title: H526 CDDO biol rep 2

type: RNA

city: Heidelberg

first: Nikolas

last: Gunkel

state: *Not Applicable

address: Im Neuenheimer Feld 280

department: Research Group Cancer Drug Development

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Hybridization (16 h at 45 °C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Clariom S type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

label: biotin

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel).

treatment_protocol: The cells were treated with 50 nM CDDO-me for 6 h.

value: small cell lung cancer


title: H526 DMSO biol rep 2

status: Public on Nov 11 2024

country: Germany

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: H526 CDDO biol rep 1


title: AFB132

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description: ethnicity: European descent

hyb_protocol: Bisulfite converted DNAs were hybridized to beadchips provided the Illumina Infinium MethylationHM450K BeadChip Kit

data_processing:
Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus
Normalized Beta values

molecule: genomic DNA

source_name: Blood

label_protocol: Sample barcoding and staining were carried out by following the instructions of Illumina provided in the Infinium MethylationHM450K BeadChip Kit

growth_protocol: Monocyte DNA samples were obtained from PBMCs frozen in 90% fetal calf serum (FCS) and 10% dimethyl sulfoxide dimethyl sulfoxid

extract_protocol: Each DNA sample was extracted from 2x106 primary monocytes by a standard phenol/chloroform protocol followed by ethanol precipitation. Prior to DNA methylation profiling, DNAs were then bisulfite converted and processed using the Illumina Infinium MethylationEPIC BeadChip Kit, according to the manufacturer's instructions followed by ethanol precipitation

treatment_protocol: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions

tag: cell type

value: CD14+ Monocytes, resting cells

value: Blood

value: CD14+ Monocytes

tag: treatment


title: RNA-seq AOMDSS WT4

type: SRA

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description:
AOMDSS_WT4
AOMDSS_deseq2_normalized_counts.txt

library_source: transcriptomic

data_processing:
The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software by the standard workflow.
The sequencing reads were aligned onto Mus musculus GRCm38/mm10 reference genome using the TopHat v2.1.0 software or Kallisto v0.45.0. The mapped reads were transformed into the count matrix with default parameters using the HTSeq v0.8.0 software, then normalized using the DESeq v2 software. Differentially expressed genes (DEGs) were identified using the same software based on a negative binomial generalized linear model. Sleuth was used to analyze statistical significance of kallisto data.
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including transcript identifiers, length, expected count, and TPM
Supplementary_files_format_and_content: a text file including gene identifiers and normalized counts

molecule: polyA RNA

organism: Mus musculus

source_name: Colitis-induced cancer cells from azoxymethane and dextran sodium sulfate treated wild type mice

growth_protocol: Colon cancer organoids (AKP and KO) were isolated as single cell or multple cells using Gibco TrypLETM Express Enzyme (12605101) following the manufacture's protocols. Those  isolated cells were plated in 1:1 ratio of Matrigel (Corning, 356231) and the minimal medium mix. The minimal medium contained 1x B27 supplement (Thermo, 12587010), 1x Glutamax (Gibco, 35050061) and 1x Penicillin/Streptomycin (Thermo, 15140122) in advanced DMEM-F12 (Thermo, 12634010). Organoids were cultured in the minimal medium and the medium was replaced every other day. Eight days cultured organoids were harvested for sequencing.

extract_protocol:
RNA was purified from colon cancer organoids using QIAGEN miRNeasy kit (217004) with on-column DNase digestion according to the manufacturer’s instructions.
RNA-seq libraries were constructed following Illumina TruSeq Stranded mRNA protocol (20020594). The RNA-seq libraries were sequenced on the Illumina Nextseq 500 (42 bp paired-end run) and Illumina HiSeq 2500 instrument platform (76 bp single-end sequencing) for organoids and colitis-induced cancer cells, respectively.

treatment_protocol: 12.5 mg/kg of azoxymethane (AOM, Sigma, A5486) was administered to 6 weeks old Lgr5CreERT2-IRES-EGFP/+-Dkk2fl/fl mice via intra-peritoneal injection. Lgr5+/+-Dkk2fl/fl littermate mice were used as controls.  After 5 days, mice were treated with 2.5 % of dextran sodium sulfate (DSS, MP biomedicals, molecular mass 36,000–50,000 Da) in the drinking water for 5 days followed by 14 days of regular water. This cycle was performed three times. 7 days after DSS treatment in each cycle, 200 μl of tamoxifen (10 mg/ml in sunflower oil, Sigma, T5648) was delivered into Lgr5CreERT2-IRES-EGFP/+-Dkk2fl/fl mice and their littermate controls by intra-peritoneal injection every other day, total three injections per DSS cycle.

tag: strain

value: C57BL/6 Dkk2fl/fl mice

value: Colon

value: Primary cancer cells


title: H526 DMSO biol rep 3


title: AFB129

description: ethnicity: European descent

scan_protocol: Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: RNA-seq AOMDSS WT3

description:
AOMDSS_WT3
AOMDSS_deseq2_normalized_counts.txt


title: K562_dtagknockin_DMSO_6hr_CTCF_HiChIP_rep2

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

country: USA

institute: Harvard University

library_source: genomic

data_processing:
HiChIP reads for each sample were aligned to hg38 and processed with HiC Pro (v 3.0.0) using the default settings with a DPNii digested genome generated with the digest_genome script. This produced .allvalidpairs files.
Hichipper (v 0.7.7) with default parameters was used to produce unfiltered loop lists(.mango files)
Assembly: hg38
Supplementary files format and content: .allvalidpairs files contain all pairs output by HiC-Pro for a given sample.
Supplementary files format and content: .mango files contains a list of all loops identified by hichipper for a given sample along with the associated P value and PET number.

growth_protocol: K562 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin. HCT116 cells were grown in McCoy's 5A medium supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Cells were fixed in 1% formaldehyde, washed, snap frozen, and stored at -80ºC. Nuclei were isolated and chromatin was subjected to DPNII digestion, biotin fill-in, and in situ ligation. Chromatin was then sheared with a Covaris sonicator and CTCF-bound chromatin was immunoprecipitated overnight.
DNA was tagmented with Tn5 and amplified by PCR.
HiChIP

treatment_protocol: For DNMT1i experiments, cells were treated at 10uM DNMT1i or 0.1% DMSO for 3 days. For dTAG-13 experiments, cells were treated at 500nMM dTAG-13 or 0.1% DMSO for 6 hours. All treatments were in duplicate separate cultures.

tag: cell line

value: chronic myeloid leukemia


title: K562_dtagknockin_DMSO_6hr_CTCF_HiChIP_rep1


title: AFB101

description: ethnicity: European descent


title: sgMKNK1-2_R3

city: Montreal

first: Sonia

last: del Rincón

state: QC

address: 3755 Chemin de la Cote Ste Catherine

institute: McGill University

data_processing:
Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0, reads were filtered against the species reference genome using STAR-Salmon and computes transcript counts using CPM.
Counts of technical replicates were summed up using DESeq2 before performing normalization and differential expression analysis for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include log10 CPM values for each Sample

source_name: 4T1 sgMKNK1-2

growth_protocol: 4T1 tumor cells were maintained in DMEM High Glucose supplemented with 10% FBS, 1.5 g/L sodium bicarbonate, 10 mM HEPES and antibitics, in a humidifed atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the Absolutely RNA Miniprep Kit (Agilent). RNA concentration and quality was assessed using a BioAnalyzer (Agilent).
RNA library preparation was performed using the KAPA mRNA HyperPrep kit (Roche).

value: 4T1 sgMKNK1-2

value: Breast invasive ductal carcinoma tumor cells

tag: genotype

value: MNK1 knockout


title: K562_dtagknockin_dtag13_6hr_CTCF_HiChIP_rep2


title: RNA-seq AOMDSS WT2

description:
AOMDSS_WT2
AOMDSS_deseq2_normalized_counts.txt


title: K562wt_DNMT1i_3days_rep1

data_processing:
UMIs were extracted with umi-tools (v 1.1.1) extract and adapters were  trimmed with cutadapt (v 2.7)
Reads were aligned to hg38 using Star aligner (v 2.6.0) with a genome generated using the Ensembl hg38 primary assembly and Ensembl GTF file v 104 with the following settings: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -- peOverlapNbasesMin 40 --peOverlapMMp 0.8 --outSAMattributes NH HI NM MD
Reads were deduplicated with umi-tools dedup ( v 1.1.1) with flags multimapping-detection-method=NH and unpaired-reads=discard
For gene expression analysis, HTseq – count ( v 0.11.2) was used to count reads in genes and generate counts files. For differential exon analysis, the dexseq_prepare_annotation script was used with the -r no option to prepare gff annotation files from ensemble gtf file (v 104) and the dexseq_count.py script was used to create counts files (dexseq.counts files).
DESeq2 (v 1.28) with R (v 4.0.2) was used to process expression count files to get gene expression foldchange values (deseq2_results.csv files). DEXSeq(v 1.34.1). with R (v 4.0.2) was used to process  exon count files and get normalized exon inclusion changes (dexseq_results.csv files)
Assembly: hg38
Supplementary files format and content: The HTSeq raw count files for genes for each individual sample are provided (.counts files). The DEXSeq raw count files for exons for each individual sample are provided (dexseq.counts files).
Supplementary files format and content: The DESeq2 results files with gene folchange and basemean values are provided for each experiment (deseq2_results.csv files). The DEXSeq results files with exon foldchange and basemean values are provided for each experiment (dexseq_results.csv files).

extract_protocol:
RNA was harvested using the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared using the PolyA enrichment kit and Corral mRNA Library Prep Kit  (Lexogen)

treatment_protocol: For DNMT1i experiments, cells were treated at 10uM DNMT1i or 0.1% DMSO for 3 days. For dTAG-13 experiments, cells were treated at 500nM dTAG-13 or 0.1% DMSO for 6 hours. All treatments were in triplicate separate cultures.


