title: 200gLib_TeloHAEC_Dialout_1.1

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive

institute: Stanford University

description:
dialout for 1 of 2 biological replicates. Technical replicate library #1.
Dialout library to link CBCs to guides

data_processing:
Fastq files were de-multiplexed by index primer
Demultiplexed fastq files for the same sample, with the same index, and from the same sequencing run were concatenated
Note, for each scRNAseq library, there were four 10xGenomics index primers for each library, designated SAMPLEID_1 _2 _3 & _4 (for 50 gene library fastq files) or _a, _b, _c & _d (for 200 gene library files)
See the Sample Information column, for information about cases where libraries were resequenced, or where multiple libraries were made from the same sample
1) We ran CellRanger (which maps reads to the human genome, assigns reads to the distinct CellBarcodes (CBCs) for each droplet, and counts reads in each droplet for all transcripts in the human genome.
1) CellRanger distinguishes droplets with true cells from droplets with debris or ambient RNA, and generates a matrix of genes by CBCs (the filtered feature barcode matrix), which was used for downstream analysis.
2) Dialout libraries linking CBCs to guides were sequenced to saturation (~40x coverage) using either Illumina NextSeq or Novaseq (as detailed in the Sample Information column).
2) Dialout read 1 covers the 10x Genomics barcode/CBC and UMI. Read 2 covers 24 invariant bases of U6 promoter sequence before reading into the guide protospacer sequence
Dialout analysis: 1) dialout reads with fewer than 4 exact duplicate were removed to reduce noise from PCR chimeras, 2) for each cell barcode x guide combination, the number of distinct Unique Molecular Identifiers (UMIs) was counted. The guide with the highest number of UMIs, plus 2nd, 3rd and 4th place guides were recorded.
Processed dialout data was used to assign whether each CellRanger cell barcode had one cell (singlet) or multiple cells (multiplet). Singlet status & the ID of top guides for singlets is available in the …calls.tsv files associated with each scRNAseq sample (also described further, under "processed data files format")
For the Supplementary files: 200gLib_TeloHAEC_DE_{p.values,log2fcs}.txt, we subset the cell ranger genes x barcodes matrix to only those barcodes corresponding to singlet cells (1 cell & 1 guide, as defined by in the calls.tsv files for each library), & combined the data from both bioreps. We then applied edgeR to the RDS genes x singlets table, to detect differentially expressed genes for singlet cells with guides to each target (up to 15 guides) versus singlet cells with non-targeting or safe targeting guides. Individual edgeR results tables for each contrast were then aggregated to give genes x perturbation tables of log2 fold changes & p.values, respectively.
Assembly: hg19
Supplementary files format and content: Matrix files (.mtx). Filtered feature barcode matrices with rows=genes and columns=cell barcodes, and values=read counts, for all high quality cells called by CellRanger. Includes all reads from each sample (both Novaseq runs). To read, in R, do: library(Matrix);mymatrix=readMM("filename")
Supplementary files format and content: Barcodes files (barcodes.tsv). The list of cell barcodes (CBCs) for high quality cells. Use for column names of the extracted matrix file.
Supplementary files format and content: Features files (features.tsv). Tab delimited table of gene names (symbols & ENSEMBL gene numbers) quantified by CellRanger. User for row names of the extracted matrix file. Features should be the same for all sample matrices.
Supplementary files format and content: Singlet calls files (calls.tsv). Tab delimited table, with header row, with columns: CBC_10x (cell barcode, in the same order as barcodes.tsv), Guide (guide protospacer sequence), Gene(gene/target of top guide), UMI_count (# of UMIs for guide with most UMIs), Good_singlet (1 if cell is a singlet, 0 otherwise), Multiplet (1 if singlet, 2, 3 or 4 for doublet, triplet or quadruplet, 0 or NA if no guide was assigned to the cell. Specific column names may vary by file, but denote these same things. For the 50 gene library singlets were defined as cells that had 6+ UMIs for the top guide and less than 1/5th of this for the 2nd most abundant guide. For the 200 gene library, singlets were defined as cells with 4+ UMIs for the top guide and <1/5th this for the 2nd most abundant guide.

source_name: Vascular

growth_protocol: Eahy926 cells (a HUVEC-A549 hybrid cell line, commonly used as an endothelial cell culture model), was grown in DMEM +10% FBS. Telomerase-immortalized human aortic endothelial cells (TeloHAEC) and were purchased from ATCC, and grown in Lifeline VEGF endothelial cell media with 1x Penn/Strep. TeloHAEC were plated at a density of 0.5-1.0 x 106 cells per 10cm plate and split before reaching 4 x 106/plate (3 to 4 days).

extract_protocol:
Cells were either loaded at the maximum recommended concentration (16,000 cells/lane, "16k"), or "superloaded" at 150,000 cells per 10X Chromium controller lane ("150k"). 1 lane was used for each cell line/loading condition for the 50gene library, and 2 per cell line (superloading only) for the 200 gene library. scRNA-seq and dialout libraries were prepared as described below.
1) scRNA-seq libraries were prepared using 3’ scRNA-seq V3 kits (10X Genomics), according to manufacturer instructions. For the Eahy926 50 gene 150k loading, three techical replicate libraries were made from the amplified cDNA from a single lane (denoted "scRNAseq.1, .2 or .3, in library names & "_A2", "_A3" & "_A4" in fastq filenames). Note that the 10x Indexes were a mix of 4 oligos for each library (each starting with a different base to avoid sequencing biases). Thus each scRNAseq library has 4 fastq files for each read direction (denoted _1, _2, _3 & _4 in fastq file names).
2) From the initial amplified cDNA, we used a two stage PCR protocol to generate “dialout” libraries, for each lane. Because the CROP-seq vector expresses a PolII polyadenylated transcript that ends just downstream of the guide sequence, the dialout libraries identify the sgRNA sequences associated with each droplet.

treatment_protocol:
1) To create the TeloHAEC CRISPRi line, cells were transduced with lentiviral vectors containing 1) dox-inducible (tetracycline operator controlled) dCas9-KRAB-BFP (CRISPRi machinery, which targets epigenetic repressors to efficiently silence enhancers or promoters58–60) and 2) rtTA (tetracycline activator) with a hygromycin marker. After hygromycin selection (250ug/ml for 4 days), cells were treated with 1 ug/ml doxycycline (dox, a stable tetracycline analogue) for 3 days before FACS sorting for the top 15% of BFP positive cells, and after a period in culture without dox, treated again with dox and re-sorted.  CRISPRi Eahy926 were created the same way, except that the rtTA vector bore puromycin resistance & was selected for that marker, and only one round of FACS sorting was performed.
2) For Perturb-seq CRISPRi TeloHAEC & Eahy926 were transduced with a Lentivirus library carrying guide RNAs against the promoters of ~50 genes (the "50gene" library, 3 guides per target + 9 control guides),  in a CROP-opti-blast backbone, selected for blasticidin resistance (15ug/ml) for 3 to 4 days, and then treated for 7 days with 1ug/ml doxycycline to induce the CRISPRi machinery. Additionally, the CRISPRi TeloHAEC line was transduced with a Lentivirus library carrying guide RNAs against the promoters of ~200 genes (the "200gene" library, with 15 guide per target), followed by the same steps. Guides and targets for each library are listed in the supplementary files: 200gLib_targets_n_guides.txt & 50gLib_targets_n_guides.txt.

value: Vascular

value: CRISPRi TeloHAEC

value: Endothelial

value: Transduced with "200gene" guide library (see supplementary files)


title: Enteroendocrine cell differentiation plus BMP 2b

status: Public on Nov 01 2022

type: SRA

city: Utrecht

first: Joep

last: Beumer

address: Uppsalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: transcriptomic

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg38. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Assembly: hg38
Supplementary files format and content: The data are in csv format. The table contains UMI deduplicated counts normalized between samples.

molecule: total RNA

organism: Homo sapiens

source_name: Intestine

extract_protocol:
RNA from whole organoids was extracted using Trizol isolation
RNA was processed using the previously described SORT-seq technique (for bulk samples), which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.

treatment_protocol: Organoids were differentiated towards enteroendocrine cells as described previously, in the presence or absence of BMP2/4

tag: tissue

value: Intestine

tag: cell line

value: Adult stem cell - derived organoid

tag: cell type

value: Enteroendocrine cells

tag: genotype

value: WT

tag: treatment


title: Enteroendocrine cell differentiation minus BMP 1b


title: Enteroendocrine cell differentiation minus BMP 1a


title: Enteroendocrine cell differentiation plus BMP 2a


title: 50gLib_TeloHAEC_150K_Dialout_1

country: USA

description:
2 libraries dialout were made from amplified cDNA from the single 10X lane used for scRNAseq (denoted as "_1" & "_2" in library names & "_14" & "_15" in fastq file names).
Dialout library to link CBCs to guides

value: Transduced with "50gene" guide library (see supplementary files)


title: 50gLib_TeloHAEC_150K_Dialout_2

description:
2 dialout libraries were made from amplified cDNA from the single 10X lane used for scRNAseq (denoted as 14 & 15).
Dialout library to link CBCs to guides


title: 200gLib_TeloHAEC_Dialout_2.1

description:
dialout for 2 of 2 biological replicates. Technical replicate library #1.
Dialout library to link CBCs to guides


title: RNA_K562_0090min_rep1

city: Chapel Hill

first: Marielle

last: Bond

state: North Carolina

address: 104 Manning Drive Thurston Building Room 4012

department: Genetics Curriculum

institute: UNC Chapel Hill

data_processing:
Adapters and low-quality reads were trimmed from paired-end reads using Trim Galore! (version 0.4.3)
Salmon was used in quant mode to quantify reads to hg19 transcripts (version 1.4.0)
Reads were aligned to the hg38 genome using HISAT2 (version 2.1.0)
Alignments were indexed using samtools (version 1.9)
Replicates were merged with samtools (version 1.9)
Alignments were converted to bigwigs using deeptools (version 3.0.1)
Reads were summarized to a gene level using txImport (R version 3.3.1, tximport version 1.2.0)
Differential analysis was completed in DESeq2 (R version 3.3.1, DESeq version 1.33.5)
Assembly: hg38
Supplementary files format and content: quant.sf: tab-delimted file of transcript-level quantifications including transcript ID, length, effective length, TPM, and NumReads from Salmon; .bw: bigwig files of signal tracks; .tsv: tab-delimited text file containing gene-summarized information including chromosome, start, end coordinates, ENSEMBL and HGNC IDs, differential gene cluster, DESeq adjusted LRT p-values, raw counts, variance-stabilized transformed counts, DESeq shrunken log2(fold-change); txt: text file summarizing all log2fold-changes and corresponding padj for each sample, counts, and differential gene cluster

growth_protocol: K562 cells maintained with RPMI + 10% FBS + 1% Pen/Strep and were grown to a density of 1x10^5 cells/mL

extract_protocol:
Qiagen RNeasy with Dnase I treatment. RNA integrity numbers were confirmed with a Tapestation High-Sensitivity RNA tape, concentration confirmed with Qubit BR assay
KAPA RNA Hyperprep with Riboerase

treatment_protocol: Megakaryocyte differentiation induced by treatment with 25 nM PMA for the 0h, 0.5h, 1.5h, 3h, 6h, 24h, 48h, and 72h. Media was changed after 24h and 48h

value: Human leukemia

tag: time point

value: 90 min

value: PMA (megakaryocyte differentiation)


title: 50gLib_Eahy926_150K_Dialout

description:
Dialout library for all 3 technical replicate Eahy 150k scRNAseq libraries (made from amplified cDNA from which all 3 of those libraries were derived)
Dialout library to link CBCs to guides

value: CRISPRi Eahy926


title: 50gLib_Eahy926_16K_Dialout

description:
Dialout library for Eahy926 16k scRNAseq library
Dialout library to link CBCs to guides


