title: 4Sa_3D_4Sa5

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-G04

status: Public on May 12 2022

type: SRA

city: Cambridge

first: Karthik

last: Jagadeesh

state: MA

address: 415 Main St

department: Human Cell Atlas

country: USA

institute: Broad Institute

library_source: transcriptomic

data_processing:
Library strategy: NanoString whole-transcriptome digital spatial profiling
Process FASTQ sequencing files (from Illumina NGS run) to DCC digital count files using Nanostring GeoMx NGS Pipeline v1.0
Generate raw and normalized count matrices using Nanostring azorius and hydra scripts, as described in associated manuscript
Assembly: Nanostring GeoMx human whole transcriptome atlas; found in geomx_ngs_data_second_acquisition_WTA_Hs_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: Txt file of uncollapsed raw counts matrix; found in hPDAC_WTA_20210222T2101_TargetCountMatrix.txt
Supplementary files format and content: Txt file of bioprobe QC counts matrix; found in hPDAC_WTA_20210222T2101_BioProbeCountMatrix.txt
Supplementary files format and content: Txt file of negative probe normalized counts matrix; found in hPDAC_WTA_20210222T2101_NegNorm_TargetCountMatrix.txt
Supplementary files format and content: Txt file of q3 normalized counts matrix; found in hPDAC_WTA_20210222T2101_Q3Norm_TargetCountMatrix.txt

molecule: total RNA

organism: Homo sapiens

source_name: Pancreas

extract_protocol:
In brief, we sectioned clinical FFPE blocks at 5 um onto SuperFrost Plus microscopy slides and then followed the manufacturer instructions for RNA (NanoString) with minor modifications as noted in the associated manuscript.
Libraries were constructed according to manufacturer protocols (NanoString) for sequencing on a NovoSeq S2 (Illumina) with the following paired end read configuration: read 1, 27 nt; read 2, 27 nt; index 1, 8 nt; index 2, 8 nt.

treatment_protocol: 14 specimens received no treatment prior to resection; 7 specimens received neoadjuvant chemotherapy, radiotherapy, losartan, and/or nivolumab prior to resection

tag: tissue

value: Pancreas

tag: treatment / other annotation

value: Untreated


title: DSP-1001660004526-D-H11


title: sciRNA_lib-p1B8

city: Seattle

first: Anna

last: Minkina

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
rna_raw_cell_by_gene_counts.gz
p1B8-RNA_CCGTCGGAGG_S20

library_source: transcriptomic single cell

data_processing:
demultiplex using bcl2fastq
adaptor trimming using trim_galore
align to reference genome using STAR
reads deduplicated by UMIs
(All code available at: https://github.com/minkinaa/TheLorax)
sciRNA_lib:
Sequencing was performed as previously described (Cao et al. 2017). Reads were adapter-trimmed using trim_galore and aligned to the reference genome (hg38) using STAR. Non-unique mappers were removed. Reads were then deduplicated using a custom script (190223_sciRNA_remove_duplicates.cpp), taking into account both UMIs and cell indices to call a duplicated read. Only cells with at least 2048 deduplicated non-mitochondrial UMIs were used for subsequent analyses.
A custom script (190704_process_sciRNA_mapped_file.cpp) was used to map reads to genes. Reads which overlapped multiple genes but only fell in an exon in one gene were counted towards that gene.
RNA processing to generate the cell by gene raw counts file is implemented in script 190807_sciRNA_wrapper_ALL.txt, with user-defined UMI cutoff of 2^11.
sciATAC_lib:
For processing sci-ATAC-seq sequencing reads, we first compare observed and expected lists of single cell indices, correcting any indices with a likely off-by-one error. All reads are then adaptor trimmed using trimmomatic (parameters: TRAILING:3 SLIDINGWINDOW:4:10 MINLEN:20), and all reads associated with a single cell are then aligned to the genome using bowtie2 (hg38 genome build). Reads are then deduplicated by UMIs using a custom script (191226_CROPt_process_atac_bedfile.cpp). Both cell by gene and cell by interval counts were generated using a custom script (191226_CROPt_make_cell_by_interval_count_file.cpp).
Lineage_wRNA & Lineage_wATAC:
Processing of raw data to generate the categorical processed data file is described in associated manuscript ("Computational processing and edit calling from lineage target sequencing data") with all associated code at https://github.com/minkinaa/TheLorax.
Cell IDs found in the processed data file are related to raw fastq files as follows:
sciRNA_lib: Each fastq pair file contains information from 25 cells (or less). The cell IDs are a combination of the plate/batch, PCR well index (index #2) during combinatorial indexing (in fastq file name), and index #1, the last 10 bases of the read1 sequence. E.g. the raw data for the cell called "p1A10_ACTAATTGAG", can be found in the raw data file "p1A10-RNA_CCAGGTCTAC_S10", with those sequences with "ACTAATTGAG" as the last 10 bases in the R1 file corresponding to this cell. The first 8 bases of R1 are the UMI.
sciATAC_lib: Cell IDs corresponding to those found in the processed file can be found in the sequence name in the fastq (e.g. "@p2H1_TGAGCTACTT-R1.1" --> cell ID = "p2H1_TGAGCTACTT")
Lineage_wRNA & Lineage_wATAC: Cell IDs are related to fastq file names as described for "sciRNA_lib" except index #1 is located in positions 9-18 in the R1 fastq file. The first 8 bases of R1 are the UMI. Read structure is further describe in manuscript Materials & Methods, and at https://github.com/minkinaa/TheLorax.
A list of index #1's can be found in supplementary file "Index_1_List.txt".
Assembly: hg38
Supplementary files format and content: Tab-separated values, raw cell by gene/tss counts matrices

extract_protocol:
sci-RNA-seq: whole cells, methanol fixes; sci-ATAC-seq: nuclei
sci-RNA-seq-2level, sci-ATAC-seq2level, targeted lineage mRNA capture as described

tag: cell type

tag: data type

value: sci-RNA-seq


title: DSP-1001660004526-D-H02


title: DSP-1001660004526-D-H08


title: DSP-1001660004526-D-G11


title: Healthy Volunteer 2 - FA R1

city: New York

first: Shruti

last: Naik

state: NY

address: 435 East 30th Street

department: Pathology

institute: NYU Langone Health

description:
st_images.gz
Sample name: HV2_S1_R1
sample id v2: ST-HF-1

data_processing:
Sequencing output and the histology images were processed using space ranger software (10X Genomics).  The space ranger mkfastq function was used for sample demultiplexing and to converting spatial barcodes and reads into FASTQ format.
The space ranger count function was used to align reads from FASTQ files to human genome (hg38) and then align microscopic slide image and transcriptome to generate barcode/UMI counts, feature spot matrices, cluster data, and perform gene expression analysis.
Assembly: hg38
Supplementary files format and content: Filtered feature-barcode matrices (filtered_feature_bc_matrix) containing only spot barcodes in MEX format for each sample. Spatial folder output from space ranger count function containing QC images for aligned fiducials and detetected tissue in jpg format, scalefactors_json.json, high and low resolution versions of the input image in png format, and tissue_positions_list.csv.  All spatial outputs (Spatial image data) are stored in st_images.tar.gz.
Library strategy: spatial transcriptomics

source_name: Skin

growth_protocol: Three to four millimeter skin punch biopsies were obtained from lesional and non-lesional skin of healthy controls and subjects with psoriatic disease.

extract_protocol: Tissues were embedded in OCT and frozen in liquid nitrogen-chilled isopentane within 5 minutes of devascularization. 10-µm cryosections were mounted onto the ST arrays (10X Visium)  where reverse transcription of cellular transcripts took place in situ after tissue permeabilization.

treatment_protocol: Subjects were biologic-naïve (untreated)

tag: individual

value: Healthy Volunteer 2

value: Skin punch biopsy

tag: sequencing run / batch

tag: disease state

value: control

tag: disease status

value: Healthy

tag: pasi score


title: 4Sa_2D_4Sa55

city: Hangzhou

first: Xiaowen

last: Shi

state: Zhejiang

address: 866 Yuhangtang Road NongshenghuanA443

department: College of Agriculture and Biotechnology

country: China

institute: Zhejiang University

description:
rpm_miRNA.txt
results_counts_miRNA.txt

data_processing:
1. the 3' end of the reads was trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly-G using cutadapt version 1.16.
2. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q33 -q20 -p80).
3. Reads mapped to known structural RNAs (rRNAs, tRNAs, sn-RNAs, and sno-RNAs) from Rfam 14.0 using bowtie 2 were removed.
4. Reads of 18-30 nt without poly(A) tails were aligned to the maize reference genome W22v2, the maize chloroplast, and mitochondrial genomes.
5. Read counts were normarlized with RPM and differential gene expression analysis were performed via edgeR.
Supplementary_files_format_and_content: Tab-delimited text files include raw count table of mapped miRNA generated by ShortStack and RPM normalized counts.

organism: Zea mays

source_name: Leaf tissue

growth_protocol: 45-day grown in the greenhouse

extract_protocol:
Extracted by mirVana™ miRNA Isolation Kit
sRNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: diploid aneuploids, disomy, whole-ploidy, or b chromosome

value: diploid aneuploids comparison (TB-4Sa)


title: sciRNA_lib-p1B7

description:
rna_raw_cell_by_gene_counts.gz
p1B7-RNA_TGATTCCTCA_S19


title: DSP-1001660004526-D-F03


title: 4Sa_1D_4Sa53

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-F12


title: sciRNA_lib-p1B6

description:
rna_raw_cell_by_gene_counts.gz
p1B6-RNA_GTCGCTCAGT_S18


title: DSP-1001660004526-D-H10


title: DSP-1001660004526-D-H12


title: sciRNA_lib-p1B5

description:
rna_raw_cell_by_gene_counts.gz
p1B5-RNA_ACTCTCTCAA_S17


title: DSP-1001660004526-D-H07


title: 4Sa_1D_4Sa51

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-H06


title: DSP-1001660004526-D-H09


title: sciRNA_lib-p1B4

description:
rna_raw_cell_by_gene_counts.gz
p1B4-RNA_GGAACGATGG_S16


title: DSP-1001660004526-D-G12


title: 4Sa_1D_4Sa50

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1B3

description:
rna_raw_cell_by_gene_counts.gz
p1B3-RNA_GAACTGCATC_S15


title: DSP-1001660004526-D-H05


title: 8Lc_2D_8Lc23

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-8Lc)


title: DSP-1001660004526-D-H04


title: DSP-1001660004526-D-G10


title: DSP-1001660004526-D-H03


title: sciRNA_lib-p1D5

description:
rna_raw_cell_by_gene_counts.gz
p1D5-RNA_TCTAGAACTA_S41


title: sciRNA_lib-p1B2

description:
rna_raw_cell_by_gene_counts.gz
p1B2-RNA_GGACTCATTG_S14


title: DSP-1001660004526-D-G08


title: 4Sa_1D_4Sa52

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-F06


title: DSP-1001660004526-D-G09


title: sciRNA_lib-p1B1

description:
rna_raw_cell_by_gene_counts.gz
p1B1-RNA_TTAACGTACC_S13


title: DSP-1001660004526-D-G06


title: DSP-1001660004526-D-H01


title: sciRNA_lib-p1B12

description:
rna_raw_cell_by_gene_counts.gz
p1B12-RNA_TGAGGTAGAA_S24


title: 4Sa_2D_4Sa34

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 4Sa_3D_4Sa25

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1B11

description:
rna_raw_cell_by_gene_counts.gz
p1B11-RNA_TTGAGTATCA_S23


title: DSP-1001660004526-D-F09


title: DSP-1001660004526-D-E08


title: 1Sb_3D_1Sb7

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-1Sb)


