title: DND41_resistant_YY1_ChIPseq_rep2

extract_protocol:
ChIP-seq for histone marks was performed as previously described (Petrovic et al., 2019). Briefly, 1 x 10^7 cells were crosslinked with 1% formaldehyde and lysed. Nuclei were extracted and resuspended in 1% SDS and sonicated using Brandson 450 sonicator with 25% amplitude, 0.5s on, 1s off for a total of 4min 30s on. Solubilized chromatin was then diluted and cleared with IgG (CST cat# 2729S) and recombinant protein G–conjugated Agarose beads (Invitrogen #15920-010) for 1 hour at 4°C. The cleared supernatant was subsequently immunoprecipitated with antibodies recognizing H3K27ac (Active Motif cat# 39133) or H3K4me1 (Abcam cat# ab8895) overnight at 4°C. Buffers in all steps above were supplemented with protease inhibitors (Roche cat# 11697498001). Antibody-chromatin complexes were captured with recombinant protein G–conjugated Agarose beads, washed with low salt wash buffer, high salt wash buffer, LiCl wash buffer and TE buffer with 50mM NaCl and eluted. Input sample was prepared by the same approach without immunoprecipitation. ChIP-seq for transcription factors was performed as previously described (Bossen et al., 2015). Briefly, Dynabeads Protein G (ThermoFisherScientific cat# 10003D) was incubated with antibodies recognizing MAML1 (D3K7B) (CST cat# 12166S), TCF1/TCF7 (C46C7) (CST cat# c2206S), LEF1 (D6J2W) (CST cat# 76010S), EBF1 (Boller et al., 2016), SMC1a (Bethyl, cat# A300-055A), YY1 (Active motif cat# 61779) and CTCF (EMD Millipore cat# 07-729) for 8-12 hours in PBS+0.5% BSA at 4°C. 4 x 10^7 cells were crosslinked with 1% formaldehyde and 1.5mM EGS (ThermoFisherScientific cat# 21565) and sonicated using Brandson 450 sonicator with 17% amplitude, 10s on, 1min off for 10 times. Lysate was then cleared by centrifuging for 5min at 16 Kg, 4°C and incubated with antibody-bound beads and 1% Triton Tx-100 (Roche cat# 10789704001) overnight at 4°C. Buffers in all steps above were supplemented with protease inhibitors (Roche cat# 11697498001). Antibody-chromatin complexes captured on beads were then separated on magnet and washed with wash buffer 1, 2, 3, LiCl wash Buffer and TE buffer and eluted.
Following elution of histone mark and transcription factor samples, RNase (Roche cat# 10109169001) and Proteinase K (Invitrogen cat# 25530-049) treatments were performed and reverse crosslinked at 65°C overnight. DNA was purified with QiaQuick PCR Purification Kit (Qiagen, cat# 28106). Libraries were then prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB cat# E7645S) with single (NEB cat# E7335, cat# E7710) or dual (NEB cat# E7600, cat# E7780) indexing. Two replicates were performed for each condition. Indexed libraries were validated for quality and size distribution using a TapeStation 4150 (Agilent), quantified by KAPA Library Quantification Kit (Roche cat# KK4824) and paired-end sequenced (38 bp+38 bp) on Illumina NextSeq 550.


title: P-524

status: Public on Feb 21 2022

type: SRA

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

description:
Tumor biopsy
Explorative_cohort_miRNA_counts_matrix.txt
Explorative_cohort_miRNA_normRPM_matrix.txt

library_source: transcriptomic

data_processing:
Single-end sequencing of 50 bases of each cDNA
Real-time analysis, base calling, adapter clipping and filtering of low quality reads performed by Illumina software according to standard protocols.
Quality assessment was based on the reads using the FASTQC quality control
Read alignment software: miRDeep2 v.2.0.0.5 with mirBase v.21 for annotation of mature miRNAs
Genome_build: Hg19
Supplementary_files_format_and_content: Explorative_cohort_miRNA_counts_matrix.txt: matrix with raw counts for every miRNA in every sample in the Explorative cohort. Duplicate mature miRNA ID are included in the dataset due to annotation of identical mature miRNA IDs to different precursor miRNA ID by the miRDeep2 algorithm.
Supplementary_files_format_and_content: Explorative_cohort_miRNA_normRPM_matrix.txt: matrix with normalized counts (RPM) for every miRNA in every sample in the Explorative cohort. Duplicate mature miRNA ID are included in the dataset due to annotation of identical mature miRNA IDs to different precursor miRNA ID by the miRDeep2 algorithm.
Supplementary_files_format_and_content: Validation_cohort1_miRNA_counts_matrix.txt: matrix with raw counts for every miRNA in every sample in the Explorative cohort. Duplicate mature miRNA ID are included in the dataset due to annotation of identical mature miRNA IDs to different precursor miRNA ID by the miRDeep2 algorithm.
Supplementary_files_format_and_content: Validation_cohort1_miRNA_normRPM_matrix.txt: matrix with normalized counts (RPM) for every miRNA in every sample in the Explorative cohort. Duplicate mature miRNA ID are included in the dataset due to annotation of identical mature miRNA IDs to different precursor miRNA ID by the miRDeep2 algorithm.

molecule: total RNA

organism: Homo sapiens

source_name: Cervical tumor

growth_protocol: 1-4 tumor samples were collected from each patient at the time of diagnosis

extract_protocol:
In the Explorative cohort, total RNA was extracted by use of the miRNeasy mini kit. In the validation cohort 1, total RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with Agilent Bioanalyser.
Small RNA preparation for sequencing was performed according to Illumina TruSeq Small RNA library protocols. Briefly, indexed 3’- and 5’end RNA adapters were ligated to 1 ug of isolated total RNA per sample followed by reverse transcription and library amplification. The cDNA was purified on a PAGE gel by cutting out bands corresponding to 140-160 bp (length of miRNA + adapter and index sequences), pooled and ethanol precipitated.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis.

tag: figo stage

tag: lymph node status (0=negative, 1=positive)

tag: tumor volume (mm3)

tag: histology

value: Squamous cell carcinoma

tag: cohort

value: Explorative cohort

tag: total number of reads from small rna seq.


title: DND41_DMSO_Arima_HiC_rep1

city: Philadelphia

first: YEQIAO

last: ZHOU

state: PA

address: 421 Curie Boulevard

department: Pathology

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Raw reads for each HiC sample were processed with HiC-Pro (version v2.5.0) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE and GENOME_FRAGMENT provided by Arima.
Genome_build: hg19
Supplementary_files_format_and_content: .hic formatted file for juicebox viewing of contact matrices

molecule: genomic DNA

source_name: DND41 cell line

growth_protocol: DND41 (male) cells were grown in RPMI 1640 (Corning, cat# 10-040-CM) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 11140-050), 1mM sodium pyruvate (Gibco, cat#11360-070) and 0.1mM of 2-mercaptoethanol (Sigma, cat# M6250).

extract_protocol:
1-2x10^6 cells were washed with 1xPBS containing 3% BSA and fixed with 2% formaldehyde and proceeded with Arima-HiC Kit per manufacturer’s instructions.
Samples passing Arima-QC1 were used for library construction with Accel-NGS 2S Plus DNA Library Kit (Swift cat# 21024) and 2S SET A INDEXING KIT (Swift cat# 26148) and assessed with Arima-QC2. Samples passing Arima-QC2 were subsequently PCR amplified based on Arima-QC2 calculations, quantified with TapeStation 4150 (Agilent) and KAPA Library Quantification Kit (Roche cat# KK4824) and paired-end (38bp+38bp) sequenced on Illumina NextSeq 550.

treatment_protocol: To generate GSI-resistant DND41, parental DND41 was treated with 125nM gamma-secretase inhibitor (GSI) compound E (Calbiochem cat# 565790) for 7-12 weeks with regular refreshment of media and maintained in 125nM GSI. To generate GSI-resistant-reversed cells, GSI-resistant DND41 were cultured in media without GSI for 6-8 weeks.

tag: cell line

value: DND41 cell line

tag: cell type

value: T-ALL cell line

tag: lentiviral transduction

tag: drug treatment

value: DMSO


title: DND41_resistant_YY1_ChIPseq_rep1

data_processing:
Reads were trimmed with Trim Galore (version 0.4.1) with parameters -q 15 --phred33 --gzip --stringency 5 -e 0.1 --length 20. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 6. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.25.0) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 329).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing

tag: chip antibody

value: GSI


title: DND41_DMSO_YY1_ChIPseq_rep2


title: P-519


title: P-531


title: P-520


title: P-516


title: P-532


title: DND41_resistant_CTCF1_ChIPseq_rep1

value: CTCF


title: DND41_resistant_SMC1_ChIPseq_rep2


title: DND41_DMSO_YY1_ChIPseq_rep1


title: DND41_DMSO_SMC1_ChIPseq_rep2


title: P-512


title: DND41_resistant_CTCF1_ChIPseq_rep2


title: DND41_resistant_SMC1_ChIPseq_rep1


title: P-513


title: P-509


title: DND41_DMSO_H3K27me3_CnR_rep2

data_processing:
Library strategy: Cut&Run
Reads were trimmed with Trim Galore (version 0.4.1) with parameters -q 15 --phred33 --gzip --stringency 5 -e 0.1 --length 20. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 6. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.25.0) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 329).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing

extract_protocol:
CUT & RUN was performed as described (Skene and Henikoff, 2017). Briefly, 5x10^5 cells were immobilized on Concanavalin-coated magnetic beads (Bangs Laboratories cat# cBP531) and incubated with Tri-Methyl-Histone H3 (Lys27) (C36B11) antibody (CST cat# 9733S) overnight at 4°C. Beads were washed with digitonin wash buffer and mixed in pA-MNase (gift from Henikoff lab) at 4°C for 1 hour. After activation by Ca2+ on wet ice for 30min, 2XSTOP buffer was added and incubated 37°C for 10min to release CUT & RUN fragments from the insoluble nuclear chromatin.
DNA was then extracted from the supernatant using Phenol-chloroform-isoamyl alcohol 25:24:1 (PCI; Invitrogen cat# 15593049) method. Library construction, quantification and sequencing were done as described above for ChIP-seq.