title: 50gLib_Eahy926_150K_scRNAseq.3

description:
3 technical replicate libraries made from the same 10x lane, each sequenced twice (files from 2nd Nextseq run denoted by "2ndRun" in the fastq filenames)
3' mRNA scRNAseq
50gLib_Eahy926_150K_scRNAseq_matrix.mtx
50gLib_Eahy926_150K_scRNAseq_barcodes.tsv
50gLib_Eahy926_150K_scRNAseq_features.tsv
50gLib_Eahy926_150K_scRNAseq_calls.tsv

library_source: transcriptomic single cell


title: 50gLib_Eahy926_150K_scRNAseq.2


title: 50gLib_Eahy926_16K_scRNAseq

description:
single scRNAseq library from one 10X lane
3' mRNA scRNAseq
50gLib_Eahy926_16K_scRNAseq_matrix.mtx
50gLib_Eahy926_16K_scRNAseq_barcodes.tsv
50gLib_Eahy926_16K_scRNAseq_features.tsv
50gLib_Eahy926_16K_scRNAseq_calls.tsv


title: 50gLib_Eahy926_150K_scRNAseq.1

description:
3 technical replicate libraries made from the same 10x lane, each sequenced twice (files from 2nd Nextseq run denoted by "2ndRun" in the fastq filenames), "processed data" files are CellRanger output for all 3 libraries combined
3' mRNA scRNAseq
50gLib_Eahy926_150K_scRNAseq_matrix.mtx
50gLib_Eahy926_150K_scRNAseq_barcodes.tsv
50gLib_Eahy926_150K_scRNAseq_features.tsv
50gLib_Eahy926_150K_scRNAseq_calls.tsv


title: TeloHAEC_G10_KLF2_KD

data_processing:
Fastq files were de-multiplexed by index primer
Demultiplexed fastq files for the same sample were concatenated
Reads were mapped to the human genome using Bowtie2
Read counts in transcripts were measured using Kallisto
Assembly: hg19
Supplementary files format and content: All_bulk_RNAseq_TPM_by_Symbol.txt. Contains TPM calls for all samples from Kallisto. Column names are the same as library ID & title. Note: A newer gtf file was used for the the CRISPRi TeloHAEC RNAseqs, so some Symbols have TPM values only for that set or for the parental TeloHAEC/Eahy926 set. To avoid data loss, we have preserved all symbols from both sets.

molecule: polyA RNA

growth_protocol: The Eahy926 human endothelial hybrid line was purchased from ATCC, and grown in DMEM media with 10% FBS & 1x Penn/Strep. Telomerase-immortalized human aortic endothelial cells (TeloHAEC) were purchased from ATCC, and grown in Lifeline VEGF endothelial cell media with 1x Penn/Strep. TeloHAEC were plated at a density of 0.5-1.0 x 106 cells per 10cm plate and split before reaching 4 x 106/plate (3 to 4 days).

extract_protocol:
Total RNA was harvested from TeloHAEC (parental or CRISPRi lines) by Qiagen RNeasy kit, DNAse treated (TURBO DNAse 15’ 37C), and purified on MyOne Silane beads. mRNA was purified from 1 ug of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation module (NEB)
NEBNext Ultra II RNA Library Kit for Illumina (NEB), according to manufacturer's protocol, and index primers specific for each library

treatment_protocol: 1) To create the TeloHAEC CRISPRi line, cells were transduced with lentiviral vectors containing 1) dox-inducible (tetracycline operator controlled) dCas9-KRAB-BFP (CRISPRi machinery, which targets epigenetic repressors to efficiently silence enhancers or promoters58–60) and 2) rtTA (tetracycline activator) with a hygromycin marker. After hygromycin selection (250ug/ml for 4 days), cells were treated with 1 ug/ml doxycycline (dox, a stable tetracycline analogue) for 3 days before FACS sorting for the top 15% of BFP positive cells, and after a period in culture without dox, treated again with dox and re-sorted. 2) To study parental or CRISPRi TeloHAEC responses to CAD-associated cytokines, cells were untreated (control), or treated with 10ng/ml recombinant human IL-1beta (Millipore IL038) or 10ng/ml recombinant TNF-alpha (Millipore GF023) for 24 hours. 3) To study the effects of gene perturbations, CRISPRi TeloHAEC were transduced with Lentivirus carrying single guide RNAs against the promoters of the indicated genes,  in a CROP-opti-blast backbone, selected for blasticidin resistance (15ug/ml) for 3 to 4 days, and then treated for 5 days with 2ug/ml doxycycline to induce the CRISPRi machinery.

value: Transduced with sgRNA to KLF2:GAAGTCCGCAACCCGGGGAT

value: normal growth medium+ 2ug/ml Doxycycline for 5 days


title: TeloHAEC_G8_ITGB1BP1_KD

value: Transduced with sgRNA to ITGB1BP1:GCCGCGGTATATAAGCCGGC


title: TeloHAEC_F6_CCM2_KD

value: Transduced with sgRNA to CCM2:GAGCCGCTACATGCTCGACCC


title: TeloHAEC_F4_neg_ctrl_KD

value: Vascular

value: Transduced with non-targeting control sgRNA:GCTGGGCGGACGTTGGGATA


title: TeloHAEC_G1_PDCD10_KD

value: Endothelial

value: Transduced with sgRNA to PDCD10:GCCGCTTTACGCCACTCGCGT


title: TeloHAEC_D8_neg_ctrl_KD

value: Transduced with non-targeting control sgRNA:GGTGGTTCGGTTTGCGTGGCC


title: TeloHAEC_D7_NFAT5_KD

value: Transduced with sgRNA to NFAT5:GGTCCCCGTCCCGCCGGGGG


title: TeloHAEC_D12_MESDC1_KD

value: Transduced with sgRNA to MESDC1:GCCTCCGGCAGCCCCTGCGGG


title: TeloHAEC_D2_neg_ctrl_KD

value: Transduced with non-targeting control sgRNA:GTGGTTCACAACCGGACCCA


title: TeloHAEC_D11_PDCD10_KD

value: Transduced with sgRNA to PDCD10:GACCGAGCAGAAGAGGTCTA


title: 50gLib_TeloHAEC_150K_scRNAseq

description:
single scRNAseq library from one lane w/ 150,000 cells
3' mRNA scRNAseq
50gLib_TeloHAEC_150K_scRNAseq_matrix.mtx
50gLib_TeloHAEC_150K_scRNAseq_barcodes.tsv
50gLib_TeloHAEC_150K_scRNAseq_features.tsv
50gLib_TeloHAEC_150K_scRNAseq_calls.tsv

value: CRISPRi TeloHAEC

value: Transduced with "50gene" guide library (see supplementary files)


title: TeloHAEC_C9_KLF2_KD

value: Transduced with sgRNA to KLF2:GGACCCGGGGAGAAAGGACG


title: TeloHAEC_B3_MESDC1_KD

value: Transduced with sgRNA to MESDC1:GTGGCTGCGCCGCCGCCCGCA


title: TeloHAEC_C10_MEF2A_KD

value: Transduced with sgRNA to MEF2A:GCGGCGCGAAGCGCTGGTGG


title: TeloHAEC_B6_neg_ctrl_KD

value: Transduced with non-targeting negative sgRNA:GCAACGGTGTACCGCGGATC

value: normal growth medium+ 2ug/ml Doxycycline for 5 days


title: TeloHAEC_C2_CCM2_KD

value: Transduced with sgRNA to CCM2:GGCAAGAAGGTGAGCGTGCG


title: TeloHAEC_B5_MAP2K5_KD

value: Vascular

value: Transduced with sgRNA to MAP2K5:GTCTGCCCCACCCGGAGACAC


title: TeloHAEC_B8_CDH5_KD

value: Endothelial

value: Transduced with sgRNA to CDH5:GCCAGCTGGAAAACCTGAAG


title: TeloHAEC_C7_ITGB1BP1_KD

value: Transduced with sgRNA to ITGB1BP1:GAAGGCCGCGGCACTCCCACG


title: TeloHAEC_C3_MAP3K3_KD

value: Transduced with sgRNA to MAP3K3:GCCAATAACAAGAAGGAAGT


title: TeloHAEC_VEGF_1.2

value: TeloHAEC

value: parental

value: growth media lacking VEGF (a normal component of LifeLine VEGF Endothelial cell medium) for 24hrs


title: TeloHAEC_A11_MAP2K5_KD

value: Transduced with sgRNA to MAP2K5:GCCGAGGCCGCGCGGACTGG


title: TeloHAEC_VEGF_1.3


title: TeloHAEC_TNFa_1.2

value: growth media supplemented with 10ng/ml TNF-alpha for 24hrs


title: TeloHAEC_D4_NFAT5_KD

value: Transduced with sgRNA to NFAT5:GGCCTCGCTTCCTGCCGGCG


title: TeloHAEC_TNFa_1.3


title: TeloHAEC_IL1b_1.2

value: growth media supplemented with 10ng/ml IL1-beta for 24hrs


title: TeloHAEC_ctrl_1.3

value: normal growth medium


title: TeloHAEC_IL1b_1.3


title: TeloHAEC_IL1b_1.1


title: TeloHAEC_H10_MEF2A_KD

value: Transduced with sgRNA to MEF2A:GACTGAATTATCCTCTCGGT


title: TeloHAEC_TNFa_1.1


title: TeloHAEC_ctrl_1.2


title: TeloHAEC_ctrl_1.1


title: TeloHAEC_A4_MAP3K3_KD

value: Transduced with sgRNA to MAP3K3:GTTCCTGAGGTGGAGAACGG

value: normal growth medium+ 2ug/ml Doxycycline for 5 days


title: TeloHAEC_D5_CDH5_KD

value: Vascular

value: Transduced with sgRNA to CDH5:GTTGGACTGCCTGTCCGTCCA


title: Eahy926_VEGF_1.3

value: Endothelial

value: growth media supplemented with VEGF (1x concentration for LifeLine VEGF Endothelial cel medium) for 24hrs


title: Eahy926_VEGF_1.2


title: Eahy926_VEGF_1.1


title: TeloHAEC_VEGF_1.1


title: Eahy926_TNFa_1.3


title: Eahy926_IL1b_1.3


title: Eahy926_TNFa_1.2


title: Eahy926_ctrl_1.3


title: Eahy926_ctrl_1.1


title: Eahy926_ctrl_1.2


title: Eahy926_IL1b_1.2


title: TeloHAEC_ctrl_0.2


title: TeloHAEC_ctrl_0.1


title: TeloHAEC, VEGF, ChIP, 1.2

description: H3K27acetyl ChIP-seq

library_source: genomic

data_processing:
Fastq files were de-multiplexed by index primer
Demultiplexed fastq files for the same sample were concatenated
Reads were mapped to the human genome using Bowtie2
Peaks were identified using MACS2
Assembly: hg19
Supplementary files format and content: Text format Macs2 peak calls (.txt extension)
Supplementary files format and content: TDF format read density traces, for rapid viewing in IGV (.tdf extension)

molecule: genomic DNA

growth_protocol: The Eahy926 human endothelial hybrid line was purchased from ATCC, and grown in DMEM media with 10% FBS & 1x Penn/Strep. Telomerase-immortalized human aortic endothelial cells (TeloHAEC) were purchased from ATCC, and grown in Lifeline VEGF endothelial cell media with 1x Penn/Strep.

extract_protocol:
Chromatin immunoprecipitation for histone H3 lysine 27 acetylation (H3K27ac) was performed as described in (Fulco, C. P., Nasser, J., Jones, T. R. & Munson, G. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations. Nature (2019)).
ChIP-seq libraries were prepared from immunoprecipitated or input control (INPUT) fragments using the KAPA Hyper Prep Kit (KAPA Biosystems). Libraries were prepared on two different days, designated (under library name & title) as CELLLINE_CONDITION_0 & _1. Biological replicate numbers are indicated after a dot, e.g. _1.1 & _1.2.

treatment_protocol: To study parental or CRISPRi TeloHAEC responses to CAD-associated cytokines, cells were untreated (control), or treated with 10ng/ml recombinant human IL-1beta (Millipore IL038) or 10ng/ml recombinant TNF-alpha (Millipore GF023) for 24 hours. For responses to VEGF, VEGF (1x concentration, from the LifeLine EC media kit) was added to the Eahy926 media (which normally lacks VEGF) or omitted from the TeloHAEC media (which normally contains it).