title: sciRNA_lib-p1B10

description:
rna_raw_cell_by_gene_counts.gz
p1B10-RNA_CGAAGGACGA_S22


title: 4Sa_2D_4Sa43

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-G07


title: 1Sb_3D_1Sb6

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-F10


title: 4Sa_3D_4Sa42

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 1Sb_3D_1Sb4

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-E09


title: DSP-1001660004526-D-G02


title: sciRNA_lib-p1A7

description:
rna_raw_cell_by_gene_counts.gz
p1A7-RNA_TTAGATTCCG_S7


title: DSP-1001660004526-D-G05


title: sciRNA_lib-p1A8

description:
rna_raw_cell_by_gene_counts.gz
p1A8-RNA_GATCAGTCAT_S8


title: 1Sb_3D_1Sb2

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-G03


title: DSP-1001660004526-D-E12


title: DSP-1001660004526-D-D12


title: sciRNA_lib-p1A6

description:
rna_raw_cell_by_gene_counts.gz
p1A6-RNA_TGATAGAACG_S6


title: 1Sb_3Sb_5Lb_2D_1Sb26

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-1Sb, 3Sb, 5Lb)


title: DSP-1001660004526-D-G01


title: 1Sb_3Sb_5Lb_2D_1Sb25

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-F04


title: DSP-1001660004526-D-F07


title: 1Sb_1D_1Sb1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-F08


title: sciRNA_lib-p1A9

description:
rna_raw_cell_by_gene_counts.gz
p1A9-RNA_TCGATATTGA_S9


title: sciRNA_lib-p1A4

description:
rna_raw_cell_by_gene_counts.gz
p1A4-RNA_CTCGTCTAGG_S4


title: 1Sb_1D_1Sb18

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-E06


title: DSP-1001660004526-D-F05


title: DSP-1001660004526-D-E10


title: 1Sb_1D_1Sb17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-F01


title: DSP-1001660004526-D-E03


title: sciRNA_lib-p1A5

description:
rna_raw_cell_by_gene_counts.gz
p1A5-RNA_GCTCTAACGA_S5


title: DSP-1001660004526-D-F11


title: sciRNA_lib-p1A2

description:
rna_raw_cell_by_gene_counts.gz
p1A2-RNA_CGACTACCAA_S2


title: 1Sb_3Sb_5Lb_2D_1Sb16

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1A11

description:
rna_raw_cell_by_gene_counts.gz
p1A11-RNA_TTGGTCATAA_S11


title: DSP-1001660004526-D-D01


title: sciRNA_lib-p1A12

description:
rna_raw_cell_by_gene_counts.gz
p1A12-RNA_AACGGACCAA_S12


title: DSP-1001660004526-D-D10


title: DSP-1001660004526-D-F02


title: DSP-1001660004526-D-E11


title: 1Sb_3Sb_5Lb_2D_1Sb24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-E04


title: 6Lc_1D_6Lc9e

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-6Lc)


title: DSP-1001660004526-D-C04

value: CRT


title: sciRNA_lib-p1A10

description:
rna_raw_cell_by_gene_counts.gz
p1A10-RNA_CCAGGTCTAC_S10


title: 6Lc_3D_6Lc8H

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-E07


title: DSP-1001660004526-D-C10


title: sciRNA_lib-p1A1

description:
rna_raw_cell_by_gene_counts.gz
p1A1-RNA_CTCGATGGAG_S1


title: 6Lc_1D_6Lc8e

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-E02


title: 8Lc_3D_8Lc10

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-D04


title: 6Lc_3D_6Lc7H

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 1Sb_1D_1Sb14

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-E05


title: DSP-1001660004526-D-D08


title: 6Lc_2D_6Lc6e

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-C09


title: DSP-1001660004526-D-D11


title: DSP-1001660004526-D-C03


title: DSP-1001660004526-D-D06


title: DSP-1001660004526-D-D09


title: Cp190[0] 2-6 hour old embryos, rep2

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: Capture-C library

library_source: genomic

data_processing:
To extract the FASTQ read pairs corresponding to each of the captured regions, the sequence of the capture probes were split in consecutive 25-mers and a Perl script was used to scan all the read pairs from the raw fastq files and generate a specific pair of fastq files per region where either read of the pair has an exact match to one of the 25-mers.
The read pairs were mapped to the dm6 genome using STAR with parameters tuned to map the expected chimeric read pairs generated by the HiC protocol (--chimOutType WithinBAM, --chimSegmentMin 10, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.04, --scoreGapNoncan 0, --scoreGapGCAG 0, --scoreGapATAC 0, --alignIntronMax 1,  --chimScoreJunctionNonGTAG 0). Only chimeric read pairs (as defined by STAR) were retained, and likely PCR duplicates were discarded. Each read was assigned to the genomic region (fragment) defined by the nearest upstream and downstream restriction sites.
For each captured viewpoint per sample, only read pairs with at least one read mapping to the viewpoint restriction fragment or one of its 2 neighboring restriction fragments were retained. A vector of counts between the viewpoint and other regions on the genome was obtained by partitioning the genome into 1 kb bins (rounded to the nearest restriction site) and evaluating, for each bin, the number of read pairs with one end associated with the viewpoint and the other end restriction fragment overlapping the bin. Bins with center located <2 kb or >100 kb from the viewpoint restriction fragment center were discarded. For each sample, raw counts per bin were then scaled by dividing by the total number of remaining read pairs and multiplying by 10^6 to represent reads per million mapped reads (RPM) within ±100 kp windows around viewpoints.
Genome_build: dm6
Supplementary_files_format_and_content: Scaled number of read pairs (RPM) within ±100 kb window around the viewpoint restriction fragment (excluding the ±2 kb window around the viewpoint restriction fragment) in bedgraph format.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: 2-6 hour old embryos

growth_protocol: standard Drosophila culture at 25°C

extract_protocol:
100 embryos were dechorionated, then homogenized in RPMI supplemented with 10% fetal bovine serum with a micropestle. Cells were crosslinked then subjected to Hi-C, cutting sequentially with MseI and Csp6I restriction enzymes. Hi-C libraries underwent two successive rounds of capture with biotinylated capture probes.
NEBNext Ultra II DNA Library Prep kit for Illumina

treatment_protocol: Animals were not subjected to any particular treatment.

tag: strain

value: whole embryo

value: 2-6 hour old

tag: genotype


title: Cp190[0] 2-6 hour old embryos, rep3

description: Capture-C library


title: DSP-1001660004526-D-B03


title: Cp190[0] 2-6 hour old embryos, rep1

description: Capture-C library


title: SF1[KO] 2-6 hour old embryos, rep3

description: Capture-C library


title: DSP-1001660004526-D-D07


title: SF1[KO] 2-6 hour old embryos, rep1

description: Capture-C library


title: 6Lc_2D_6Lc1e

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1A3

description:
rna_raw_cell_by_gene_counts.gz
p1A3-RNA_GTTGACGGCC_S3


title: 6Lc_2D_6Lc2e

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 6Lc_2D_6Lc3e

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-B01


title: WT 2-6 hour old embryos, rep3

description: Capture-C library


title: DSP-1001660004526-D-E01


title: 6Lc_3D_6Lc3H

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: WT 2-6 hour old embryos, rep2

description: Capture-C library


title: DSP-1001660004526-D-D03


title: WT 2-6 hour old embryos, rep1

description: Capture-C library


title: SF1[KO] 2-6 hour old embryos, rep2

description: Capture-C library


title: DSP-1001660004526-D-C11


title: DSP-1001660004526-D-C06


title: DSP-1001660004526-D-D05


title: 5Lb_3D_5Lb48

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-5Lb)


title: DSP-1001660004526-D-B07


title: 6Lc_1D_6Lc12e

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: CapStarr_pR-Ea

city: Marseille

first: Nori

last: SADOUNI

address: 169 Avenue Luminy

country: France

institute: TAGC INSERM U1090

data_processing:
FastQ files were trimmed using sickle with -q 20 option and mapped to the mm9 reference genome using bowtie2 with default parameters
Sam files were converted using samtools to BAM files. BAM files of all replicates were pooled and converted into bed files using BedTools (v2.28.0)
Input and cDNA files were concatenated into a reference file using cat from bash. Reads were reduced to 1bp.
Number of occurrence of each unique read was calculated using the reference file and BedTools intersect with -c option to count each overlap. Then reads length was restored to original captured fragments size
Activity of each fragments (= reads) is computed using cDNA count / input count normalized by number of reads
Assembly: mm9
Supplementary files format and content: bed

molecule: polyA RNA

organism: Mus musculus

source_name: P5424 Cell line

growth_protocol: Mouse P5424 T cells were cultured in RPMI medium supplemented with 10% FBS (PAA) at 37 °C, 5% CO2.

extract_protocol: Library preparation was carried out as per manufacturer’s instructions (Illumina). Samples were subsequently size-selected via gel migration and extraction, with average cut sizes at about 400bp. Sequencing was carried out on an Illumina NextSeq 500. The quality of libraries was checked with the Bioanalyser DNA High sensitivity and by Q-PCR.

treatment_protocol: PMA/Ionomycin

tag: cell amout

tag: cell line

value: P5424 Cell line


title: DSP-1001660004526-D-A10

value: Pancreas


title: CapStarr_pPGK_PMA_I

treatment_protocol:
PMA/I
PMA/Ionomycin


title: CapStarr_pPGK, input


title: DSP-1001660004526-D-D02

value: Untreated


title: DSP-1001660004526-D-B11


title: 6Lc_3D_6Lc10H

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 6Lc_1D_6Lc11e

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-A12


title: DSP-1001660004526-D-C07


title: DSP-1001660004526-D-C05


title: 5Lb_1D_5Lb23

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-C12


title: DSP-1001660004526-D-B05


title: CapStarr_pR-Ea, input


title: 5Lb_3D_5Lb1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 5Lb_1D_5Lb28

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 5Lb_3D_5Lb18

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-B04


title: CapStarr_pPGK


title: DSP-1001660004526-D-A11


title: liver_PtenE2f78TKO_3 [TKO_b4]

city: Utrecht

first: Bart

last: Westendorp

address: Uppsalalaan 8

department: Molecular Health Sciences

country: Netherlands

institute: Utrecht University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BWA
Trimmed sequence reads were mapped to GrCM38/mm10 using BWA
Mapped reads were counted with the R package GenomicAlignments
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver

extract_protocol:
Frozen pieces of ~100 mg liver tissue were pulverized on dry ice and RNA was extracted using Quagen's Rneasy kit.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq PolyA kit (illumina).