title: DND41_DMSO_H3K27me3_CnR_rep1


title: P-507


title: P-506


title: DND41_DMSO_SMC1_ChIPseq_rep1


title: DND41_DMSO_CTCF_ChIPseq_rep2


title: P-505


title: P-504


title: P-503


title: P-493


title: DND41_DMSO_EBF1_ChIPseq_rep2


title: P-500


title: P-510


title: DND41_resistant_LEF1_ChIPseq_rep2


title: DND41_DMSO_EBF1_ChIPseq_rep1


title: DND41_resistant_LEF1_ChIPseq_rep1


title: P-488


title: P-484


title: P-485


title: DND41_DMSO_LEF1_ChIPseq_rep2


title: DND41_resistant_TCF1_ChIPseq_rep2


title: P-487


title: DND41_DMSO_TCF1_ChIPseq_rep2


title: P-482


title: DND41_resistant_TCF1_ChIPseq_rep1


title: P-481


title: P-479


title: DND41_DMSO_CTCF_ChIPseq_rep1


title: DND41_resistant_MAML_ChIPseq_rep2


title: DND41_resistant_EBF1_ChIPseq_rep2


title: P-478


title: DND41_resistant_MAML_ChIPseq_rep1


title: DND41_resistant_EBF1_ChIPseq_rep1


title: P-474


title: DND41_DMSO_MAML_ChIPseq_rep2


title: P-491


title: DND41_DMSO_MAML_ChIPseq_rep1


title: P-471


title: P-469


title: P-483


title: P-468


title: DND41_resistant_H3K4me1_ChIPseq_rep2


title: DND41_DMSO_LEF1_ChIPseq_rep1


title: P-467


title: P-466


title: P-460


title: DND41_resistant_H3K4me1_ChIPseq_rep1


title: DND41_reverse_24hrGSI_H3K27ac_ChIPseq_rep2


title: DND41_DMSO_H3K4me1_ChIPseq_rep2


title: P-464


title: DND41_DMSO_H3K4me1_ChIPseq_rep1


title: DND41_reverse_DMSO_H3K27ac_ChIPseq_rep1


title: DND41_DMSO_TCF1_ChIPseq_rep1


title: P-457


title: DND41_reverse_24hrGSI_H3K27ac_ChIPseq_rep1


title: P-455


title: DND41_reverse_DMSO_H3K27ac_ChIPseq_rep2


title: P-454


title: DND41_resistant_H3K27ac_ChIPseq_rep1


title: P-443


title: DND41_24hrGSI_H3K27ac_ChIPseq_rep2


title: DND41_resistant_H3K27ac_ChIPseq_rep2


title: P-442


title: P-438


title: DND41_24hrGSI_H3K27ac_ChIPseq_rep1


title: DND41_DMSO_H3K27ac_ChIPseq_rep2


title: P-433


title: DND41_DMSO_H3K27ac_ChIPseq_rep1


title: P-434


title: DND41Cas9_TCF1g5_ATAC_rep3

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013) and three replicates were performed for each condition. Briefly, 50,000 cells were pelleted at 800 x g and washed with 50 μl of ice cold 1 x PBS (Corning cat# 21031CV), followed by 2min treatment with 50 μl lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% Igepal cat# CA-630). Pelleted nuclei were resuspended in 50 μl of transposition buffer (25 μl of 2 x TD buffer, 22.5ul of molecular biology grade water and 2.5 μl Tn5 transposase (Illumina cat# FC-121-1030) to tag the accessible chromatin for 45min at 37°C.
Tagmented DNA was purified with MinElute Reaction Cleanup kit (Qiagen cat# 28204) and amplified with 5 PCR cycles. Additional number of PCR cycles was determined from the side reaction and ranged from 10-12 total cycles of PCR. Libraries were purified using QiaQuick PCR purification kit (Qiagen cat# 28106) and eluted in 20 μl EB buffer. Indexed libraries were assessed for nucleosome patterning on TapeStation 4150 (Agilent) and paired-end sequenced (38bp+38bp) on Illumina NextSeq 550.

value: Cas9 and TCF1-targeting sgRNA


title: P-429


title: P-427


title: DND41Cas9_TCF1g5_ATAC_rep2


title: P-423


title: P-421


title: DND41Cas9_LEF1g3_ATAC_rep3

value: Cas9 and LEF1-targeting sgRNA


title: DND41Cas9_TCF1g5_ATAC_rep1


title: DND41Cas9_LEF1g3_ATAC_rep1


title: DND41Cas9_LEF1g3_ATAC_rep2


title: DND41Cas9_LEF1_TCF1_KO_d9_ATAC_rep3

value: Cas9 and LEF1+TCF1-targeting sgRNA


title: P-413


title: P-420


title: P-417


title: DND41Cas9_LEF1_TCF1_KO_d9_ATAC_rep2


title: P-418


title: DND41Cas9_LEF1_TCF1_KO_d6_ATAC_rep3


title: P-412


title: P-411


title: DND41Cas9_LEF1_TCF1_KO_d6_ATAC_rep2


title: P-410


title: DND41Cas9_LEF1_TCF1_KO_d3_ATAC_rep3


title: DND41Cas9_LEF1_TCF1_KO_d3_ATAC_rep2


title: P-406


title: P-401


title: P-426


title: DND41Cas9_ctrl_ATAC_rep3

value: Cas9 and control sgRNA


title: DND41Cas9_LEF1_TCF1_KO_d3_ATAC_rep1


title: P-397


title: DND41Cas9_ctrl_ATAC_rep2


title: DND41Cas9_LEF1_TCF1_KO_d9_ATAC_rep1


title: DND41Cas9_ctrl_ATAC_rep1


title: P-391

description:
Tumor biopsy
Validation_cohort1_miRNA_counts_matrix.txt
Validation_cohort1_miRNA_normRPM_matrix.txt

value: Validation cohort 1


title: P-390


title: DND41ResCas9_EBF1g7_day9_ATAC_rep3

value: Cas9 and EBF1-targeting sgRNA


title: DND41ResCas9_EBF1g7_day9_ATAC_rep2


title: P-374


title: P-389


title: DND41Cas9_LEF1_TCF1_KO_d6_ATAC_rep1


title: DND41ResCas9_EBF1g7_day6_ATAC_rep2


title: P-372


title: DND41ResCas9_EBF1g7_day6_ATAC_rep3


title: P-376


title: DND41ResCas9_EBF1g7_day6_ATAC_rep1


title: P-371


title: DND41ResCas9_EBF1g7_day9_ATAC_rep1


title: P-368


title: DND41ResCas9_EBF1g7_day3_ATAC_rep3


title: DND41ResCas9_EBF1g7_day3_ATAC_rep2


title: DND41ResCas9_EBF1g7_day3_ATAC_rep1


title: P-361


title: P-399


title: P-360


title: DND41ResCas9_ctrl_ATAC_rep3


title: P-392


title: DND41ResCas9_ctrl_ATAC_rep1


title: DND41ResCas9_ctrl_ATAC_rep2


title: P-355


title: P-354


title: P-352


title: P-353


title: DND41_resistant_ATAC_rep3


title: P-350


title: DND41_24hrGSI_ATAC_rep2


title: P-349


title: P-351


title: P-367


title: DND41_resistant_ATAC_rep1


title: P-346


title: DND41_24hrGSI_ATAC_rep3


title: DND41_DMSO_ATAC_rep3


title: DND41_DMSO_ATAC_rep2


title: P-343


title: P-337


title: DND41_24hrGSI_ATAC_rep1


title: MB157pIndEBF1_10dox_ATAC_rep3

source_name: MB157 cell line

growth_protocol: MB157 (female) cells were grown in DMEM (Corning, cat# 10-013-CV) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03) and 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI). When passaged cells were detached with 0.25% trypsin, EDTA-free (Gibco, cat# 15090-046) to avoid activation of Notch signaling.

treatment_protocol: MB157pInducer cells were generated by lentivirus infection and G418 selection. To ectopically express LEF1, TCF1 or EBF1, 10ug/ml doxycycline was added and cells were harvested at 72hr.

value: MB157 cell line

value: Triple-negative breast cancer cell line

value: doxycycline


title: P-336


title: MB157pIndEBF1_10dox_ATAC_rep2


title: P-335


title: MB157pIndEBF1_10dox_ATAC_rep1


title: P-333


title: P-332


title: P-331


title: MB157pIndTCF1_10dox_ATAC_rep2


title: DND41_resistant_ATAC_rep2


title: MB157pIndTCF1_10dox_ATAC_rep1


title: P-326


title: P-340


title: MB157pIndLEF1_10dox_ATAC_rep2


title: MB157pIndLEF1_10dox_ATAC_rep3


title: P-325


title: MB157pIndLEF1_10dox_ATAC_rep1


title: P-322


title: P-310


title: MB157_sorted_ATAC_rep1


title: P-308


title: MB157_sorted_ATAC_rep2


title: DND41_DMSO_ATAC_rep1


title: P-302


title: P-319


title: MB157_sorted_ATAC_rep3


title: P-303


title: MB157pInd20EBF1_10dox_SMC1_HiChIP

data_processing:
Library strategy: HiChIP
Raw reads for each HiChIP sample were processed with HiC-Pro (version v2.5.0) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GATCGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The valid pairs (allValidPairs file) from HiC-Pro were used to generate .hic file using Juicer tools (version 1.7.6) ‘pre’ command.
Genome_build: hg19
Supplementary_files_format_and_content: .hic formatted file for juicebox viewing of contact matrices

extract_protocol:
SMC1 HiChIP was performed as previously described (Petrovic et al., 2019). DMSO and GSI-washout treated MB157 HiChIP samples were previously published (Petrovic et al., 2019). Briefly, 2 x 107 cells were crosslinked with 1% formaldehyde (Thermo Fisher Scientific, cat# 28908) for 10 min and subsequently quenched with 0.125M glycine (Invitrogen, cat# 15527-013). Chromatin was digested using MboI restriction enzyme (NEB, cat# R0147), followed by biotin incorporation with Biotin-14-dATP (Invitrogen, cat# 19524-016 or Jena Bioscience cat# NU-835-BIO14-S). DNA was then ligated with T4 ligase (NEB cat# M0202L) and sonicated on Covaris LE220. Sheared chromatin was 4-fold diluted with ChIP dilution buffer (16.7mM Tris pH 7.5, 167mM NaCl, 1.2mM EDTA, 0.01% SDS, 1.1% Triton X-100), cleared with IgG (CST cat# 2729S) and then incubated with anti-SMC1 antibody (Bethyl, cat# A300-055A) at 4°C overnight. Chromatin-antibody complexes were captured by Protein-A magnetic beads (Pierce, cat# 88846) and subsequently washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and eluted.
DNA was purified with MinElute PCR Purification Kit (Qiagen, cat# 28004) and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851). 50-150ng was used for capture with Dynabeads MyOne Streptavidin C-1 (Invitrogen, cat# 65001) and an appropriate amount of Tn5 enzyme was added to captured DNA to generate sequencing library. Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.