tag: chip antibody


title: Eahy926_IL1b_1.1


title: TeloHAEC, VEGF, ChIP, 1.1

description: H3K27acetyl ChIP-seq


title: TeloHAEC, TNFa, ChIP, 1.1

description: H3K27acetyl ChIP-seq


title: Eahy926_ctrl_0.2


title: TeloHAEC, ctrl, ChIP, 1.1

description: H3K27acetyl ChIP-seq


title: TeloHAEC, ctrl, ChIP, 1.2

description: H3K27acetyl ChIP-seq


title: TeloHAEC, IL1b, ChIP, 1.1

description: H3K27acetyl ChIP-seq


title: Eahy926, VEGF, ChIP, 1.2

description: H3K27acetyl ChIP-seq


title: Eahy926, VEGF, ChIP, 1.1

description: H3K27acetyl ChIP-seq


title: Eahy926, TNFa, ChIP, 1.2

description: H3K27acetyl ChIP-seq


title: Eahy926_TNFa_1.1


title: Eahy926, TNFa, ChIP, 1.1

description: H3K27acetyl ChIP-seq


title: Eahy926, IL1b, ChIP, 1.2

description: H3K27acetyl ChIP-seq


title: Eahy926, IL1b, ChIP, 1.1

description: H3K27acetyl ChIP-seq


title: Eahy926, ctrl, ChIP, 1.2

description: H3K27acetyl ChIP-seq


title: Eahy926, ctrl, ChIP, 1.1

description: H3K27acetyl ChIP-seq


title: TeloHAEC, ctrl, INPUT, 0.1

description: Input chromatin (not immunoprecipitated)


title: TeloHAEC, ctrl, ChIP, 0.2

description: H3K27acetyl ChIP-seq


title: Eahy926, ctrl, ChIP, 0.2

description: H3K27acetyl ChIP-seq


title: Eahy926_ctrl_0.1


title: Eahy926, ctrl, INPUT, 0.1


title: TeloHAEC, TNFa, ChIP, 1.2

description: H3K27acetyl ChIP-seq


title: Eahy926, ctrl, INPUT, 0.2


title: TeloHAEC, VEGF, 1.3

description: Tn5 tagmentation enzyme fragments (ATAC)

extract_protocol:
One well of a 12-well plate (~200,000 cells) was directly lysed using a custom TN5 buffer (33mM Tris Acetate pH 7.8, 66mM Potassium Acetate, 10 mM Magnesium Acetate, 16% dimethylformamide & 0.1% NP40). 47.5 ul of lysed cells was added to 2.5 ul Tn5 tagmentation enzyme (Illumina) & incubated at 37C for 1hr, and the reaction stopped by addition of 20 ul buffer RLT (Qiagen). Products were purified by addition of 1.8 volumes Ampure XP beads (Beckman-Coulter) & magnetic separation of beads, followed by two 80% ethanol washes, brief drying of pellets & resuspension in 23 ul water. Barcoded ATAC-seq libraries were then generated as described in (Fulco, C. P., Nasser, J., Jones, T. R. & Munson, G. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations. Nature (2019)), and sequenced to a depth of 10-20 million reads per library.
Amplification with custon ATAC-seq oligos to give ATAC fragments flanked by read1, read2 sequences, and an 8 base index sequence specific to each library. Libraries were prepared on two different days, designated (under library name & title) as CELLLINE_CONDITION_0 & _1. Biological replicate numbers are indicated after a dot, e.g. _1.1, _1.2 & _1.3.

treatment_protocol: To study parental or CRISPRi TeloHAEC responses to CAD-associated cytokines, cells were untreated (control), or treated with 10ng/ml recombinant human IL-1beta (Millipore IL038) or 10ng/ml recombinant TNF-alpha (Millipore GF023) for 24 hours. For responses to VEGF, VEGF (1x concentration from the LifeLine EC media kit) was added to the Eahy926 media (which normally lacks VEGF) or omitted from the TeloHAEC media (which normally contains it).


title: TeloHAEC, VEGF, 1.2


title: TeloHAEC, TNFa, 1.3


title: TeloHAEC, TNFa, 1.2


title: TeloHAEC, TNFa, 1.1


title: TeloHAEC, IL1b, 1.1


title: TeloHAEC, ctrl, 1.3


title: TeloHAEC, IL1b, 1.3


title: TeloHAEC, IL1b, ChIP, 1.2

description: H3K27acetyl ChIP-seq


title: TeloHAEC, IL1b, 1.2


title: TeloHAEC, VEGF, 1.1


title: TeloHAEC, ctrl, INPUT, 0.2


title: TeloHAEC, ctrl, 1.2


title: CNR_K562_0360min_CTCF_rep2

data_processing:
library strategy: CUT&RUN
Adapters and low-quality reads were trimmed from paired-end reads using Trim Galore! (version 0.4.3)
Reads were aligned to the hg19 genome using BWA mem (version 0.7.17)
Alignments were sorted using Samtools (version 1.9)
Duplicates were removed with PicardTools (version 2.10.3)
Alignments were index using Samtools (version 1.9)
Replicates were merged with samtools (version 1.9)
Alignments were converted to bigwigs using deeptools (version 3.0.1)
Peaks were called from merged alignments using MACS2 (-f BAM -q 0.01 -g hs --nomodel --shift 0 --extsize 200 --keep-dup all -B --SPMR; version 2.1.1.20160309)
Peaks were merged using bedtools (version 2.26)
Counts at merged peaks were extacted from BAM files using bedtools multicov (version 2.26)
Assembly: hg38
Supplementary files format and content: narrowPeak: tab-delimited BED-style file containing peak info from MACS2 (chr, start, end coordinates, peakID, score, strand, signal, p-value, q-value, peak summit position); .bw: bigwig signal tracks; .tsv: counts of all peaks included in analysis for each antibody

growth_protocol: K562 cells maintained with RPMI + 10% FBS + 1% Pen/Strep

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min, quenched with 2.0M glycine for 5 min, washed in PBS, and split into 5x10^5 cell pellet aliquots
KAPA Hyperprep kit

treatment_protocol: Megakaryocyte differentiation induced by treatment with 25 nM PMA for the length of each timepoint

value: Human leukemia

value: WT

value: PMA (megakaryocyte differentiation)

tag: antibody

value: CTCF


title: TeloHAEC, ctrl, ChIP, 0.1

description: H3K27acetyl ChIP-seq

value: TeloHAEC

value: parental


title: TeloHAEC, ctrl, 1.1


title: Eahy926, VEGF, 1.3


title: Eahy926, VEGF, 1.1


title: Eahy926, TNFa, 1.3

value: growth media supplemented with 10ng/ml TNF-alpha for 24hrs


title: Eahy926, TNFa, 1.2


title: Eahy926, TNFa, 1.1


title: Eahy926, IL1b, 1.2


title: Eahy926, ctrl, 1.2


title: Eahy926, ctrl, 1.3


title: Eahy926, ctrl, ChIP, 0.1

description: H3K27acetyl ChIP-seq


title: Eahy926, IL1b, 1.1


title: Eahy926, ctrl, 1.1


title: TeloHAEC, ctrl, 0.3


title: TeloHAEC, ctrl, 0.1


title: TeloHAEC, ctrl, 0.2


title: Eahy926, VEGF, 1.2


title: Eahy926, ctrl, 0.3


title: Eahy926, ctrl, 0.2


title: PROseq, RANKL, replicate 3

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

data_processing:
Low-quality reads and adapter sequences were assessed with Fastqc v0.11.9, and filtered out with Skewer v0.2.2.
The filtered reads were then aligned to hg19 genome with STAR v2.7.3a with default parameters. The resulting alignment files were sorted by positions.
From alignment files, strand-specific bigWig files were generated with Bedtools genomecov (v2.27.1) and bedGraphToBigWig v4.
bigWig files were used as inputs for dREG and dREG-HD runs (default parameters).
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: PRO-seq

source_name: Blood

growth_protocol: Monocytes were obtained from peripheral blood using anti-CD14 magnetic beads. Monocyte-derived osteoclast precursors (OCPs) were obtained by culturing for 1 day with 20 ng ml-1 of M-CSF in a-MEM medium supplemented with 10 % fetal bovine serum.

extract_protocol:
Cells were incubated in polymerase run-on reactions with ribonucleotide triphosphate (NTP) substrates at a final concentration of 19 μM biotin-11-CTP, 19 μM biotin-11-UTP, 0.19 mM ATP, and 0.19 mM GTP at 37 °C for 3 min.
Biotin-labeled nascent RNA is extracted and fragmented and passed through P-30 size exclusion column (BioRad). The RNA is bound to streptavidin-magnetic beads (ThermoFisher). The purified biotin-labeled RNA is processed through 3' RNA adaptor (pUGGAAUUCUCGGGUGCC AAGG-/inverted dT/) ligation, 2nd streptavidin purification, 5' RNA decapping, 5' RNA adaptor ligation, 3’rd streptavidin purification, and reverse transcription. cDNA is amplified through 15–20 cycles of PCR amplification with Illumina TRU-seq single barcode multiplexing primers.

value: Blood

value: Osteoclast Precursor Cells

value: M-CSF + RANKL


title: PROseq, CTL, replicate 3

value: M-CSF


title: PROseq, RANKL, replicate 2


title: Eahy926, ctrl, 0.1

value: normal growth medium


title: PROseq, RANKL, replicate 1


title: PROseq, CTL, replicate 2


title: PROseq, CTL, replicate 1


title: WT_rep1 [ATAC-Seq]

city: Irvine

first: Jefferson

middle: K

last: Chen

address: UC Irvine

institute: UC Irvine

data_processing:
FASTQC was used to check read quality. Adapters were removed with cutadapt v2.9 (parameter: -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT) and sequences were aligned and mapped to mm10 (UCSC) with Bowtie2. Reads mapped to mitochondrial DNA were excluded. PCR duplicates were then removed based on the list of duplicate generated from Genrich (v0.6, available at github.com/jsh58/Genrich). Properly paired and mapped reads with mapping quality over 30 were kept for downstream analysis. To explore the feature of the uniquely mapped reads, deeptools (v3.4.2, parameter: -of bigwig --effectiveGenomeSize 2652783500 --normalizeUsing RPKM -e --ignoreDuplicates -bs 10) was used to convert aligned reads into a coverage track in BigWig format after read normalization based on RPKM. ChIPseeker (v1.24.0) was used to annotate the function of peaks and genomic region ontology was conducted with GREAT. ATACseq and RNAseq co-analysis was conducted with BETA using standard BETA plus parameters.
Assembly: mm10
Supplementary files format and content: bed

organism: Mus musculus

source_name: hair follicle stem cell

extract_protocol:
HFSC (Ly-6A/E- CD34+ CD45f+) were FACS sorted and lysed.
Nuclei were incubated in 50uL of Tn5 transposition buffer for 30mins at 37C. DNA isolation was preformed with Qiagen MinElute Cleanup kit.
Library preparation with Illumina TrueSeq library preparation kit and paired end Illumina HiSeq 2500 sequencing (80million reads per sample) was performed at the University of California, Irvine High Throughput Genomics Facility.

value: hair follicle stem cell


title: WT_rep2 [ATAC-Seq]


title: Eahy926, IL1b, 1.3

value: Vascular

value: growth media supplemented with 10ng/ml IL1-beta for 24hrs


title: Irx5KO_rep1

data_processing:
Read alignment was preformed using Bowtie2, and Deseq2 was used to identify differentially expressed genes. Gene ontology was conducted using Metascape
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cell

extract_protocol:
P20 back skin was dissected and incubated in 0.25% trypsin (Invitrogen 1505-065) for 2hrs at 34C. The epidermal side was mechanically separated and resuspended in 2% FBS PBS. Debris was removed with 40uM and 70uM mesh filters. Whole epidermis samples were processed for bulk RNA-seq.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
RNA quality was determined with Aglient Bioanalyzer; only samples with RNA Integrity Number > 8 were used. Library preparation with Illumina TrueSeq library preparation kit and single end Illumina HiSeq 2500 sequencing was performed at the University of California, Irvine High Throughput Genomics Facility.