treatment_protocol: Livers from conditional knockout mice aged 16 weeks were obtained by taking out the livers immediately from euthanized animals, and flash-freezing the tissue using liquid nitrogen

value: liver

value: bulk tissue

value: Alb-Cre-Pten/E2f7/E2f8 knockout

value: 16 weeks


title: DSP-1001660004526-D-A06


title: DSP-1001660004526-D-C02


title: DSP-1001660004526-D-B12


title: DSP-1001660004526-D-C01


title: DSP-1001660004526-D-B10


title: DSP-1001660004526-D-B09


title: DSP-1001660004526-D-B06


title: 5Lb_1D_5Lb26

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 5Lb_1D_5Lb27

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: liver_PtenE2f78TKO_1 [TKO_b1]


title: DSP-1001660004525-B-H07


title: CapStarr_SCP1, input


title: DSP-1001660004526-D-B08


title: DSP-1001660004526-D-A09


title: 5Lb_3D_5Lb17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-A04


title: liver_PtenE2f78TKO_2 [TKO_b2]


title: 3Sb_3D_3Sb5

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-3Sb)


title: liver_PtenE2f78TKO_4 [TKO_b5]


title: DSP-1001660004525-B-H05


title: liver_PtenKO_2 [PtenKO_v2]

value: Alb-Cre Pten knockout


title: DSP-1001660004525-B-H12


title: DSP-1001660004526-D-A07


title: DSP-1001660004525-B-F11


title: 3Sb_1D_3Sb24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-A08


title: DSP-1001660004526-D-A03


title: 3Sb_1D_3Sb6

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004526-D-B02


title: 3Sb_3D_3Sb8

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-H10


title: CapStarr_SCP1


title: 3Sb_1D_3Sb25

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 3Sb_1D_3Sb21

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-H02


title: liver_PtenKO_1 [PtenKO_b3]


title: DSP-1001660004526-D-A05


title: 3Sb_3D_3Sb1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: liver_control_4 [con_w1]

value: Alb-Cre control


title: liver_PtenKO_3 [PtenKO_v3]


title: liver_control_3 [con_v4]


title: liver_PtenKO_4 [PtenKO_w2]


title: 3Sb_3D_3Sb2

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: liver_control_1 [con_p2]


title: DSP-1001660004526-D-C08


title: DSP-1001660004526-D-A01

value: No Template Control


title: DSP-1001660004525-B-H11


title: 4Lb_1D_4Lb30

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-4Lb)


title: DSP-1001660004526-D-A02


title: liver_control_2 [con_q2]


title: DSP-1001660004525-B-H08


title: DSP-1001660004525-B-G11


title: liver_E2f78DKO_2 [78DKO_q1]

value: Alb-Cre E2f7/E2f8 knockout


title: 4Lb_2D_4Lb35

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: liver_E2f78DKO_4 [78DKO_q4]


title: DSP-1001660004525-B-H03

value: CRT


title: DSP-1001660004525-B-H09


title: liver_E2f78DKO_3 [78DKO_q3]


title: DSP-1001660004525-B-H06


title: DSP-1001660004525-B-G10


title: DSP-1001660004525-B-G12


title: 4Lb_2D_4Lb37

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 4Lb_1D_4Lb28

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: KO_d3_rep3

city: Münster

first: Marisol

last: Herrera-Rivero

state: NRW

address: Albert-Schweitzer-Campus 1

country: Germany

institute: University of Münster

description: ATAC-seq

data_processing:
Sequence analysis was performed by mapping the paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing (using NextSeq 500) to the genome using the BWA algorithm with default settings (“bwa mem”). Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) were removed. BAM files were used to perform peak calling with MACS2, using paired-end mode with a bandwidth of 200 and q-value cutoff of 0.01. BedGraph files were converted to BigWig format for visualization with the Integrative Genomics Viewer (IGV) using bedGraphToBigWig. Differential accessibility analyses for all possible comparisons between WT and/or C/EBPδ KO in day 0 and day 3 groups were carried out with GUAVA v1. Differential peaks were defined as those merged intervals within a window of 5000 bp upstream and 3000 bp downstream of the transcription start site (TSS) showing an adjusted p-value < 0.05 and log2 fold change ≥ ±1.5.
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol: Precursor and day 3 differentiated WT and C/EBPδ KO ER-Hoxb8 cells were harvested, washed and cryopreserved in 50% FBS/ 40% growth media/ 10% DMSO using a freezing container at -80 °C overnight. Sequence analysis was performed by mapping the paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing (using NextSeq 500) to the genome using the BWA algorithm with default settings (“bwa mem”).

value: differentiated


title: DSP-1001660004525-B-H01


title: 4Lb_2D_4Lb25

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: liver_E2f78DKO_1 [78DKO_p1]


title: DSP-1001660004525-B-G09


title: 4Lb_1D_4Lb27

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-G07


title: 4Lb_1D_4Lb26

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-G08


title: DSP-1001660004525-B-G02


title: DSP-1001660004525-B-F07


title: KO_d3_rep2

description: ATAC-seq


title: DSP-1001660004525-B-E10

value: CRTl


title: 4Lb_2D_4Lb24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-G01


title: DSP-1001660004525-B-G04


title: 4Lb_3D_4Lb20

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-D12


title: KO_d0_rep3

description: ATAC-seq

value: precursor


title: DSP-1001660004525-B-G05


title: 4Lb_3D_4Lb19

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-E09


title: DSP-1001660004525-B-G06


title: KO_d0_rep1

description: ATAC-seq


title: KO_d0_rep2

description: ATAC-seq


title: KO_d3_rep1

description: ATAC-seq


title: DSP-1001660004525-B-F08


title: DSP-1001660004525-B-F01


title: DSP-1001660004525-B-G03


title: 4Lb_3D_4Lb15

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: WT_d3_rep1

description: ATAC-seq

value: WT


title: DSP-1001660004525-B-F03

value: Pancreas


title: DSP-1001660004525-B-F05


title: DSP-1001660004525-B-F10


title: 3La_2D_3La9

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-3La)


title: DSP-1001660004525-B-F06


title: 3La_2D_3La8

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-E06


title: 3La_1D_3La36

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 3La_1D_3La30

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: WT_d3_rep2

description: ATAC-seq


title: DSP-1001660004525-B-F12


title: 4Lb_3D_4Lb17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: WT_d0_rep3

description: ATAC-seq


title: 3La_2D_3La5

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-F09


title: WT_d0_rep2

description: ATAC-seq


title: WT_d3_rep3

description: ATAC-seq


title: DSP-1001660004525-B-E05


title: 3La_3D_3La24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-E03


title: DSP-1001660004525-B-E12


title: Ctrl_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

description: freshly isolated MuSCs

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.7.10a  with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 20 --alignIntronMax 200000" (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Duplicate reads were removed with Picard 2.25.5 (https://github.com/broadinstitute/picard).
The number of reads aligning to genes was counted with featureCounts 2.0.2 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
A combined raw count matrix was produced and used for differential expression analysis using DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10 / GRCm38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Muscle stem cells

growth_protocol: Freshly isolated MuSCs

extract_protocol:
For RNA-seq, RNA was isolated from 100-200 FACS sorted satellite cells using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent).
All isolated RNA (1-5ng) was then used as input for ribosomal depletion with RiboGone-Mammalian (Takara Bio) followed by library preparation using SMARTer Stranded Total RNA Sample Prep Kit (Takara Bio). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry with 1x75bp single end setup.

value: Muscle stem cells

tag: mouse strain

value: Wild type


title: WT_d0_rep1

description: ATAC-seq


title: DSP-1001660004525-B-F04


title: Ctrl_2

description: freshly isolated MuSCs


title: DSP-1001660004525-B-D02


title: 3La_3D_3La21

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-E01


title: DSP-1001660004525-B-E08


title: DSP-1001660004525-B-E11


title: Ctrl_1

description: freshly isolated MuSCs


title: DSP-1001660004525-B-C10


title: DSP-1001660004525-B-D01


title: 3La_3D_3La22

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Sirt6mKO_2

description: freshly isolated MuSCs


title: DSP-1001660004525-B-E02


title: 3La_2D_3La1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-F02


title: Sirt6mKO_3

description: freshly isolated MuSCs


title: DSP-1001660004525-B-E07


title: DSP-1001660004525-B-D11


title: 3La_1D_3La17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-E04


title: 3La_3D_3La19

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-D07


title: Muscle_Sirt6-mKO_3

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38.p5) using STAR 2.6.1d with parameters “--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignMatesGapMax 2000 --alignIntronMax 200000” (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.3 from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: mm10 / GRCm38
Supplementary_files_format_and_content: Tab-delimited matrix with DESeq normalized gene counts.

source_name: Muscle tissue

extract_protocol:
Total RNA was isolated from muscle tissue using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen)
300 ng of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme)

value: mdx, Sirt6-mKO


title: 10L18_3D_10L80

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-10L18)


title: 3La_1D_3La16

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Muscle_Sirt6-mKO_2


title: DSP-1001660004525-B-C03


title: DSP-1001660004525-B-D05


title: DSP-1001660004525-B-D04


title: DSP-1001660004525-B-D08


title: 10L18_3D_10L76

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-D09


title: Muscle_Sirt6-mKO_1


title: DSP-1001660004525-B-D10


title: Muscle_mdx_3

value: mdx


title: 10L18_3D_10L74

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-B02


title: DSP-1001660004525-B-D06


title: DSP-1001660004525-B-B07


title: 10L18_3D_10L59

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Sirt6mKO_1

description: freshly isolated MuSCs


title: 10L18_2D_10L38

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-B10


title: Muscle_mdx_2


title: DSP-1001660004525-B-H04


title: DSP-1001660004525-B-C06


title: DSP-1001660004525-B-C01


title: Muscle_mdx_1


title: 10L18_4D_10L34

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-C12


title: Muscle_Control_3

value: wild type


title: DSP-1001660004525-B-C11


title: DSP-1001660004525-B-D03


title: DSP-1001660004525-B-C09


title: Muscle_Control_2


title: 10L18_4D_10L26

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 10L18_2D_10L30

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 10L18_4D_10L32

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Nupr1_KO_HSCs_4

city: Guangzhou

first: Tongjie

last: Wang

address: No.190 Kaiyuan Road

institute: Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences

data_processing:
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to mm10 genome by HISAT2 and generated raw counts values by featureCounts of Subread package.
Gene expression levels of different saMacles were normalized by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw count table was a csv file
Supplementary_files_format_and_content: gene expression value

source_name: HSCs

growth_protocol: All mice in this study were kept in C57BL/6J backgroud. HSCs were sorted from wild type mice and Nupr1-/- mice.

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA is based on published methods(PMID:20203668).
Libraries were prepared according to Illumina's instructions accompanying the  illumina Nextera XT DNA Sample Preparation Kit (FC-131-1096).

treatment_protocol: Target cells were sorted from the bone marrow nucleated cells.

value: Bone marrow

tag: genotype/variation


title: Nupr1_KO_HSCs_3

tag: tissue


title: DSP-1001660004525-B-C07

tag: treatment / other annotation


title: 10L18_2D_10L1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 10L18_4D_10L13

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-B08


title: Muscle_Control_1


title: DSP-1001660004525-B-A06


title: DSP-1001660004525-B-C04


title: DSP-1001660004525-B-C08


title: DSP-1001660004066-H-C02

value: CRTln


title: Nupr1_KO_HSCs_2


title: DSP-1001660004525-B-A12


title: DSP-1001660004525-B-C05


title: DSP-1001660004525-B-C02


title: Nupr1_KO_HSCs_1


title: 10L18_1D_10L106

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: WT_HSCs_4

value: Wildtype


title: DSP-1001660004525-B-A10


title: 10L18_1D_10L103

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-B06


title: WT_HSCs_3


title: DSP-1001660004525-B-B11


title: DSP-1001660004525-B-B04


title: WT_HSCs_2


title: 10L18_1D_10L101

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 10L18_2D_10L10

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-A08


title: WT_HSCs_1


title: 4X_2C_Z62

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: whole-ploidy comparison(tetraploid)


title: DSP-1001660004525-B-B12

value: CRT


title: DSP-1001660004525-B-B03


title: 10L18_1D_10L102

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 4X_2C_Z61

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: KPPC PDAC cell line

city: Houston

first: Yang

last: Chen

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

data_processing:
STAR
HTSEQ
DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Mouse pancreatic cancer cell total RNA

growth_protocol: Cancer cells cultured in DMEM with 10%FBS and 1% PS

extract_protocol:
Direct-zol RNA extraction kit (Zymo)
Illumina TrueSeq stranded mRNAseq Library

treatment_protocol: Cells received no treatment

value: KPPC

tag: detailed genotype


title: DSP-1001660004525-B-B09


title: DSP-1001660004525-B-A04


title: scRNAseq

city: Shanghai

first: Zhe

state: Shanghai

address: Siping Road, Shanghai

institute: Tongji university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebrospinal fluid cells

extract_protocol:
Cerebrospinal fluid cells were isolated by Fluorescence-activated cell sorting (FACS)
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell type

value: Cerebrospinal fluid cells


title: DSP-1001660004066-H-C08


title: DSP-1001660004525-B-A07


title: DSP-1001660004525-B-A11


title: DSP-1001660004525-B-B05


title: 4X_2C_Z63

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: KPPC;Col1pdxKO PDAC cell line


title: DSP-1001660004066-H-A10


title: DSP-1001660004525-B-A02


title: DSP-1001660004525-B-A09


title: DSP-1001660004066-H-C06


title: DSP-1001660004066-H-B05


title: SKBR3 Breast siGCDH Rep1

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

state: CA

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina Truseq adapter, polyA, and polyT sequences were trimmed using cutadapt version 2.3.
Trimmed reads were aligned to human genome version hg38 and Ensembl gene annotations version 84 using STAR aligner version 2.7.0d_0221 and ENCODE long RNA-seq pipeline parameters (https://github.com/ENCODE-DCC/long-rna-seq-pipeline). Gene expression levels were quantified using RSEM version 1.3.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited table with normalized gene expression (TPM)

growth_protocol: For RNA-seq analysis, 0.3-0.5x105 cells were seeded O/N in triplicate in 6-well plate before transfection. Cells were harvested 48 hr after siGCDH transfection for studies designed to analyze gene expression changes upon inhibition of GCDH protein expression.