title: MB157pInd20TCF1_10dox_SMC1_HiChIP


title: P-293


title: MB157pInd20TCF1_10dox_YY1_ChIP_rep1


title: P-292


title: MB157pInd20EBF1_10dox_YY1_ChIP_rep2


title: MB157pInd20TCF1_10dox_YY1_ChIP_rep2


title: P-294


title: MB157pInd20EBF1_10dox_YY1_ChIP_rep1


title: MB157_YY1_ChIP_rep2


title: MB157pIndTCF1_10dox_ATAC_rep3


title: P-290


title: P-289


title: MB157pInd20TCF1_10dox_CTCF_ChIP_rep2


title: MB157_YY1_ChIP_rep1


title: MB157pInd20TCF1_10dox_CTCF_ChIP_rep1


title: P-283


title: P-282


title: MB157pInd20EBF1_10dox_CTCF_ChIP_rep1


title: P-281


title: MB157_CTCF_ChIP_rep1


title: MB157pInd20EBF1_10dox_CTCF_ChIP_rep2


title: MB157pInd20EBF1_10dox_SMC1_ChIPseq_rep2


title: P-298


title: P-277


title: MB157pInd20EBF1_10dox_SMC1_ChIPseq_rep1


title: P-276


title: P-278


title: P-274


title: MB157pInd20TCF1_10dox_SMC1_ChIPseq_rep1


title: MB157_CTCF_ChIP_rep2


title: P-272


title: P-291


title: MB157_SMC1_ChIPseq_rep1


title: P-270


title: P-288


title: MB157pInd20EBF1_10dox_EBF1_ChIPseq_rep2


title: P-267


title: MB157pInd20EBF1_10dox_EBF1_ChIPseq_rep1


title: P-264


title: P-265


title: MB157_EBF1_ChIPseqc_rep2


title: MB157_SMC1_ChIPseq_rep2


title: MB157_EBF1_ChIPseq_rep1


title: MB157pInd20TCF1_10dox_TCF1_ChIPseq_rep2


title: P-263


title: P-284


title: P-261


title: P-262


title: MB157_TCF1_ChIPseq_rep2


title: P-257


title: P-258


title: P-318


title: MB157pInd20TCF1_10dox_TCF1_ChIPseq_rep1


title: P-247


title: P-251


title: MB157_TCF1_ChIPseq_rep1


title: P-246


title: MB157pInd20TCF1_10dox_H3K27ac_ChIP_rep2


title: MB157pInd20EBF1_10dox_H3K27ac_ChIP_rep1


title: P-244


title: MB157_DMSO_H3K27ac_ChIP_rep2


title: MB157_DMSO_H3K27ac_ChIP_rep1


title: P-243


title: T3_con_rep4

type: RNA

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

hyb_protocol: 825 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 4x180k format for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red & Green and PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 042279_D_F_20120723) to obtain mean Red or Green intensities and median Red or Green background intensities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizing was done.

organism: Enchytraeus crypticus

source_name: pool of 10 animals

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Low Input Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 10 adult animals which had a visible clitellum were used for the experiment

extract_protocol: Total RNA was extracted from all animals, using the SV Total RNA isolation System (Promega).

treatment_protocol: 10 adult animals per sample were exposed to two concentrations of zinc (EC10 and EC50) or control in LUFA2.2 soil for 1,2,3 or 4 days. 4 replicates per condition were used

tag: time point

tag: agent

value: none, control

tag: age

value: adult whole animal


title: P-240

value: Squamous cell carcinoma


title: MB157pInducer20EBF1_RNAseq_rep3

data_processing:
RNA-seq data was aligned to Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using STAR (version 2.5) with parameters --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 100000 --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 25  --chimJunctionOverhangMin 25.
Strand-specific read counts were quantified using Subread (version 1.5.1) featureCounts with parameters -t exon -g gene_id -s 1 -T 6 and used as input to differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with read count; bigWig files for genome browser viewing

extract_protocol:
5x10^5 cells were washed with 1 x PBS and lysed with 350 μl RLT Plus buffer (Qiagen) supplemented with 2-mercaptoethanol, vortexed briefly and immediately proceeded to RNA isolation with RNeasy Plus Micro Kit (Qiagen #74034).
RNA integrity numbers were determined using TapeStation 4150 (Agilent), and all samples used for RNA-seq library preparation had RIN numbers greater than 9.5. 500-800 ng of total RNA was used, and libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit-HI Mammalian (Clontech cat# 634873). Libraries were paired-end sequenced (38bp+38bp) on Illumina NextSeq 550.


title: P-252


title: MB157pInducer20EBF1_RNAseq_rep2


title: P-239


title: P-236


title: T2_10_rep4

value: zinc (EC10)


title: MB157pInducer20EBF1_RNAseq_rep1


title: MB157pInd20TCF1_10dox_SMC1_ChIPseq_rep2


title: T3_10_rep4


title: T2_con_rep4


title: MB157pInducer20TCF1_RNAseq_rep3


title: P-235


title: T3_10_rep3


title: MB157pInd20EBF1_10dox_H3K27ac_ChIP_rep2


title: T3_50_rep3

value: zinc (EC50)


title: T2_10_rep3


title: MB157pInducer20TCF1_RNAseq_rep2


title: P-232


title: MB157pInducer20TCF1_RNAseq_rep1


title: MB157pInd20TCF1_10dox_H3K27ac_ChIP_rep1


title: T3_50_rep4


title: T4_10_rep4


title: T4_50_rep4


title: P-231


title: rice cv. Nipponbare,rep1

city: Shijiazhuang

first: Caili

last: Bi

state: Hebei

address: No.20 Road East. 2nd Ring South, Yuhua District

department: College of life sciences

country: China

institute: Hebei Normal University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Oryza sativa

source_name: wild-type rice seedling

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Rice seedlings of OsUBA-overexprssed, OsUBA-RNA interferenced,and the wild type were normally-grown at 28 ℃ until the fourth leave arises

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: no treatment.

tag: tissue

value: four-leaf seedlings


title: OsUBA-RNA interferenced rice,rep2

source_name: OsUBA-RNA interferenced rice seedling


title: OsUBA-RNA interferenced rice,rep1


title: MB157_DMSO_RNAseq_rep3

value: DMSO


title: OsUBA-overexpressing rice,rep1

source_name: OsUBA-overexpressing rice seedling


title: OsUBA-overexpressing rice,rep2


title: rice cv. Nipponbare,rep2


title: P-229

value: Explorative cohort


title: T1_50_rep4


title: T3_50_rep2


title: T1_con_rep4


title: T3_con_rep3


title: T2_50_rep4


title: MB157_DMSO_RNAseq_rep2


title: T3_10_rep2


title: MB157_DMSO_RNAseq_rep1


title: T2_50_rep3


title: T2_con_rep3


title: T4_con_rep4


title: Mouse 2 somites

city: Baltimore

first: James

last: Saba

state: MD

address: 725 N Wolfe St, 714 PCTB

department: Molecular Biology and Genetics

institute: Johns Hopkins

description: Barcode = CCTGAG at the 5' end of read

data_processing:
Library strategy: nAnTi-CAGE
Illumina HiSeq 2500
CAGE-seq reads were aligned to the mouse genome (mm10) using STAR v2.7.3a
vM24
Genome_build: Mus musculus mm10 (GRCm38)
Supplementary_files_format_and_content: WIGGLE (.wig) files contain chromosome mapping locations for the first non-barcode nucleotide of each read (mapped using STAR v2.7.3a). Signal values for each nucleotide position are normalized to reads per million (RPM)

organism: Mus musculus

source_name: E11.5 somites and neural tube

growth_protocol: C56BL/6J mice were used for timed mating; the date when a vaginal pug is present is assigned as embryonic day (E) 0.5 per convention.

extract_protocol:
Embryos were placed in dissection media (DMEM/F-12 1:1, 10% FBS, and 1% penn-strep; GIBCO) and chilled on ice in a 60 mm petri dish (Falcon) until dissection. Each embryo was sequentially transferred to a small dissection dish with Sylgard bottom (Living Systems Instrumentation) in the same media, pinned facing down by small dissection pins (Living Systems Instrumentation), and the neural tube and somites were dissected out using two angled scissors (2.5 mm and 4 mm cutting edge; FST) from the first somite to the tail end. Prior to transferring the dissected somite/neural tube to a 1.5 ml RNase-free microfuge tube (ThermoFisher Scientific), any remaining ventral endoderm-derived tissue was removed. To the dissected somite/neural tube (~100 µl, after removing as much media as possible), 400 µl of Trizol reagent (Invitrogen) was added. The tube was vortexed until the tissue was dissolved, and then immediately frozen on dry ice and stored at -80 °C until RNA isolation. Total RNA was isolated using the Direct-zol RNA Miniprep kit (Zymogen), followed by quantification and analyses using Nanodrop One (ThermoFisher Scientific) and Bioanalyzer (Agilent), respectively, and stored at -80 °C until use.
No-amplification non-tagging cap analysis of gene expression (nAnT-iCAGE) libraries were prepared using the cap-trap method as described in a detailed protocol (Murata et al., Methods Mol. Biol., 2014). In brief, 5 µg total mouse somite RNA was reverse transcribed (Superscript III, ThermoFisher) using random hexamer primers. Following cleanup with Agencourt RNAClean XP (Beckman Coulter), the RNA ends of RNA:cDNA hybrids were oxidized with NaIO4 (11.3 mM) on ice in the dark for 45 min, cleaned with Agencourt RNAClean XP, and biotinylated with biotin hydrazide (0.83 mM) at RT overnight. Single-stranded RNA was cleaved using RNAseONE ribonuclease and biotinylated RNA:cDNA hybrids were purified by incubation with Dynabeads M-270 streptavidin for 30 min, followed by washing and elution on a magnetic stand as previously described (Murata et al., Methods Mol. Biol., 2014)). Hybrid RNA was degraded with RNAseH, and any remaining free RNA was degraded with RNAse ONE. cDNA was concentrated in a centrifugal concentrator to ~5-10 µl and ligated to the pre-annealed double-stranded 5’linker containing a 6-nt barcode using ligation Mighty Mix at 16 °C for 16 hours. Following cDNA purification with Agencourt AMPure XP, cDNA was ligated to the pre-annealed 3’linker using ligation Mighty Mix at 16 °C for 16 hours. cDNA was treated with shrimp alkaline phosphatase and USER enzyme, followed by cleanup, second-strand synthesis using DeepVent DNA polymerase, primer degradation with Exonuclease I, and a final AMPure XP cleanup. Total cDNA was analyzed for quality and quantified using a Bioanalyzer (Agilent). DNA was pooled to a final concentration of 2 nM and sequenced on 2 lanes of a HiSeq FlowCell (Illumina) with 50 bp read length.

treatment_protocol: No treatment

value: E11.5 somites and neural tube

tag: strain

tag: treatment

value: untreated

tag: seq method

value: nAnT-iCAGE sequencing (Murata 2014)

tag: molecule

value: cDNA generated from 5'-cap selected mRNA (random hexamer RT)


title: P-211

tag: figo stage

tag: lymph node status (0=negative, 1=positive)

tag: tumor volume (mm3)


title: Mouse 1 somites

description: Barcode = AGGTTT at the 5' end of read


title: Mouse 3 somites

description: Barcode = GAACCC at the 5' end of read


title: T4_10_rep2


title: P-210

tag: histology

tag: cohort

value: Validation cohort 1

tag: total number of reads from small rna seq.


title: P-227


title: T4_50_rep2


title: TREGPD1_4

city: Chapel Hill

first: Jonathan

middle: S

last: Serody

state: NC

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
bcl2fastq (illumina pipeline software)
QC using FastQC module
BBDuk to trim anything under 50bp fragments.  Alignment to the murine genome using BBMap.
Differential gene expression analysis performed using DESeq2
Feature counts were obtained using UCSC mm10 gene annotation file (featureCounts v1.5.2)
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 results (.txt);  gene feature expression

source_name: claudin-low TNBC tumors (T11)_murine anti-PD-1 (J43)

extract_protocol:
Tumors were harvested at 150 mm2, digested with Liberase TL (Roche #5401020001), DNase I (Sigma #D4527), Hyaluronidase (Sigma), and Collagenase XI (Sigma #C9697),  enriched for lymphocytes by isolating cells at the interface of a 44% Percoll (Sigma #P1644) in media and Lympholyte-M (Cedarlane #CL5031) gradientand GFP+ Tregs were sorted to greater than 90% purity using MoFlo XDP cell sorter. RNA was isolated from sorted Tregs using RNeasy Micro Kit according to manufacturer's protocol
RNA-Seq libraries constructed with NuGEN Ovation SoLo (NuGEN Technologies)

treatment_protocol: Foxp3-GFP mice were injected with 1 x 10^4 T11 (claudin-low) cells and were untreated or treated with 200 µg ⍺-PD1 antibody (J43) injected IP twice a week

tag: cell type

value: FoxP3+ Treg cells

value: BALB/c

value: murine anti-PD-1 (J43)


title: T4_con_rep3


title: T4_50_rep3


title: P-208


title: P-214


title: TREGPD1_5


title: T1_con_rep3


title: P-201


title: T2_50_rep2


title: No.4 pig intreatment group

city: Hangzhou

first: Haiguang

last: Mao

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then then mapped to reference genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Sus_scrofa.Sscrofa11.1.96
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: ovary