title: HaCaT DMSO biol rep 2

source_name: HaCaT

value: normal skin


title: HaCaT CDDO biol rep 1


title: HaCaT CDDO biol rep 2


title: sgMKNK1-2_R2


title: sgMKNK1-1_R4

source_name: 4T1 sgMKNK1-1

value: 4T1 sgMKNK1-1


title: AFB091

description: ethnicity: European descent


title: H526 DMSO biol rep 1


title: H526 CDDO biol rep 3


title: AFB108

description: ethnicity: European descent


title: AFB105

description: ethnicity: European descent


title: RNA-seq AOMDSS WT1

description:
AOMDSS_WT1
AOMDSS_deseq2_normalized_counts.txt


title: AFB095

description: ethnicity: European descent


title: sgMKNK1-2_R1


title: HaCaT CDDO biol rep 3


title: H82 CDDO biol rep 1


title: sgMKNK1-1_R1


title: AFB093

description: ethnicity: European descent


title: HaCaT DMSO biol rep 1


title: HCT116wt_DMSO_3days_CTCF_HiChIP_rep2

value: colorectal carcinoma


title: HCT116wt_DMSO_3days_CTCF_HiChIP_rep1


title: H82 CDDO biol rep 2


title: sgMKNK1-1_R3


title: AFB090

description: ethnicity: European descent


title: HCT116wt_DNMT1i_3days_CTCF_HiChIP_rep2


title: AFB087

description: ethnicity: European descent


title: K562wt_DNMT1i_3days_CTCF_HiChIP_rep2


title: K562_dtagknockin_dtag13_6hr_CTCF_HiChIP_rep1


title: H82 DMSO biol rep 3


title: H82 CDDO biol rep 3


title: AFB081

description: ethnicity: European descent


title: HCT116wt_DNMT1i_3days_CTCF_HiChIP_rep1


title: AFB084

description: ethnicity: European descent


title: Cas9CTL_R4

source_name: 4T1 Cas9CTL

value: 4T1 Cas9CTL

value: WT


title: Beas-2b CDDO biol rep 2

value: normal lung


title: K562wt_DMSO_3days_CTCF_HiChIP_rep2


title: K562_dtagknockin_DMSO_6hr_CTCF_input_rep2

data_processing:
Reads were aligned to hg38 using Burrow-Wheeler Aligner (BWA-mem, v  0.7.15)
Sam files were converted to bam files and sorted using Samtools view and sort (v 1.5)
Identical ChIP-seq sequence reads were collapsed to avoid PCR duplicates using Picard Tools MarkDuplicates(v 2.18.5) with Java (v 1.8.0) with parameters VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=true
Peaks were called using Homer (v. 4.11) getDifferentialPeaksReplicates where -t was replicate ChIP files, -i was the corresponding replicate input files, with parameters -F 10 and -L 4.  Reactivated DNMT1i peaks were called using Homer (v. 4.11) getDifferentialPeaksReplicates where -t was replicate ChIP files for DNMT1i treatment, -b was the replicate ChIP files for DMSO treatment, and -p was the peaks called in the corresponding DNMT1i treatment condition
Bigwig files were constructed from deduplicated bam files using Deeptools2 (v 3.4.3) bamCoverage with --normalizeUsing RPKM and default settings.
Assembly: hg38
Supplementary files format and content: RPKM normalized bigwig files are provided for each ChIP sample.
Supplementary files format and content: Replicate homer peak files are provided for each ChIP condition. Reactivated peak files for 3 days of DNMT1i v. DMSO are also provided.

extract_protocol:
Cells were fixed in 1% formaldehyde, washed, snap frozen, and stored at -80ºC. Cells were lysed and DNA was sonicated with a Branson Sonicator. Immunoprecipitations were carried out overnight for ChIP samples.
ChIP or input DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.


title: sgMKNK1-1_R2


title: AFB083

description: ethnicity: European descent

value: CD14+ Monocytes, resting cells


title: H82 DMSO biol rep 1

value: small cell lung cancer


title: Cas9CTL_R3


title: K562wt_DMSO_3days_CTCF_HiChIP_rep1


title: Cas9CTL_R2


title: Beas-2b CDDO biol rep 3


title: K562_dtagknockin_DMSO_6hr_CTCF_input_rep1


title: AFB075

description: ethnicity: European descent

value: Blood

value: CD14+ Monocytes


title: H82 DMSO biol rep 2


title: Mouse_SI_perturb_rep2_Xenium

city: Seattle

first: Maximilian

last: Heeg

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Immunology

hyb_protocol: not applicable

scan_protocol: Xenium analyzer and MERSCOPE were used to image target RNA positions and cell boundaries. Proprietary software was used to decode and return RNA positions as outputs from each machine, along with raw images of cell nucleus and boundary stainings.

data_processing:
Cell nuclei were segmented using Cellpose 2.0 (Pachitariu et al. 2022). Cell boundaries were predicted using the nuclear staining and transcript positions using Baysor (Petukhov et al. 2021). Experiments were integrated using scVI (Lopez et al 2018). Celltypes were assigned manually, and the processed object is stored as an Anndata object in h5ad format containing both metadata and raw gene expression counts (Wolf et al 2018).
Raw detected RNA counts per cell

source_name: FFPE block

label_protocol: not applicable

extract_protocol: 5 um-thick microtome sections of Formalin-Fixed Paraffin-Embedded tissues.

value: Small Intestine

value: infection with LCMV

tag: timepoint

value: day 7 after infection


title: AFB079

description: ethnicity: European descent

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: AFB071

description: ethnicity: European descent


title: Beas-2b CDDO biol rep 1


title: RNA-seq Dkk2 KO2

source_name: Dkk2 knockout colon cancer organoids carrying mutations in Apc, Kras and Tp53 genes

value: Colon

value: Organoids


title: K562_dtagknockin_dtag13_6hr_CTCF_input_rep1

value: chronic myeloid leukemia


title: RNA-seq Dkk2 KO5


title: AFB077

description: ethnicity: European descent


title: Cas9CTL_R1

value: Breast invasive ductal carcinoma tumor cells


title: AFB070

description: ethnicity: European descent


title: K562wt_DNMT1i_3days_CTCF_HiChIP_rep1


title: RNA-seq Dkk2 KO1


title: RNA-seq Dkk2 KO4


title: K562_dtagknockin_dtag13_6hr_CTCF_input_rep2


title: Mouse_SI_uninfected_rep2_Xenium

value: uninfected


title: Beas-2b DMSO biol rep 2


title: K562_dtagknockin_DMSO_6hr_CTCF_ChIP_rep1


title: Beas-2b DMSO biol rep 3


title: RNA-seq Dkk2 KO3


title: Mouse_SI_perturb_rep1_Xenium


title: AFB082

description: ethnicity: European descent


title: K562_dtagknockin_DMSO_6hr_CTCF_ChIP_rep2


title: Beas-2b DMSO biol rep 1


title: Mouse_SI_day90_rep1_Xenium

value: day 90 after infection


title: K562_dtagknockin_dtag13_6hr_CTCF_ChIP_rep1


title: RNA-seq AKP3

source_name: Colon cancer organoids carrying mutations in Apc, Kras and Tp53 genes


title: Mouse_SI_uninfected_rep1_Xenium


title: ATAC-seq KO 2

data_processing:
The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software by the standard workflow.
Sequenced reads were trimmed with adaptor sequences (cutadapt v1.9.1, (Martin, 2011)) and mapped to the mouse genome (GRCm38, emsembl release 93) by Bowtie2 (v2.3.4.1, (Langmead and Salzberg, 2012)). Mitochondrial and duplicated reads were removed by SAMtools (v1.9, (Li et al., 2009)) and Picard (v2.9.0, https://broadinstitute.github.io/picard/), respectively.
Peaks were found by MACS2 (v.2.1.1, (Zhang et al., 2008)) and visualized by deepTools (v3.1.1, Ramirez et al., 2014, NAR).
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a narrowPeak file including Chrom, ChromStart, ChromEnd, Name, Score, Strand, SignalValue, pValue, qValue, and Peak.
Supplementary_files_format_and_content: a bigWig file

growth_protocol: Colon cancer organoids (AKP and KO) were isolated as single cell or multple cells using Gibco TrypLETM Express Enzyme (12605101) following the manufacture's protocols. Those  isolated cells were plated in 1:1 ratio of Matrigel (Corning, 356231) and the minimal medium mix. The minimal medium contained 1x B27 supplement (Thermo, 12587010), 1x Glutamax (Gibco, 35050061) and 1x Penicillin/Streptomycin (Thermo, 15140122) in advanced DMEM-F12 (Thermo, 12634010). Colon cancer organoids were cultured in the minimal medium. Normal colonic organoids were cultured in the IntesticultTM organoid culutre medium (STMECELL 06005). The culture medium was replaced every other day. Eight days cultured organoids were harvested for sequencing.

extract_protocol:
Eight days cultured organoids were isolated as single cells using TrypLE (Thermo, 12605010) and fluorescent activated cell sorting (FACS). Dead cells were excluded by Zombie aquaTM (Biolegend 423102) staining. Genomic DNAs were extracted by DNA Clean & Concentrator (Zymo).
ATAC-seq libraries were constructed with 50K cells from each condition following Omni-ATAC protocol (Illumina 20034197(Corces et al., 2017))


title: AFB060

description: ethnicity: European descent


title: AFB068

description: ethnicity: European descent


title: AFB067

description: ethnicity: European descent


title: HCT116wt_DMSO_3days_CTCF_input_rep2

value: colorectal carcinoma


title: RNA-seq AKP2


title: K562_dtagknockin_dtag13_6hr_CTCF_ChIP_rep2


title: Mouse_SI_day90_rep2_Xenium


title: AFB062

description: ethnicity: European descent


title: RNA-seq AKP1


title: HCT116wt_DNMT1i_3days_CTCF_input_rep2


title: Mouse_SI_day30_rep2_Xenium

value: day 30 after infection


title: HCT116wt_DMSO_3days_CTCF_input_rep1


title: ATAC-seq KO 1


title: Mouse_SI_day30_rep1_Xenium


title: AFB055

description: ethnicity: European descent


title: Mouse_SI_day8_rep1_Xenium

value: day 8 after infection


title: AFB057

description: ethnicity: European descent

value: CD14+ Monocytes, resting cells


title: AFB053

description: ethnicity: European descent


title: K562wt_DMSO_3days_CTCF_input_rep2


title: Mouse_SI_day6_rep2_Xenium

value: day 6 after infection


title: ATAC-seq AKP 1


title: AFB048

description: ethnicity: European descent

value: Blood


title: ATAC-seq Normal 2

source_name: Normal colonic organoids


title: HCT116wt_DNMT1i_3days_CTCF_input_rep1


title: ATAC-seq Normal 1


title: AFB061

description: ethnicity: European descent

value: CD14+ Monocytes


title: Mouse_SI_day6_rep1_Xenium

value: Small Intestine


title: K562wt_DMSO_3days_CTCF_input_rep1


title: C&R,WT,Gaf,Rep6

city: philadelphia

first: Mustafa

last: Mir

state: PA

address: 3501 Civic Center Boulevard, CTRB 9030

institute: Children's Hospital of Philadelphia

data_processing:
For ATAC-seq and CUT&RUN, reads were aligned to the Berkeley Drosophila Genome Project (version six) reference genome using bowtie2 with the ‘--sensitive-local’ setting. Samtools was used to convert from .sam to .bam, index, sort, and remove duplicate, unmapped, and multi-mapped reads. For Cut and Run, peaks were called using macs2 using the ‘-f BAMPE’, ‘-g 129789873’, and ‘--bw 300’ settings using IgG as a control. For ATAC-seq, no IgG was used as a control and --nomodel --nolambda settings were used. Consensus peaks were called using the ‘diffbind’ package in R. Peaks were annotated using the CHIPseeker package and ‘TxDb.Dmelanogaster.UCSC.dm6.ensGene’ annotation. Bigwig files were generated using the Bamcoverage function from the deeptools package using the a ‘--binSize 20’, ‘--smoothLength 60’, ‘--centerReads’, ‘--normalizeUsing RPKM’, ‘--effectiveGenomeSize 142573017’.
Assembly: DM6
Supplementary files format and content: .bw files with averaged RPKM with a bine size of 20
Library strategy: Cut&Run

organism: Drosophila melanogaster

extract_protocol:
Embryos were staged to NC12-NC13 and were placed and briefly dried on a double-sided tape . Using a sterile 18 gauge metal needle, embryos were popped into pools of the wash buffer previously described in Panday, A. 2022. Extracted contents were quickly moved in the wash buffer into a 1.5ul tube and temporarily stored at room temperature while samples were collected. Nuclei were collected by slow centrifugation at room temperature at 1500 RCF for 10 minutes.
Cut & Run libraries were made using NEBNext Ultra II NGS library kit and size selected using AMPure XP beads using manufacturer’s protocols.