extract_protocol:
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).
Following transfection for 48 hr, total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).

tag: treatment

value: siGCDH


title: SKBR3 Breast siGCDH Rep2


title: 4X_4C_Z54

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 4X_4C_Z47

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 4X_4C_Z38

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004525-B-B01


title: DSP-1001660004066-H-C04


title: DSP-1001660004525-B-A05


title: 4X_4C_Z30

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: SKBR3 Breast siControl Rep3

value: siControl


title: SKBR3 Breast siControl Rep2


title: 4X_2C_Z14

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: SKBR3 Breast siGCDH Rep3


title: 200491250039_R05C01

type: genomic

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

institute: IARC

description:
200491250039_R05C01_Grn.idat
200491250039_R05C01_Red.idat

hyb_protocol: 500 ng of bissulfite-modified DNA were hybridized to Illumina Infinium 450K beadchip assay

scan_protocol: Arrays were imaged with standard recommended Illumina sacanner settings

data_processing:
Idat files were loaded into R and analyzed using R/Biocondutor packages (minfi, limma)
Processed data files include: Normalized betas (FunNorm normalisation - minf R package). Probres were filtered out for cross-reactive probes and XY chromosomes

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: DNA Mini Qiasymphony kit (Qiagen)

treatment_protocol: All samples are prior to any treatment

value: melanoma

tag: histological type

tag: gender

value: M

tag: uv signature

value: No

tag: specimen type

value: Primary


title: SKBR3 Breast siControl Rep1


title: DSP-1001660004066-H-B10

value: Pancreas


title: 200491250024_R01C01

description:
200491250024_R01C01_Grn.idat
200491250024_R01C01_Red.idat

tag: disease state

value: F


title: DSP-1001660004066-H-A06


title: 1X_1C_H23

description:
rpm_miRNA.txt
results_counts_miRNA.txt

tag: age

tag: diploid aneuploids, disomy, whole-ploidy, or b chromosome

value: whole-ploidy comparison(haploid)


title: DSP-1001660004066-H-C07


title: 200491250034_R06C01

description:
200491250034_R06C01_Grn.idat
200491250034_R06C01_Red.idat

value: Metastasis


title: DSP-1001660004066-H-A05


title: SK-Hep1 Liver siGCDH Rep3


title: DSP-1001660004066-H-C05


title: DSP-1001660004525-B-A01

value: No Template Control


title: DSP-1001660004066-H-B12

value: CRTln


title: SK-Hep1 Liver siGCDH Rep2


title: 1X_1C_H21

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 1X_2C_D26

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: SK-Hep1 Liver siGCDH Rep1


title: DSP-1001660004525-B-A03


title: 1X_1C_H25

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 200491250045_R04C01

description:
200491250045_R04C01_Grn.idat
200491250045_R04C01_Red.idat


title: 200491250046_R06C02

description:
200491250046_R06C02_Grn.idat
200491250046_R06C02_Red.idat


title: 200491250017_R04C02

description:
200491250017_R04C02_Grn.idat
200491250017_R04C02_Red.idat


title: SK-Hep1 Liver siControl Rep3


title: DSP-1001660004066-H-B08


title: SK-Hep1 Liver siControl Rep2


title: 200491250017_R02C01

description:
200491250017_R02C01_Grn.idat
200491250017_R02C01_Red.idat


title: DSP-1001660004066-H-C03


title: 1X_1C_H22

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004066-H-A11


title: SK-Hep1 Liver siControl Rep1


title: DSP-1001660004066-H-A09


title: 200491250045_R02C01

description:
200491250045_R02C01_Grn.idat
200491250045_R02C01_Red.idat


title: A375 Melanoma siGCDH Batch2 Rep3


title: DSP-1001660004066-H-C01


title: A375 Melanoma siGCDH Batch2 Rep2


title: 1X_2C_D25

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 5Sc_2D_5SCS6

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-5Sc)


title: 200491250048_R05C02

description:
200491250048_R05C02_Grn.idat
200491250048_R05C02_Red.idat


title: A375 Melanoma siGCDH Batch2 Rep1


title: 5Sc_1D_5SCS5

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 200491250034_R04C01

description:
200491250034_R04C01_Grn.idat
200491250034_R04C01_Red.idat


title: 200491250017_R05C01

description:
200491250017_R05C01_Grn.idat
200491250017_R05C01_Red.idat


title: 1X_2C_D22

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: A375 Melanoma siControl Batch2 Rep3


title: A375 Melanoma siControl Batch2 Rep2


title: 200491250047_R06C01

description:
200491250047_R06C01_Grn.idat
200491250047_R06C01_Red.idat


title: 5Sc_2D_5SCS4

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004066-H-B11


title: 200491250046_R05C01

description:
200491250046_R05C01_Grn.idat
200491250046_R05C01_Red.idat


title: DSP-1001660004066-H-A12


title: 5Sc_2D_5SCS3

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: A375 Melanoma siControl Batch2 Rep1


title: DSP-1001660004066-H-B09


title: 5Sc_3D_5SCS42

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004066-H-B04


title: 5Sc_3D_5SCS8

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 200491250039_R02C02

description:
200491250039_R02C02_Grn.idat
200491250039_R02C02_Red.idat


title: A375 Melanoma siGCDH Batch1 Rep3

extract_protocol:
Libraries were prepared from total RNA using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen. Barcoded libraries were pooled and single end sequenced (1×75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).
Following transfection for 48 hr, total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).


title: 5Sc_4D_5SCS38

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 1X_2C_D21

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 200491250034_R01C01

description:
200491250034_R01C01_Grn.idat
200491250034_R01C01_Red.idat


title: 5Sc_4D_5SCS34

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 200491250048_R03C01

description:
200491250048_R03C01_Grn.idat
200491250048_R03C01_Red.idat


title: DSP-1001660004066-H-B06


title: A375 Melanoma siGCDH Batch1 Rep1


title: 200491250039_R01C02

description:
200491250039_R01C02_Grn.idat
200491250039_R01C02_Red.idat


title: DSP-1001660004064-F-H08


title: 5Sc_4D_5SCS30

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 5Sc_3D_5SCS25

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004066-H-B03


title: 200491250034_R03C02

description:
200491250034_R03C02_Grn.idat
200491250034_R03C02_Red.idat

value: Cutaneous


title: A375 Melanoma siControl Batch1 Rep2


title: 200491250024_R03C02

description:
200491250024_R03C02_Grn.idat
200491250024_R03C02_Red.idat

value: Yes


title: DSP-1001660004066-H-A07


title: 200491250039_R01C01

description:
200491250039_R01C01_Grn.idat
200491250039_R01C01_Red.idat


title: 5Sc_4D_5SCS20

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 5Sc_3D_5SCS24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: A375 Melanoma siGCDH Batch1 Rep2


title: A375 Melanoma siControl Batch1 Rep1


title: 5Sc_1D_5SCS18

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Kidney Organoids ACE2 KO G7

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

data_processing:
Demultiplexing, alignment to the Homo sapiens (hg38) genome and quantification using the annotation from Ensembl v93 was performed using 10X Genomics Cell Ranger (v4.0.0)
Downstream analysis steps (quality control filtering, normalization, integration, clustering and differential expression) were performed using the R package Seurat (v3.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix containing a Gene x Cells UMI count matrix

source_name: Human Kidney Organoid

growth_protocol: hPSCs were maintained in Essential 8 medium (Life Technologies #A1517001) in p10 culture plates coated with vitronectin (Fisher Scientific S.L. A14700) in a 37ºC incubator with 5% CO2 and were passaged every 5-6 days.

extract_protocol:
After the indicated treatments kidney organoids were collected and washed twice with PBS, and further dissociated into a single cell suspension by treating them with Accumax (07921, Stem Cell Technologies) for 15 min at 37ºC followed by Trypsin-EDTA 0.25% (wt/vol) trypsin (25300-054, Life Technologies)  for additional 15 min at 37ºC. The reaction was deactivated by adding 10% FBS. The cell suspension was then passed through a 40μm cell strainer. After centrifugation at 1,000 RPM for 5 minutes cell numbers and viability were analyzed using Countess Automated Cell Counter (Invitrogen). This method generated single cell suspension with greater than 90% viability. Cell suspensions were frozen until further use. For library construction cells were thawed and centrifuged at 1,000 RPM for 5 minutes. Cell numbers and viability were analyzed using Countess Automated Cell Counter (Invitrogen) and cell suspensions were loaded onto a well of a 10X Chromium Single Cell instrument. Barcoding and cDNA synthesis were performed according to the manufacturer´s instructions. The cDNA libraries were constructed using the 10X Chromium Single cell 3' Library Kit v3 according to the manufacturer's original protocol and sequenced either with a NovaSeq 6000 (R1:28,R2:94,i7:8) or a NextSeq 500 (R1:28, R2:55, i7:8) instrument.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hPSCs grown on vitronectin were washed twice with PBS (Life Technologies #1001-015) and dissociated into small clusters with EDTA (Sigma #E9884). Cells were then seeded onto vitronectin pre-coated culture dishes at a density of 50.000-150.000 cells per cm2 in Essential 8 Medium. After overnight culture, the differentiation was initiated (day -4) by treatment with 8µM CHIR99021 (Sigma #SML1046-5MG) in basic differentiation medium [Advanced RPMI 1640(Life technologies #12633-012) + 1 × 1-GlutaMAX (Life Technologies #35050-038) + Penicillin/Streptomycin (Life Technologies #15140122)] for 3 days. On day -1, CHIR99021 was removed by washing once with PBS and cells were exposed to 200 ng ml-1 FGF9 (PeproTech House#100-23B), 1 µ ml -1 Heparin (Sigma#H3149-10KU) and 10 ng ml-1 Activin A (Vitro S.A #338-AC-050) in basic differentiation media for 24h. On day 0, cells were mechanically dissociated into single cells and resuspended in basic differentiation medium supplemented with 3μM CHIR99021, 200 ng ml-1 FGF9 and 1µg ml-1 Heparin. Cells were then placed in 96-well, round bottom, ultra-low attachment plates at a density of 500.000 cells per well. Cells were spun down at x300g for 2 min form a pellet and then cultured at 37ºC, 5% CO2 for 2 days additional days without media change. On day 2, the pellets were transferred onto a Transwell 0.4µm pore polyester membrane (Sigma#3460) and treated with basic differentiation media supplemented with 3μM CHIR99021, 200 ng ml-1 FGF9 and 1µg ml-1 Heparin. On day 3, CHIR99021 was removed and the organoids were switched to basic differentiation media supplemented with 200 ng ml-1 FGF9 and 1µg ml-1 Heparin for another 4 days. From that point, organoids were cultured in basic differentiation medium and maintained without additional growth factors. For experiments employing glucose challenge, day 16 kidney organoids were diexposed to low glucose DMEM (ThermoFisher) supplemented with 1% Penicillin-Streptomycin for 6h (starvation period). After this time, normoglycemic conditions were assessed exposing organoids into DMEM supplemented with 5mM D-Glucose changing medium every day until day 23. Hyperglycaemic-like organoids were incubated with DMEM supplemented with 5mM D-Glucose on even days or with 25mM of D-Glucose on odd days until day 23 (5-25mM oscillatory hyperglycaemic condition).