value: primary cell

value: epithelial cells


title: Irx5KO_rep1 [ATAC-Seq]


title: Irx5KO_rep2


title: BMSC, mmHg-200

city: Guangzhou

first: Ziling

last: Lin

state: Guangdong

address: No.12 Jichang Road

country: China

institute: Guangzhou University of Chinese Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed reads were mapped to the rat genome rn6 using HISAT2, and tag counts were summarized at the gene level using SAMtools.
Read count extraction and normalization were performed using featureCounts v1.5.0-p3
Assembly: rn6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

growth_protocol: BMSCs were seeded separately in T25 plates at a density of 3 × 105 cells per plate and cultured at 37 °C for 72 h

extract_protocol:
BMSCs were collected and harvested, and total RNA was prepared using the GenCatch TM Total RNA Extraction Kit (Epoch Life Sciences, 1,660,050)
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The air outlet channel was connected to a vacuum pump (VSD Medical Technology Co., Ltd., customized, China) to generate a continuous NP. The air inlet channel was installed in a valve to adjust the air exchange. The NP was controlled and adjusted using a vacuum pump with a pressure sensor. The applied pressures of NP treatment were −80 mmHg, −120 mmHg, −160 mmHg, and −200 mmHg with a continuous 48 h for each experiment.

value: bone marrow

value: Bone mesenchymal stem cells

value: -200 mmHg NP treatment pressure


title: BMSC, mmHg-160

value: WT

value: -160 mmHg NP treatment pressure


title: BMSC, mmHg-120

value: -120 mmHg NP treatment pressure


title: BMSC, mmHg-80

value: -80 mmHg NP treatment pressure


title: BMSC, control

value: 0 mmHg NP treatment pressure


title: WT_rep1


title: WT_rep2


title: DDX6-AID 6h-1

city: Mishima

first: Yumiko

last: Saga

state: Shizuoka

address: 1111 Yata

department: Department of Gene Function and Phenomics

country: Japan

institute: National Institute of Genetics

data_processing:
Low-quality sequences, adapters were trimmed or removed using fastp (version 0.22.0).
Trimmed reads were were aligned to the Mus musculus genome supported with gene annotation file (the Ensembl GRCm38) using Hisat2 (version 2.2.1)
Only the read counts that uniquely aligned to the exon regions were summarised at the gene level by featureCounts (version 2.0.3).
Supplementary files format and content: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include raw read count values for each Sample

source_name: D6AdP cell line

growth_protocol: The D6AdP cell line (ES cells) were maintained in ES medium (Yagi et al., 1993) supplied with PD0325901 and CHIR99021, and Leukemia inhibiting factor in a 37-degree humid incubator with 5% CO2.

extract_protocol:
The 2 x 105 ES cells were passaged on the Mitomycin-C treated fibroblast feeder cells in each well of the 24 well plate, and treated with IAA for 0, 3, 6 hr.
Total RNA was isolated using the RNAiso Plus (Takara), treated with DNase I (Invitrogen). The quality of collected RNAs was examined using Bioanalyzer (Agilent), and RINs of them were confirmed to be over 8.0. cDNA libraries were prepared from polyA RNAs originally from 500-1000 ng of total RNAs. RNA libraries for RNA-seq were prepared using the Truseq Stranded mRNA Library Prep kit (Illumina) following manufacturer's protocols.

treatment_protocol: 500 nM 5-Ph-indole-3-acetic acid (IAA) was added in the maintenance medium.

value: D6AdP cell line

value: ES cell

value: DDX6-AID-mCherry/DDX6-AID-mCherry; DCP1a-EGFP/+; OsTIR1-FLAG Tg

value: 6hr after IAA treatment (IAA6hr)


title: DDX6-AID 0h-2

value: Before IAA treatment (IAA0h)


title: DDX6-AID 3h-1

value: 3hr after IAA treatment (IAA3hr)


title: DDX6-AID 0h-1


title: I17R023h08

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

country: Germany

institute: Saarland University

data_processing:
Read quality of RNA-seq data in fastq files was assessed using FastQC (v0.11.9) to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using STAR (v2.7.9a) allowing gapped alignments to account for splicing against the Ensembl MusMusculus genome v104 and the human SNCA transgene
Raw counts describing gene-level abundances were derived from DESeq2 (v1.32.0) (Love et al., 2014)
Genome_build: Ensembl MusMusculus genome v104 including the human SNCA transgene
Supplementary_files_format_and_content: comma seperated text file containing raw read counts per gene identified by Ensembl gene ID

source_name: hippocampus

extract_protocol:
Hippocampus and brainstem were removed, flash-frozen on dry ice, and RNA was harvested using the AllPrep DNA/RNA Mini Kit (Qiagen). TruSeq RNA Sample Prep Kit (Illumina) was used with 500 ng of RNA to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Poly(A)-selected single-end sequencing libraries (75 bp) were generated according to the manufacturer’s instructions. All libraries were sequenced on an Illumina HiSeq 2500 platform at a depth of 10–25 million reads each.

tag: strain

value: wildtype

tag: diet

value: high fat diet


title: I17R023h07


title: I17R023h05


title: I17R023h04


title: I17R023h06


title: I17R023h03


title: I17R023g06

value: standard diet


title: I17R023g08


title: I17R023g05


title: I17R023g07


title: I17R023g04


title: I17R023f07

value: transgenic


title: I17R023g03


title: I17R023f08


title: I17R023f05


title: DDX6-AID 3h-2


title: I17R023f03


title: I17R023f06


title: I17R023f04


title: I17R023e07


title: I17R023e05


title: Irx5KO_rep2 [ATAC-Seq]

value: hair follicle stem cell


title: I17R023e04


title: I17R023e06


title: I17R023e08


title: I17R023d08

source_name: brainstem


title: I17R023e03


title: I17R023d02


title: I17R023d03


title: I17R023d07


title: I17R023d01


title: DDX6-AID 6h-2


title: I17R023c07


title: I17R023c06


title: I17R023c04


title: I17R023c08


title: I17R023b01


title: I17R023b03


title: I17R023b07


title: I17R023b06


title: I17R023a08


title: I17R023b08


title: I17R023a07


title: I17R023a05


title: I17R023a02


title: I17R023a01


title: I17R023b04


title: RB_THC_3

city: Ottawa

first: Ruth

middle: S

last: Slack

state: ON

address: 451 Smyth Rd

department: Brain and Mind Research Institute

country: Canada

institute: University of Ottawa

data_processing:
FastQ files were aligned to Hisat2 GRCm38 index using HiSat2, following default parameters.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm, as part of the Subread package.
Expression data was normalized in R using the DESeq2 package, and batch-adjusted to account for preparation date.
Differentially expressed genes were identified using the DESeq2 algorithm, adjusting p-value using Independent Hypothesis Weighting as part of the IHW package.
Genome_build: version 101 of mouse reference genome GRCm38
Supplementary_files_format_and_content: comma separated values file including log2 fold change, DESeq2 and IHW adjusted p-value and normalized counts for each sample

source_name: FACS-isolated SVZ cells

growth_protocol: Inducible NestinCreERT2/R26;EYFP mice of each genotype were aged 6-10 weeks upon initial intervention. Mice were administered tamoxifen gavage at 200 mg/kg/d for 5 days to induce recombination. Ten days following final gavage, SVZ of multiple mice were microdissected and pooled to obtain minimum 200000 YFP-expressing cells per sample after FACS isolation. Cells were stored at -80º as pellets.

extract_protocol:
Total RNA was isolated using the Arcturus PicoPure RNA Isolation Kit, processed as per manufacturer’s instructions, and moved forward if QC reflected 260/280 ≥ 2 and RQN ≥ 8.0.
cDNA conversion from minimum 35ng of Total RNA used the SMART-Seq v4 Ultra Low Input RNA Kit, and was followed by Library Preparation using the Nextera XT DNA Library Preparation Kit, both according to the manufacturer’s instructions.

value: FACS-isolated SVZ cells

tag: background strain

tag: batch

value: November


title: RB_TKO_3


title: RB_THC_1

value: February


title: I17R023d04


title: RB_TKO_1


title: RB_TKO_2


title: I17R023a06


title: EHT_C


title: EKO_A


title: RB_THC_2


title: EKO_C


title: I17R023c01


title: EHT_A


title: Infarct 2

first: Dan

last: Lu

address: No.601, West Huangpu Avenue

department: Neurology and Stroke center

institute: Jinan University

description:
T02
circRNA

data_processing:
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 poly-N and low quality reads from raw data. At the same time, Q20, Q30, and GC-content were calculated. All the downstream analyses were based on clean data with high quality. The clean reads were mapped to the reference genome sequence by TopHat2 version 2.0.10 which is an efficient sequence alignment software based on Bowtie software and then identified the Splicing Junction between exons.
CIRI (CircRNA Identifier) tools to identification circRNA, it scans SAM files twice and collects sufficient information to identify and characterize circRNAs. Briefly, during the first scanning of SAM alignment, CIRI detects junction reads with PCC signals that reflect a circRNA candidate. Preliminary filtering is implemented using paired-end mapping (PEM) and GT-AG splicing signals for the junctions. After clustering junction reads and recording each circRNA candidate, CIRI scans the SAM alignment again to detect additional junction reads and meanwhile performs further filtering to eliminate false positive candidates resulting from incorrectly mapped reads of homologous genes or repetitive sequences. Finally, identified circRNAs are output with annotation information.
We performed circRNA analysis using "Medical combined transcriptome analysis platform tools" on the platform BMKCloud (www.biocloud.net).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: circRNA_gene_counts.list.txt: Tab-delimited matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: circ_gene_fpkm.list.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: circRNA.fa: FASTA file

source_name: brain tissue

extract_protocol:
Brain tissues of penumbra, Infarct1, infarct2 and SHAM were removed after cardiac perfusion by ice PBS. RNA of flash tissues was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
A total of 2 μg RNA per sample was used as input for RNA sequencing. First, ribosomal RNA was removed using an Epicenter Ribo-zero™ rRNA Removal Kit (Epicenter, USA), and rRNA-free residue was washed by ethanol precipitation. Subsequently, sequencing libraries were generated using rRNA-depleted RNA by an NEBNext® Ultra™ Directional RNA Library Prep kit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to the attribute sequences in each sample.

value: MCAO

value: core tissues close to occipital lobe


title: Infarct 1

description:
T01
circRNA

value: core tissues close to frontal lobe


title: EKO_B


title: Patient Tissue 37229-S

city: Houston

first: Michael

middle: T

last: Lewis

state: TX

address: 1 Baylor Plaza N1210

department: Breast Center

institute: Baylor College of Medicine

description: RNAseq of human TNBC tumor tissue

data_processing:
For PDX models, raw reads were split into human/epithelial (graft) and murine/stromal (host) reads using Xenome v1.0.1. For Patient models, reads were not split as all reads are from human tissue.
Human and Mouse reads were aligned to hg38 and mm10 reference genomes respectively using RSEM/STAR v2.5.3a_modified
The above STAR run was run internally by rsem-calculate-expression (RSEM v1.2.31), which then quantified transcripts and genes, producing isoform and gene level results.
Assembly: hg38/mm10
Supplementary files format and content: A matrix file was generated using expected counts values from RSEM results. Each row represents a gene and each column represents a xenograft model

source_name: Patient Tumor Tissue

extract_protocol:
NEBNext Ultra II Directional RNA-Seq Sample Preparation with rRNA Depletion protocol (p/n E7760S/L, version 1.0, April 2017) using 100, 50, or 2.5ng RNA input, along with ThermoFisher’s ERCC RNA Spike-In Control Mixes Protocol (publication number 4455352, rev. D).
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.