value: sfGFP-ZLD

tag: antibody

value: GAF


title: AFB047

description: ethnicity: European descent

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: ATAC-seq AKP 2

value: Colon


title: Human_Ileum_donor2_rep2_Xenium

value: Ileum


title: AFB045

description: ethnicity: European descent


title: C&R,WT,Gaf,Rep5


title: K562wt_DNMT1i_3days_CTCF_input_rep2

value: chronic myeloid leukemia


title: Human_Ileum_donor2_rep1_Xenium


title: Mouse_SI_day8_rep2_Xenium

value: infection with LCMV


title: K562wt_DNMT1i_3days_CTCF_input_rep1


title: HCT116wt_DMSO_3days_CTCF_ChIP_rep2


title: AFB043

description: ethnicity: European descent


title: AFB041

description: ethnicity: European descent


title: C&R,WT,Gaf,Rep3


title: C&R,WT,Gaf,Rep4


title: Human_Ileum_donor1_rep1_Xenium


title: Human_Ileum_donor1_rep2_Xenium


title: HCT116wt_DMSO_3days_CTCF_ChIP_rep1


title: AFB038

description: ethnicity: European descent


title: Liver,MOCA treated female F1-TKm30 mice-4

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

data_processing:
Quality trimming and adapter clipping of the read data were performed using Trimmomatic version 0.38.
Trimmed reads were mapped to the transcript in the human  reference sequence mm10 using Bowtie2 aligner within RSEM.
Read count extraction and normalization were performed using edgeR program.
Assembly: mm10
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Liver

extract_protocol:
RNeasy Mini Kit was performed according to the manufacturer's instructions.
The sequencing libraries were prepared from 200 ng of total RNA with MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd.) according to the manufacturer's instructions.

treatment_protocol: Female 17- or 21-week-old C57BL mice were treated with 0 or 0.05% 4,4'-Methylenebis(2-chlorobenzenamine) (MOCA) for 4 weeks.

value: Liver

tag: Sex

value: female

value: MOCA

tag: time

value: 4 weeks


title: HCT116wt_DNMT1i_3days_CTCF_ChIP_rep2

value: colorectal carcinoma


title: C&R,Zf5,Gaf,Rep3

value: mNG-ZF5 GLC


title: C&R,Zf5,Gaf,Rep4


title: Liver,MOCA treated female F1-TKm30 mice-3


title: AFB035

description: ethnicity: European descent

value: CD14+ Monocytes, resting cells


title: AFB031

description: ethnicity: European descent

value: Blood


title: Liver,MOCA treated female F1-TKm30 mice-2


title: K562wt_DMSO_3days_CTCF_ChIP_rep2


title: K562wt_DMSO_3days_CTCF_ChIP_rep1


title: Liver,MOCA treated female F1-TKm30 mice-1


title: AFB028

description: ethnicity: European descent

value: CD14+ Monocytes


title: K562wt_DNMT1i_3days_CTCF_ChIP_rep2


title: C&R,Zf5_het,Zld,Rep6

value: mNG-ZF5 Het GLC

value: Zelda


title: C&R,Zf5_het,Zld,Rep7


title: Liver, control female F1-TKm30 mice-4

value: Control


title: K562wt_DNMT1i_3days_CTCF_ChIP_rep1


title: Liver, control female F1-TKm30 mice-3


title: AFB040

description: ethnicity: European descent

value: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions


title: C&R,Zf5_het,Zld,Rep5


title: AFB022

description: ethnicity: European descent


title: C&R,Zf5_het,Zld,Rep4


title: AFB026

description: ethnicity: European descent


title: Liver, control female F1-TKm30 mice-2


title: AFB018

description: ethnicity: European descent


title: HCT116wt_DNMT1i_3days_CTCF_ChIP_rep1


title: C&R,Zf5_het,Zld,Rep3


title: C&R,Zf5,Gaf,Rep2

value: GAF


title: KMS28BM_B

city: 南京

first: yang

last: shu

state: 江苏

address: xianlin road

country: China

institute: Nanjin university of Chinese medicin

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 mapped to mm8 whole 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: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Multiple myeloma cells

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: Homo multiple myeloma cells

value: before sorting


title: AFB013

description: ethnicity: European descent


title: H929_A

value: after sorting


title: HaCaT DMSO biol rep 3

value: normal skin


title: C&R,Zf5_het,Zld,Rep1


title: Male_female_young_old

city: Boston

first: Kseniia

last: Petrova

address: 200 Longwood

department: System's biology

institute: HMS

library_source: transcriptomic single cell

data_processing:
inDrops standard pipeline
Assembly: Daphnia Magna DM3 genome assembly BioProject ID: PRJNA624896; Fields et al
Supplementary files format and content: .mtx contains counts in csc format; genes.tsv files contain list of genes, corresponding to columns in the mtx file; barcodes.tsv file contains sample information for each cell corresponding to rows of .mtx file

organism: Daphnia magna

source_name: whole body

extract_protocol:
dissociation with collagenase (4 mg / ml) treatment
according to the inDrops protocol ()

treatment_protocol: standard Daphnia lab protocol

value: whole body


title: H929_B


title: Liver, control female F1-TKm30 mice-1

value: Liver

value: female


title: Bacteroides fragilis str. NCTC 9343, filtered culture, nascent transcript sequencing

city: Madison

first: Robert

last: Landick

state: WI

address: 1550 Linden Drive

department: Biochemistry

institute: University of Wisconsin-Madison

description: Native elongating transcript sequencing (NET-seq) was performed on nascent transcripts derived from a filtered Bacteroides fragilis culture and identifies known pauses

library_source: other

data_processing:
NET-seq data were processed using a combination of custom scripts and standard tools. Briefly, adapters, linker, and control oligos potentially contaminating each sample were trimmed from raw reads using cutadapt (v3.4). Reads with a minimum length of 14 nts were mapped to the B. fragilis genome (NC_003228.3) using Bowtie (v1.3.0) allowing both one mismatch and random assignment of reads mapping to multiple loci based on alignment stratum (Bowtie options --best -a -M 1 -v 1). Alignments were converted to BAM and BED files using samtools (v1.16.1) and bedtools (v2.30.0). The specific 3' end counts for each genome position were determined using bedtools (options -d -strand - -5 [plus strand] or -d -strand + -5 [minus strand]).
Assembly: NC_003228.3
Supplementary files format and content: Tab-delimited text file. In this file Col1: strand (+ or -), Col2: genome position, Col3: total counts of that genome position at any position in a read, Col4: total counts of that genome position as a 3' end in a read, and Col5: ratio of 3' end counts to totat counts anywhere in a mapped read for that position.
Library strategy: NET-seq

molecule: other

organism: Bacteroides fragilis NCTC 9343

source_name: Bacterial cell

growth_protocol: Bacteroides fragilis NCTC 9343 rpoC-3xFLAG was streaked onto supplemented brain heart infusion (BHIS) plates and incubated at 37 °C anaerobically for 2 days. A swab from a dense area on the plate was used to inoculate overnight cultures. The next day, 10 mL of the overnight culture was used to inoculate 500 mL supplemented basal medium (SBM) (starting apparent OD600 0.04 as measured by a Denville® CO8000 Personal Cell Density Meter). When the apparent OD600 measured 0.65, cultures were removed from the anaerobic chamber and 300 mL was used for subsequent steps.

extract_protocol:
To harvest nascent transcripts for the NET-seq workflow, cultures were filtered between two vacuum filtration systems using a 0.45 µm pore nitrocellulose filter (GVS Micron Sep, 1215305). Cells were scraped off each filter using a spatula and plunged immediately into liquid nitrogen (i.e., cells from the same culture were combined into the same 50 mL conical tube containing ~25 mL liquid nitrogen). Collected cells were cryo-lysed using a RETSCH mixer mill (MM 400) as previously described (Larson, M. H. et al. 2014. Science 344: 1042-47), with the exception that 50 mL stainless steel canisters and a 25 mm stainless steel ball were used to perform the cryomilling.
To isolate nascent transcripts, we performed a modified 3xFLAG-IP protocol with previously described buffers Larson, M. H. et al. 2014. Science 344: 1042-47). Specifically, the thawed grindate volume was scaled to 5.5 mL with lysis buffer (1x lysis stock [20 mM Tris, pH 8.0, 0.4% Triton X-100, and 0.1% NP-40 substitute], 100 mM NH4Cl, 1x EDTA-free cOmplete Mini protease inhibitor cocktail [Roche Diagnostics GmbH, 11836170001], 10 mM MnCl2, and 50 U/mL RNasin [Promega, N211B], and 0.4 mg/mL puromycin), DNA was partially digested for 20 min with RQ1 DNase (0.054 U/mL [0.02 U/mL for the E. coli-only NET-seq pilot experiment])[Promega, M6101], and digestion reactions were stopped by addition of EDTA to 28 mM (final concentration). RNAP-nascent transcript complexes were directly immunoprecipitated using Anti-FLAG M2 affinity gel (Sigma, A2220) (i.e., without buffer exchange), and the precipitated RNAP-nascent transcript complexes were subsequently washed four times (1x lysis stock, 100 mM NH4Cl, 300 mM KCl, 1 mM EDTA, and 50 U/mL RNasin) [Promega, N2515]. RNAP-nascent transcript complexes were eluted twice with 3xFLAG peptide (Sigma, F4799) (1x lysis stock, 100 mM NH4Cl, 2 mg/mL 3xFLAG peptide, 1 mM EDTA, and 50 U/mL RNasin). Nascent transcripts were purified using a miRNeasy kit [Qiagen, 217084] as previously described (Larson, M. H. et al. 2014. Science 344: 1042-47). However, to reduce phenol and chaotropic salt contamination, nascent transcripts were subjected to an additional overnight isopropanol-GlycoBlue (Invitrogen, AM9516) precipitation at -20 °C.
For nascent transcript library generation, we followed a modification of a previous NET-seq workflow (Larson, M. H. et al. 2014. Science 344: 1042-47 and Churchman, L. S. & Weissman, J. S. 2011. Nature 469: 368-73). Specifically, our workflow included using custom adaptors compatible with an Illumina NovaSeq X instrument. Likewise, the DNA adapter used for nascent transcript 3' end ligation was adenylated using components from a NEB 5' DNA Adenylation kit (E2610; 6µM DNA linker [/5Phos/NNNNNNNNNNgcagctCTGTAGGCACCATCAATGATCGTCGGA/3ddC/], 80 µM ATP, 6 µM Mth RNA ligase, and 1X Adenylation Reaction Buffer). The adenylation reaction was incubated for 4 h incubation at 65 °C, inactivated at 85 °C for 5 min, and precipitated overnight at -20 °C with isopropanol and GlycoBlue (Invitrogen AM9516). The precipitated, adenylated DNA linker was ligated to 750 ng of precipitated nascent transcripts, in duplicate, using components of a NEB T4 RNA Ligase 2, truncated (T4 Rnl2tr) kit (M0242; 10% DMSO, 22% PEG8000, 3 µM adenylated DNA linker, T4 Rnl2tr [14.7 U/µL], RNasin [2U/µL], and 1x T4 RNA Ligase Reaction Buffer). These ligation reactions were incubated at 37 °C for 4 h. After this incubation, T4 Rnl2tr was inactivated by incubation with Proteinase K (0.04 U/µL) (NEB, P8107) at 37 °C for 1 h. RNAs were fragmented, resolved, gel extracted, and precipitated as previously described (Larson, M. H. et al. 2014. Science 344: 1042-47 and Churchman, L. S. & Weissman, J. S. 2011. Nature 469: 368-73), with the exception that the gel extraction incubation at 70 °C was increased to 25 min. cDNAs were synthesized using a custom adapter (/5Phos/AGATCGGAAGAGCACACGTCTGAAC/iSp18/CACTCA/iSp18/CCTACACGACGCTCTTCCGATCTTCCGACGATCATTGATGGTGCCTACAG) and a previously described protocol (Larson, M. H. et al. 2014. Science 344: 1042-47 and Churchman, L. S. & Weissman, J. S. 2011. Nature 469: 368-73), with the exception that the reaction time was increased to 1 h. Circularization of gel extracted and precipitated cDNAs was performed using a protocol previously described (Larson, M. H. et al. 2014. Science 344: 1042-47 and Churchman, L. S. & Weissman, J. S. 2011. Nature 469: 368-73), with the exception that the circularization reaction incubation period was increased to 3 h and the gel extraction incubation period was increased as above. After circularization, cDNA libraries were PCR amplified using minimal cycles and custom adapters (AATGATACGGCGACCACCGAGATCTACACAGCGAGCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCCGACGATC and CAAGCAGAAGACGGCATACGAGATAAGGATGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT), gel extracted, and precipitated as previously described (Larson, M. H. et al. 2014. Science 344: 1042-47 and Churchman, L. S. & Weissman, J. S. 2011. Nature 469: 368-73). Library concentration and amplified product size distribution were determined using an Agilent TapeStation 4150. NET-seq libraries were sequenced by the University of Wisconsin-Madison Biotechnology Center on an Illumina NovaSeq X Plus instrument.