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

value: fpFSH


title: P-202


title: T4_10_rep3

value: adult whole animal


title: P-203

value: Squamous cell carcinoma


title: TREGUN_1

source_name: claudin-low TNBC tumors (T11)_untreated


title: No.2 pig in treatment group


title: No.5 pig in treatment group


title: No.3 pig in treatment group


title: TREGPD1_6


title: T1_10_rep4

value: zinc (EC10)


title: P-215


title: TREGUN_2


title: T1_con_rep2

value: none, control


title: P-200


title: No.1 pig in treatment group


title: TREGUN_3


title: No.5 pig in control group


title: P-198


title: T1_50_rep3

value: zinc (EC50)


title: SM_6

city: Clayton

first: Stephanie

middle: Irene

last: Studniberg

state: VIC

address: 19 Innovation Walk

department: Microbiology

country: Australia

institute: Monash Biomedicine Discovery Institute

data_processing:
The base calling and quality scanning were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilised bcl2fastq conversion software v2.15.0.4
Reads were aligned to the human genome by Rsubread v2.0.1
Fragment (read-pair) counts were summarised by Entrez Gene ID using the featureCounts function in Rsubread v2.0.1
Genes were identified using the the inbuilt RefSeq annotation in Rsubread v2.0.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt: columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

source_name: Peripheral blood_Symptomatic malaria

extract_protocol:
Isolate II RNA Mini Kit (Bioline) following manufacturers' instructions, with the final elution step repeated once and RNA eluted into 40uL total RNAse-free water
Illumina TruSeq RNA Library Prep Kit (<100ng) following manufacturers' instructions

treatment_protocol: PBMCs were frozen at collection

tag: disease status

value: Symptomatic malaria

tag: Sex

value: F

value: Peripheral blood

value: Peripheral blood mononuclear cells


title: P-196


title: T4_10_rep1

tag: time point


title: P-194


title: No.3 pig in control group

value: untreated


title: SM_5


title: SM_4

value: M


title: P-193

value: Validation cohort 1


title: P-191


title: T3_10_rep1

tag: agent


title: SM_1

tag: age


title: No.2 pig in control group

tag: tissue


title: No.1 pig in control group


title: T3_con_rep2


title: 21323_RpoC_HS_i5006_DY330_rep3

city: Ithaca

first: B. Franklin

last: Pugh

state: NY

address: 465 Biotechnology Building

institute: Cornell University

data_processing:
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
peaks were called using GeneTrack using the parameters -s 5 -e 10 -F 1
Genome_build: W3110
Supplementary_files_format_and_content: gff format

organism: Escherichia coli

growth_protocol: Cells were grown in 50 ml of LB media at 30˚C in a shaking incubator with a starting OD600=0.1, then crosslinked when the final OD600=0.7-0.8.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; Reference paper:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054642/
ChIP-exo

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

tag: antibody

value: TAP-tag:Sigma i5006

tag: strain

value: 6 min heat shock


title: P-188


title: 21324_RpoC_HS_i5006_DY330_rep4

tag: treatment


title: P-189


title: AM_5

source_name: Peripheral blood_Asymptomatic malaria

value: Asymptomatic malaria


title: AM_4


title: 20232_RpoC_HS_i5006_DY330_rep2


title: 20231_RpoC_HS_i5006_DY330_rep1


title: No.4 pig in control group

value: ovary


title: T1_10_rep3


title: T2_10_rep1


title: P-184


title: T4_con_rep1


title: AM_3


title: P-182


title: 21317_RpoC_MHS_i5006_DY330_rep4


title: T2_10_rep2


title: SM_2


title: SM_3


title: P-190


title: T2_50_rep1


title: AM_2


title: P-180


title: T4_con_rep2


title: AM_1


title: P-179

value: Explorative cohort


title: T3_50_rep1

value: adult whole animal


title: 21316_RpoC_MHS_i5006_DY330_rep3


title: 20224_RpoC_MHS_i5006_DY330_rep2


title: T3_con_rep1


title: HC_5

source_name: Peripheral blood_Healthy immune control

value: Healthy immune control


title: P-177

value: Squamous cell carcinoma


title: T2_con_rep2

value: none, control


title: T1_10_rep2

value: zinc (EC10)


title: 20230_RpoN_HS_i5006_DY330_rep2


title: 20229_RpoN_HS_i5006_DY330_rep1


title: HC_4


title: T4_50_rep1

value: zinc (EC50)


title: P-172


title: HC_6


title: 20223_RpoC_MHS_i5006_DY330_rep1


title: HC_2

value: F


title: HC_1

value: Peripheral blood


title: 20222_RpoN_MHS_i5006_DY330_rep2


title: 20221_RpoN_MHS_i5006_DY330_rep1


title: T1_10_rep1


title: T1_50_rep2


title: P-149


title: P-162


title: T1_50_rep1


title: BM1172

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

country: Germany

institute: Institute of Bioinformatics

data_processing:
Accurate quantification was performed with the QuantiFluor dsDNA system (Promega).
The size range of the generated cDNA libraries was measured with the DNA 1000 chip on the Bioanalyzer 2100 (280 bp).
Amplification and sequencing of cDNA libraries were performed using the cBot and HiSeq 2000 (Illumina, SR, 1x51 bp, 8-9 gigabases, >40 mio reads per sample).
Sequence images were transformed with Illumina software BaseCaller to bcl-files, which were demultiplexed to fastq-files with CASAVA (v1.8.2).
Quality check was done via FastQC (v0.10.1, Babraham Bioinformatics).
Sequence reads were aligned with the reference genome GRCh37 using the STAR RNA-Seq alignment tool.
Gene-level abundances were estimated using the RNA-seq by expectation-maximization (RSEM) algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with RSEM gene counts for every gene and every sample

source_name: brain metastases

growth_protocol: All brain metastases samples were obtained with informed consent as approved by the local ethics committee (24/10/05).

extract_protocol:
Total RNA was isolated with the Trizol reagent from fresh frozen tissue and RNA integrity was checked with the Bioanalyzer 2100 (Agilent Technologies).
cDNA library preparation was carried out using the TruSeq Stranded Total RNA sample preparation kit (Illumina).

treatment_protocol: Samples of brain metastases were collected from patients previously diagnosed with primary breast cancer during neurosurgical removal.

value: brain metastases,primary breast cancer

value: neurosurgical removal


title: P-174


title: 20227_HimD_HS_i5006_DY330_rep1


title: P-146


title: BM1146


title: T1_con_rep1


title: 21320_HimD_MHS_i5006_DY330_rep3


title: T2_con_rep1


title: HC_3

value: M

value: Peripheral blood mononuclear cells


title: P-133

value: Validation cohort 1


title: CDX2-CnR-Gastricorg

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Library strategy: Cut and Run
Alignment: ChIP-seq, ATAC-seq:bowtie2; RNA-seq: STAR; scATAC: CellRanger
CHIP-seq peak calling, ATAC-seq peak calling: MACS, version 2.0
Genome_build: hg19, mm10
Supplementary_files_format_and_content: ATAC-seq, ChIP-seq, CUT&RUN: bigwig file for visualizing aligned sequence tags; RNA-seq: unprocessed gene counts; scATAC-seq: unfiltered peak-cell counts

source_name: Mouse gastric organoids

extract_protocol:
Orgnaoids were removed from matrigel using cell recovery solution and digested to single cells using Trypsin. Fresh viable single cells were isolated using flow sorting.
Whole nuclei were immobilized on Concanavalin A beads followed by antibody incubation overnight, pA-Mnase digestion in an ice bath for one hour followed by extraction of DNA using phenol chloroform.
Libraries were prepared using NEB Next UltraII and 42bp paired end sequencing was performed on the Miniseq

value: Mouse gastric organoids

value: Cell Signaling technology, #12306 (CDX2 Clone D11D10)


title: BM1115


title: P-138


title: 20219_HimD_MHS_i5006_DY330_rep1

value: TAP-tag:Sigma i5006


title: P-129


title: BM1101


title: P-126


title: TM335

city: Zhanjiang

first: Yan

last: Zeng

address: No. 236 Yuanzhu Road, Chikan District, Zhanjiang , Guangdong

institute: Precision clinical laboratory Central People's Hospital of Zhanjiang

data_processing:
Data were sequenced using Illumina HiSeq X high-throughput sequencing platform
FastQC software was used to assess sequencing quality
Clean reads are obtained after data filtering to remove splice sequences and low quality reads
Genome_build: miRBase
Supplementary_files_format_and_content: Using bowtie2 software to match the quality-controlled Clean Data to the miRBase database of human mature miRNA sequences.
Supplementary_files_format_and_content: The miRNA expression abundance was then assessed and the miRNA expression count matrix was calculated.

source_name: PBMC

extract_protocol:
The exoRNeasy Serum/Plasma Maxi and Midi Kits from QIAGEN from QIAGEN were used to extract and purify exosomal RNA from the separated blood samples, and the obtaining exosomal RNA was used for miRNA library construction using the QIAseq miRNA Library Kit.
miRNA libraries were prepared for sequencing using standard Illumina protocols

tag: blood

value: pbmc

tag: disease state

value: normal


title: TM334


title: TM333


title: 21307_RpoA_HS_i5006_DY330_rep3

value: 6 min heat shock


title: TM332


title: P-148

source_name: Cervical tumor

tag: figo stage

tag: lymph node status (0=negative, 1=positive)

value: Squamous cell carcinoma


title: BM1097


title: BM1100


title: 19790_RpoA_HS_i5006_DY330_rep1


title: BM1164


title: P-124

tag: tumor volume (mm3)

tag: histology


title: TM331


title: P-121

tag: cohort

tag: total number of reads from small rna seq.