value: Human breast tumor tissue

value: untreated


title: Patient Tissue 39918-S

description: RNAseq of human TNBC tumor tissue


title: Patient Tissue 4179-S

description: RNAseq of human TNBC tumor tissue


title: Patient Tissue 39608-S

description: RNAseq of human TNBC tumor tissue


title: Patient Tissue 32176-S

description: RNAseq of human TNBC tumor tissue


title: Patient Tissue 3522-S

description: RNAseq of human TNBC tumor tissue


title: Patient Tissue 3120-S

description: RNAseq of human TNBC tumor tissue


title: Patient Tissue 3273-S

description: RNAseq of human TNBC tumor tissue


title: EHT_B


title: Patient Tissue 3664-S

description: RNAseq of human TNBC tumor tissue


title: Patient Tissue 2382-S

description: RNAseq of human TNBC tumor tissue


title: Patient Tissue 15076-S

description: RNAseq of human TNBC tumor tissue


title: H3K4WT

city: Shanghai

first: Shi

last: Jiao

address: 320 Yue Yang Road

institute: Shanghai Institutes of Biological Sciences

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 0.12.8.
peaks were called using MACS version 1.4.2 and Different peaks were caculated by DiffBind in R with the Fold change >=2 and p value <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: peaks files were generated by MACS version 1.4.2 20120305. Fold_enrichment reprensent fold change. Fold change >=2 and p value <0.05.

source_name: mouse peritoneal macrophages

growth_protocol: The thioglycollate broth-induced peritoneal macrophages are harvested and are cultured in 10 cm dishes with 10%FBS DMEM cultures.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed according to standard Illumina protocols.

value: thioglycollate broth induced peritoneal macrophages

tag: age

value: 8 weeks

value: H3K4me3 (abcam, ab8580)

value: wild type


title: H3K9KO

value: H3K9me3 (abcam, ab8898)

value: Sun-/-


title: H3K9WT

value: WT


title: Patient Tissue 4353-S

description: RNAseq of human TNBC tumor tissue


title: H3K4KO


title: hepatocyte rep2

city: Portland

first: Amita

last: Tiyaboonchai

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Pediatrics

institute: Oregon Health & Science University

data_processing:
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
Custom bowtie indexes were built containing the gene targets for custom sequence integration.
Libraries were aligned to these custom indexes using bowtie 1.0.0 using a 50 base wide sliding window.  The window was offset in 15 base steps along the sequence reads until an alignment was found or the end was reached.  This allowed us to place the integrated sequence relative to specific genes from the reference genome and verify that it was at the expected integration site.
These windowed alignments were parsed to generate the matrix of unique counts provided as processed data.
Assembly: mm9
Supplementary files format and content: text file includes matrix of unqiue counts using the custom index alignment for integrated sequences

source_name: Liver

extract_protocol:
RNA lysis buffer is TRIzol reagent
RNA libraries were prepared with standard Illumina protocols

value: Liver

value: No treatment

tag: selection

value: No selection


title: hepatocyte rep4


title: Patient Tissue 4570-S

description: RNAseq of human TNBC tumor tissue


title: Penumbra

description:
T03
circRNA

value: penumbra tissues


title: hepatocyte rep3


title: Patient Tissue 15056-S

description: RNAseq of human TNBC tumor tissue


title: Patient Tissue 15063-S

description: RNAseq of human TNBC tumor tissue


title: SHAM

description:
T04
circRNA
Sham operation

value: Sham

value: Cortex tissues corresponding to core and penumbra tissues


title: LPS

type: RNA

city: Suita

first: Tomohiko

last: Murakami

state: OSAKA

address: 1-8 Yamada-Oka

institute: Osaka University

description: Gene expression data from bone marrow derived macrophages

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label: biotin

source_name: macrophages_treated with LPS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Bone marrow derived macrophages were cultured with RPMI containing 10% FBS and MCSF.

extract_protocol: Total RNA was extracted with Nucleospin RNA plus kit

treatment_protocol: Bone marrow derived macrophages were treated with or without LPS.

value: bone marrow

value: macrophages


title: hepatocyte rep1


title: control


title: Trdn-as KO-3

city: Augusta

first: Hongyan

last: Xu

state: GA

department: Population Health Sciences

institute: Augusta University

data_processing:
Salmon 1.5.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 transcriptome and quantified using Salmon 1.5.2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: heart

extract_protocol:
Hearts were dissected out and flash frozen in liquid nitrogen.  RNA was harvested using Trizol reagent.  1 ug of total RNA was used for the construction of sequencing libraries .
RNA libraries were prepared for sequencing using standard Illumina protocols by the BGI Group (Shenzhen, CN).

value: heart

value: 5 months


title: Trdn-as KO-1

value: 14 months


title: MEF_4F_2wks

description: Total RNA extracted from mouse embryonic fibroblasts infected with retroviruses carrying Gata4, Hand2, Mef2C, and Tbx5 2 weeks post-infection.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Cartridge  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Normalized data file includes MAS5.0 signal intensity

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (GeneChip WT Plus Reagent Kit, 2013, Affymetrix).

growth_protocol: Cells were cultured in medium composed of DMEM/199 (4:1) (Gibco), 10% FBS (Gemini), 5% horse serum (Gemini), antibiotics (Gibco), 1X  non-essential amino acids (Gibco), 1X essential amino acids (Gibco), 1 B-27 (Gibco), 1 insulin–selenium–transferin (Gibco), 1 MEM vitamin solution (Gibco) and 1X sodium pyruvate (Gibco). The medium was changed every 2–3 days until cells were harvested for RNA extraction.

extract_protocol: Total RNA were extracted using TRizol reagent (Ambion) and the RNeasy Plus Universal Mini Kit (Qiagen).

treatment_protocol: Cells were infected with retroviruses carrying  carrying Gata4, Hand2, Mef2C, and Tbx5 and cultured for various time period.

value: embryonic fibroblasts

tag: infected with

value: Gata4, Hand2, Mef2C, and Tbx5

tag: time post infection

value: 2 weeks


title: WT-1


title: MEF_4F_O_1m

description: Total RNA extracted from mouse embryonic fibroblasts infected with retroviruses carrying Gata4, Hand2, Mef2C, and Tbx5 1 month post-infection.

value: 1 month


title: MEF_4F_D5

description: Total RNA extracted from mouse embryonic fibroblasts infected with retroviruses carrying Gata4, Hand2, Mef2C, and Tbx5 day 5 post-infection.

value: 5 days


title: Trdn-as KO-2


title: MEF_4F_D3

description: Total RNA extracted from mouse embryonic fibroblasts infected with retroviruses carrying Gata4, Hand2, Mef2C, and Tbx5 day 3 post-infection.

value: 3 days


title: MEF_4F_3wks

description: Total RNA extracted from mouse embryonic fibroblasts infected with retroviruses carrying Gata4, Hand2, Mef2C, and Tbx5 3 weeks post-infection.

value: 3 weeks


title: WT-2


title: NMCM

description: Neonatal mouse cardiomyocytes.

source_name: Neonatal mouse cardiomyocytes.

value: neonatal mouse cardiomyocytes


title: R0929TAT

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner (bwa) version 0.7.15
Non-uniquely mapped/redundant reads were discarded.
Narrow peaks were called using MACS version 2.1.2 on deduplicated bam files using the following command: macs2 callpeak --SPMR -B -q 0.01 --keep-dup 1 -g hs -f BAMPE --extsize 146 --nomodel -t {treat.bam} -c {input.bam}.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig and peak text files (BED) were generated

source_name: Chromophobe

extract_protocol:
Using a 2 mm2 core needle, one core was extracted from frozen RP tissue blocks in the areas marked on the corresponding slide. Frozen cores were pulverized using the Covaris CryoPrep system.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced on an Illumina HiSeq 4000 to generate 150-bp paired-end reads (Novogene).

tag: tumor stage

tag: grade

value: III

tag: tumor tissue source (primary versus metastasis)

value: Primary


title: R0957TAT

source_name: Clear cell RCC


title: S22741_IN

value: IV


title: R1152TAT

value: II


title: WT-3

tag: tissue


title: MEF_4F_D7

description: Total RNA extracted from mouse embryonic fibroblasts infected with retroviruses carrying Gata4, Hand2, Mef2C, and Tbx5 day 7 post-infection.

tag: cell type

value: 7 days


title: R1097TAT


title: R1149TAT


title: R0998TAT

source_name: Papillary RCC


title: S21429_IN


title: MEF_4F_D9

description: Total RNA extracted from mouse embryonic fibroblasts infected with retroviruses carrying Gata4, Hand2, Mef2C, and Tbx5 day 9 post-infection.

value: 9 days


title: R991T1AT


title: DCL1_ChIP_WT_input_rep1

city: Poznan

first: Jakub

middle: Jacek

last: Dolata

address: Uniwersytetu Poznanskiego 6

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

data_processing:
For small RNA studies reads coresponding to miRNAs were selected using 'mirnasoft' package and counted, analysis was performed using 'DESeq2'
For ChIPseq studes, reads were mapped to the tair10 genome (Bowtie), PCR duplicates were removed (samtools), bam files were used to draw metaplots (ngs.plot), bed files were generated (bedtools) to count reads for particular genomic regions.
Genome_build: tair10
Supplementary_files_format_and_content: small RNA processed data files (txt) contains counted reads coresponding to miRNAs

organism: Arabidopsis thaliana

source_name: seedlings, WT, 14 days

growth_protocol: temp 22°C, long day, 14 days old seedlings were grown on 1/2 MS plates, 21 days old plants were grown on soil

extract_protocol:
according to manufacturers instructions
ChIPseq libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode), smallRNA libraries were prepared using TruSeq SmallRNA Library Preparation Kit (Illumina)

value: seedlings

tag: genotype

value: WT

value: 14 days


title: DCL1_ChIP_prp40ab_input_rep1

source_name: seedlings, prp40ab, 14 days


title: MEF_4F_D4

description: Total RNA extracted from mouse embryonic fibroblasts infected with retroviruses carrying Gata4, Hand2, Mef2C, and Tbx5 day 4 post-infection.

value: embryonic fibroblasts

value: 4 days


title: DCL1_ChIP_noAb_rep1


title: DCL1_ChIP_prp40ab_DCL1_rep1


title: DCL1_ChIP_WT_DCL1_rep1


title: MEF

description: Total RNA extracted from mouse embryonic fibroblasts.

source_name: mouse embryonic fibroblasts.


title: S20449_IN


title: PolII_ChIP_prp40ab_input_rep1


title: RT998_IN


title: PolII_ChIP_WT_input_rep1


title: PolII_ChIP_prp40ab_PolII_total_rep1


title: PolII_ChIP_WT_noAb_rep1


title: RT991_IN


title: RT929_IN


title: RT957_IN


title: Monocytes from severe COVID19 patient number 76

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

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

country: Spain

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
iDATs were analyzed using a standard pipeline, with the shinyepico package (1.0.0) of the Bioconductor project
Matrix_processed.txt contains Normalized (minfi preprocessNoob + preprocessQuantile) Beta values