value: kidney organoid

value: ACE2 KO


title: DSP-1001660004066-H-B07

extract_protocol:
In brief, we sectioned clinical FFPE blocks at 5 um onto SuperFrost Plus microscopy slides and then followed the manufacturer instructions for RNA (NanoString) with minor modifications as noted in the associated manuscript.
Libraries were constructed according to manufacturer protocols (NanoString) for sequencing on a NovoSeq S2 (Illumina) with the following paired end read configuration: read 1, 27 nt; read 2, 27 nt; index 1, 8 nt; index 2, 8 nt.


title: 200491250047_R02C02

description:
200491250047_R02C02_Grn.idat
200491250047_R02C02_Red.idat


title: DSP-1001660004066-H-B02


title: 200491250047_R05C02

description:
200491250047_R05C02_Grn.idat
200491250047_R05C02_Red.idat


title: DSP-1001660004064-F-H02

value: CRT


title: OX_PDC22_A1B3_068_E1

city: Oxford

first: Lars

last: Fugger

address: The MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

country: United Kingdom

institute: University of Oxford

data_processing:
ST pipeline v1.5.1 available from https://github.com/SpatialTranscriptomicsResearch/st_pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: Count data was saved as sparse matrix in the Market Exchange Format (MEX)
Supplementary_files_format_and_content: Tissue coordinates for each spot transcriptome were derived using ST Spot Detector v 2.0.2 available from https://github.com/SpatialTranscriptomicsResearch/st_spot_detector and are provided together with spatial annotations as csv file
Supplementary_files_format_and_content: Microscopy images of HE stained brain tissue linked to spot transcriptomes are provided as png files

source_name: Contr. brain 2

extract_protocol:
Fresh-frozen brain tissues from SPMS patients and non-MS controls used in this study were provided by the UK Multiple Sclerosis Society Tissue Bank at Imperial College London
Spatial transcriptomics as previously described by Stahl et al. 2016

value: brain cortex

value: HI

tag: ChIP

tag: well


title: Kidney organoids ACE2 WT B10

value: ACE2 WT


title: 5Sc_2D_5SCS17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: A375 Melanoma siControl Batch1 Rep3

tag: cell line

value: siControl


title: 200491250039_R02C01

description:
200491250039_R02C01_Grn.idat
200491250039_R02C01_Red.idat

value: melanoma

value: M

value: No


title: 5Sc_1D_5SCS11

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: OX_PDC22_A1B3_068_D2


title: OX_PDC22_A1B3_068_D1


title: 200491250024_R05C01

description:
200491250024_R05C01_Grn.idat
200491250024_R05C01_Red.idat

value: Primary


title: DSP-1001660004066-H-A02

data_processing:
Library strategy: NanoString whole-transcriptome digital spatial profiling
Process FASTQ sequencing files (from Illumina NGS run) to DCC digital count files using Nanostring GeoMx NGS Pipeline v1.0
Generate raw and normalized count matrices using Nanostring azorius and hydra scripts, as described in associated manuscript
Assembly: Nanostring GeoMx human whole transcriptome atlas; found in geomx_ngs_data_second_acquisition_WTA_Hs_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: Txt file of uncollapsed raw counts matrix; found in hPDAC_WTA_20210222T2101_TargetCountMatrix.txt
Supplementary files format and content: Txt file of bioprobe QC counts matrix; found in hPDAC_WTA_20210222T2101_BioProbeCountMatrix.txt
Supplementary files format and content: Txt file of negative probe normalized counts matrix; found in hPDAC_WTA_20210222T2101_NegNorm_TargetCountMatrix.txt
Supplementary files format and content: Txt file of q3 normalized counts matrix; found in hPDAC_WTA_20210222T2101_Q3Norm_TargetCountMatrix.txt

value: Pancreas


title: 5Sc_1D_5SCS10

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004066-H-B01


title: OX_PDC22_A1B3_068_C2


title: 6Sa_4D_6SA50

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-6Sa)


title: 200491250045_R02C02

description:
200491250045_R02C02_Grn.idat
200491250045_R02C02_Red.idat

value: Metastasis


title: DSP-1001660004064-F-H06


title: OX_PDC22_A1B3_068_C1


title: DSP-1001660004066-H-A08

value: CRTln


title: 200491250034_R02C02

description:
200491250034_R02C02_Grn.idat
200491250034_R02C02_Red.idat

value: Cutaneous


title: 6Sa_3D_6SA38

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 200491250046_R02C02

description:
200491250046_R02C02_Grn.idat
200491250046_R02C02_Red.idat

value: F


title: OX_342_P5B4_067_E2

source_name: MS brain 1

value: MS


title: DSP-1001660004066-H-A04


title: 6Sa_3D_6SA33

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 6Sa_4D_6SA32

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: OX_342_P5B4_067_E1


title: DSP-1001660004066-H-A03


title: 200491250046_R01C02

description:
200491250046_R01C02_Grn.idat
200491250046_R01C02_Red.idat


title: DSP-1001660004064-F-H07


title: DSP-1001660004064-F-H10


title: 200491250047_R02C01

description:
200491250047_R02C01_Grn.idat
200491250047_R02C01_Red.idat


title: DSP-1001660004064-F-G11


title: OX_342_P5B4_067_C2


title: 6Sa_4D_6SA61

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004064-F-G08


title: 6Sa_3D_6SA29

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 200491250048_R05C01

description:
200491250048_R05C01_Grn.idat
200491250048_R05C01_Red.idat

value: Yes


title: 6Sa_4D_6SA25

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 6Sa_3D_6SA30

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: OX_342_P5B4_067_C1


title: 200491250017_R03C01

description:
200491250017_R03C01_Grn.idat
200491250017_R03C01_Red.idat


title: 200491250034_R05C01

description:
200491250034_R05C01_Grn.idat
200491250034_R05C01_Red.idat


title: 200491250048_R01C02

description:
200491250048_R01C02_Grn.idat
200491250048_R01C02_Red.idat


title: DSP-1001660004064-F-H09

value: CRT


title: DSP-1001660004064-F-H12


title: OX_530_P2F2_061_E1

source_name: MS brain 6

value: brain cortex


title: OX_342_P5B4_067_D2


title: OX_342_P5B4_067_D1


title: DSP-1001660004064-F-G05

value: Untreated


title: 200491250039_R05C02

description:
200491250039_R05C02_Grn.idat
200491250039_R05C02_Red.idat


title: 200491250045_R01C02

description:
200491250045_R01C02_Grn.idat
200491250045_R01C02_Red.idat


title: 6Sa_2D_6SA24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004066-H-A01

value: No Template Control


title: 6Sa_2D_6SA22

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 200491250034_R06C02

description:
200491250034_R06C02_Grn.idat
200491250034_R06C02_Red.idat


title: OX_530_P2F2_061_D1


title: 6Sa_2D_6SA23

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: DSP-1001660004064-F-H11


title: OX_535_P4C2_053_E2

source_name: MS brain 10


title: 200491250047_R04C02

description:
200491250047_R04C02_Grn.idat
200491250047_R04C02_Red.idat


title: DSP-1001660004064-F-G10


title: IDlib_control_5min_2rep

city: Baltimore

first: Taekjip

last: Ha

state: Maryland

address: 3400 N. Charles Street

institute: Johns Hopkins University

data_processing:
Trim Illumina adaptor using Trim Galore software
Merge the pair-end reads with FLASh software
Reads alignment with Bowtie2 software
Calling the sequence identity and DNA cleavage location by using custom python script
Data imputation by linear regression with custom python script
Supplementary files format and content: .data file including estimated nucleosome positioning scores and cleavage counts for each sequence in the library

organism: synthetic construct

source_name: indel library

growth_protocol: nucleosome libraries are reconstituted by salt-dialysis methods from synthetic DNA pools with Xenopus laevis histone octamers

extract_protocol:
phenol chloroform extraction of DNA
single-stranded 3’ end DNA fragments were converted into double-stranded DNA by Bst polymerase (NEB Bst 2.0 WarmStart). And NGS library was prepared with NEBUltraII kit (NEBNext Ultra II DNA Library Prep Kit) for Illumina sequecing.

treatment_protocol: nucleosomal DNA was photo-crosslinked site-specifically and cleavaged by alkaline treatment

tag: base sequence

value: Widom 601 DNA

tag: perturbation type

value: no bulge control

tag: chd1 sliding

value: 5 min Chd1 sliding


title: DSP-1001660004064-F-H05

city: Cambridge

first: Karthik

address: 415 Main St

institute: Broad Institute

source_name: Pancreas

tag: tissue

tag: treatment / other annotation


title: 6Sa_2D_6SA21

description:
rpm_miRNA.txt
results_counts_miRNA.txt

extract_protocol:
Extracted by mirVana™ miRNA Isolation Kit
sRNA libraries were prepared for sequencing using standard Illumina protocols