value: Bacterial cell

value: Bacteroides fragilis str. NCTC 9343 culture filtered, flash frozen, and nascent transcripts isolated


title: AFB017

description: ethnicity: European descent

value: CD14+ Monocytes, resting cells


title: Hela cells expressing 3×Flag-TFEB,Torin1, rep3

status: Public on Nov 10 2024

city: Avenida da Universidade Taipa

first: Chen

last: Ming

address: Macau

department: Faculty of Health Sciences

country: Macau

institute: the University of Macau

description:
gene.expression.txt
Torin1vsCtrl.txt

data_processing:
Three replicates of paired-end reads were trimmed and filtered by Fastp and qualified by FastQC, reads were aligned to the hg38 RefSeq database using HISAT2.
The gene count matrix and transcript count matrix were generated by Stringtie.
Genes with FPKM (fragments per kilobase per million mapped reads) larger than or equal to 0.1 were included.
Differential gene expression was performed using DESeq2.
Differential expression genes (DEGs) were selected based on corrected p-value using the Benjamini-Hochberg method (Padj) <0.05 and fold change (FC) > 1.5 or < -1.5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include DEG results

source_name: Hela cells

growth_protocol: Cells were cultured using DMEM containing 10% FBS and 1% PS

extract_protocol:
For RNA-seq, total RNA was extracted from Hela cells expressing 3×Flag-TFEB using RNA stabilization and storage solution (RNAlater™, Thermo, AM7020)
For RNA-seq, the RNA extraction was followed by reverse transcription with an oligo-dT primer, RNA library preparation, and paired-end sequencing was performed at the DNBSeq platform by Bioyi Biotechnology Co., Ltd. Wuhan.

treatment_protocol: CCCP (20µM) for 6h; sucrose (150mM) for 8h; Torin1 (1µM) for 6h

value: Hela cells

value: Cervical cancer cells

value: expressing 3xFlag-TFEB


title: Jurkat, MYB dTAG Jurkat, MYB (L) OE rep2

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

data_processing:
RNA-seq reads were mapped to transcript sequences of curated RefSeq (Release 105.20190906; NM and NR transcripts) and MYB (S)  using salmon (version 1.4.0) with the options “--gcBias --seqBias –validateMappings”.
The index file for the transcript sequences was created with default settings.
Transcript-level read counts were converted to gene-level read counts using tximport (version 1.20.0).
Genes that did not have more than 5 read counts in at least two samples were removed.
Gene-level read counts were normalized by upper-quantile normalization.
Differentially expressed genes were then estimated using DESeq2 (version 1.32.0).
Assembly: hg19
Supplementary files format and content: Tab-delimited files include transcript-level read counts (salmon output files)

source_name: Jurkat

growth_protocol: Jurkat cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the DNBSEQ platform were performed at the BGI Genomics.

treatment_protocol: Jurkat cells were infected with MYB (L)/(S)-expressing lentiviruses and treated with dTAG.

value: Jurkat

value: FKBP-MYB knock-in, MYB (L) overexpression

value: dTAG


title: Hela cells expressing 3×Flag-TFEB, sucrose, rep2

description:
gene.expression.txt
SucrosevsCtrl.txt

value: Sucrose


title: MYB dTAG MYB (S) OE rep2

value: FKBP-MYB knock-in, MYB (S) overexpression


title: Hela cells expressing 3×Flag-TFEB, sucrose, rep1

description:
gene.expression.txt
SucrosevsCtrl.txt


title: KMS28BM_A

value: Homo multiple myeloma cells


title: Hela cells expressing 3×Flag-TFEB, sucrose, rep3

description:
gene.expression.txt
SucrosevsCtrl.txt


title: Jurkat, MYB dTAG Control rep2

value: FKBP-MYB knock-in


title: C&R,Zf5_het,Zld,Rep2

value: mNG-ZF5 Het GLC

value: Zelda


title: Jurkat, MYB DMSO Control rep2

value: DMSO


title: MYB dTAG MYB (S) OE rep1


title: Jurkat, MYB dTAG Jurkat, MYB (L) OE rep1


title: Hela cells expressing 3×Flag-TFEB, CCCP, rep2

description:
gene.expression.txt
CCCPvsCtrl.txt

value: CCCP


title: Jurkat, MYB dTAG Control rep1


title: Hela cells expressing 3×Flag-TFEB, CCCP, rep1

description:
gene.expression.txt
CCCPvsCtrl.txt


title: Hela cells expressing 3×Flag-TFEB, CCCP, rep3

description:
gene.expression.txt
CCCPvsCtrl.txt


title: Hela cells expressing 3×Flag-TFEB,Torin1, rep1

description:
gene.expression.txt
Torin1vsCtrl.txt


title: Hela cells expressing 3×Flag-TFEB,Torin1, rep2

description:
gene.expression.txt
Torin1vsCtrl.txt


title: Jurkat, MYB DMSO Control rep1


title: Jurkat, 24h dTAG rep1 (spike-in)

data_processing:
RNA-seq reads were mapped to transcript sequences of curated RefSeq (Release 105.20190906; NM and NR transcripts) with ERCC spike-in controls using salmon (version 1.4.0) with the options “--gcBias --seqBias –validateMappings”.
The index file for the transcript sequences was created with default settings.
Transcript-level read counts were converted to gene-level read counts using tximport (version 1.20.0).
Genes that did not have more than 5 read counts in at least two samples were removed.
Gene-level read counts were normalized by upper-quantile normalization.
The gene-level read counts of spike-in controls were applied to RUVSeq (version 1.26.0) for estimating a factor (k=1) of unwanted variation between samples.
Differentially expressed genes were then estimated using DESeq2 (version 1.32.0).
The estimated unwanted factor was incorporated to the design formula of DESeq2 for spike-in normalization.
Assembly: hg19
Supplementary files format and content: Tab-delimited file includes transcript-level read counts (salmon output) for each sample.

growth_protocol: FKBP-MYB Jurkat cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen), ERCC spike-in RNA (Invitrogen) was added per manufacturer's instructions.
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the DNBSEQ platform were performed at the BGI Genomics.

treatment_protocol: Jurkat cells with FKBP knock-in at the MYB locus was treated with DMSO or dTAG.

value: T lymphoblast

value: 24 hours


title: Jurkat, 24h dTAG rep2 (spike-in)


title: Jurkat, 24h DMSO rep2 (spike-in)


title: Inland annual, floral bud stage, sample 10

city: EAST LANSING

first: David

middle: Bryant

last: Lowry

state: MI

address: 612 WILSON RD RM 166

department: Plant Biology

institute: Michigan State University

description: Rapid Run flow cells (v2)

data_processing:
Raw reads were filtered for quality with FastQC before processing to remove adapter sequences with Cutadapt. Cutadapt was applied with an adapter mismatch error threshold of 20% of primer length. Primer trimming began with the 5’ end (NNNN followed by 3-5 G’s with a first step to cut 8 bases and a second step to cut and remaining 5’ G’s). Trimming of the 3’ end was done by removing 15bp of the 3’ end of each read to remove the poly-A primer and any readthrough. To retain only high-quality sequences after trimming, any bases on either end with a quality score < 30 were removed and we required the last two bases of each read to match the poly-A primer while discarding any reads <30bp in length. These parameters align with the requirements for the Tag-Seq methodology to remove both adapter sequences and non-template bases created during library preparation. Trimmed sequence files were concatenated and aligned to the Mimulus guttatus v2.0 reference genome using the memory-efficient Borrows-Wheeler Aligner (BWA-MEM). Aligned reads were filtered to include only high-quality, primary alignments using Samtools. The total number of aligned reads retained for each sample was calculated with Samtools. Counting the number of reads aligned per gene per sample was done with HT-seq v.0.6.1 with “stranded” and “union” parameter options. Count files were filtered to remove genes with < 5 aligned reads to exclude non-expressed genes or alignment artifacts.
Assembly: Mimulus guttatus v2.0 reference genome
Supplementary files format and content: csv file of count data for each of the 80 samples in the experiment

organism: Erythranthe guttata

source_name: bud

growth_protocol: To identify patterns of gene expression divergence between the ecotypes, we selected one coastal perennial (SWB-4) and one inland annual (LMC-17) accession for a detailed study throughout development. Surface-sterilized Mimulus guttatus seeds were placed on 60 mm diameter x 15mm height Petri dishes containing half-strength Linsmaier and Skoog (LS) medium: 1.5% w/v sucrose and 0.25% Phytagel (P8169, Sigma). Seeds were then stratified at 4°C in the dark for 14 days. After cold treatment, plants were grown at 20°C under a 16 h 100 mE light / 8 h dark cycle for 5 to 14 days in a Percival (Percival Scientific, Perry, IA) chamber. Cotyledon-stage seedlings were transferred to 3.5-inch square pots containing SureMix Perlite (Michigan Grower Products, Galesburg, MI) and grown in a BioChambers FXC-19 flex growth chamber (BioChambers, Winnipeg, Manitoba) in the same conditions as in the Percival chamber. Three key steps were taken to minimize the effects of environmental heterogeneity within the growth chamber. First, the locations of plants were fully randomized across trays within the chamber. Second, the tray position within the chamber was haphazardly rotated daily. Third, the developmental stage at which each plant was sampled was assigned randomly. Developmentally equivalent leaf pairs and floral buds were collected in a time series manner. Only one tissue was collected per plant to avoid induced responses and repeated measures. Each tissue collection was harvested in a fixed time window (14:00 to 14:30) during the simulated daylight period. Tissue was immediately flash frozen on liquid nitrogen and stored in a -80° C freezer. For the inland annual plants, we sampled at the two-leaf, four-leaf, and floral bud stages because plants often flowered after producing four true leaves. Because the coastal perennial plants flowered at a later developmental stage, we sampled at the two-leaf, four-leaf, six-leaf, eight-leaf, and floral bud stages. All tissue samples were collected before anthesis. Overall, we collected 10 biological replicates for each developmental stage x ecotype combination (N = 80 total tissue samples).