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Monocytes were isolated from severe COVID19 patients and Healthy donors using CD14 positive and CD15 negative selection by sorter

extract_protocol: Total DNA was isolated using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to manufacturer’s instruction

tag: cell tnype

value: monocyte

tag: gender

value: Male


title: RT970_IN

tag: antibody


title: Monocytes from severe COVID19 patient number 37


title: Monocytes from severe COVID19 patient number 38


title: Monocytes From HD number 10

source_name: Healthy Donor


title: RT1265_IN


title: Monocytes from severe COVID19 patient number 86


title: RT1205_IN


title: S21381_IN


title: RT1152_IN


title: RT1168_IN


title: RT1184_IN


title: Monocytes from severe COVID19 patient number 81


title: Monocytes From HD number 6


title: RT1143_IN


title: PolII_ChIP_prp40ab_noAb_rep1


title: PolII_ChIP_WT_PolII_total_rep1


title: RT1240_IN


title: Monocytes from severe COVID19 patient number 79


title: Monocytes from severe COVID19 patient number 67


title: Monocytes from severe COVID19 patient number 30


title: Monocytes from severe COVID19 patient number 28


title: Monocytes from severe COVID19 patient number 29

value: Female


title: RT1059_IN


title: RT1149_IN


title: Monocytes from severe COVID19 patient number 94


title: RT1043_IN


title: Monocytes from severe COVID19 patient number 61


title: RT1047_IN


title: Monocytes From HD number 24


title: RT1056_IN


title: Monocytes From HD number 3


title: Monocytes from severe COVID19 patient number 69


title: Monocytes from severe COVID19 patient number 100


title: Monocytes from severe COVID19 patient number 66


title: Monocytes from severe COVID19 patient number 56


title: Monocytes from severe COVID19 patient number 63


title: Monocytes from severe COVID19 patient number 84


title: RT1039_IN


title: Monocytes from severe COVID19 patient number 58


title: Monocytes from severe COVID19 patient number 88


title: RT1131_IN

value: Metastatic


title: Monocytes from severe COVID19 patient number 70


title: RT1097_IN


title: RT1002_IN


title: Monocytes from severe COVID19 patient number 90


title: Monocytes from severe COVID19 patient number 48


title: Monocytes from severe COVID19 patient number 82


title: RT1046_IN


title: Monocytes from severe COVID19 patient number 62


title: Monocytes from severe COVID19 patient number 68


title: RT0638_IN


title: Monocytes from severe COVID19 patient number 72


title: RT0642_IN


title: RT0301_IN


title: Monocytes From HD number 15


title: Monocytes from severe COVID19 patient number 55


title: Monocytes from severe COVID19 patient number 47


title: Monocytes from severe COVID19 patient number 32


title: IN968M

source_name: Clear Cell


title: RT0356_IN


title: Monocytes From HD number 9


title: Monocytes from severe COVID19 patient number 85


title: IN962T


title: Monocytes from severe COVID19 patient number 89


title: IN951T


title: Monocytes From HD number 20


title: IN716T


title: Monocytes from severe COVID19 patient number 80


title: Monocytes from severe COVID19 patient number 54


title: Monocytes From HD number 30


title: IN233T


title: Monocytes from severe COVID19 patient number 83


title: IN1247A


title: Monocytes from severe COVID19 patient number 64


title: Monocytes from severe COVID19 patient number 31


title: Monocytes from severe COVID19 patient number 53


title: Monocytes from severe COVID19 patient number 87


title: IN1120T


title: Monocytes From HD number 14


title: IN1226T


title: Monocytes from severe COVID19 patient number 75


title: Monocytes from severe COVID19 patient number 78


title: IN1091T


title: Monocytes from severe COVID19 patient number 50


title: Monocytes from severe COVID19 patient number 97


title: Monocytes from severe COVID19 patient number 52


title: Monocytes from severe COVID19 patient number 57


title: Monocytes from severe COVID19 patient number 65


title: IN1014T


title: Monocytes from severe COVID19 patient number 49


title: Monocytes from severe COVID19 patient number 35


title: Monocytes From HD number 5


title: 1059T1AT


title: 1056T1AT


title: 1039T2AT


title: Human, kidney, wild type, biol rep 2

city: BALTIMORE

first: KAUSHAL

middle: VIJAY

last: ASRANI

state: MD

address: 1550 ORLEANS

institute: JOHNS HOPKINS MEDICINE

data_processing:
Sequencing reads were mapped to the hg38 human genome using STAR.v2.7.3a. All subsequent analyses were performed in R. Gene level abundance was quantitated using the GenomicAlignments Bioconductor package.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include TPM-normalized data and raw-counts.

source_name: Embryonic kidney

extract_protocol:
Total cellular RNA was extracted using RNeasy Mini kit (#74104, Qiagen) according to manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis.

treatment_protocol: All cell lines were maintained in DMEM high glucose medium with l-glutamine, 10% heat-inactivated FBS and 1% penicillin/ streptomycin at 37°C in 5% CO2.

value: Embryonic kidney

tag: cell line

value: Kidney


title: Monocytes From HD number 2


title: Human, kidney, TSC1/TSC2 KO, biol rep 2

value: TSC1/TSC2 KO


title: Human, kidney, wild type, biol rep 1


title: S22741_H3K4me2

value: Primary

value: H3K4me2 antibody, Millipore C07030


title: Human, kidney, TSC1/TSC2 KO, biol rep 1


title: S21381_H3K4me2

value: II


title: Human, xenograft, TSC2/TFE3/TFEB KO, biol rep 1

source_name: Xenograft

value: Xenograft

value: TSC2/TFE3/TFEB KO


title: Human, xenograft, TSC2/TFE3 KO, biol rep 3

value: TSC2/TFE3 KO


title: IN1058T

value: III


title: Human, xenograft, TSC2/TFE3 KO, biol rep 2


title: Human, xenograft, TSC2/TFEB KO, biol rep 3

value: TSC2/TFEB KO


title: Human, xenograft, TSC2/TFE3 KO, biol rep 1


title: RT998_H3K4me2


title: Human, xenograft, TSC2/TFEB KO, biol rep 2


title: Human, xenograft, TSC2 KO, biol rep 3

value: TSC2 KO


title: RT991_H3K4me2

value: IV


title: RT970_H3K4me2


title: Human, xenograft, TSC2/TFEB KO, biol rep 1


title: Human, kidney, wild type, biol rep 3

value: WT


title: Human, xenograft, wild type, biol rep 3


title: RT957_H3K4me2


title: Human, xenograft, TSC2 KO, biol rep 1


title: Human, kidney, TSC1/TSC2 KO, biol rep 3


title: Human, xenograft, wild type, biol rep 2


title: Human, xenograft, TSC2/TFE3/TFEB KO, biol rep 2


title: Human, xenograft, wild type, biol rep 1


title: RT1265_H3K4me2


title: Human, xenograft, TSC2/TFE3/TFEB KO, biol rep 3


title: RT929_H3K4me2


title: RT1240_H3K4me2


title: RT1168_H3K4me2


title: RT1152_H3K4me2


title: RT1149_H3K4me2


title: Human, xenograft, TSC2 KO, biol rep 2


title: RT1056_H3K4me2


title: OE-19 cells

city: New York

first: Luigi

last: Scotto

state: NY

address: 650 West 168th Street, P&S 8-460

department: Medicine

institute: Columbia University Medical Center

data_processing:
Kallisto
Kallisto to pseudoalign and quantify RNA-seq reads to transcripts
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: Esophageal adenocarcinoma

growth_protocol: Cells were maintained in appropiate media 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 kit (Qiagen). .
RNA libraries prepared from poly-A pull-down enrich mRNAs from total RNA samples (Illumina TruSeq RNA prep kit)

treatment_protocol: no treatment

value: Esophageal adenocarcinoma

tag: cell culture

value: Adherent


title: NCI-H82 cells

source_name: Small cell lung carcinoma

value: Small cell lung carcinoma

value: Suspension


title: NH6 cells

source_name: Neuroblastoma

value: Neuroblastoma


title: SNU-119 cells

source_name: Serous ovarian adenocarcinoma

value: Serous ovarian adenocarcinoma


title: UOK-269 cells

source_name: Renal cell carcinoma

value: Renal cell carcinoma


title: RT1059_H3K4me2

value: Primary

value: H3K4me2 antibody, Millipore C07030


title: NCI-H2342 cells

source_name: Lung ademocarcinoma

value: Lung ademocarcinoma


title: Dph015 input 2

first: Marcus

last: Noyes

address: 435 East 30th Street

department: Department of Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

data_processing:
Reads were mapped to hg38 using bowtie2 version 2.2.5
samtools version 1.7 was used to filter out reads that were not uniquely aligned
MACS2 version 2.2.7.1 was used to call peaks using input DNA as the control
Assembly: hg38
Supplementary files format and content: BedGraph files containing comparison of treatment of control

growth_protocol: Gibco High Glucose DMEM , 10% fetal bovine serum, no antibiotics prior to treatments,. cells were cultured at 37Cͦ and 5% CO2.

extract_protocol:
Cells were fixed with 2.7% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor sonication device..
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: colony selection was carried in 200ug/ml of hygromycin, 24 hours prior to fixing the cells were treated with 100ng/ml of doxycyclin.

value: Human embryonic kidney

tag: chip antibody

value: ab290 abcam


title: Kelly cells

value: Kelly


title: YY1 input DNA


title: Dph015 input 1


title: CDKN1C array #125 8Q input DNA


title: YY1 biol rep 2


title: CDKN1C array #125 8R input DNA


title: CDKN1C array #200 8R input DNA


title: YY1 biol rep 1


title: GCIY cells

source_name: Gastric adenocarcinoma

value: Gastric adenocarcinoma

value: GCIY


title: RT1046_H3K4me2

value: III


title: Dph015 array #200 8R biol rep 1


title: Dph015 array #200 8R biol rep 2


title: Clone 19 of HeLa-Cas9 cell line with SNAPC4-Knockdown small, RNA

city: Rockville

first: May Christine

middle: V

last: Malicdan

address: 5625 Fisher's Ln

department: National Human Genome Research Institute

institute: National Institutes of Health

data_processing:
For polyA RNA-Seq, the data was processed using RTA version 3.4.4. Reads were then aligned to GRCh37 using HISAT2, and reads were assembled and counted using StringTie and counts were generated using DESeq2.
For small RNA-Seq, reads were then aligned to GRCh37 by BGI and reads were assembled and counted using StringTie. Next, counts were generated using DESeq2
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Cervix

extract_protocol:
For polyA RNA-Seq, total RNA was extracted from HeLa cells using the Maxwell RSC simplyRNA Cells Kit (AS1390, Promega), and from patient-derived fibroblasts using the Maxwell RSC miRNA from Tissue Kit (AS1460, Promega), according to the manufacturer’s specifications.
For small RNA-seq total RNA was extracted from HeLa cells and patient-derived fibroblasts using the Maxwell RSC miRNA from Tissue Kit (AS1460, Promega) according to the manufacturer’s specifications.
For polyA RNA-seq, stranded poly-A selected mRNA libraries were constructed from 1 µg total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs) and NEBNext Ultra II Directional RNA Library Prep for Illumina with Sample Purification Beads (E7765, New England Biolabs). Amplification was performed using 8 cycles of PCR to avoid over-amplification. Unique dual-indexed barcode adapters were applied to each library.
Small RNA-seq library construction was carried out by BGI Genomics (Shenzhen, China).

value: Cervix

value: HeLa line stably expressing Cas9

tag: treatment


title: Clone 12 of HeLa-Cas9 cell line with SNAPC4-Knockdown, small RNA


title: RT1039_H3K4me2

source_name: Chromophobe


title: RT1043_H3K4me2

source_name: Clear cell RCC

value: IV


title: CDKN1C array #200 8R biol rep 2


title: RT1047_H3K4me2


title: Parental HeLa-Cas9 cell line, small RNA

value: WT


title: RT0642_H3K4me2

source_name: Papillary RCC

value: II


title: RT0301_H3K4me2


title: CDKN1C array #125 8R biol rep 1


title: CDKN1C array #200 8R biol rep 1


title: Control skin fibroblast cell line 2, small RNA

source_name: Skin

value: Skin

value: Primary Skin Fibroblasts


title: RT0638_H3K4me2


title: Control skin fibroblast cell line 1, small RNA


title: CDKN1C array #125 8Q biol rep 2


title: RT0356_H3K4me2


title: CDKN1C array #125 8R biol rep 2


title: AML2_control_UTX

city: Birmingham

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham

data_processing:
All sequencing reads were mapped to the human genome (hg19) using the Bowtie2 (v2.2.3), and reads with a mapping score > 20 were selected for data analysis with PCR duplicated reads removed by Picardtools (v2.27.0). MACS2 (v2.2.7.0) was used to call ChIP-seq peaks with input as controls using default parameters in paired-end mode. Bigwig files were generated by bamCoverage and used for visualization in Integrative Genomics Viewer (IGV).
Assembly: hg19
Supplementary files format and content: bigwig files

growth_protocol: Cells were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Briefly, 20-50 million cells were cross-linked by formaldehyde (1%) and then quenched with 0.125 M glycine. After washing with cold PBS, cells were suspended in lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5%NP-40, 0.25% TritonX-100, and protease inhibitor) and subjected to sonication to shear the chromatin DNA into sizes ranging from 200 to 500 bp. The fragmented chromatin was pre-cleared by centrifugation at 4°C (15,000 rpm, 30 min). The supernatant was incubated with primary antibody and Protein A or G Dynabeads magnetic beads (Invitrogen) at 4°C overnight. The following primary antibodies were used: anti-UTX (Bethyl, A302-374A) and anti-H3K27ac (Abcam, ab4729). After six times wash with RIPA wash buffer (50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na-Deoxycholate) and once wash with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, and 50 mM NaCl), chromatin was eluted from beads in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS). After reverse crosslinking, ChIP DNA was purified using a DNA clean-up kit (Zymo Research).
ChIP-seq library was prepared using NEBNext Library Prep Kit following the instructions and samples were sequenced on the NovaSeq 6000 PE150 platform.