title: 200491250024_R04C01

description:
200491250024_R04C01_Grn.idat
200491250024_R04C01_Red.idat

value: melanoma


title: 200491250039_R04C02

description:
200491250039_R04C02_Grn.idat
200491250039_R04C02_Red.idat

value: M

value: Primary


title: DSP-1001660004064-F-H03

value: Pancreas


title: OX_530_P2F2_061_D2


title: OX_530_P2F2_061_C2


title: IDlib_control_0min_2rep

value: No Chd1 sliding


title: IDlib_control_5min_1rep


title: DSP-1001660004064-F-H04


title: OX_535_P4C2_053_E1


title: DSP-1001660004064-F-G12


title: 200491250024_R06C01

description:
200491250024_R06C01_Grn.idat
200491250024_R06C01_Red.idat


title: OX_530_P2F2_061_E2


title: IDlib_bubble_5min_2rep

value: insertion bulge


title: 200491250017_R02C02

description:
200491250017_R02C02_Grn.idat
200491250017_R02C02_Red.idat

value: Cutaneous


title: OX_535_P4C2_053_D1


title: 200491250017_R04C01

description:
200491250017_R04C01_Grn.idat
200491250017_R04C01_Red.idat


title: OX_535_P4C2_053_D2


title: DSP-1001660004064-F-G09


title: 200491250048_R03C02

description:
200491250048_R03C02_Grn.idat
200491250048_R03C02_Red.idat


title: IDlib_control_0min_1rep


title: OX_535_P4C2_053_C1


title: OX_535_P4C2_053_C2


title: IDlib_bubble_0min_1rep


title: mmlib_control_5min_2rep

source_name: mismatch library

value: no mismatch control


title: 200491250047_R03C02

description:
200491250047_R03C02_Grn.idat
200491250047_R03C02_Red.idat

value: Metastasis


title: DSP-1001660004064-F-F03


title: DSP-1001660004064-F-G02


title: IDlib_bubble_5min_1rep


title: 200491250039_R06C01

description:
200491250039_R06C01_Grn.idat
200491250039_R06C01_Red.idat

value: F

value: Yes


title: DSP-1001660004064-F-F12


title: mmlib_control_5min_1rep


title: mmlib_control_0min_2rep


title: OX_530_A5C4_052_C2

value: brain cortex

value: MS


title: 200491250039_R03C02

description:
200491250039_R03C02_Grn.idat
200491250039_R03C02_Red.idat


title: DSP-1001660004064-F-G04

value: Untreated


title: OX_530_A5C4_052_C1


title: DSP-1001660004064-F-G03


title: DSP-1001660004064-F-G06


title: mmlib_bubble_5min_2rep

value: Widom 601 DNA

value: mismatch bubble


title: mmlib_control_0min_1rep


title: OX_530_A5C4_052_D1


title: OX_530_P4D4_049_E2


title: OX_530_P4D4_049_E1


title: OX_530_A5C4_052_D2


title: mmlib_bubble_5min_1rep

value: 5 min Chd1 sliding


title: 200491250034_R04C02

description:
200491250034_R04C02_Grn.idat
200491250034_R04C02_Red.idat

value: melanoma


title: 200491250046_R03C01

description:
200491250046_R03C01_Grn.idat
200491250046_R03C01_Red.idat

value: M


title: OX_530_P4D4_049_D2


title: DSP-1001660004064-F-G07


title: 200491250046_R04C01

description:
200491250046_R04C01_Grn.idat
200491250046_R04C01_Red.idat


title: OX_530_P4D4_049_D1


title: DSP-1001660004064-F-E06


title: mmlib_bubble_0min_1rep


title: mmlib_bubble_0min_2rep


title: DSP-1001660004064-F-E09


title: DSP-1001660004064-F-F10


title: DSP-1001660004064-F-G01


title: 200491250048_R02C01

description:
200491250048_R02C01_Grn.idat
200491250048_R02C01_Red.idat


title: 200491250045_R04C02

description:
200491250045_R04C02_Grn.idat
200491250045_R04C02_Red.idat


title: 200491250017_R05C02

description:
200491250017_R05C02_Grn.idat
200491250017_R05C02_Red.idat


title: OX_530_P4D4_049_C1


title: 200491250048_R01C01

description:
200491250048_R01C01_Grn.idat
200491250048_R01C01_Red.idat

value: No


title: 200491250017_R01C02

description:
200491250017_R01C02_Grn.idat
200491250017_R01C02_Red.idat


title: 200491250024_R05C02

description:
200491250024_R05C02_Grn.idat
200491250024_R05C02_Red.idat


title: DSP-1001660004064-F-F11

value: Pancreas


title: OX_530_P4D4_049_C2


title: OX_527_A5B7_048_E1

source_name: MS brain 9


title: 200491250017_R06C02

description:
200491250017_R06C02_Grn.idat
200491250017_R06C02_Red.idat


title: OX_527_A5B7_048_D2


title: OX_527_A5B7_048_E2


title: DSP-1001660004064-F-F04


title: HeLa cells, CTT251236 8 hours replicate 2

city: Heidelberg

first: George

last: Reid

address: Waldhofer Strasse

institute: WMT AG

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38 using CLC genomic benchwork (parameters- mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HeLa

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

extract_protocol:
RNA was harvested using Trizol (Thermofisher) and RNA quality was determined by an Agilent 2100 Bioanalyzer system. All samples had a RIN of 10.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with 1 micromolar CTT251236 for 8 and for 24 hours. The final concentration of DMSO was 0.05% v/v.

value: HeLa

tag: cell type

value: cervical carcinoma

tag: genotype

value: WT

value: 1 micromolar CTT251238

tag: time point

value: 8 hours


title: 200491250024_R01C02

description:
200491250024_R01C02_Grn.idat
200491250024_R01C02_Red.idat

tag: histological type

value: Cutaneous

tag: gender

value: Metastasis


title: HeLa cells, CTT251236 24 hours replicate 1

tag: treatment

value: 24 hours


title: DSP-1001660004064-F-F06

last: Jagadeesh


title: HeLa cells, CTT251236 24 hours replicate 2


title: DSP-1001660004064-F-F09


title: HeLa cells, CTT251236 8 hours replicate 1


title: HeLa cells, DMSO 8 hours replicate 3

value: solvent control


title: DSP-1001660004064-F-E10

value: Untreated


title: HeLa cells, CTT251236 8 hours replicate 3


title: 200491250046_R04C02

description:
200491250046_R04C02_Grn.idat
200491250046_R04C02_Red.idat

tag: disease state

tag: uv signature

value: Yes

tag: specimen type

value: Primary


title: OX_527_A5B7_048_C1

value: brain cortex

value: MS

tag: ChIP


title: HeLa cells, DMSO 8 hours replicate 2


title: 200491250039_R06C02

description:
200491250039_R06C02_Grn.idat
200491250039_R06C02_Red.idat

value: melanoma

value: M


title: OX_527_A5B7_048_D1

tag: well


title: OX_527_A5B7_048_C2


title: 200491250045_R06C01

description:
200491250045_R06C01_Grn.idat
200491250045_R06C01_Red.idat

value: F


title: HeLa cells, CTT251236 24 hours replicate 3

tag: cell line

value: HeLa


title: OX_528_P4D6_047_E2

source_name: MS brain 5


title: 200491250034_R02C01

description:
200491250034_R02C01_Grn.idat
200491250034_R02C01_Red.idat


title: OX_528_P4D6_047_E1


title: 200491250046_R01C01

description:
200491250046_R01C01_Grn.idat
200491250046_R01C01_Red.idat


title: HeLa cells, DMSO 8 hours replicate 1

value: cervical carcinoma


title: 200491250045_R05C02

description:
200491250045_R05C02_Grn.idat
200491250045_R05C02_Red.idat


title: DSP-1001660004064-F-F08

value: Pancreas


title: 200491250034_R01C02

description:
200491250034_R01C02_Grn.idat
200491250034_R01C02_Red.idat


title: DSP-1001660004064-F-F02


title: OX_528_P4D6_047_C2


title: OX_528_P4D6_047_D1


title: DSP-1001660004064-F-F07


title: DSP-1001660004064-F-F01


title: DSP-1001660004064-F-H01

value: CRT


title: DSP-1001660004064-F-F05


title: OX_528_A3B5_045_E1


title: DSP-1001660004064-F-D04


title: OX_528_A3B5_045_E2


title: OX_528_A3B5_045_D2


title: OX_528_P4D6_047_C1


title: OX_528_A3B5_045_D1


title: 200491250047_R05C01

description:
200491250047_R05C01_Grn.idat
200491250047_R05C01_Red.idat


title: 200491250046_R05C02

description:
200491250046_R05C02_Grn.idat
200491250046_R05C02_Red.idat


title: 200491250045_R06C02

description:
200491250045_R06C02_Grn.idat
200491250045_R06C02_Red.idat


title: DSP-1001660004064-F-E08


title: DSP-1001660004064-F-E03


title: 200491250024_R02C02

description:
200491250024_R02C02_Grn.idat
200491250024_R02C02_Red.idat


title: RNAseq_CdLS_Fibroblast_rep2

city: Changsha

first: Jiankang

state: Hunan

address: Lushan

institute: School of biology

data_processing:
Sequencing reads were aligned to human reference genome (hg38) using Bowtie version 1.2.2 with “-n2 -m1” parameters
Peak calling was performed using MACS2 version 2.2.6 with default settings
Htseq version 0.11.3 was then utilized with default parameters to generate a count table
Genome_build: hg38
Supplementary_files_format_and_content: bed files of ChIP-seq peak; gene count table of RNA-seq

source_name: CdLS Fibroblast

growth_protocol: RPE cells and MCF-7 cells (JCRB Cell Bank) were cultured in DMEM containing 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Komata, M., et al., Chromatin immunoprecipitation protocol for mammalian cells. Methods Mol Biol, 2014. 1164: p. 33-8.).  Total RNA was extracted using TRIzol (Life Technologies) and Nucleospin RNA (Macherey-Nagel) following the manufacturers' instructions.
ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (New England BioLabs).

treatment_protocol: RPE cells were cultured in serum-free medium for 48 hours and then incubated in DMEM containing 10% FBS for 30 min. MCF-7 cells were maintained in phenol red-free medium containing charcoal-dextran stripped FBS (Life Technologies) at 70-80% confluency for 2 days before treatment with 50nM E2 ligand (SIGMA) for the indicated times.

value: CdLS Fibroblast

tag: antibody

value: Non-treatment


title: DSP-1001660004064-F-E11


title: DSP-1001660004064-F-E04


title: 200491250045_R03C02

description:
200491250045_R03C02_Grn.idat
200491250045_R03C02_Red.idat

value: Cutaneous

value: Metastasis


title: DSP-1001660004064-F-D12


title: RNAseq_Normal_Fibroblast_rep2

source_name: Healthy Fibroblast

value: Healthy Fibroblast


title: RNAseq_CHOP_Fibroblast_rep1

source_name: CHOPS Fibroblast

value: CHOPS Fibroblast


title: OX_528_A3B5_045_C2


title: OX_C36_A2C2_044_C2

source_name: Contr. brain 6

value: HI


title: 200491250048_R04C01

description:
200491250048_R04C01_Grn.idat
200491250048_R04C01_Red.idat

value: Yes


title: DSP-1001660004064-F-E12

value: Untreated


title: DSP-1001660004064-F-E05


title: DSP-1001660004064-F-D08


title: 4M+

type: RNA

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

description: Gene expression data from Tom+ MEx3a WT adenoma cell

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChip™ MG-430 PM Array Strip arrays were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: Arrays were processed in Bioconductor, using RMA background correction, quantile normalization and RMA summarization.

label: biotin

source_name: Epcam positive Tomato positive cells sorted by FACs coming from colon adenomas

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Adenomas were induced by Tamoxifen treatment in Mex3a WT and KO animals. Animals were sacrified two months afetr the induction, when there were adenomas in the colon.

extract_protocol: RNA was isolated using magnetic beads from 2000 cels. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 24 cycles.

treatment_protocol: Adenomas were manually resected and disgregated using Colagenase IV. Epcam staining was used to sort Tom+ Epethilial cells.

value: WT


title: RNAseq_Normal_Fibroblast_rep1


title: OX_528_A3B5_045_C1

value: brain cortex

value: MS


title: OX_C36_A2C2_044_D2


title: DSP-1001660004064-F-E07


title: 200491250039_R03C01

description:
200491250039_R03C01_Grn.idat
200491250039_R03C01_Red.idat

value: melanoma

value: F

value: Primary


title: IDlib_bubble_0min_2rep

tag: base sequence

value: Widom 601 DNA

tag: perturbation type

value: insertion bulge

value: No Chd1 sliding


title: RNAseq_CdLS_Fibroblast_rep1

value: CdLS Fibroblast

value: Non-treatment


title: RNAseq_CHOP_Fibroblast_rep2


title: OX_C36_A2C2_044_D1

tag: tissue


title: DSP-1001660004064-F-D07

value: Pancreas

tag: treatment / other annotation

value: CRT


title: OX_C36_A2C2_044_E2


title: DSP-1001660004064-F-D10


title: OX_C36_A2C2_044_E1


title: 7M+

description: Gene expression data from Tom+ MEx3a KO adenoma cell

value: KO


title: OX_527_A5C7_043_D2


title: DSP-1001660004064-F-B11


title: RNAseq_MCF7_KD_E2_rep2

source_name: MCF7 cell line

tag: cell type

value: MCF7 cell line

value: Estrogen +

tag: sirna


title: OX_527_A5C7_043_D1


title: OX_C36_A2C2_044_C1

value: HI


title: RNAseq_MCF7_WT_E2_rep2


title: 5M+

tag: genotype

value: WT


title: 9M+


title: RNAseq_MCF7_WT_Ctrl_rep2

value: Estrogen -


title: RNAseq_MCF7_WT_E2_rep1


title: DSP-1001660004064-F-C11


title: DSP-1001660004064-F-C05


title: MKL367 ki/+ Mex3A- LGR5 - Adenoma 2000 cells

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization using the normqc function of Bioconductor's MDA package