title: BM1092


title: 21299_RpoA_MHS_i5006_DY330_rep3


title: BM1110


title: BM1088


title: P-115


title: TM233


title: 20236_RpoA_MHS_i5006_DY330_rep2


title: BM1072


title: 19784_RpoA_MHS_i5006_DY330_rep1


title: 20240_RpoA_HS_i5006_DY330_rep2


title: TM229


title: TM158


title: P-093


title: P-097

value: Explorative cohort


title: BM1069


title: TM156


title: 21313_RpoH_HS_i5006_DY330_rep3


title: P-091


title: TM157


title: BM1057


title: BM1054


title: P-087


title: P-166


title: TM155


title: 20220_HimD_MHS_i5006_DY330_rep2


title: 17265_RpoH_HS_i5006_DY330_rep1


title: P-081


title: P-125


title: TM154


title: P-080


title: 21314_RpoH_HS_i5006_DY330_rep4


title: BM1022


title: 21306_RpoH_MHS_i5006_DY330_rep4


title: TM152


title: 21305_RpoH_MHS_i5006_DY330_rep3


title: TM153


title: P-074


title: P-072


title: P-068


title: TM150


title: 17273_RpoH_MHS_i5006_DY330_rep2


title: 17257_RpoH_MHS_i5006_DY330_rep1


title: BM1006


title: TM151


title: BM0071


title: 17280_RpoH_HS_i5006_DY330_rep2


title: P-067


title: BM1029


title: BM0070


title: BM0046


title: BM0049


title: 17276_RpoD_HS_i5006_DY330_rep2


title: TM149


title: 17261_RpoD_HS_i5006_DY330_rep1


title: TM148


title: P-055


title: P-053


title: BM0045


title: TM30


title: 17253_RpoD_MHS_i5006_DY330_rep1


title: P-042


title: 17269_RpoD_MHS_i5006_DY330_rep2


title: 21322_RpoB_HS_i5006_DY330_rep3


title: BM0026


title: 17275_RpoB_HS_i5006_DY330_rep2


title: BM0033


title: TM27


title: TM29


title: 17260_RpoB_HS_i5006_DY330_rep1


title: BM0025


title: TM147


title: 21315_RpoB_MHS_i5006_DY330_rep3


title: P-028


title: P-025


title: BM0009


title: P-018


title: P-014


title: 17268_RpoB_MHS_i5006_DY330_rep2


title: BM0008


title: P-009


title: TM25


title: BM0044


title: BM0006


title: TM24


title: 17252_RpoB_MHS_i5006_DY330_rep1


title: BM0005


title: TM28


title: 20238_Fis_HS_i5006_DY330_rep2


title: TM23


title: BM0003


title: TM26


title: 19786_Fis_HS_i5006_DY330_rep1


title: 20234_Fis_MHS_i5006_DY330_rep1


title: mcf7_pROR2_3

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2.  RNA sequencing data were first quality checked via FastQC (Babraham Bioinformatics). For MCF-7 the reads were then mapped against the reference genome GRCh38 with the STAR RNA-Seq alignment tool and gene-level abundances were estimated using the RSEM algorithm. For SK-BR-3 and BT-474 cells sequence reads were aligned with the reference genome GRCh38 using the HISAT2 (v2.1.0) alignment tool, while incorporating database information from Ensembl (v38.87) during the reference indexing step.   Gene-level abundances were estimated using featureCounts (v1.6.3).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with gene-level counts for every sample

source_name: MCF-7 cells

growth_protocol: MCF-7 and SK-BR-3 cells were cultured in RPMI-1640, BT-474 cells in DMEM/F12, all supplemented with 10% heat-inactivated (56°C, 30 min) fetal calf serum (FCS).

extract_protocol:
Total RNA was isolated with the Trizol reagent for MCF-7 cells and with the High Pure RNA isolation kit (Roche) for BT-474 and SK-BR-3 cells. RNA concentration was measured at the Nanodrop ND-1000 and RNA integrity was checked with the Bioanalyzer 2100 (Agilent).
For MCF-7 cells, library preparation for RNA-Seq was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) starting from 1,000 ng of total RNA. For SK-BR-3 and BT-474 cells libraries for RNA-Seq were prepared with the NEBNext Ultra RNA II directional kit including NEBNext mRNA enrichment. RNA and library quality control was checked by TapeStation (Agilent).

treatment_protocol: To achieve gene overexpression, cells were transfected with Fugene HD transfection reagent (Promega) and stable clones generated by geneticin or zeocin selection (750 µg/ml or 100 µg/ml, respectively).  For siRNA-mediated gene knockdown, cells were transfected with 10 nM siRNA (santa cruz) using the RNAimax transfection reagent (Invitrogen). Cells were used 72h post transfection for expression analysis.

tag: cell line

value: MCF7 (ATCC  HTB-22)

value: mammary gland, breast; derived from metastatic site:pleural effusion

tag: cell type

value: epithelial

value: transfected with a hROR2 overexpression plasmid (pROR2). Cells were treated with control siRNA (siCTL, #sc-37007, santa cruz).


title: TM22


title: TM21


title: TM20


title: 19780_Fis_MHS_i5006_DY330_rep1


title: mcf7_pROR2_2


title: control-shRNA replicate 2

city: Winston-Salem

first: Swapan

last: Das

address: Bowman Gray Center for Medical Education, 475 Vine St

department: Department of Internal Medicine, Section of Endocrinology and Metabolism

institute: Wake Forest School of Medicine

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: monocyte

growth_protocol: THP1 cells (American Type Culture Collection, Manassas, VA), a model for human macrophages were obtained from the Wake Forest Cell and Viral Vector Core Laboratory and cultured in RPMI-1640 Medium (ATCC® 30-2001™), supplemented with 10% fetal bovine serum (Bench Mark FBS, Gemini, West Sacramento, CA), L-glutamine, and antibiotics. Cells were cultured at 37°C in a humidified incubator maintaining a 5% CO2 atmosphere.

extract_protocol:
Total RNA from gene specific-shRNA and control-shRNA expressing THP1 cells were isolated at baseline and 48hr PMA treated condition using RNAeasy kit (Qiagene). RNA samples were reverse transcribed using Qiagen QuantiTect reverse transcription kit (Qiagen) based on manufacturer’s protocol. To confirm shRNA mediated downregulation, expression of NPL was measured in cDNA by quantitative real-time PCR (qRT-PCR) using Power SYBR green chemistry (Applied Biosystems, Inc., Foster City, CA).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit II for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: For stable RNA interference the NPL gene was silenced by infecting the THP1 cells with gene-specific lentiviral (lv) shRNA (sc-88481-V, Santcruz biotechnology Inc., Dallas, TX)  in the presence of polybrene (sc-134220, Santacruz; 8g/ml) according to an optimized method based on the manufacturer’s protocol. A Control shRNA lentiviral Particles-A (sc-108080, Santacruz) was used a negative control (encodes a scrambled shRNA sequence that will not lead to the specific degradation of any known cellular mRNA). Cells successfully transduced and stably expressing shRNA were selected using 2g/ml of puromycin (A1113803, Gibco, Thermo Fisher Scientific, USA).

value: 48hr PMA treatment

tag: shRNA

value: control shRNA


title: NPL-shRNA replicate 2

value: NPL-shRNA


title: NPL-shRNA replicate 1


title: NPL-shRNA replicate 3


title: control-shRNA replicate 3


title: mcf7_pROR2_1


title: 17274_MglB_HS_i5006_DY330_rep2


title: mcf7_pROR2_siWNT11_3

value: transfected with a hROR2 overexpression plasmid (pROR2). Cells were treated with siRNA against WNT11 (siWNT11, #sc-41120, santa cruz).


title: 17259_MglB_HS_i5006_DY330_rep1


title: Donor_12_AMD

city: Iowa City

first: Andrew

middle: P

last: Voigt

state: IA

address: 375 Newton Road

institute: University of Iowa

description:
GSM4037989
all_metadata.csv
all_normalized_expression_data.csv

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build GRCh38 with CellRanger (v6.0.0) using the CellRanger human GTF
Cells were filtered with the Seurat (v4.0.3) subset function. Cells with nUMIs less than 500 (to remove cells with poor read quality) or greater than 7000 (to remove cells likely to be doublets) were removed. Cells with greater than 15% of reads originating from mitochondrial genes  or 25% of reads originating from ribosomal reads were also removed.
For each of the eight libraries, reads were normalized with the Seurat (v4.0.3) NormalizeData function, and variable features were found with the following commands: my _object <- NormalizeData(my_object, normalization.method = "LogNormalize", scale.factor = 10000), my_object <- FindVariableFeatures(my_object, selection.method = “vst”, nfeatures = 2000)
Integration anchors from the first 24 dimensions of the canonical correlation analysis were used to integrate data with the following commands: choroid.anchors <- FindIntegrationAnchors(object.list = my_object_list, dims=1:25), choroid.combined <- IntegrateData(anchorset = choroid.anchors, dims = 1:25)
Data scaling, principal component analysis, and clustering were performed with the following commands: choroid.combined <- ScaleData(choroid.combined, verbose = FALSE), choroid.combined <- RunPCA(choroid.combined, npcs = 30, verbose = FALSE), choroid.combined <- RunUMAP(choroid.combined, reduction = "pca", dims = 1:23), choroid.combined <- FindNeighbors(choroid.combined, reduction = "pca", dims = 1:23), choroid.combined <- FindClusters(choroid.combined, resolution = 0.35)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format for count(*_count.csv) and processed/normalized (*_normalized.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

extract_protocol:
An 8 or 12-mm macular centered punch of RPE/choroid was acquired from twenty human donors. After dissection away from the retina and sclera, the RPE/choroid was finely diced into small squares (approximately 1 mm x 1 mm) with a razor blade. The resulting suspension was dissociated in 450 units/mL of collagenase II (Gibco, Grand Island NY) reconstituted in Hank’s Balanced Salt Solution containing calcium chloride and magnesium chloride (Life technologies, Grand Island NY). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Cryopreserved cells from single-cell donors were rapidly thawed before pre-enrichment for endothelial cells. Cells were incubated for 15 minutes with anti-CD31 microbeads (Miltenyi Biotech, Bergisch Gladbach Germany) according to the manufacturer’s instructions before automated autoMACs magnetic separation (Miltenyi Biotech, Bergisch Gladbach Germany) into CD31+ fractions. Sequencing of CD31-positive fractions was performed on pooled libraries using the Illumina NovaSeq platform (San Diego, CA).
Single-cell RNA-Seq

tag: condition

value: AMD

tag: region

value: macula


title: TM178


title: 17267_MglB_MHS_i5006_DY330_rep2


title: mcf7_pROR2_siWNT11_2

tag: tissue


title: Donor_11_AMD

description:
GSM4037987
all_metadata.csv
all_normalized_expression_data.csv
donor_11_nAMD


title: TM176


title: mcf7_pROR2_wt_3

value: transfected with a hROR2 overexpression plasmid (pROR2).


title: Donor_2_control

description:
GSM4037990
all_metadata.csv
all_normalized_expression_data.csv

value: control


title: 17251_MglB_MHS_i5006_DY330_rep1

tag: antibody

value: TAP-tag:Sigma i5006


title: TM177

value: pbmc

value: normal


title: TM175


title: mcf7_pROR2_wt_2


title: Human bone marrow mononuclear cells RNA-seq [Sample 14]

city: Rochester

first: Mrinal

middle: M.

last: Patnaik

state: MN

address: 200 First Street SW

department: Division of Hematology

institute: Mayo Clinic

description: Sample 14

data_processing:
FastQC (v0.11.8) pre-alignment quality and adapter trimming, STAR (v2.7.3a) alignment, post-alignment quality control, Subread/featureCounts (v2.0.0)
Genome_build: GRCh38 / hg38
Supplementary_files_format_and_content: Raw feature counts for the transcripts annotated in GRCh38 / hg38 in tab-delimited TXT file generated by Subread/featureCounts (v2.0.0)

source_name: Bone marrow mononuclear cells

extract_protocol:
Total RNA
Illumina TruSeq Stranded Total RNA

value: Bone marrow

tag: cell selection

value: Ficoll-gradient selected mononuclear cells


title: TM19


title: mcf7_pROR2_wt_1

value: MCF7 (ATCC  HTB-22)

tag: treatment


title: mcf7_pcDNA_siWNT11_3

value: mammary gland, breast; derived from metastatic site:pleural effusion

value: transfected with an empty vector (pcDNA). Cells were treated with siRNA against WNT11 (siWNT11, #sc-41120, santa cruz).