treatment_protocol: Cells were lentivirally infected with indicated sgRNA for gene knockout

value: Acute myeloid leukemia cells

value: anti-UTX (Bethyl, A302-374A)


title: S22741_H3K27ac

value: Primary

value: H3K27ac anitbody, Diagenode C15410196


title: Individual 6, Skin biopsy-derived fibroblasts, small RNA

value: Derived from skin biopsy


title: Individual 4, Skin biopsy-derived fibroblasts, small RNA


title: RT1002_H3K4me2

value: Metastatic

value: H3K4me2 antibody, Millipore C07030


title: Control skin fibroblast cell line 3, small RNA


title: AML2_sgUTX_4_H3K27ac

value: anti-H3K27ac (Abcam, ab4729)


title: S21381_H3K27ac


title: Individual 3, Skin biopsy-derived fibroblasts, small RNA


title: AML2_sgUTX_2_H3K27ac


title: S21429_H3K27ac


title: Individual 2, Skin biopsy-derived fibroblasts, small RNA


title: CDKN1C array #125 8Q biol rep 1

value: Human embryonic kidney

value: ab290 abcam


title: RT998_H3K27ac

value: III


title: Individual 1, Skin biopsy-derived fibroblasts, small RNA


title: AML2_sgUTX_4_Input


title: S20449_H3K27ac


title: AML2_sgUTX_2_Input


title: Recipient cow 1

city: Zhengzhou

first: Shijie

last: Lyu

address: Huayuan Road 116

institute: Henan Academy of Agricultural Sciences

data_processing:
Agilent Technologies 2100 Bioanalyze was used to check the size and purity of the library.
Clean reads were mapped to the bovine genome (ARS-UCD 1.2) using HISAT2
Htseq package was used to get gene counts
Assembly: ARS-UCD 1.2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Bos taurus

source_name: uterine flushing fluids

growth_protocol: Ten Xianan cows were selected as donors for synchronous estrus and superovulation. The artificial insemination was performed after superovulation. Another 23 Xianan cows were selected as recipients for synchronous estrus.

extract_protocol:
Total RNA in exosomes from uterine flushing fluids was extracted using the miRNeasy Serum/Plasma Kit (Qiagen, Germany)
A total of 10 ng total RNA was used to construct the small RNA library using the TruSeq Small RNA Sample Prep Kits (Illumina, USA).

treatment_protocol: On the 7th day after artificial insemination of donors, 100 ml bovine UFs were collected by uterine flushing using sterile Gibco Minimum Essential Media with 0.7% 200mM Tris buffer (pH = 7.2) controls.Three donor cows with well-developed blastocysts were used for further analysis . Three recipient cows having similar body weight and age were selected as matched.

value: uterine flushing fluids

tag: breed

value: Xianan

tag: rna popoulation

value: exosomal miRNA


title: Recipient cow 2


title: AML2_control_Input


title: Donor cow 1


title: HIC_K562_0000min_biorep4_techrep2_seqrep2

city: Chapel Hill

first: Marielle

last: Bond

address: 104 Manning Drive Thurston Building Room 4012

institute: UNC Chapel Hill

data_processing:
Hi-C maps for each sample were generated using the Juicer pipeline as initially described in Rao et al. 2014 (version 1.5.6).
Merged Hi-C maps for each time point as well as a total "mega" map were generated using Juicer (version 1.5.6)
Loops were called from merged timepoint maps at 5kb resolution using SIP (-g 2 -t 2000 -fdr 0.05, version 1.6.1)
Loops were called from merged mega map at 5kb resolution using SIP (-g 1 -t 2000 -fdr 0.05, version 1.6.1)
Loops were extrapolated to 10kb and concatenated, then merged using DBScan while keeping the mean of modes for anchor coordinates (epsilon = 20kb manhattan distance, version 1.1.8)
Counts for merged loops were extracted from Hi-C files of each sample using strawR (no normalization, 10kb resolution, version 0.0.9)
Raw counts were used as input for differential analysis with DESeq2 (LRT, full design ~techRep + bioRep + time, reduced ~techRep + bioRep, version 1.33.5). Significant results were determined based on an absolute LFC greater than 0.585 (fold-change of ±1.5) and an adjusted p-value below 0.05.
Assembly: hg38
Supplementary files format and content: .hic: chromatin contact matrices; .tsv tab-delimited text file containing information on all HiC loops (anchor, chr, start, end coords, SIP outputs, loop names, differential clusteres, DESeq adjusted LRT p-values, raw un-normalized counts, variance-stabilized transformed counts

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min, quenched with 2.0M glycine for 5 min, washed in PBS, and split into 3x106 cell pellet aliquots
in situ Hi-C

treatment_protocol: Megakaryocyte differentiation induced by treatment with 25 nM PMA for the 0h, 6h, and 72h. Media was changed after 24h and 48h

value: Human leukemia

value: WT

value: PMA (megakaryocyte differentiation)


title: RT991_H3K27ac

value: IV


title: RT957_H3K27ac


title: RT1205_H3K27ac

value: II


title: RT1265_H3K27ac

value: Primary


title: HIC_K562_0360min_biorep3_techrep2_seqrep2


title: Donor cow 3


title: RT1240_H3K27ac

value: H3K27ac anitbody, Diagenode C15410196


title: RT970_H3K27ac


title: HIC_K562_0360min_biorep4_techrep2_seqrep2


title: RT929_H3K27ac


title: w1118_5wk_2 (ATAC-seq)

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

data_processing:
Reads were aligned using bowtie2, converted to uncompressed BAM files, sorted and index using: bowtie2-X2000 --mm --local -1 $fastq1 -2 $fastq2 | samtools view -Su /dev/stdin | samtools sort & index > xxx.PE2SE.bam &.bai 2> align.log. Poorly mapped, (<30 mapping score), duplicate, multimapped, and mitochondrial reads were removed using samtools and picard. Tn5 adapters were removed by truncating + end reads by 4 base pairs and – end reads by 5 base pairs, and then written to final output BAMs.
BAM files were  sorted and indexed with samtools. Peakcalling was performed using MACS2 using the following commands: callpeak -f BAMPE -g dm - -q 0.01 --nomodel --shift -100 --extsize 200 --keep-dup all.
Genome_build: dm6
Supplementary_files_format_and_content: narrow peak

organism: Drosophila melanogaster

source_name: Heart

extract_protocol:
Hearts were exposed and removed, and transferred to 1ml glass douncer with Nuclei EZ Prep kit detergent. Hearts were sheared with 20 loose and 15 tight strokes, then transferred to eppendorf for remainder of SigmaAldrich Nuclei EZ prep kit instructions. Samples were permeabilized in cold nuclear permeabilization buffer ((0.2% IGEPAL-CA630 (I8896, Sigma), 1 mM DTT (D9779, Sigma), Protease inhibitor (05056489001, Roche), and 5% BSA (A7906, Sigma) in PBS (10010-23, Thermo Fisher Scientific)) for 5 minutes on a rotator at 4°C followed by centrifugation for 5 min at 500g at 4°C. After decanting supernatant, the pellet was resuspended in cold tagmentation buffer ((33 mM Tris-acetate (pH = 7.8) (BP-152, Thermo Fisher Scientific), 66 mM K-acetate (P5708, Sigma), 11 mM Mg-acetate (M2545, Sigma), 16% DMF (DX1730, EMD Millipore) in molecular biology grade water (46000-CM, Corning)) followed by incubation with Tagmentation enzyme (FC-121-1030; Illumina) at 37°C with shaking at 500 rpm for 30 min. Tagmented DNA was purified using MinElute PCR purification kit (28004, QIAGEN).
The resulting libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72°C for 5 minutes, denaturation at 98°C for 30 s, followed by 8 cycles of denaturation at 98°C for 10s, annealing at 63°C for 30s and extension at 72°C for 60s. After purification of amplified libraries using MinElute PCR purification kit (28004, QIAGEN), double sided size selection was performed using SPRIselect beads (B23317, Beckman Coulter) with 0.55X beads and 1.5X to sample volume.

value: Heart

tag: age

value: 5 weeks

tag: strain


title: w1118_5wk_3 (ATAC-seq)


title: Donor cow 2


title: Recipient cow 3


title: HIC_K562_4320min_biorep3_techrep2_seqrep2


title: w1118_5wk_1 (ATAC-seq)


title: HIC_K562_0000min_biorep3_techrep2_seqrep2


title: AML2_control_H3K27ac

value: Acute myeloid leukemia cells


title: w1118_1wk_3 (ATAC-seq)

value: 1 week


title: RT1168_H3K27ac

tag: tumor stage


title: RT1184_H3K27ac

tag: grade


title: HIC_K562_0360min_biorep4_techrep2_seqrep1


title: HIC_K562_4320min_biorep4_techrep2_seqrep1


title: w1118_1wk_1 (ATAC-seq)


title: LamBiR_1wk_4 (ATAC-seq)

value: attp40, LamB iR


title: HIC_K562_4320min_biorep4_techrep1_seqrep2


title: LamBiR_1wk_3 (ATAC-seq)


title: LamBiR_1wk_5 (ATAC-seq)


title: w1118_1wk_2 (ATAC-seq)


title: HIC_K562_0000min_biorep4_techrep2_seqrep1


title: RT1059_H3K27ac

tag: tumor tissue source (primary versus metastasis)


title: RT1149_H3K27ac


title: RT1131_H3K27ac

value: Metastatic


title: HIC_K562_4320min_biorep3_techrep2_seqrep1


title: HIC_K562_0360min_biorep3_techrep2_seqrep1


title: HIC_K562_4320min_biorep3_techrep1_seqrep2


title: RT1152_H3K27ac


title: RT1097_H3K27ac

value: III


title: LamCiR_1wk_4 (ATAC-seq)

tag: tissue

value: attp2, LamC iR


title: LamBiR_1wk_2 (ATAC-seq)


title: RT1143_H3K27ac


title: HIC_K562_4320min_biorep4_techrep2_seqrep2

tag: cell type


title: HIC_K562_0360min_biorep4_techrep1_seqrep2

tag: genotype


title: HIC_K562_0360min_biorep3_techrep1_seqrep2


title: RT1056_H3K27ac


title: LamBiR_1wk_1 (ATAC-seq)


title: HIC_K562_0000min_biorep4_techrep1_seqrep2


title: HIC_K562_0000min_biorep3_techrep1_seqrep2


title: RT1047_H3K27ac


title: HIC_K562_0000min_biorep3_techrep2_seqrep1


title: LamCiR_1wk_3 (ATAC-seq)


title: RT1046_H3K27ac


title: RT1043_H3K27ac


title: RT1002_H3K27ac


title: HIC_K562_4320min_biorep4_techrep1_seqrep1


title: LamCiR_1wk_1 (ATAC-seq)


