipose

extract_protocol:
Visceral adipose tissue (1g) was placed in the cold 1× homogenization buffer (320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 1× protease inhibitors (Roche, cOmplete), and 167 μM β-mercaptoethanol, in water), homogenized with Dounce homogenizer, and residual debris were precleared by using 80 um nylon mesh filter. The nuclei were then collected by layering with iodixanol mixture.
50,000 counted nuclei were transferred to a tube containing the transposition mix (25 μl 2× TD buffer, 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl water) and mixed by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns. Library amplification was done with 2x KAPA HiFi mix (Kapa Biosystems) and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min.
ATAC-seq was carried out using the Omni-ATAC protocol.

value: Adipose

value: 8-weeks old

value: Control


title: Cont, Adipose, ATACseq, Rep1


title: cre_d_EC8_S52439

value: duodenum


title: cre_d_EC5_S52449


title: MG_Cort_ATGLi_p48

value: Cort ATGLi

value: Nondiabetic (ND)


title: MG_Cort_CON_p46


title: MG_Cort_CON_p49


title: Tumor_158