extract_protocol:
RNA was extracted from tissue samples using a Spectrum Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO).
We prepared genomic libraries using a 3’-Tag-Seq procedure, which restricts sequencing to the 3’ end of RNAs and dramatically reduces the cost for RNA-seq studies. Each sample was assigned a fully randomized position across four pools of 20 samples before library construction. The MSU Genomics Core Facility conducted sequencing in Illumina HiSeq 2500 Rapid Run flow cells (v2) in the 1x100bp conformation. Sequencing of the four pooled libraries was conducted across three different flow cells, with two pools being sequenced in two separate flow cells and the other pools only being sequenced on a single flow cell each.
3' Tag RNA-Seq

treatment_protocol: All samples were collected from plants grown under the same environmental conditions.

value: bud

tag: ecotype

value: Inland

tag: library pool

tag: barcode


title: Inland annual, floral bud stage, sample 1

description: Rapid Run flow cells (v2)


title: Jurkat, 06h DMSO rep2 (spike-in)

value: 6 hours


title: Jurkat, 02h dTAG rep2 (spike-in)

value: 2 hours


title: Jurkat, 24h DMSO rep1 (spike-in)

value: Jurkat


title: Inland annual, floral bud stage, sample 4

description: Rapid Run flow cells (v2)


title: Inland annual, floral bud stage, sample 3

description: Rapid Run flow cells (v2)


title: Jurkat, 06h dTAG rep1 (spike-in)


title: Jurkat, 02h DMSO rep2 (spike-in)


title: Inland annual, floral bud stage, sample 6

description: Rapid Run flow cells (v2)


title: Jurkat, 02h DMSO rep1 (spike-in)


title: Inland annual, floral bud stage, sample 8

description: Rapid Run flow cells (v2)


title: Inland annual, floral bud stage, sample 9

description: Rapid Run flow cells (v2)


title: Jurkat, 06h DMSO rep1 (spike-in)


title: Inland annual, floral bud stage, sample 5

description: Rapid Run flow cells (v2)


title: Jurkat, 06h dTAG rep2 (spike-in)


title: Inland annual, floral bud stage, sample 7

description: Rapid Run flow cells (v2)


title: Jurkat, 02h dTAG rep1 (spike-in)


title: Jurkat 96h dTAG rep1

data_processing:
RNA-seq reads were mapped to transcript sequences of curated RefSeq (Release 105.20190906; NM and NR transcripts) using salmon (version 1.4.0) with the options “--gcBias --seqBias –validateMappings”.
The index file for the transcript sequences was created with default settings.
Transcript-level read counts were converted to gene-level read counts using tximport (version 1.20.0).
Genes that did not have more than 5 read counts in at least two samples were removed.
Gene-level read counts were normalized by upper-quantile normalization.
Differentially expressed genes were then estimated using DESeq2 (version 1.32.0).
Assembly: hg19
Supplementary files format and content: Tab-delimited file includes transcript-level read counts (salmon output) for each sample.

value: 96 hours


title: Inland annual, floral bud stage, sample 2

description: Rapid Run flow cells (v2)


title: Inland annual, four-leaf stage, sample 7

description: Rapid Run flow cells (v2)


title: Inland annual, four-leaf stage, sample 3

description: Rapid Run flow cells (v2)


title: Jurkat 96h DMSO rep1


title: Jurkat 96h dTAG rep2

value: dTAG


title: Inland annual, four-leaf stage, sample 2

description: Rapid Run flow cells (v2)


title: Inland annual, four-leaf stage, sample 10

description: Rapid Run flow cells (v2)


title: Jurkat 48h dTAG rep2

value: 48 hours


title: Jurkat 96h DMSO rep2


title: Jurkat 48h dTAG rep1


title: Inland annual, four-leaf stage, sample 4

description: Rapid Run flow cells (v2)


title: Jurkat 48h DMSO rep1


title: Inland annual, four-leaf stage, sample 5

description: Rapid Run flow cells (v2)


title: Inland annual, four-leaf stage, sample 6

description: Rapid Run flow cells (v2)


title: Inland annual, two-leaf stage, sample 1

description: Rapid Run flow cells (v2)


title: Inland annual, two-leaf stage, sample 7

description: Rapid Run flow cells (v2)


title: Inland annual, four-leaf stage, sample 1

description: Rapid Run flow cells (v2)


title: Jurkat 16h dTAG rep1

value: 16 hours


title: Inland annual, two-leaf stage, sample 9

description: Rapid Run flow cells (v2)


title: Jurkat 48h DMSO rep2


title: Jurkat 24h DMSO rep2


title: Jurkat 24h dTAG rep1


title: Jurkat 16h dTAG rep2


title: Inland annual, two-leaf stage, sample 3

description: Rapid Run flow cells (v2)


title: Jurkat 24h DMSO rep1


title: Inland annual, four-leaf stage, sample 9

description: Rapid Run flow cells (v2)


title: Inland annual, four-leaf stage, sample 8

description: Rapid Run flow cells (v2)


title: Inland annual, two-leaf stage, sample 5

description: Rapid Run flow cells (v2)


title: Inland annual, two-leaf stage, sample 4

description: Rapid Run flow cells (v2)


title: Jurkat 16h DMSO rep2


title: Jurkat 16h DMSO rep1


title: Inland annual, two-leaf stage, sample 10

description: Rapid Run flow cells (v2)


title: Jurkat 08h DMSO rep2

value: 8 hours


title: Jurkat 08h DMSO rep1

value: FKBP-MYB knock-in


title: Inland annual, two-leaf stage, sample 2

description: Rapid Run flow cells (v2)


title: Inland annual, two-leaf stage, sample 8

description: Rapid Run flow cells (v2)


title: Jurkat 08h dTAG rep1


title: Coastal perennial, floral bud stage, sample 1

description: Rapid Run flow cells (v2)

value: Coast


title: Jurkat 24h dTAG rep2


title: Jurkat 06h dTAG rep2


title: Inland annual, two-leaf stage, sample 6

description: Rapid Run flow cells (v2)


title: Coastal perennial, floral bud stage, sample 10

description: Rapid Run flow cells (v2)


title: Coastal perennial, floral bud stage, sample 4

description: Rapid Run flow cells (v2)


title: Jurkat 06h DMSO rep2


title: Coastal perennial, floral bud stage, sample 9

description: Rapid Run flow cells (v2)


title: Coastal perennial, floral bud stage, sample 7

description: Rapid Run flow cells (v2)


title: Coastal perennial, floral bud stage, sample 8

description: Rapid Run flow cells (v2)


title: Jurkat 06h DMSO rep1


title: Jurkat 06h dTAG rep1


title: Jurkat 08h dTAG rep2


title: Coastal perennial, floral bud stage, sample 6

description: Rapid Run flow cells (v2)


title: Jurkat 04h DMSO rep2

value: 4 hours


title: Jurkat 04h dTAG rep2


title: Jurkat 04h dTAG rep1


title: Coastal perennial, floral bud stage, sample 2

description: Rapid Run flow cells (v2)


title: Coastal perennial, floral bud stage, sample 5

description: Rapid Run flow cells (v2)


title: Jurkat 02h dTAG rep2


title: Jurkat 02h dTAG rep1


title: Coastal perennial, eight-leaf stage, sample 10

description: Rapid Run flow cells (v2)


title: Coastal perennial, eight-leaf stage, sample 8

description: Rapid Run flow cells (v2)


title: Coastal perennial, eight-leaf stage, sample 2

description: Rapid Run flow cells (v2)


title: Jurkat 01h dTAG rep2

value: 1 hour


title: Coastal perennial, eight-leaf stage, sample3

description: Rapid Run flow cells (v2)


title: Coastal perennial, floral bud stage, sample 3

description: Rapid Run flow cells (v2)


title: Jurkat 04h DMSO rep1

value: DMSO


title: Coastal perennial, eight-leaf stage, sample 9

description: Rapid Run flow cells (v2)


title: Jurkat 01h dTAG rep1

value: T lymphoblast


title: Jurkat 01h DMSO rep2


title: Coastal perennial, eight-leaf stage, sample 4

description: Rapid Run flow cells (v2)


title: Jurkat 01h DMSO rep1


title: Coastal perennial, eight-leaf stage, sample 1

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB dTAG pMYB rep2

data_processing:
CUT&RUN reads were mapped to the hg19 genome (no alt analysis set) including E. coli K12 MG1655 DNA using bowtie2 (version 2.4.2) with the options “-X 1000 --very_sensitive --dovetail”.
Duplicated reads were marked using GATK MarkDuplicates (version 4.1.9.0) with the default settings.
Reads with MAPQ < 10 and duplicated reads were filtered out.
Reads mapped to blacklisted regions (v2) including chrEBV and chrMT were filtered out as well.
The number of spike-in reads mapped to the E. coli DNA was counted for each sample.
Read coverage profile was generated using deepTools bamCoverage (version 3.4.1) with the options “--normalizeUsing None --binSize 1 --extendReads --scaleFactor <scale_factor>”.
The scale factor was calculated for each sample by the minimum spike-in read count in all samples / the spike-in read count of the sample.
Assembly: hg19
Supplementary files format and content: bigWig, Read coverage profile
Library strategy: CUT&RUN

extract_protocol:
The cells were incubated with CUTANA pA/G-Mnase. Chromtin fragments were purified utilizing a Cutana DNA purification kit. Libraries were generated using a NEBNext Ultra II DNA library prep kit and analyzed on Illumina Novaseq at GENEWIZ Azenta Life Sciences Co. Ltd.
Library construction from the CUT&RUN-seq samples and sequencing of paired-end-150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.