title: RT1039_H3K27ac


title: RT0642_H3K27ac


title: HIC_K562_0360min_biorep4_techrep1_seqrep1


title: HIC_K562_0000min_biorep4_techrep1_seqrep1


title: RT0638_H3K27ac


title: HIC_K562_4320min_biorep3_techrep1_seqrep1


title: attp2_1wk_3 (ATAC-seq)


title: attp2_1wk_1 (ATAC-seq)


title: attp2_1wk_2 (ATAC-seq)


title: HIC_K562_0360min_biorep3_techrep1_seqrep1


title: S20449_H3K4me2

value: H3K4me2 antibody, Millipore C07030


title: LamCiR_1wk_2 (ATAC-seq)


title: K27968M

source_name: Clear Cell


title: RT0301_H3K27ac


title: attp40_1wk_3 (ATAC-seq)


title: attp40_1wk_2 (ATAC-seq)


title: HIC_K562_4320min_biorep2_techrep3_seqrep1


title: K27962T


title: attp40_1wk_1 (ATAC-seq)


title: K27951T


title: K27716T


title: attp2_1wk_4 (ATAC-seq)


title: HIC_K562_0360min_biorep2_techrep3_seqrep1


title: HIC_K562_4320min_biorep1_techrep3_seqrep1


title: HIC_K562_0000min_biorep2_techrep3_seqrep1


title: E16.5

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Science

institute: Sichuan University

data_processing:
The Cell Ranger (v3.0.2) software was obtained from 10x Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters.
Genome_build: mm10
Supplementary_files_format_and_content: feature_bc_matrix

source_name: Molar at embryonic day 16.5

growth_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committee at College of Life Sciences, Sichuan University. All animals were maintained under standardized conditions with the temperature- and light-controlled (12 hr light/dark cycle), in individually ventilated cages always with companion mice and had free access to food and water. Knock-in transgenic mice (Pitx2-P2A-copGFP and Msx1-P2A-tdTomato) were generated by Biocytogen, Inc (Beijing).

extract_protocol:
The molar tooth germs were physically separated from the mandibular using dissection needles under a stereo-fluorescent microscope. Tissues surrounding the tooth germs were eliminated and tooth germs were collected into a clean culture plate. Next, the tooth germs were washed twice with D-PBS and incubated with 0.8 ml 0.75 mg/ml Dispase in 1% FBS D-PBS for 20-45 min (E12.5 20 min; E14.5 30 min; E16.5 35 min; PN1 40 min; PN7 45 min). After that, 3 ml culture medium supplied with 20 µl 5 mg/ml DNase was used to neutralize the enzymes and prevent cell aggregates. The epithelium and mesenchyme were then separated and dissociated with 0.25% Trypsin-EDTA for 5 min and 9 min respectively in an incubator at 37°C with 5% CO2. Finally, single-cell suspensions were collected through a 70 μm strainer and centrifuged at 550 g for 5 min. Cell number and viability were assessed by an automatic cell counter.
Using single cell 3’ Library and Gel Bead Kit V3 (10x Genomics) and Chromium Single Cell B Chip Kit (10x Genomics), the cell suspension (300-600 living cells per micro-liter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cell recovered was estimated to be about 3,000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53℃ for 45 min, followed by 85℃ for 5 min, and hold at 4℃. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200. According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3. The libraries were finally sequenced using an Illumina HiSeq X or MiSeq sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

value: molar

tag: timepoint


title: K27233T


title: PN7

source_name: Molar at post-natal day 7

value: day 7


title: K271247A


title: RT0356_H3K27ac


title: HIC_K562_0360min_biorep1_techrep3_seqrep1

value: Human leukemia

value: WT


title: PN1

source_name: Molar at post-natal day 1

value: day 1


title: E12.5

source_name: Molar at embryonic day 12.5


title: K271226T


title: db/m4

city: Guangzhou

first: Li

last: Xiong

address: 58 Zhongshan Road 2

department: Department of Endocrinology

institute: The First Affiliated Hospital of Sun Yat-sen University

description: processed data file: all.counts.exp.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all.counts.exp.txt: Tab-delimited text file contains counts for each sample.

source_name: islet cells

extract_protocol:
Islets were isolated by collagenase digestion followed by purification on Histopaque (Sigma Aldrich, Germany) density gradient and used directly for RNA extraction.
The library for sequencing was constructed by removing ribosomal RNA from the total RNA.

tag: strain/background

tag: genotype/variation

value: Wild type

value: Pancreas


title: HIC_K562_0000min_biorep3_techrep1_seqrep1

tag: cell line

value: PMA (megakaryocyte differentiation)


title: HIC_K562_0000min_biorep1_techrep3_seqrep1


title: db/db4

description: processed data file: all.counts.exp.txt

value: Lepr-/-


title: HIC_K562_4320min_biorep2_techrep2_seqrep1


title: HIC_K562_0360min_biorep2_techrep2_seqrep1


title: K271120T

value: II

tag: antibody

value: H3K27ac anitbody, Diagenode C15410196


title: K271091T


title: K271058T


title: HIC_K562_0000min_biorep2_techrep2_seqrep1


title: HIC_K562_4320min_biorep1_techrep2_seqrep1


title: K271014T

value: IV

value: Primary


title: HIC_K562_0360min_biorep1_techrep2_seqrep1


title: HIWI1_PARCLIP_rep2

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

data_processing:
Library strategy: PAR-CLIP
Trimming: Adapter sequences and low quality ends were trimmed using cutadapt (version 1.4.1), keeping all reads longer than 14bp.
Alignment: All remaining reads were aligned againts hg38 genome and CDS database (Ensembl Genes V82) using PARA-suite pipeline (version 1.0.0).
Binding site detection: Only uniquely aligned reads were used for binding site detection using PARA-suite pipeline (version 1.0.0) with mostly default parameters (T2C conversion rate > 25%; min reads > 200). For data integration with additional data, coordinates have been lifter over to hg19 using UCSC liftOver tool.
Annotation: All identified binding sites were annotated using homer annotatePeaks.pl function
Visualization: For visualization, we created a bigwig track using DeepTools (version 2.5.7) with special parameters --binSize 25 and --smoothLength 75
Genome_build: hg19
Supplementary_files_format_and_content: tsv; bed

source_name: AML cell line

growth_protocol: THP-1 cells were cultured in RPMI supplemented with 10% FBS and 1% penicillin streptomycin

extract_protocol:
Cells were lysed using the NP40 lysis buffer and partial RNase T1 digestion of mRNAs was performed at a final concentration of 1 U μl−1 and incubate in a water bath for 15 min at 22 °C to facilitate the recovery of cross-linked mRNPs. A 10-μl aliquot was removed as an input control. Protein G magnetic beads (10ul/ml lysate) were conjugated to anti-FLAG antibody to a final concentration of 0.25 mg/ml lysate and incubate on a rotating wheel for 40 min at room temperature. The antibody-conjugated magnetic beads were incubated with RNase T1-treated cell lysate on a rotating wheel for 1 h at 4 °C. Magnetic beads were washed with IP wash buffer twice. The second RNaseT1 treatment was performed at final concentration of 100 U/μl, in a 22 °C water bath for 15 min. The beads were washed with high salt buffer and dephosphorylation buffer. Release of the protein-RNA complex from the beads was achieved by incubating the complex at 90 °C and separating on an SDS gel . The protein-RNA complex based on the size (18 – 28 bases) was excised from the gel. Proteinase K digestion was performed and RNA was precipitated with phenol-chloroform extraction and ethanol precipitation.
The 5'- 32P-phosphorylated RNA was then subjected to a standard cDNA library preparation protocol (Hafner et al. Methods 2012 ). The RNA was ligated with adaptors at 3'   and 5' ends followed by reverse transcription. The resulting  cDNA was amplified by adaptor-specific primers and  sequenced

treatment_protocol: THP-1 cell overexpressing FLAG-PIWIL4 were expanded in culture and grown to ~80% confluence. 14h prior to harvesting cell, crosslinking was performed by adding 4-thiouridine (4SU) to a final concentration of 100 μM directly to the cell culture. Cells were harvested and placed in a 10cm plate on a tray with ice and irradiate uncovered with 0.2 J cm−2 of 365-nm UV light in a Stratalinker 2400. The crosslinked cells were pelleted to get 1-2 ml of wet cell pellet per experiment.

tag: par-clip antibody

value: Anti-FLAG (Sigma-Aldrich, F3165)

value: AML


title: HIC_K562_0000min_biorep1_techrep2_seqrep1

department: Genetics Curriculum

tag: treatment


title: HIWI1_PARCLIP_rep1


title: TG_Spongy

city: pune

first: vineet

last: jha

state: Maharashtra

address: 9 A/12 Pingale Aryabhatta Persistent Tower,

department: LABS

country: India

institute: Persistent systems

description: Spongy fruit mesocarp of 5 days after harvest

data_processing:
Basecalls performed using CASAVA version 1.8.2
A merged de novo transcriptome was  generated using Velvet-Oases (k-mer 55)
Mapping by Bowtie 2 version 2.2.3
DESeq2 for differential gene expression

organism: Mangifera indica

source_name: Fruit mesocarp

extract_protocol:
Total RNA isolation was carried out for all the tissues sampled for current study using RNeasy Plus mini kit (Quiagen, Venlo, The Netherlands).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Alphonso

tag: tissue type

value: Mesocarp

tag: ripening stage

value: Table green


title: TG_Healthy

description: Healthy fruit mesocarp of 5 days after harvest


title: MiR_Spongy

description: Spongy fruit mesocarp of 10 days after harvest

value: Mid ripe


title: HIC_K562_4320min_biorep2_techrep1_seqrep1

value: Human leukemia


title: E14.5

source_name: Molar at embryonic day 14.5

tag: strain

value: molar


title: HIC_K562_0360min_biorep2_techrep1_seqrep1

value: WT


title: HIC_K562_0000min_biorep2_techrep1_seqrep1


title: HIC_K562_4320min_biorep1_techrep1_seqrep1


title: HIC_K562_0000min_biorep1_techrep1_seqrep1


title: HIC_K562_0360min_biorep1_techrep1_seqrep1


title: MiR_Healthy

description: Healthy fruit mesocarp of 10 days after harvest


title: ATAC Day_26_R1881_2

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

data_processing:
Sequenced samples were trimmed with Trimmomatic, mapped using Bowtie2 and replicate mapped files merged with SAM tools. Coverage files were generated with deepTools. Open chromatin chromatin was detected with MACS2 using a p value < 1x10-7 and a q value of less than 0.1 and differentially regulated regions identified with DiffBind using a 2-fold enrichment threshold and lower than 0.01 p value. Bed files were analyzed with Bedtools, and visualized alongside coverage files on IGV and Sparkpy.
Assembly: hg38
Supplementary files format and content: Genomic tracks as BigWig files

source_name: LNCaP

extract_protocol:
Libraries were prepared using the Nextera DNA library Prep Kit (Illumina) adapting a published protocol. Cells were washed in PBS and then lysed for 3 min in 10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630, 0.1% Tween-20, 0.01% Digitonin, 1% BSA (all SIGMA). Cold wash buffer (same as lysis buffer without Igepal and digitonin) was added to the lysate and mixed three times by inverting the tubes and immediately spun 500 x g for 5 min, 4°C. Supernatant was discarded and nuclei resuspended in 2.5 μl TDE1 (Nextera Tn5, 100 nM final), 0.5 μl 1% Digitonin (0.01% final), 0.5ul 10% Tween-20 (1% final) 16.5 μl PBS and 5 μl water and incubated for 30 min at 37°C with gentle mixing (1000 RPM).
DNA was purified with the QIAGEN MinElute PCR Purification Kit (Thermo Fisher Scientific). PCR amplification was performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs) using custom Nextera PCR Primers containing barcodes. Adaptors were removed with AMPure XP beads according to manufacturer’s protocol. Libraries were quantified with the Qubit and sequenced with a NovaSeq 6000 (Illumina).

value: LNCaP

tag: time point

value: Day 26


title: ATAC Day_26_R1881_1


title: ATAC Day_26_Veh_2

value: Vehicle


title: ATAC Day_5_R1881_2

value: Day 5