label: Biotin

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

extract_protocol: total RNA extraction

tag: mex3a status

value: negative

tag: lgr5 status


title: MKL367 ki/+ Mex3A+ LGR5- Adenoma 2000 cells

value: positive


title: MKL367 ki/+ Mex3A- LGR5 + Adenoma 2000 cells


title: RNAseq_MCF7_WT_Ctrl_rep1

tag: treatment


title: 3M+


title: OX_527_A5C7_043_E1

value: brain cortex

tag: disease state

value: MS


title: DSP-1001660004064-F-D11


title: RNAseq_MCF7_KD_E2_rep1


title: OX_527_A5C7_043_C1


title: OX_527_A5C7_043_E2


title: OX_527_A5C7_043_C2


title: ChIPseq_Fibroblast_Input_Normal

value: Healthy Fibroblast

value: Input


title: 6M+


title: ChIPseq_Fibroblast_Input_CHOPS

value: CHOPS Fibroblast


title: DSP-1001660004064-F-D06


title: 2M+


title: DSP-1001660004064-F-E02

value: Untreated


title: DSP-1001660004064-F-C10


title: OX_523_P2B2_042_E2

source_name: MS brain 8


title: MKL347 ki/+ Mex3A- LGR5 - Adenoma 2000 cells


title: OX_523_P2B2_042_D1


title: ChIPseq_Fibroblast_Input_CdLS

value: CdLS Fibroblast

value: Non-treatment


title: MKL347 ki/+ Mex3A- LGR5 + Adenoma 2000 cells


title: MKL367 ki/+ Mex3A+ LGR5 + Adenoma 2000 cells


title: DSP-1001660004064-F-C02

value: Pancreas

value: CRT


title: ChIPseq_Fibroblast_Rad21_Normal


title: RNAseq_MCF7_KD_Ctrl_rep2

value: MCF7 cell line


title: MKL347 ki/+ Mex3A+ LGR5 + Adenoma 2000 cells


title: OX_523_P2B2_042_D2


title: OX_523_P2B2_042_E1


title: DSP-1001660004064-F-E01


title: ChIPseq_Fibroblast_Rad21_CdLS


title: ChIPseq_Fibroblast_Pol2ser5_Normal

value: RNA Pol2ser2


title: RNAseq_MCF7_KD_Ctrl_rep1


title: DSP-1001660004064-F-D09


title: DSP-1001660004064-F-D02


title: ChIPseq_Fibroblast_Rad21_CHOPS


title: MKL347 ki/+ Mex3A+ LGR5- Adenoma 2000 cells


title: ChIPseq_HeLa_Rad21_WT_rep2

source_name: HeLa cell line

value: HeLa cell line


title: MKL358 ki/+ Mex3A- LGR5 + Adenoma 500 cells


title: OX_523_P2B3_041_E2


title: ChIPseq_Fibroblast_Pol2ser5_CdLS


title: MKL358 ki/+ Mex3A+ LGR5- Adenoma 500 cells


title: DSP-1001660004064-F-B12


title: DSP-1001660004064-F-C12


title: ChIPseq_Fibroblast_Pol2_Normal

value: RNA Pol2


title: OX_523_P2B3_041_C2


title: DSP-1001660004064-F-D03


title: DSP-1001660004064-F-C08


title: OX_523_P2B3_041_D2


title: OX_523_P2B2_042_C2


title: OX_523_P2B2_042_C1


title: OX_523_P2B3_041_E1


title: ChIPseq_Fibroblast_Pol2ser5_CHOPS


title: ChIPseq_Fibroblast_Pol2_CHOPS


title: DSP-1001660004064-F-D05


title: MKL358 ki/+ Mex3A+ LGR5 + Adenoma 500 cells


title: OX_510_P4C5_040_E1

source_name: MS brain 7


title: DSP-1001660004064-F-D01


title: ChIPseq_Fibroblast_NIPBL_Normal

value: NIPBL


title: DSP-1001660004064-F-C09


title: 4C-seq of K5aSE: ESCs-K5aSE-4C-bat3-Rep2

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

description: 4C-seq of K5aSE in Mus musculus: ESCs-K5aSE-4C-bat3-Rep2

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.2.1)
Expression levels of all genes were counted and expression profile matrix was constructed with featureCounts (2.0.3)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with q value < 0.05 and fold change > 2 or < 1/2
Clean reads of 4C-seq were mapped to mm10 with Bowtie2(2.4.4). Then we obtained the interaction regions by R package FourCSeq
Assembly: mm10
Supplementary files format and content: Text files include genes counts values and bedGraph files include 4C interaction regions
Library strategy: 4C-seq

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs (E14) were grown in culture dishes coated with 0.1% gelatin in DMEM supplemented with 15% FBS, 100 nM NEAA, 200 mM L-Glutamate, 1% Penicillin-streptomycin, 50 μM β-mercaptoethanol, 10 ng/mL LIF, 1 μM PD0325901 and 3 μM CHIR99021. The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
1. For RNA-seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions.
2. For 4C-seq：Briefly, 10^7 ESCs were trypsinised into single cells and resuspended in 9.5 ml of DMEM/15% FBS. Cells were then cross-linked by adding 0.6 ml of 16% formaldehyde for 10 min. After centrifugation at 4 degrees (2000 g), cells were lysed in 5 ml of lysis buffer (10 mM Tris-HCl [pH 7.5]; 10 mM NaCl; 5 mM MgCl2; 0.1 mM EGTA; 1 x protease inhibitor) for 10 min (placed ice with constant light shaking) and centrifuged to remove the supernatant. The nuclei were then digested with DpnII at 37°C. After inactivation with 1.6% SDS for 20 minutes at 65°C, samples were diluted in 6.125 ml of 1.15× ligation buffer and 100 U T4 ligase and incubated for 4 hours at 16°C, followed by 30 minutes at 25°C. The ligated chromatin was digested by proteinase K, purified by phenol-chloroform extraction and the DNA was precipitated by ethanol. The purified product was further digested with NlaIII and then cyclised with T4 ligase. After purification, PCR reactions containing 100 ng DNA were performed using the bait-primers. PCR products were purified by Agencourt AMPure XP paramagnetic beads and the purified products were sequenced at Novogene (Tianjin city, China).
1. RNA-seq Library. Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Then 3 µl USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
2. 4C-seq Library. After the DNA samples were tested and passed, the DNA fragments specifically enriched by the 4C technique were subjected to end repair, addition of A-tails, addition of sequencing connectors, purification and PCR amplification to complete the entire library preparation. After library construction, initial quantification was performed using Qubit 2.0 to dilute the library, followed by detection of the insert fragment using Agilent 2100. After the insert fragment size met the expectation, the effective concentration of the library was accurately quantified using Q-PCR method to ensure the quality of the library. After the libraries passed the assay, the different libraries were pooled into flowcell according to the effective concentration and the target downstream data volume. cBOT was clustered and sequenced using Illumina high-throughput sequencing platform NovaSeq 6000.

treatment_protocol: RNA-seq was performed using undifferentiated and EB-differentiated （5d) WT and KO ESCs. Undifferentiated ESCs (WT) were used for 4C-seq.

value: blastocyst

value: ESC

value: WT


title: OX_523_P2B3_041_C1

value: brain cortex

value: MS


title: 4C-seq of K5aSE: ESCs-K5aSE-4C-bat4-Rep1

description: 4C-seq of K5aSE in Mus musculus: ESCs-K5aSE-4C-bat4-Rep1


title: OX_510_P4C5_040_D2


title: DSP-1001660003872-E-F03


title: ChIPseq_Fibroblast_NIPBL_CdLS


title: OX_523_P2B3_041_D1


title: 4C-seq of K5aSE: ESCs-K5aSE-4C-bat4-Rep2

description: 4C-seq of K5aSE in Mus musculus: ESCs-K5aSE-4C-bat4-Rep2


title: MKL358 ki/+ Mex3A- LGR5 - Adenoma 500 cells

value: negative


title: ChIPseq_Fibroblast_Pol2_CdLS


title: 4C-seq of K5aSE: ESCs-K5aSE-4C-bat2-Rep1

description: 4C-seq of K5aSE in Mus musculus: ESCs-K5aSE-4C-bat2-Rep1


title: 4C-seq of K5aSE: ESCs-K5aSE-4C-bat2-Rep2

description: 4C-seq of K5aSE in Mus musculus: ESCs-K5aSE-4C-bat2-Rep2


title: ChIPseq_HeLa_Rad21_WT_rep1


title: OX_510_P4C5_040_D1


title: DSP-1001660004064-F-C06


title: OX_510_P4C5_040_E2


title: ChIPseq_Fibroblast_H3K27ac_Normal

value: Healthy Fibroblast


title: 4C-seq of K5aSE: ESCs-K5aSE-4C-bat1-Rep2

description: 4C-seq of K5aSE in Mus musculus: ESCs-K5aSE-4C-bat1-Rep2


title: 4C-seq of K5aSE: ESCs-K5aSE-4C-bat3-Rep1

description: 4C-seq of K5aSE in Mus musculus: ESCs-K5aSE-4C-bat3-Rep1


title: DSP-1001660004064-F-B06

value: Untreated


title: DSP-1001660004064-F-C03


title: DSP-1001660004064-F-C07


title: OX_510_P4B2_039_D1


title: ChIPseq_Fibroblast_NIPBL_CHOPS

value: CHOPS Fibroblast


title: DSP-1001660004064-F-C04


title: ChIPseq_Fibroblast_H3K27ac_CHOPS

value: Non-treatment


title: OX_510_P4C5_040_C2


title: OX_510_P4C5_040_C1


title: DSP-1001660004064-F-C01

value: Pancreas


title: ChIPseq_Fibroblast_H3K27ac_CdLS

value: CdLS Fibroblast


title: DSP-1001660004064-F-B03


title: RNA-Seq: EBd5-Tbc1d4-KO-Rep1

description: RNA-Seq of Mus musculus: EBd5-Tbc1d4-KO-Rep1

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.2.1)
Expression levels of all genes were counted and expression profile matrix was constructed with featureCounts (2.0.3)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with q value < 0.05 and fold change > 2 or < 1/2
Clean reads of 4C-seq were mapped to mm10 with Bowtie2(2.4.4). Then we obtained the interaction regions by R package FourCSeq
Assembly: mm10
Supplementary files format and content: Text files include genes counts values and bedGraph files include 4C interaction regions