title: SQ53 Replicate 1

city: Cuernavaca

first: Jose

last: Utrilla

state: Morelos

address: Av. Universidad sn

department: Centro de Ciencias Genómicas

country: Mexico

institute: Universidad Nacional Autonoma de México

description: MG1655 mutant with four rRNA operons deleted

data_processing:
Base-calling was performed in the Illumina Next-Seq 500 platform
Raw sequenced reads were trimmed with Trim-galore using automatic adapter detection and quality filtering was verified using FastQC
Alignment of reads was performed using Bowtie2 with reference genome (GCF_000005845.2_ASM584v2).
Raw transcript table counts were obtained using the summarize overlaps function from the GenomicAlignments R bioconductor package
Normalization of table counts and significance tests for differential expression were performed with the DeSeq2 R bioconductor package. Additional analysis performed with cufflinks tool.
Genome_build: GCF_000005845.2_ASM584v2
Supplementary_files_format_and_content: Spreadsheet file includes tables with FPKM values for each strain, gene names, DEGs, uniprot accession numbers, log2 fold change, p values, gene products, GO terms for biological process, cellular component, molecular function and its final functional category

source_name: Cell culture

growth_protocol: Cells were grown at 37°C in M9 minimal medium supplemented with glucose (4 g/L). Cultures were innoculated with a passage from an overnight culture in the same media.

extract_protocol:
Samples at early exponential growth phase were mixed  and incubated with RNA protect reagent, lysed enzymatically with lysozyme and RNA was purificated using the Quick-RNA Miniprep kit from Zymo Research. 5 ug were treated with the Zymo-Seq RiboFree Total RNA Library kit for the construction of sequencing libraries.
TruSeq stranded mRNA kit from Illumina

tag: strain

tag: genotype

value: -rrnGBAD


title: SQ53 Replicate 2


title: Donor_1_control

description:
GSM4037988
all_metadata.csv
all_normalized_expression_data.csv


title: 20228_HimD_HS_i5006_DY330_rep2

value: 6 min heat shock


title: TM162

tag: blood

tag: disease state


title: MG1655 Replicate 2

value: wild type


title: Human bone marrow mononuclear cells RNA-seq [Sample 13]

description: Sample 13


title: MG1655 Replicate 1


title: 21327_HimD_HS_i5006_DY330_rep3


title: Human bone marrow mononuclear cells RNA-seq [Sample 12]

description: Sample 12


title: control-shRNA replicate 1

value: 48hr PMA treatment

value: control shRNA


title: TM161


title: mcf7_pcDNA_siWNT11_2

value: epithelial


title: rad16set2_UV2hr_A3_1bp

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

data_processing:
Library strategy: CPD-seq
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3 or SacCer3+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools
Background values dipyrimidine sequences were generated in WIG file using custom perl script
Genome_build: SacCer3
Supplementary_files_format_and_content: WIG files containing counts of DNA CPD lesion reads filtered for only dipyrimidine mapping sequences and including background value of 0.0 at nucleotides associated with dipyrimidines with no mapped sequencing reads. A sequencing read count was  assigned to each nucleotide in the lesion-containing dipyrimidine sequence.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cultures were grown in YPD (yeast extract, peptone, dextrose) media to an OD600=~0.8 in an incubator shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A/T1 (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O. The purified genomic DNA was quantified and 5 μg of DNA was used for each sequencing library preparation.
CPD-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by terminal transferase and dideoxy-ATP.  CPD lesions were  cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor  A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT A4: ATCGCGAT; A5: TACTGGAT; and A6: GAACTGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Yeast cells were harvested and resuspended in sterile deionized H2O and irradiated with 125 J/m2 UVC. Following UV irradiation, cells were spun down and resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) to allow for repair. Aliquots (10 ml of yeast culture) were taken before UV irradiation (No UV), immediately after UV irradiation (0hr), and at 2 hours after UV irradiation (2hr). Cells were spun down and stored at -80˚C until genomic DNA isolation.

value: UV irradiated 125 J/m2

tag: repair time

value: 2 hr


title: TM160


title: Human bone marrow mononuclear cells RNA-seq [Sample 11]

description: Sample 11


title: mcf7_pcDNA_siWNT11_1


title: TM163


title: Human bone marrow mononuclear cells RNA-seq [Sample 09]

description: Sample 09


title: TM159


title: TM220

value: breast cancer


title: mcf7_pcDNA_wt_2

value: transfected with an empty vector (pcDNA).


title: rad16wtH3K36_UV2hr_A5_1bp

value: rad16delta histone WT


title: rad16set2_UV0hr_A2_1bp

value: 0 hr


title: mcf7_pROR2_siWNT11_1

value: transfected with a hROR2 overexpression plasmid (pROR2). Cells were treated with siRNA against WNT11 (siWNT11, #sc-41120, santa cruz).


title: Human bone marrow mononuclear cells RNA-seq [Sample 10]

description: Sample 10

value: Bone marrow

value: Ficoll-gradient selected mononuclear cells


title: Human bone marrow mononuclear cells RNA-seq [Sample 06]

description: Sample 06


title: Human bone marrow mononuclear cells RNA-seq [Sample 07]

description: Sample 07


title: mcf7_pcDNA_wt_1

value: MCF7 (ATCC  HTB-22)

value: mammary gland, breast; derived from metastatic site:pleural effusion


title: rad16wtH3K36_UV0hr_A4_1bp


title: TM218

value: pbmc


title: rad16H3K36A_UV0hr_A4_1bp


title: rad16H3K36A_UV2hr_A5_1bp


title: wtH3K36_UV2hr_A3_1bp

value: histone WT


title: TM219


title: Human bone marrow mononuclear cells RNA-seq [Sample 05]

description: Sample 05


title: TM217


title: Human bone marrow mononuclear cells RNA-seq [Sample 04]

description: Sample 04


title: wtH3K36_UV0hr_A2_1bp


title: TM216


title: TM215


title: Human bone marrow mononuclear cells RNA-seq [Sample 08]

description: Sample 08


title: Semaglutide 8w Rep 7

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

data_processing:
Reads were mapped to the GRCm38.p96 Ensembl mouse genome using STAR v.2.5.2a with default parameters.
Counts in protein coding genes was quantified using STAR and can be found in supplementary.
Genome_build: GRCm38
Supplementary_files_format_and_content: .txt file of RPKM-normalized gene expression

source_name: Liver

extract_protocol: Illumina TruSeq Stranded mRNA Library Prep kit (#20020594, Illumina, San Diego, CA, USA)

value: Semaglutide 8w

tag: weeks treatment


title: TM214


title: Semaglutide 8w Rep 8


title: wtH3K36_NoUV_A1_1bp


title: TM213


title: H3K36A_UV2hr_A3_1bp


title: Human bone marrow mononuclear cells RNA-seq [Sample 02]

description: Sample 02


title: H3K36A_UV0hr_A2_1bp


title: Semaglutide 8w Rep 5


title: Semaglutide 8w Rep 10


title: TM211


title: Semaglutide 8w Rep 9


title: Human bone marrow mononuclear cells RNA-seq [Sample 01]

description: Sample 01


title: H3K36A_NoUV_A1_1bp


title: Semaglutide 8w Rep 4


title: Semaglutide 8w Rep 3


title: TM210


title: SW872_RNA_rep1

first: Ian

middle: Johnathan

last: Davis

state: North Carolina

address: 450 West Dr.

department: Genetics

data_processing:
RNA-seq fastqs: Adaptor sequences were trimmed using (cutadapt v1.12). Reads were filtered using fastq quality filter in FASTX-Toolkit (v0.0.12) with options -Q 33, -p 90, and q 20.  Reads were aligned to hg19 genome using STAR (v2.5.2b) with options: --quantMode TranscriptomeSAM, --outFilterMismatchNmax 2, --alignIntronMax 1000000, --alignIntronMin 20, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1. Salmon (v0.11.3) was used to calculate gene expression (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: sf files (Salmon output) provide TPM (transcirpt per million values) for each transcript. DESeq2 files contain list of differential expressed genes found between the FUS-CHOP positive MLS402, DL221 cell lines and the FUS-CHOP control SW872 control cell line.

source_name: SW872 Cell line

extract_protocol:
Direct-zol (Trizol) extraction
Ribozero rRNA removal kit (Illumina) depletion, NEBNextUltra RNA Library Kit for Illumina

value: myxoid liposarcoma

tag: fus-chop status

value: negative


title: SW872_RNA_rep3


title: TM18


title: rad16set2_UV2hr_rep2_A3_1bp

treatment_protocol: Yeast cells were harvested and resuspended in sterile deionized H2O and irradiated with 125 J/m2 UVC. Following UV irradiation, cells were spun down and resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) to allow for repair. Aliquots (10 ml of yeast culture) were taken before UV irradiation (No UV), immediately after UV irradiation (0hr), and at 2 hours or 3 hours after UV irradiation (2hr or 3 hr). Cells were spun down and stored at -80˚C until genomic DNA isolation.


title: TM17


title: rad16set2_UV0hr_rep2_A2_1bp


title: Semaglutide 8w Rep 1


title: Human bone marrow mononuclear cells RNA-seq [Sample 03]

description: Sample 03


title: Semaglutide 8w Rep 6


title: DL221_RNA_rep1

source_name: DL221 Cell line

value: positive


title: rad16set2_NoUV_rep2_A1_1bp


title: TM16


title: Semaglutide 12w Rep 10

value: Semaglutide 12w


title: TM15


title: TM43


title: Semaglutide 12w Rep 9


title: set2_2hrUV_rep2_A5_1bp

value: UV irradiated 125 J/m2

value: 2 hr


title: mcf7_pcDNA_wt_3

value: epithelial

value: transfected with an empty vector (pcDNA).


title: set2_3hrUV_rep2_A6_1bp

value: 3 hr


title: Semaglutide 12w Rep 8


title: MLS402_RNA_rep2

source_name: MLS402 Cell line


title: MLS402_RNA_rep1


title: set2_0hrUV_rep2_A4_1bp

value: 0 hr


title: SW872_H3K27ac

data_processing:
Library strategy: CUT&RUN
CUT&RUN fastqs: Adaptor sequences were removed from reads using (cutadapt v1.12), and reads were then quality filtered using fastq quality filter in FASTX-Toolkit (v0.0.12) with options -Q 33, -p 90, and q 20. Reads were aligned to a custom hg19-eColi-K12 genome using STAR (v.2.5.2b) with the following options: --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --alignMatesGapMax 1000, --outFilterScoreMin 1, --outFilterMultimapNmax 1
Genome_build: custom hg19-eColi-K12 genome
Supplementary_files_format_and_content: bigWig files contain total read depth normalized signal, and is the signal shown in tracks.  BED files contian peak calls defined by MACS2. Input controls were used for peak calling when available.