treatment_protocol: FKBP-MYB Jurkat cells were treated with DMSO or dTAG.

value: phospho-MYB


title: Coastal perennial, eight-leaf stage, sample 6

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB dTAG pMYB rep1


title: Coastal perennial, eight-leaf stage, sample 5

description: Rapid Run flow cells (v2)


title: Coastal perennial, six-leaf stage, sample 10

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB dTAG pMYB rep3


title: Jurkat 24h MYB dTAG H3K4me3 rep3


title: Jurkat 24h MYB dTAG H3K4me3 rep1


title: Coastal perennial, six-leaf stage, sample 4

description: Rapid Run flow cells (v2)


title: Coastal perennial, six-leaf stage, sample 8

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB dTAG H3K27ac rep3


title: Coastal perennial, six-leaf stage, sample 1

description: Rapid Run flow cells (v2)


title: Jurkat 02h DMSO rep2


title: Jurkat 24h MYB dTAG H3K27ac rep2


title: Jurkat 02h DMSO rep1


title: Coastal perennial, six-leaf stage, sample 7

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB dTAG H3K27ac rep1


title: Coastal perennial, six-leaf stage, sample 2

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB DMSO pMYB rep3


title: Coastal perennial, six-leaf stage, sample 3

description: Rapid Run flow cells (v2)


title: Coastal perennial, eight-leaf stage, sample 7

description: Rapid Run flow cells (v2)


title: Coastal perennial, six-leaf stage, sample 6

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB DMSO pMYB rep2


title: Coastal perennial, six-leaf stage, sample 9

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB dTAG H3K4me3 rep2


title: Coastal perennial, six-leaf stage, sample 5

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB DMSO pMYB rep1


title: Jurkat 24h MYB DMSO H3K4me3 rep2


title: Coastal perennial, four-leaf stage, sample 3

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB DMSO H3K4me3 rep1


title: Jurkat 24h MYB DMSO H3K27ac rep3


title: Jurkat 24h MYB dTAG rep2

data_processing:
ATAC-seq reads were mapped to the hg19 genome (no alt analysis set) using bowtie2 (version 2.4.2) with the default settings.
Duplicated reads were marked using GATK MarkDuplicates (version 4.1.9.0) with the default settings.
Reads with MAPQ < 10 and duplicated reads were filtered out.
Reads mapped to blacklisted regions (v2) including chrEBV and chrMT were filtered out as well.
Filtered reads were shifted using ATACseqQC (version 1.14.4).
ATAC-seq peaks were detected using MACS2 (version 2.2.6) with the options “--format BAMPE --keep-dup all --qvalue 0.001 --gsize hs --call-summits”.
Read coverage profile was generated using deepTools bamCoverage (version 3.4.1) with the options “--binSize 1 --normalizeUsing BPM --extendReads <mean_fragment_size>”.
The mean fragment size was obtained from a MACS2 output.
Assembly: hg19
Supplementary files format and content: bigWig, read coverage profile

extract_protocol:
Cells were harvested in cold lysis buffer, tagmented with Tn5 transposase (Illumina), and purified with a Genomic DNA Clean & Concentrator kit (Zymo research).
Tagmented DNA was amplified with NEBNext High Fidelity 2X Master Mix (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) and purified with a Genomic DNA Clean & Concentrator Kit (Zymo Research).

treatment_protocol: Jurkat cells with FKBP knock-in at MYB locus are treated with DMSO or dTAG.


title: Jurkat 24h MYB DMSO H3K27ac rep1


title: Coastal perennial, four-leaf stage, sample 9

description: Rapid Run flow cells (v2)


title: Coastal perennial, four-leaf stage, sample 10

description: Rapid Run flow cells (v2)


title: Coastal perennial, four-leaf stage, sample 7

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB DMSO H3K27ac rep2


title: Jurkat 24h MYB dTAG rep1


title: Coastal perennial, four-leaf stage, sample 2

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB DMSO rep2


title: Coastal perennial, four-leaf stage, sample 6

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB DMSO rep1


title: Coastal perennial, four-leaf stage, sample 4

description: Rapid Run flow cells (v2)


title: Coastal perennial, four-leaf stage, sample 8

description: Rapid Run flow cells (v2)


title: Coastal perennial, four-leaf stage, sample 5

description: Rapid Run flow cells (v2)


title: Streptococcus salivarius KSS12 replicate 2

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

institute: Kyung Hee University

data_processing:
The adpater sequences were trimmed using cutadapt and then, the processed reads were aligned to the Streptococcus salivarius ATCC 7073 genome bowtie2 (v2.5.4). For the gene annotations, RefSeq annotaion (GCF_900143035.1) was used.
Assembly: Streptococcus salivarius ATCC 7073
Supplementary files format and content: a tab-delimited text file including raw read count of each gene as a matrix format for all samples

organism: Streptococcus salivarius

growth_protocol: Streptococcus salivarius strains were grown in BHI broth under the same conditions (OD600 = 0.5–0.7, 37°C, anaerobic chamber).

extract_protocol:
After centrifugation, the supernatant was removed, and the bacterial cells were processed using the AccuPrep® Bacterial RNA Extraction Kit (Bioneer, K-3143), following the manufacturer’s protocol.
RNA libraries was prepared using Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #20020595) following manufacturer's protocols


title: Coastal perennial, two-leaf stage, sample 4

description: Rapid Run flow cells (v2)


title: Jurkat 24h MYB DMSO H3K4me3 rep3


title: Streptococcus salivarius KSS11 replicate 2


title: Coastal perennial, four-leaf stage, sample 1

description: Rapid Run flow cells (v2)


title: Coastal perennial, two-leaf stage, sample 8

description: Rapid Run flow cells (v2)


title: Coastal perennial, two-leaf stage, sample 1

description: Rapid Run flow cells (v2)


title: Streptococcus salivarius KSS10 replicate 1


title: Streptococcus salivarius KSS10 replicate 2


title: Streptococcus salivarius KSS11 replicate 1


title: Streptococcus salivarius KSS9 replicate 2


title: Coastal perennial, two-leaf stage, sample 3

description: Rapid Run flow cells (v2)


title: Coastal perennial, two-leaf stage, sample 5

description: Rapid Run flow cells (v2)


title: Streptococcus salivarius KSS9 replicate 1


title: Streptococcus salivarius KSS7 replicate 2


title: Coastal perennial, two-leaf stage, sample 10

description: Rapid Run flow cells (v2)


title: Streptococcus salivarius KSS8 replicate 2


title: Coastal perennial, two-leaf stage, sample 7

description: Rapid Run flow cells (v2)


title: Streptococcus salivarius KSS6 replicate 1


title: Hela cells expressing 3×Flag-TFEB, ChIP, Input

description: HeLa-TFEB-Flag-ChIP-seq-Input

data_processing:
Clean sequencing reads were aligned to the hg38 RefSeq database using Bowtie and then were qualified by FastQC.
After removing the reads that duplicated as the artificial product of the PCR step of library preparation, we merged the qualified reads of two replicates for further study using samtools.
Peaks were determined by MACS2 using input DNA as the negative control and the default parameters with minor modifications (i.e., “--extsize 200”, “--p 0.01”).
The peaks were annotated using the default parameters by HOMOR.
The promoter peaks were defined as those localizing from 1,000 bp downstream to 5,000 bp upstream of transcript start sites (TSS).
Assembly: hg38
Supplementary files format and content: narrow peaks format files include peak calling results
Supplementary files format and content: tab-delimited text files include peak annotation results

extract_protocol:
For ChIP-seq, the total DNA fragment and ChIPed DNA fragment was extracted using the ChIP Kit from ZYMO Research (D5209)
For ChIP-seq, was purified by the kit and subjected to library construction and high throughput sequencing by the Beijing Genomics Institution (BGI).

treatment_protocol: CCCP (20µM) for 1h; sucrose (150mM) for 6h; Torin1 (1µM) for 1h

value: Hela cells

value: Cervical cancer cells

value: expressing 3xFlag-TFEB

tag: chip antibody

value: Anti-FLAG® M2 Magnetic Beads (Sigma, M8831)


title: Hela cells expressing 3×Flag-TFEB, ChIP, Torin1, rep2

description:
HeLa-TFEB-Flag-ChIP-seq-Torin1-2
Torin1merge_rmdup_peaks.narrowPeak
Torin1merge_rmdup_peaks_anno.txt

value: Anti-FLAG® M2 Magnetic Beads (Sigma, M8830)


title: Streptococcus salivarius KSS8 replicate 1


title: Streptococcus salivarius KSS6 replicate 2


title: Coastal perennial, two-leaf stage, sample 6

description: Rapid Run flow cells (v2)


title: Coastal perennial, two-leaf stage, sample 9

description: Rapid Run flow cells (v2)


title: Streptococcus salivarius KSS5 replicate 2


title: Hela cells expressing 3×Flag-TFEB, ChIP, Torin1, rep1

description:
HeLa-TFEB-Flag-ChIP-seq-Torin1-1
Torin1merge_rmdup_peaks.narrowPeak
Torin1merge_rmdup_peaks_anno.txt

value: Anti-FLAG® M2 Magnetic Beads (Sigma, M8829)


title: Streptococcus salivarius KSS12 replicate 1


title: Coastal perennial, two-leaf stage, sample 2

description: Rapid Run flow cells (v2)


title: Hela cells expressing 3×Flag-TFEB, ChIP, sucrose, rep2

description:
HeLa-TFEB-Flag-ChIP-seq-sucrose-2
Sucrosemerge_rmdup_peaks.narrowPeak
Sucrosemerge_rmdup_peaks_anno.txt

value: Sucrose

value: Anti-FLAG® M2 Magnetic Beads (Sigma, M8828)


title: Streptococcus salivarius KSS5 replicate 1


title: Streptococcus salivarius KSS4 replicate 2


title: Hela cells expressing 3×Flag-TFEB, ChIP, sucrose, rep1

description:
HeLa-TFEB-Flag-ChIP-seq-sucrose-1
Sucrosemerge_rmdup_peaks.narrowPeak
Sucrosemerge_rmdup_peaks_anno.txt

value: Anti-FLAG® M2 Magnetic Beads (Sigma, M8827)


title: Hela cells expressing 3×Flag-TFEB, ChIP, CCCP, rep2

description:
HeLa-TFEB-Flag-ChIP-seq-CCCP-2
CCCPmerge_rmdup_peaks.narrowPeak
CCCPmerge_rmdup_peaks_anno.txt

value: CCCP

value: Anti-FLAG® M2 Magnetic Beads (Sigma, M8826)


title: Hela cells expressing 3×Flag-TFEB, ChIP, Ctrl, rep2

description:
HeLa-TFEB-Flag-ChIP-seq-Control-2
Ctrlmerge_rmdup_peaks.narrowPeak
Ctrlmerge_rmdup_peaks_anno.txt

value: Non

value: Anti-FLAG® M2 Magnetic Beads (Sigma, M8824)