value: EBs-day 5


title: RNA-Seq: EBd5-Tbc1d4-KO-Rep2

description: RNA-Seq of Mus musculus: EBd5-Tbc1d4-KO-Rep2


title: ChIPseq_Fibroblast_AFF4_Normal


title: OX_510_P4B2_039_C2


title: DSP-1001660004064-F-B08


title: RNA-Seq: EBd5-Nkx3-1-KO-Rep2

description: RNA-Seq of Mus musculus: EBd5-Nkx3-1-KO-Rep2


title: ChIPseq_Fibroblast_AFF4_CHOPS


title: DSP-1001660004064-F-B09


title: ChIPseq_Fibroblast_AFF4_CdLS


title: OX_510_P4B2_039_C1


title: RNA-Seq: EBd5-Nkx3-1-KO-Rep1

description: RNA-Seq of Mus musculus: EBd5-Nkx3-1-KO-Rep1


title: DSP-1001660004064-F-B04


title: OX_510_P4B2_039_E1


title: 4C-seq of K5aSE: ESCs-K5aSE-4C-bat1-Rep1

description: 4C-seq of K5aSE in Mus musculus: ESCs-K5aSE-4C-bat1-Rep1


title: DSP-1001660004064-F-B01


title: OX_510_P4B2_039_E2


title: RNA-Seq: EBd5-Farp1-KO-Rep2

description: RNA-Seq of Mus musculus: EBd5-Farp1-KO-Rep2


title: RNA-Seq: EBd5-Farp1-KO-Rep1

description: RNA-Seq of Mus musculus: EBd5-Farp1-KO-Rep1


title: OX_510_P4B2_039_D2


title: ChIPseq_RPE_Input_FBS+

source_name: RPE1 cell line

value: RPE1 cell line

value: Input

value: FBS +


title: OX_584_A2B4_038_E2

source_name: MS brain 2


title: ChIPseq_RPE_Input_DRB+

value: DRB +


title: OX_584_A2B4_038_E1


title: RNA-Seq: EBd5-CFNT-WT-Rep2

description: RNA-Seq of Mus musculus: EBd5-CFNT-WT-Rep2

value: blastocyst


title: ChIPseq_RPE_Input_FBS-

value: FBS -


title: OX_584_A2B4_038_D2


title: RNA-Seq: EBd5-Clybl-KO-Rep2

description: RNA-Seq of Mus musculus: EBd5-Clybl-KO-Rep2

value: Clybl-KO


title: ChIPseq_RPE_K27ac


title: DSP-1001660004064-F-B02

source_name: Pancreas


title: RNA-Seq: EBd5-Clybl-KO-Rep1

description: RNA-Seq of Mus musculus: EBd5-Clybl-KO-Rep1


title: ChIPseq_RPE_Med1_FBS-


title: OX_584_A2B4_038_C1

value: brain cortex


title: RNA-Seq: ESCs-Tbc1d4-KO-Rep1

description: RNA-Seq of Mus musculus: ESCs-Tbc1d4-KO-Rep1

value: ESC


title: DSP-1001660004064-F-A09


title: DSP-1001660003872-E-H12


title: ChIPseq_RPE_Input_FBS+DRB

value: FBS + DRB +


title: RNA-Seq: EBd5-CFNT-WT-Rep1

description: RNA-Seq of Mus musculus: EBd5-CFNT-WT-Rep1

value: WT


title: OX_584_A3C1_037_E2

value: MS


title: ChIPseq_RPE_Mau2_FBS+


title: DSP-1001660004064-F-A03

value: Untreated


title: OX_584_A2B4_038_D1


title: OX_584_A2B4_038_C2


title: ChIPseq_RPE_Input_DRB-

value: DRB -


title: DSP-1001660004064-F-B05

value: Pancreas


title: DSP-1001660004064-F-B07


title: DSP-1001660004064-F-A07


title: ChIPseq_RPE_Med1_FBS+


title: ChIPseq_RPE_Mau2_FBS-


title: DSP-1001660004064-F-B10


title: RNA-Seq: ESCs-Tbc1d4-KO-Rep2

description: RNA-Seq of Mus musculus: ESCs-Tbc1d4-KO-Rep2


title: OX_584_A3C1_037_D2


title: DSP-1001660004064-F-A11


title: DSP-1001660004064-F-A10


title: ChIPseq_RPE_Pol2_FBS+

value: RNA Pol2


title: DSP-1001660004064-F-A05


title: ChIPseq_RPE_Pol2_FBS-


title: OX_584_A3C1_037_E1


title: ChIPseq_RPE_Pol2ser2_FBS+

value: RNA Pol2ser2


title: DSP-1001660004064-F-A08


title: OX_584_A3C1_037_C1


title: RNA-Seq: ESCs-Nkx3-1-KO-Rep2

description: RNA-Seq of Mus musculus: ESCs-Nkx3-1-KO-Rep2


title: DSP-1001660004064-F-A12


title: ChIPseq_RPE_Pol2ser2_FBS-

value: RPE1 cell line


title: ChIPseq_RPE_CTCF

value: CTCF

value: Non-treatment


title: OX_584_A3C1_037_D1


title: ChIPseq_RPE_SA1_FBS+

value: FBS +


title: OX_584_A3C1_037_C2


title: OX_584_A1C2_036_E2


title: RNA-Seq: ESCs-Farp1-KO-Rep1

description: RNA-Seq of Mus musculus: ESCs-Farp1-KO-Rep1

value: blastocyst


title: RNA-Seq: ESCs-CFNT-WT-Rep1

description: RNA-Seq of Mus musculus: ESCs-CFNT-WT-Rep1


title: ChIPseq_RPE_SA1_FBS-

value: FBS -


title: DSP-1001660003872-E-H08


title: OX_584_A1C2_036_E1


title: RNA-Seq: ESCs-Klf5-KO-Rep2

description: RNA-Seq of Mus musculus: ESCs-Klf5-KO-Rep2


title: DSP-1001660003872-E-H09


title: RNA-Seq: ESCs-Clybl-KO-Rep2

description: RNA-Seq of Mus musculus: ESCs-Clybl-KO-Rep2


title: RNA-Seq: ESCs-Farp1-KO-Rep2

description: RNA-Seq of Mus musculus: ESCs-Farp1-KO-Rep2


title: OX_584_A1C2_036_D1


title: RNA-Seq: ESCs-Nkx3-1-KO-Rep1

description: RNA-Seq of Mus musculus: ESCs-Nkx3-1-KO-Rep1


title: RNA-Seq: ESCs-Clybl-KO-Rep1

description: RNA-Seq of Mus musculus: ESCs-Clybl-KO-Rep1


title: DSP-1001660004064-F-A01

value: No Template Control


title: DSP-1001660004064-F-A06


title: ChIPseq_RPE_Rad21_DRB+

value: DRB +


title: RNA-Seq: ESCs-Klf5-WT-Rep2

description: RNA-Seq of Mus musculus: ESCs-Klf5-WT-Rep2

value: ESC


title: DSP-1001660003872-E-H11


title: RNA-Seq: ESCs-Klf5-WT-Rep1

description: RNA-Seq of Mus musculus: ESCs-Klf5-WT-Rep1


title: OX_584_A1C2_036_D2

value: brain cortex


title: OX_586_A1C2_030_E2

source_name: MS brain 13


title: ChIPseq_RPE_Rad21_FBS+DRB

value: FBS + DRB +


title: ChIPseq_RPE_Rad21_FBS-


title: OX_586_A1C2_030_D2

value: MS


title: RNA-Seq: EBd5-Klf5-WT-Rep2

description: RNA-Seq of Mus musculus: EBd5-Klf5-WT-Rep2

value: EBs-day 5

value: WT


title: RNA-Seq: EBd5-Klf5-KO-Rep2

description: RNA-Seq of Mus musculus: EBd5-Klf5-KO-Rep2


title: DSP-1001660004064-F-A04

value: Pancreas

value: Untreated


title: ChIPseq_RPE_Rad21_DRB-

value: DRB -


title: ChIPseq_Fibroblast_Rad21_WT

value: Healthy Fibroblast


title: RNA-Seq: EBd5-Klf5-WT-Rep1

description: RNA-Seq of Mus musculus: EBd5-Klf5-WT-Rep1


title: ChIPseq_Bcell_Rad21_WT

source_name: Bcell

value: Bcell


title: OX_586_A1C2_030_D1


title: ChIPseq_293T_Rad21_WT

source_name: 293T cell line

value: 293T cell line

value: Non-treatment


title: OX_586_A1C2_030_E1


title: RNA-Seq: ESCs-CFNT-WT-Rep2

description: RNA-Seq of Mus musculus: ESCs-CFNT-WT-Rep2

value: blastocyst


title: OX_586_A1C2_030_C1


title: OX_584_A1C2_036_C1


title: DSP-1001660003872-E-G06


title: DSP-1001660003872-E-H06


title: RNA-Seq: ESCs-Klf5-K5aSE-KO-Rep2

description: RNA-Seq of Mus musculus: ESCs-Klf5-K5aSE-KO-Rep2


title: ChIPseq_RPE_Rad21_WT

value: RPE1 cell line


title: RNA-Seq: ESCs-Klf5-KO-Rep1

description: RNA-Seq of Mus musculus: ESCs-Klf5-KO-Rep1


title: RNA-Seq: ESCs-Klf5-K5aSE-KO-Rep1

description: RNA-Seq of Mus musculus: ESCs-Klf5-K5aSE-KO-Rep1


title: RNA-Seq: ESCs-V-K5aSE-KO-Rep2

description: RNA-Seq of Mus musculus: ESCs-V-K5aSE-KO-Rep2


title: ChIPseq_MCF7_ER_Ctrl

value: MCF7 cell line

value: ER

value: Estrogen -


title: DSP-1001660003872-E-H02


title: OX_586_A1C2_030_C2

value: brain cortex


title: ChIPseq_RPE_Rad21_FBS+

value: FBS +


title: OX_584_A1C2_036_C2

value: MS


title: OX_586_A1B3_029_D2


title: DSP-1001660004064-F-A02


title: DSP-1001660003872-E-F07


title: RNA-Seq: EBd5-Klf5-KO-Rep1

description: RNA-Seq of Mus musculus: EBd5-Klf5-KO-Rep1

value: EBs-day 5


title: OX_586_A1B3_029_D1


title: ChIPseq_MCF7_CBP_KD_E2

value: CBP

value: Estrogen +


title: OX_586_A1B3_029_C2


title: OX_586_A1B3_029_E2


title: DSP-1001660003872-E-H07

value: Pancreas

value: Untreated


title: OX_586_A1B3_029_E1


title: OX_586_A1B3_029_C1


title: RNA-Seq: ESCs-V-K5aSE-KO-Rep1

description: RNA-Seq of Mus musculus: ESCs-V-K5aSE-KO-Rep1

value: ESC


title: ChIPseq_MCF7_ER_E2


title: DSP-1001660003872-E-H10


title: ChIPseq_MCF7_CBP_KD_Ctrl


title: DSP-1001660003872-E-H04


title: OX_536_A1D1_028_E1

source_name: MS brain 11


title: RNA-Seq: ESCs-V-K5aSE-WT-Rep1

description: RNA-Seq of Mus musculus: ESCs-V-K5aSE-WT-Rep1

value: WT-Vector


title: ChIPseq_MCF7_Pol2ser2_KD_Ctrl

value: RNA Pol2ser2


title: DSP-1001660003872-E-H03


title: DSP-1001660003872-E-F12


title: ChIPseq_MCF7_Pol2ser2_KD_E2


title: OX_536_A1D1_028_D2


title: DSP-1001660003872-E-F11


title: ChIPseq_MCF7_p300_KD_Ctrl


title: RNA-Seq: EBd5-K5aSE-KO-Rep3

description: RNA-Seq of Mus musculus: EBd5-K5aSE-KO-Rep3


title: RNA-Seq: EBd5-K5aSE-KO-Rep2

description: RNA-Seq of Mus musculus: EBd5-K5aSE-KO-Rep2


title: DSP-1001660003872-E-H05


title: RNA-Seq: EBd5-K5aSE-KO-Rep1

description: RNA-Seq of Mus musculus: EBd5-K5aSE-KO-Rep1


title: RNA-Seq: ESCs-V-K5aSE-WT-Rep2

description: RNA-Seq of Mus musculus: ESCs-V-K5aSE-WT-Rep2


title: DSP-1001660003872-E-E11


title: ChIPseq_MCF7_Mau2_KD_E2


title: ChIPseq_MCF7_Pol2_KD_Ctrl

value: RNA Pol2


title: DSP-1001660003872-E-G12


title: ChIPseq_MCF7_Pol2_KD_E2


title: ChIPseq_MCF7_p300_KD_E2


title: DSP-1001660003872-E-F02


title: RNA-Seq: EBd5-K5aSE-WT-Rep2

description: RNA-Seq of Mus musculus: EBd5-K5aSE-WT-Rep2

value: blastocyst

value: WT


title: RNA-Seq: EBd5-K5aSE-WT-Rep3

description: RNA-Seq of Mus musculus: EBd5-K5aSE-WT-Rep3


title: OX_438_P6C3_026_E2

source_name: MS brain 4


title: OX_536_A1D1_028_C1