extract_protocol:
Phenol chloroform extraction
NEBNext Ultra II DNA Library Prep Kit

tag: chip antibody

value: H3K27ac (ab4729, abcam)


title: Semaglutide 12w Rep 7


title: Semaglutide 8w Rep 2


title: wtSet2_3hrUV_rep2_A3_1bp

value: WT


title: TM42

value: breast cancer


title: Semaglutide 12w Rep 6


title: TM50


title: MLS402_H3K27ac

tag: cell line


title: DL221_H3K27ac

tag: cell type


title: DL221_RNA_rep2


title: wtSet2_2hrUV_rep2_A2_1bp


title: wtSet2_0hrUV_rep2_A1_1bp


title: TM49


title: SW872_SNF2H

value: SNF2H (ABE1026, EMD Millipore)


title: TM48

value: pbmc


title: Semaglutide 12w Rep 4


title: MLS402_SNF2H


title: TM47


title: Semaglutide 12w Rep 3


title: set2d_UV2hr_A5_1bp


title: set2d_UV0hr_A4_1bp


title: HNF4A overexpressing stomach organoids CDX2 3' enhancer homozygous deletion rep 3

description:
RNA-seq
GSE160264_Suppl.Table-oragnoids_RNASeq_Rawcounts_STAR.csv

data_processing:
Alignment and gene counting by STAR
Genome_build: mm10
Supplementary_files_format_and_content: unprocessed gene counts

source_name: Stomach antrum organoids

extract_protocol:
Orgnaoids were removed from matrigel using cell recovery solution and immediately resuspended in trizol for RNA extraction.
Orgnaoids were removed from matrigel using cell recovery solution and immediately resuspended in trizol for RNA extraction. RNA was extracted using Qiagen miniRNA kit with additional on column Dnase digestion.
Libraries were made using NEB Poly-A library preparation kit and 150bp paired end sequencing was performed on Illumina platform.

value: Stomach antrum organoids

value: CDX2 3' enhancer homozygous deletion


title: set2d_NoUV_A6_1bp


title: Semaglutide 12w Rep 2


title: SW872-CHOP_input

data_processing:
ChiP-seq fastqs: Adaptor sequences were with cutadapt (v.1.12). FASTX-Toolkit (v0.0.12) with options -Q 33, -p 90, and q 20 was used to filter reads. Reads were aligned to the hg19 genome using STAR (v2.5.2b) with the following options: --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, --outFilterMultimapNmax 1.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain total read depth normalized signal, and is the signal shown in tracks.  BED files contian peak calls defined by MACS2. Input controls were used for peak calling when available.

extract_protocol:
Spin-column purification
NEBNext Ultra DNA Library Prep Kit

value: myxoid liposarcoma

value: none (input)


title: Chow+Vehicle 12w Rep 8

value: Chow+Vehicle 12w


title: HNF4A overexpressing stomach organoids CDX2 3' enhancer homozygous deletion rep 2


title: Semaglutide 12w Rep 1

value: Semaglutide 12w


title: MLS402-CHOP_input

value: positive


title: TM51


title: HNF4A overexpressing stomach organoids CDX2 3' enhancer heterozygous deletion rep 3

value: CDX2 3' enhancer heterozygous deletion


title: Chow+Vehicle 12w Rep 6


title: SW872-CHOP

value: negative

value: CHOP (Cell Signaling Technology, 2895S)


title: Semaglutide 12w Rep 5


title: Chow+Vehicle 12w Rep 7


title: Chow+Vehicle 12w Rep 5


title: HNF4A overexpressing stomach organoids CDX2 3' enhancer heterozygous deletion rep 2


title: TM110


title: MLS402-CHOP


title: HNF4A overexpressing stomach organoids CDX2 3' enhancer homozygous deletion rep 1


title: TM46


title: TM108


title: DL221_SNF2H


title: TM45


title: DL221-CHOP


title: TM109


title: HNF4A overexpressing stomach organoids CDX2 3' enhancer heterozygous deletion rep 1


title: TM107


title: TM44


title: Chow+Vehicle 12w Rep 3


title: HNF4A overexpressing stomach organoids wild type CDX2 3' enhancer rep 3


title: underground_SD+Si-2

city: Yinchuan

first: Xiang

last: Xiao

state: Ningxia

address: Shengli Street

institute: Ningxia Medical University

data_processing:
Transcriptome analysis using reference genome-based reads mapping：Low quality reads, such as only adaptor, unknown nucleotides>5%, or Q20 <20%(percentage of sequences with sequencing error rates <1%), were removed by perl script.  The clean reads that were filtered from the raw reads were mapped to honeybee (Apis mellifera) genome (OGSv3.2) using Tophat2 software. The aligned records from the aligners in BAM/SAM format were further examined to remove potential duplicate molecules. Gene expression levels were estimated using FPKM values(fragments per kilobase of exon per million fragments mapped) by the Cufflinks software.
Genome_build: Glycyrrhiza_uralensis.gdb.genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Glycyrrhiza uralensis

source_name: Glycyrrhiza uralensis Fisch.

growth_protocol: 75 water-absorbing, full-filled seeds were selected, blotted surface moisture, and sown evenly in each pot filled with 1900 g high-pressure sterilized and fully dried sand medium collected from native desert regions which do not contain any nutrients.

extract_protocol:
Glycyrrhiza uralensis Fisch. seedling in aerial and underground part were collected. Then RNA was extracted and its purity, concentration and integrity were tested. 1ug total RNA was prepared for cDNA libraries using protocol provided by Oxford Nanopore Technologies (ONT). Briefly, SuperScript IV First-Strand Synthesis System (Invitrogen) was used for full length mRNA reverse transcription and following cDNA PCR for 14 circles with LongAmp Tag (NEB). The PCR products were then subjected to FFPE DNA repair and end-repair (NEB) steps and following adaptor ligation using T4 DNA ligase (NEB). Agencourt XP beads was used for DNA purification according to ONT protocol. The final cDNA libraries were added to FLO-MIN109 flowcells and were run on PromethION platform at Biomarker Technology Company (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: (i) control with or without 2 mM Si, (ii) 35~45% of saturation moisture content (drought stress) with or without 2 mM Si, (iii) 75 mM NaCl (salt stress) with or without 2 mM Si, (iv) 35~45% of saturation moisture content + 75 mM NaCl (drought-salt stress) with or without 2 mM Si (Control treatment was added distilled water, Si was added as K2SiO3).

value: underground part

value: salt-droughtt and Si treatment

tag: age

value: 45 days

tag: stress

value: salt-drought stress


title: TM63

value: breast cancer


title: DL221-CHOP_input


title: underground_SD+Si-3

value: salt-drought and Si treatment


title: Chow+Vehicle 12w Rep 2


title: underground_SD+Si-1


title: TM120

value: pbmc


title: Chow+Vehicle 12w Rep 1


title: HNF4A overexpressing stomach organoids wild type CDX2 3' enhancer rep 1

value: Stomach antrum organoids

value: WT


title: Chow+Vehicle 12w Rep 4


title: underground_SD-3

value: salt-drought treatment


title: Lanifibranor 8w Rep 9

value: Lanifibranor 8w


title: TM119


title: underground_SD-1


title: Lanifibranor 8w Rep 10


title: TM62


title: GFPgastricorg_HNF4A_CutandRun

data_processing:
Library strategy: CUT&RUN
Alignment: bowtie2
Peak calling: MACS, version 2.0
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for visualizing aligned sequence tags

extract_protocol:
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina).
DNA libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs) and 150bp paired end sequencing was performed on the HiSeq-X (Illumina).

value: Gastric organoids

value: Wild type

tag: cut&run antibody

value: HNF4A Ab (Novus, NBP1-89679)


title: Gastric_antrum_K27Ac_ChIP_Rep2

data_processing:
Alignment: bowtie2
Peak calling: MACS, version 2.0
Genome_build: mm10
Supplementary_files_format_and_content: read density bigwig file for visualizing aligned sequence tags

tag: tissue/cell type

value: whole gastric antral glands

value: H3K27ac Ab (Active Motif, 39135)


title: Lanifibranor 8w Rep 7


title: TM117


title: Gastric_antrum_K27Ac_ChIP_Rep1


title: underground_SD-2

tag: tissue


title: HNF4Agastricorg_HNF4A_CutandRun

value: HNF4A overexpressing


title: HNF4A overexpressing stomach organoids wild type CDX2 3' enhancer rep 2


title: Lanifibranor 8w Rep 5


title: TM118


title: Intestinal_stem_cell_ATAC_Rep_1

value: Lgr5-IRES-GFP mice

value: Intestinal stem cells

tag: cell subtype

value: Flow sorted GFP+ Lgr5+ stem cells


title: Lanifibranor 8w Rep 8

tag: treatment


title: underground_S+Si-3

value: underground part

value: salt and Si treatment

value: 45 days

value: salt stress


title: TM41

value: pbmc

value: breast cancer


title: TM61


title: Gastric_stem_cell_ATAC_Rep_2

value: Gastric stem cells

tag: strain


title: underground_S+Si-2


title: underground_S-3

value: salt treatment


title: underground_S+Si-1


title: Lanifibranor 8w Rep 3

value: Lanifibranor 8w


title: TM40


title: underground_S-2


title: TM59


title: Lanifibranor 8w Rep 2


title: Lanifibranor 8w Rep 1


title: Gastric_stem_cell_ATAC_Rep_1

tag: genotype


title: CDX2-KO-CnR-Villus

source_name: Mouse small intestinal villus cells from a villin cre-er+, CDX2f/f mouse 7 days after tamoxifen injection.

extract_protocol:
Proximal 1/3rd of small intestine was incubated with 5mM EDTA for 45 minutes to extract villi which were then dissociated to single cells using TrypLE 4x for 30-40 minutes. Single viable cells were isolated using flow sorting.
Whole nuclei were immobilized on Concanavalin A beads followed by antibody incubation overnight, pA-Mnase digestion in an ice bath for one hour followed by extraction of DNA using phenol chloroform.
Libraries were prepared using NEB Next UltraII and 150bp paired end sequencing was performed on the HiSeq-X (Illumina).

value: Mouse small intestinal villus cells

tag: antibody

value: Cell Signaling technology, #12306 (CDX2 Clone D11D10)


title: CDX2-CnR-Villus-Rep3

source_name: Mouse small intestinal villus cells


title: underground_S-1


title: underground_D+Si-3

value: drought and Si treatment

value: drought stress


title: Lanifibranor 8w Rep 6


title: Intestinal_stem_cell_ATAC_Rep_2


title: TM58

tag: blood

tag: disease state


title: CDX2-CnR-Villus-Rep2


title: Lanifibranor 12w Rep 13

value: Lanifibranor 12w

tag: weeks treatment


title: underground_D+Si-1


title: TM38


title: TM37


title: CDX2-CnR-Villus-Rep1


title: TM36


title: underground_D-3

value: drought treatment


title: Lanifibranor 8w Rep 4


title: Intorg-Line2-RNASeq

data_processing:
Alignment: ChIP-seq, ATAC-seq:bowtie2; RNA-seq: STAR; scATAC: CellRanger
CHIP-seq peak calling, ATAC-seq peak calling: MACS, version 2.0
Genome_build: hg19, mm10
Supplementary_files_format_and_content: ATAC-seq, ChIP-seq, CUT&RUN: bigwig file for visualizing aligned sequence tags; RNA-seq: unprocessed gene counts; scATAC-seq: unfiltered peak-cell counts

source_name: Mouse small intestine organoids

extract_protocol:
Orgnaoids were removed from matrigel using cell recovery solution and immediately resuspended in trizol for RNA extraction.
Orgnaoids were removed from matrigel using cell recovery solution and immediately resuspended in trizol for RNA extraction. RNA was extracted using Qiagen miniRNA kit with additional on column Dnase digestion.
Libraries were made using NEB Poly-A library preparation kit and 150bp paired end sequencing was performed on  Illumina platform.