title: Streptococcus salivarius KSS3 replicate 1


title: Hela cells expressing 3×Flag-TFEB, ChIP, Ctrl, rep1

description:
HeLa-TFEB-Flag-ChIP-seq-Control-1
Ctrlmerge_rmdup_peaks.narrowPeak
Ctrlmerge_rmdup_peaks_anno.txt

value: Anti-FLAG® M2 Magnetic Beads (Sigma, M8823)


title: Streptococcus salivarius KSS3 replicate 2


title: Hela cells expressing 3×Flag-TFEB, ChIP, CCCP, rep1

description:
HeLa-TFEB-Flag-ChIP-seq-CCCP-1
CCCPmerge_rmdup_peaks.narrowPeak
CCCPmerge_rmdup_peaks_anno.txt

value: Anti-FLAG® M2 Magnetic Beads (Sigma, M8825)


title: WT24

city: Orem

first: Eric

last: Domyan

state: UT

address: 800 W University Parkway

department: Department of Biology

institute: Utah Valley University

data_processing:
Illumina Cassava software was used for base calling.
Sequence reads were aligned to the reference pigeon genome using Rsubread (Chen, Lun, & Smyth, 2016)
Differentially expressed genes were identified by DESeq2 using default parameters, with design ~ batch + phenotype (Love, Huber, & Anders, 2014).
Genome_build: Cliv_2.1
Supplementary_files_format_and_content: tab-delimited text file includes raw counts per sample for each gene, along with DESeq2 output

organism: Columba livia

source_name: regenerating feather

extract_protocol:
To harvest RNA from melanocytes, several secondary flight feathers were plucked from one wing of each pigeon to stimulate regeneration and allowed to regrow for 9-10 days. 70% ethanol was used to sterilize as well as to dampen the feathers in the area to assist in locating the regenerating feathers. Once located, each pigmented regenerating feather was plucked, and the proximal 4-5 mm was dissected, bisected longitudinally, and placed in RNA Later (Qiagen, Germantown, MD, USA) overnight at 4oC. Afterwards, the dermal pulp was discarded and the feather collar was harvested and stored at -80oC until RNA extraction with RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: wild type

tag: batch


title: Streptococcus salivarius KSS4 replicate 1


title: WT23


title: Streptococcus salivarius KSS2 replicate 1


title: Streptococcus salivarius KSS7 replicate 1


title: WT00


title: Mut14

value: recessive red

value: homozyous e2 allele (Domyan et al. Current Biology 2014)


title: WT20


title: T144-1

city: Yinchuan

last: Li

address: No. 489, Helan Mountain West Road, Xixia District, Yinchuan City, Ningxia

institute: NingXia University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic[1]. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. After removing adaptor and low quality sequences, the clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcripts by Trinity [2] (vesion: 2.4) with paired-end method. The longest transcript was choose as a unigene based on the similarity and length for subsequent analyses.
The function of the unigenes was annotated by alignment of the unigenes with the NCBI non-redundant (NR), Swiss-Prot, evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and Clusters of orthologous groups for eukaryotic complete genomes (KOG) databases using diamond[3] with a threshold e<1e-5. The proteins with the highest hits to the unigenes were used to assign functional annotations. The unigenes were also mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG)[4] database to annotate the potential pathways. Gene ontology (GO) classification was performed through the mapping relation between Swiss-Prot and GO term.
After annotation, Use the software bowtie2[5] to obtain the number of reads aligned to Unigene in each sample, and use the eXpress[6]software to calculate the expression level of Unigene (FPKM[7]). Differentially expressed unigenes (DEGs) between different groups were identified using DESeq2[8]software to calculate the fold of difference, and use NB (negative binomial distribution test) to test the significance of difference, and finally the default filter conditions for DEG was q<0.05 and foldChange >2 or foldChange < 0.5. Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of unigenes in different groups and samples. GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution. R (v 3.2.0) was used to draw the column diagram and bubble diagram of the significant enrichment term.
Assembly: aw data (raw reads) of fastq format were firstly processed using Trimmomatic[1]. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. After removing adaptor and low quality sequences, the clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcripts by Trinity [2] (vesion: 2.4) with paired-end method.
Supplementary files format and content: tabdelimited text files include RPKM values for each Sample

organism: Sitona callosus

source_name: Whole body

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.1.3 ug of tota RNA was used for the construction of sequencing libraries
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: Whole body

value: infected by Beauveria bassiana


title: Mut12

value: homozyous e1 allele (Domyan et al. Current Biology 2014)


title: T144-3


title: Mut11


title: WT22

value: heterozygous wild-type/e1 (Domyan et al. Current Biology 2014)


title: cK-1

value: cK


title: T96-3


title: Mut6


title: T96-2


title: T96-1


title: WT4


title: T48-3


title: WT3


title: Streptococcus salivarius KSS1 replicate 2


title: Streptococcus salivarius KSS2 replicate 2


title: T48-2


title: Mut5


title: T144-2


title: cK-2


title: T48-1


title: WT2


title: PDS_Visium

city: Dallas

first: Jason

middle: C

last: Klein

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: FFPE Visium 10X

data_processing:
Preprocessed by CD Genomics
the image files were unavailable
Assembly: Chromiium Flex Human Probe Panel
Supplementary files format and content: h5

source_name: Tumor

extract_protocol: CD Genomics

value: Tumor


title: WT1


title: Mut4


title: cK-3


title: Mut3


title: WT21


title: Mut7


title: Mut1


title: Streptococcus salivarius KSS1 replicate 1


title: LF1 cells, late senescence, replicate 3

city: Providence

first: Maxfield

last: Kelsey

address: 225 Dyer St.

institute: Brown University

data_processing:
Raw sequencing reads were trimmed using Fastp
Trimmed reads were aligned using STAR to a custom LF1 genome derived from the T2T-HS1 human genome, but including appended contigs representing non-reference retrotransposon insertions called using the TLDR program.
Repetitive element counts were quantified using the Telescope tool.
Differential expression was assessed using the DESeq2 R package.
Assembly: Custom LF1 genome (derived from the T2T-HS1 or Hs1, human genome)
Supplementary files format and content: resultsdf: tab-delimited text file contains DESeq2 results and DESeq2 normalized counts for each sample

growth_protocol: Cells were passaged in regular growth media (HAMS F10, 15% FBS, and 1x of Penicillin Streptomycin and Glutamine) and maintained at 37 degrees Celsius at 5% CO2 and 2.5% O2.

extract_protocol:
PRO, ESEN and LSEN cells were harvested using Trizol. Total RNA was then extracted using a Qiagen Rneasy column kit. Libraries were then prepared using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads to purify mRNA (using polyA isolation oligodT beads). The samples were then sent for sequencing to Azenta, where they were all sequenced in the same lane.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

treatment_protocol:
Proliferating (PRO) cells were harvested at 60 - 80% confluency.
Early replicative senescent (ESEN) cells were passaged in regular growth media until replicative exhaustion. These cells were maintained in the senescent state for 1 month.
Late replicative senescent (LSEN) cells were passaged in regular growth media until replicative exhaustion. These cells were maintained in the senescent state for 4 months.

value: lung fibroblasts

value: WT

value: Replicative Exhaustion + 4 months


title: LF1 cells, late senescence, replicate 2


title: LF1 cells, late senescence, replicate 4


title: Outer passage 3 meniscus cells 148

city: Durham

first: Amy

middle: L

last: McNulty

state: NC

address: DUMC Box 3093

institute: Duke University School of Medicine

data_processing:
Basecalling by Illumina RTA2
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were 20nt or longer after trimming were kept for further analysis
Reads were mapped to the Sscrofa11.1v91 version of the pig genome and transcriptome using the STAR RNA-seq alignment tool.  Reads were kept for subsequent analysis if they mapped to a single genomic location
Gene counts were compiled using the HTSeq tool
Normalization and differential expression analysis was performed using the DeSeq2 BioConductor packge in the R statistical programming language
Assembly: Sscrofa11.1v91
Supplementary files format and content: Matrix tables with raw gene counts and DESeq2 normalized counts for every gene and every sample

organism: Sus scrofa

source_name: medial meniscus

extract_protocol:
Tissues were pulverized in TRIzol under liquid nitrogen using a freezer mill. RNA was extracted by TRIzol/chloroform separation according to the manufacturer’s protocol, then resuspended in lysis buffer and column purified according to the Norgen RNA extraction kit protocol (Catalog # 48300; Norgen Biotek Corp). Cell pellets were flash frozen in liquid nitrogen and stored at -80°C until RNA extraction was performed using the Norgen Total RNA Purification Plus extraction kit.
KAPA Stranded mRNA-Seq Kit--KK8421

value: medial meniscus

value: outer zone passage 3

tag: zone

value: outer


title: Outer passage 3 meniscus cells 147

tag: tissue


title: LF1 cells, early senescence, replicate 4

tag: cell type

value: Replicative Exhaustion + 1 months


title: LF1 cells, late senescence, replicate 1

tag: treatment


title: Inner passage 3 meniscus cells 149

value: inner zone passage 3

value: inner


title: LF1 cells, early senescence, replicate 3


title: Cartilage 3

source_name: cartilage

value: cartilage

value: not applicable


title: LF1 cells, early senescence, replicate 2


title: Inner passage 3 meniscus cells 148


title: Inner passage 3 meniscus cells 147


title: LF1 cells, proliferating, replicate 2


title: Cartilage 1


title: Cartilage 2


title: LF1 cells, proliferating, replicate 4


title: LF1 cells, proliferating, replicate 3


title: Outer meniscus tissue 3


title: MCF7_rep2, PCHI-C

city: Brisbane

first: Jonathan

last: Beesley

state: QLD

address: 300 Herston Rd Herston

country: Australia

institute: QIMR Berghofer

data_processing:
PCHiC reads were analysed with HiCUP (version 0.5.9).
Raw sequencing reads were aligned to the hg38 human reference genome with Bowtie2 version 2.2.9
Chromatin interactions were identified using CHiCAGO following generation of genome indices, HindIII restriction fragment digest files, and the bait map.
The CHiCAGO pipeline was run independently for each library for quality control, followed by merging of replicates for subsequent analyses. Interactions with CHiCAGO score ≥ 5 were treated as high confidence for target gene analysis and visualisation.
Assembly: hg38
Supplementary files format and content: ChiCAGO peak matrix file for merged biological replicates, listing chromatin interactions obseverd in at least 1 sample
Library strategy: Promoter capture Hi-C

source_name: MCF7 cell line

extract_protocol:
PCHiC libraries were prepared from 4-5 x 1e7 cells per library (two biological replicates per cell line using in-nucleus ligation).
The HiC libraries were amplified using the SureSelectXT ILM Indexing pre-capture primers (Agilent Technologies) with 8 PCR amplification cycles. Each HiC library (750 ng) was hybridized and captured individually using the SureSelectXT Target Enrichment System reagents and protocol (Agilent Technologies). After library enrichment, a post-capture PCR amplification step was carried out using SureSelectXT ILM Indexing post-capture primers (Agilent Technologies) with 14–16 PCR amplification cycles.