value: Mouse small intestine organoids


title: underground_D-2


title: underground_D-1


title: TM242


title: TM39


title: Lanifibranor 12w Rep 10


title: Lanifibranor 12w Rep 12


title: Lanifibranor 12w Rep 9


title: TM241


title: Lanifibranor 12w Rep 11


title: underground_D+Si-2


title: GFP-Line2-RNASeq

value: Mouse gastric organoids


title: Intorg-Line1-RNASeq


title: underground_CK+Si-3

value: underground part

value: Si treatment

value: no stress


title: TM239


title: TM240


title: GFP-Line1-RNASeq


title: Lanifibranor 12w Rep 8


title: Lanifibranor 12w Rep 7


title: underground_CK+Si-2

value: 45 days


title: TM238

value: pbmc


title: underground_CK+Si-1


title: GFP-Line3-RNASeq


title: HNF4A-Line3-RNASeq


title: TM57

value: breast cancer


title: HNF4A-Line2-RNASeq


title: underground_CK-2

value: control treatment


title: TM223


title: Lanifibranor 12w Rep 5


title: Lanifibranor 12w Rep 4


title: HNF4A-Line1-RNASeq


title: TM56


title: Lanifibranor 12w Rep 3


title: underground_CK-1


title: aerial_SD+Si-3

value: aerial part

value: salt-drought and Si treatment

value: salt-drought stress


title: CDX2-Line3-RNASeq


title: Lanifibranor 12w Rep 2


title: aerial_SD+Si-2


title: CDX2-Line2-RNASeq


title: CDX2-Line1-RNASeq


title: Lanifibranor 12w Rep 1


title: TM221


title: Lanifibranor 12w Rep 6


title: aerial_SD+Si-1


title: TM212


title: underground_CK-3


title: DIO-NASH Vehicle 8w Rep 10

value: DIO-NASH Vehicle 8w


title: DIO-NASH Vehicle 8w Rep 9


title: aerial_SD-3

value: salt-drought treatment


title: Intorg-Line1-ATAC

extract_protocol:
Orgnaoids were removed from matrigel using cell recovery solution and digested to single cells using Trypsin. Fresh viable single cells were isolated using flow sorting.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina).
DNA libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs) and 150bp paired end sequencing was performed on the HiSeq-X (Illumina).


title: Intorg-Line2-ATAC


title: aerial_SD-2


title: TM64

extract_protocol:
The exoRNeasy Serum/Plasma Maxi and Midi Kits from QIAGEN from QIAGEN were used to extract and purify exosomal RNA from the separated blood samples, and the obtaining exosomal RNA was used for miRNA library construction using the QIAseq miRNA Library Kit.
miRNA libraries were prepared for sequencing using standard Illumina protocols


title: DIO-NASH Vehicle 8w Rep 8


title: aerial_SD-1


title: DIO-NASH Vehicle 8w Rep 7


title: GFP-Line2-ATAC

source_name: Mouse gastric organoids


title: aerial_S+Si-3

value: salt and Si treatment

value: salt stress


title: GFP-Line3-ATAC


title: TM222

source_name: PBMC


title: HepG2

city: Cincinnati

first: Tareian

middle: A

last: Cazares

state: OH

address: 3333 Burnet Avenue, MLC 7038

department: Immunobiology and Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Paired-end fastq files were trimmed with Trim-Galore! for adapter contamination removal.
Reads were aligned to the hg38 reference genome with bowtie2, we used parameters (-p 8 --very-sensitive --maxins 2000).
Reads were filtereed by applying post-alignment filters for reads with MAPQ score of ≥ 30 and samflag 3.
We removed duplicates (e.g., PCR artifacts) with samtools rmdup and samtools fixmate with parameter (-n), and further filtered for reads mapping to autosomal chromosomes.
Paired-end reads were converted to bed intervals with bedtools bamtobed and the 5' was shifted +4 on the (+) strand reads and -5 on the (-) strand reads to center the end of the read over the Tn5 cut site.
A 40 bp window was created around the 5' end of the Tn5 corrected cut site using bedtools slop. Intervals that overlapped our maxATAC blacklist were removed (see https://doi.org/10.1101/2022.01.28.478235).
Peaks were called on Tn5 cut sites using MAC2 --shift 0 --ext 40 --no-model
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file of peaks called by MACS2

source_name: Human Hepatocellular Carcinoma

growth_protocol:
Eagle's Minimum Essential Medium (EMEM) (ATCC 30-2003) with 10% Fetal Bovine Serum (FBS)
Cells were cultured per ATCC instructions in appropriate medium.

extract_protocol: OMNI ATAC-seq was performed as described by (Corces et al, 2017)

tag: cell number

value: 50k cells

value: none; untreated


title: TM55

data_processing:
Data were sequenced using Illumina HiSeq X high-throughput sequencing platform
FastQC software was used to assess sequencing quality
Clean reads are obtained after data filtering to remove splice sequences and low quality reads
Genome_build: miRBase
Supplementary_files_format_and_content: Using bowtie2 software to match the quality-controlled Clean Data to the miRBase database of human mature miRNA sequences.
Supplementary_files_format_and_content: The miRNA expression abundance was then assessed and the miRNA expression count matrix was calculated.


title: DIO-NASH Vehicle 8w Rep 6


title: GFP-Line1-ATAC

value: Mouse gastric organoids


title: LoVo

source_name: Human Colorectal Cancer

growth_protocol:
F12K Medium + 10% FBS (Catalog No. 30-2004)
Cells were cultured per ATCC instructions in appropriate medium.

value: LoVo


title: aerial_S+Si-2


title: DIO-NASH Vehicle 8w Rep 5


title: aerial_S+Si-1


title: DND41ResCas9_bioRep2_EBF1g7_Arima_HiC_rep1

city: Philadelphia

first: YEQIAO

last: ZHOU

address: 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
Raw reads for each HiC sample were processed with HiC-Pro (version v2.5.0) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE and GENOME_FRAGMENT provided by Arima.
Genome_build: hg19
Supplementary_files_format_and_content: .hic formatted file for juicebox viewing of contact matrices

source_name: DND41 cell line

extract_protocol:
1-2x10^6 cells were washed with 1xPBS containing 3% BSA and fixed with 2% formaldehyde and proceeded with Arima-HiC Kit per manufacturer’s instructions.
Samples passing Arima-QC1 were used for library construction with Accel-NGS 2S Plus DNA Library Kit (Swift cat# 21024) and 2S SET A INDEXING KIT (Swift cat# 26148) and assessed with Arima-QC2. Samples passing Arima-QC2 were subsequently PCR amplified based on Arima-QC2 calculations, quantified with TapeStation 4150 (Agilent) and KAPA Library Quantification Kit (Roche cat# KK4824) and paired-end (38bp+38bp) sequenced on Illumina NextSeq 550.

value: DND41 cell line

value: T-ALL cell line

tag: lentiviral transduction

value: Cas9 and EBF1-targeting sgRNA

tag: drug treatment

value: GSI


title: HNF4A-Line3-ATAC


title: DIO-NASH Vehicle 8w Rep 4


title: HNF4A-Line2-ATAC


title: DND41ResCas9_bioRep2_ctrl_Arima_HiC_rep1

tag: cell line

tag: cell type

value: Cas9 and control sgRNA


title: aerial_S-3

value: salt treatment

tag: age

value: 45 days

tag: stress


title: DND41_GSIweek4_Arima_HiC_rep1


title: aerial_S-2

value: aerial part


title: CDX2-Line3-ATAC


title: DIO-NASH Vehicle 8w Rep 1


title: DIO-NASH Vehicle 8w Rep 3


title: DIO-NASH Vehicle 8w Rep 2


title: HNF4A-Line1-ATAC


title: aerial_D+Si-3

value: drought and Si treatment

value: drought stress


title: HEK293

source_name: Human Embryonic Kidney

growth_protocol:
Dulbecco’s Modified Eagle’s Medium (DMEM), supplemented with Fetal Bovine Serum (FBS) to a final concentration of 10%
Cells were cultured per ATCC instructions in appropriate medium.


title: CDX2-Line2-ATAC


title: CDX2-Line1-ATAC


title: DIO-NASH Vehicle 12w Rep 10

value: DIO-NASH Vehicle 12w


title: aerial_D+Si-2


title: Donor_20_AMD

description:
all_metadata.csv
all_normalized_expression_data.csv

extract_protocol:
An 8 or 12-mm macular centered punch of RPE/choroid was acquired from twenty human donors. After dissection away from the retina and sclera, the RPE/choroid was finely diced into small squares (approximately 1 mm x 1 mm) with a razor blade. The resulting suspension was dissociated in 450 units/mL of collagenase II (Gibco, Grand Island NY) reconstituted in Hank’s Balanced Salt Solution containing calcium chloride and magnesium chloride (Life technologies, Grand Island NY). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Cryopreserved cells from single-cell donors were rapidly thawed before pre-enrichment for endothelial cells. Cells were incubated for 15 minutes with anti-CD31 microbeads (Miltenyi Biotech, Bergisch Gladbach Germany) according to the manufacturer’s instructions before automated autoMACs magnetic separation (Miltenyi Biotech, Bergisch Gladbach Germany) into CD31+ fractions. Sequencing of CD31-positive fractions was performed on pooled libraries using the Illumina NovaSeq platform (San Diego, CA).
Single-cell RNA-Seq

tag: condition

value: AMD

tag: region

value: macula


title: Donor_19_AMD

tag: tissue


title: DIO-NASH Vehicle 12w Rep 9

tag: treatment


title: aerial_D+Si-1


title: CX3CR1_neg dendritic cells (Sample_2047)

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Illumina Casava1.82 software used for basecalling and demultiplexing.
After demultiplexing, raw reads were pseudoaligned to the murine transcriptome (mm10, GENCODE general assembly release vM16) using Kallisto with default settings
Based on the pseudoalignment estimated by Kallisto, transcript levels were quantified and counts were imported into R using tximport. Transcript information was summarized on gene-level. We imported the resulting dataset and performed the downstream analysis using the DESeq2 pipeline.
Genome_build: mm10
Transcriptome_build: mm10, GENCODE general assembly release vM16
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference transcriptome

source_name: muscularis externa of the small bowel wall

extract_protocol:
For RNA sequencing, 6-25x10e5 cells were harvested for each sample and lysed in TRIzol (Invitrogen). Total RNA was extracted according to the manufacturer’s protocol.
Library preparation for subsequent RNA-sequencing analysis was performed using the TruSeq. RNA Library Prep Kitv2 (Illumina) following manufacturer’s protocol instructions

treatment_protocol: mice/cells did not receive any treatment

value: dendritic cell