value: MCF7 cell line

value: Breast cancer cell line


title: LF1 cells, proliferating, replicate 1


title: Inner meniscus tissue 5


title: MDAMB231_rep2, PCHI-C

source_name: MDAMB231 cell line

value: MDAMB231 cell line


title: MCF7_rep1, PCHI-C


title: B80T5_rep2, PCHI-C

source_name: B80T5 cell line

value: B80T5 cell line

value: Normal breast cell line


title: Inner meniscus tissue 2


title: Inner meniscus tissue 3


title: MDAMB231_rep1, PCHI-C


title: B80T5_rep1, PCHI-C


title: KO, replicate 3, scRNA seq

city: Baltimore

first: Yijun

last: Xu

state: MD

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins University School of Medicine

description: 10X Gemomics

data_processing:
The raw fastq files were demultiplexed, barcoded and counted by CellRanger 7.0.0
Assembly: GRCm39
Supplementary files format and content: The h5 files with gene count matrix, annotated with cell barcode and gene symbols

source_name: Cochlear tissue

extract_protocol:
P21 male mice (3 Tmie-/-, 4 Tmie+/- controls) were anesthetized, sacrificed by decapitation, and temporal bones were isolated and dissected in ice-cold Leibovitz’s L-15 medium. Dissected tissue consisted of the spiral ganglion, spiral limbus, inner sulcus, organ of Corti, and outer sulcus and was pooled in tubes containing ice-cold L-15. Pooled tissue was centrifuged and the supernatant was replaced with a prewarmed solution of Leibovitz containing 200 units/mL of collagenase IV (ThermoFisher, 17104-019) and incubated for 30 min at 37°C. Collagenase solution was replaced with a prewarmed solution of Earle’s Balanced Salt Solution (EBSS) containing 20 units/mL papain (Worthington, LK003150), 1mM L-cysteine, 0.5mM EDTA, 15 mM HEPES, 10units/mL DNAse I (StemCell Technologies, 7900), and 8 µL/mL RNAse inhibitor (Lucigen, 30281-1). Single cell solutions were obtained by incubation for 30 min at 37°C and gentle trituration every 10 min via pipette. Then, an equal volume of L-15 medium containing 10 mg/mL ovomucoid inhibitor, 10 mg/mL BSA (Worthington), and 8 µL/mL RNAse inihibtor was added, and the suspension was passed through a 20 µm filter to remove debris. Cells were re-pelleted at 350g for 5 min, washed twice with DMEM/F12 containing 0.04% BSA and 8 µL/mL RNase inhibitor, and pelleted again. Lastly, cells were resuspended in 60 µL of DMEM/F12 containing 0.04% BSA and 8 µL/mL RNase inhibitor.
Cell counts and viability were determined using the Cell Countess II with Trypan Blue. Cells were combined with RT reagents and loaded onto Next GEM Chip G along with 3’ v3.1 gel beads (10X Genomics, PN-1000121). The NextGEM protocol was run on the 10X Chromium Controller to create Gel Beads in emulsion (GEMs), composed of a single cell, uniquely barcoded gel bead, and reverse transcriptase reagents. Next, 100 µL of emulsion was retrieved from the chip and incubated (45 min at 53°C , 5 min at 85°C, cool to 4°C), generating barcoded cDNA from each cell. The GEMs were broken using Recovery Agent and cDNA was cleaned, following manufacturer’s instructions using MyOne SILANE beads (Invitrogen, 37002D). cDNA was amplified for 11-12 cycles based on input cell number (3 min at 98°C, 11-12 cycle:  15 sec at 98°C, 20 sec at 63°C, 1 min at 72°C; 1 min at 72°C, cool to 4°C) and samples were cleaned using 0.6X SPRIselect beads (Beckman Coulter, B23317). QC was completed using Qubit and Bioanalyzer to determine size and concentrations. 10 µL of amplified cDNA (containing 172-222 ng cDNA) was carried into library prep. Fragmentation, end repair and A-tailing were completed, and samples were cleaned up using double sided size selection (0.6X, 0.8X) with SPRIselect beads.  Adaptor ligation (15 min at 20°C, cool to 4°C), 0.8X cleanup and amplification were performed, with PCR using unique i7 index sequences.  Libraries underwent a final cleanup using double sided size selection (0.6X, 0.8X) with SPRIselect beads.  Library QC was performed using Qubit, Bioanalyzer and KAPA library quantification qPCR kit.  Libraries were sequenced on the geSa using v1.5 kits, targeting 50K reads/cell, at read lengths of 28 (R1), 8 (i7), 91 (R2).

value: Cochlear tissue

value: Tmie-/-

tag: age


title: Ishikawa_rep2, PCHI-C

source_name: Ishikawa cell line

tag: cell line

value: Ishikawa cell line

value: Endometrial cancer cell line


title: Ishikawa_rep1, PCHI-C


title: HET, replicate 4, scRNA seq

description: 10X Gemomics

tag: genotype

value: Tmie+/-


title: HET, replicate 3, scRNA seq

description: 10X Gemomics


title: ARK1_rep2, PCHI-C

source_name: ARK1 cell line

value: ARK1 cell line


title: Outer meniscus tissue 2

value: medial meniscus

value: outer


title: E6E7-hTERT_rep2, PCHI-C

source_name: E6E7-hTERT cell line

value: E6E7-hTERT cell line

value: Normal endometrial cell line


title: HET, replicate 2, scRNA seq

description: 10X Gemomics


title: LF1 cells, early senescence, replicate 1

value: lung fibroblasts

value: WT

value: Replicative Exhaustion + 1 months


title: ARK1_rep1, PCHI-C


title: KO, replicate 1, scRNA seq

description: 10X Gemomics


title: E6E7-hTERT_rep1, PCHI-C


title: HET, replicate 1, scRNA seq

description: 10X Gemomics


title: COV362_rep2, PCHI-C

source_name: COV362 cell line

value: COV362 cell line

value: Ovarian cancer cell line


title: Outer meniscus tissue 6


title: scRNA_Fosl2 cko_Rep1

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Guangdong Medical University

data_processing:
The raw sequencing data were processed with CellRanger from 10×Genomics (version 3.1.0) with default parameters.
Alignment was performed against the mouse genome reference sequence GRCm38. Uniquely mapped reads were retained for UMI counting, and gene expression levels were quantified for each detected barcode.
CellBender was employed to process the raw feature-barcode matrices with default parameters to eliminate ambient RNA molecules from each sample.The resulting clean corrected expression matrices were then analyzed using the Seurat package (version 4.1.0)
To ensure high-quality cell data, cells were filtered out if they did not meet the following criteria: 1) a minimum of 500 detected genes, 2) more than 3,000 detected UMIs, and 3) mitochondrial UMI counts constituting less than 30% of the total. Doublets were identified using scDblFinder with the parameter dbr.SD=1
These were meticulously removed based on the expression patterns of cell type/lineage -specific markers.
Assembly: mm10
Supplementary files format and content: Barcodes file for each sample, respectively.
Supplementary files format and content: Features file for each sample, respectively.
Supplementary files format and content: Matrix file for each sample, respectively.

source_name: ovary

extract_protocol:
8-week-old Fosl2flox/flox and Cyp19a1-Cre; Fosl2flox/flox female mice from the same litter were euthanized to collect ovaries tissues.
The single-cell library was meticulously prepared using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10×Genomics, 120237), strictly following the manufacturer's protocol. Briefly, cell viability was confirmed to be >70% in ovaries tissues from Fosl2-deficient and control mice using trypan blue exclusion. Cell suspensions were filtered using a 70 μm strainer, and dissociated cells were pelleted and re-suspended with 0.04% BSA in PBS. Single-cell suspensions were loaded on the Chromium Controller (10×Genomics, USA) to generate Gel Bead-In-Emulsions (GEMs)

value: ovary

value: Fosl2 cKO in GCs


title: COV362_rep1, PCHI-C


title: scRNA_Ctrl_Rep2


title: scRNA_Ctrl_Rep1


title: OVCAR4_rep1, PCHI-C

source_name: OVCAR4 cell line

value: OVCAR4 cell line


title: FT282_rep1, PCHI-C

source_name: FT282 cell line

value: FT282 cell line

value: Fallopian tube cell line


title: LPS-4

city: Harbin

first: JingYi

last: Ren

address: No. 148, BaoJian Road, Nangang District, Harbin City, Heilongjiang Province

institute: Second Affiliated Hospital of Harbin Medical University

data_processing:
HISAT2
Assembly: Mus musculus (Mouse) Genome Reference Assembly, GRCm39 (mm39)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the  manufacturer’s protocol.
RNA integrity was assessed using the Agilent 2100  Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using  VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Lung

value: Epithelial cell


title: PC3_rep2, PCHI-C

source_name: PC3 cell line

value: PC3 cell line

value: Prostate cancer cell line


title: LPS-3


title: LPS-2


title: LNCAP_rep2, PCHI-C

source_name: LNCAP cell line

value: LNCAP cell line


title: LPS-1


title: EXO-3


title: EXO-4


title: EXO-2


title: RWPE1_rep2, PCHI-C

source_name: RWPE1 cell line

value: RWPE1 cell line

value: Normal prostate cell line


title: EXO-1


title: LNCAP_rep1, PCHI-C


title: DEX-25170, APOE4, LDLR, batch_C, tech_replicate_2

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Sequencing data was processed using nf-core/rnaseq (v3.11.2) of the nf-core collection of workflows, using STAR (v2.7.9a) and salmon (v1.10.1) for alignment of reads to the GRCh38 human reference genome and quantification of Gencode (v42) gene models, respectively.
One library (HSA-000031753) failed QC (fewer than 1 million total counts) and was excluded from downstream analysis.
Differential expression analysis was performed for protein-coding genes with the edgeR (v3.42.4) and limma (v 3.56.2) Bioconductor packages using R v4.3.1. In brief, count matrices were subset to protein-coding genes, and library size factors were calculated with the TMM method. Gene-wise linear models with experimental group and collection batch as covariates were fit with the voomLmFit function, setting the sample weights argument to TRUE. The relationships of technical and biological replicates were specified via the block argument. Fold changes and p-values for the contrasts of interest were obtained with the eBayes function.
Assembly: GRCh38
Supplementary files format and content: Microsoft excel file with three worksheets: 1) sample metadata, 2) raw counts for all protein-coding genes, 3) normalized counts-per-million for all protein-coding genes

source_name: Human Episomal iPSC Line A18968

growth_protocol: Hematopoietic progenitor cells (HPCs) were generated based on a protocol published by Guttikonda et al, 2021 with modifications. To differentiate HPCs into microglia (iMG), frozen vials of HPCs were thawed in 37°C water bath. Cryoprotectant was washed away by titrating cells into DMEM-F12 and centrifuging at 500 g for 5 min. Cells were resuspended in Microglia Differentiation Medium (STEMCELL Technologies, Catalog No. 100-0019) and differentiated according to the manufacturer’s protocol with suggested medium changes and splitting. After 24 days of differentiation, cells were switched into Microglia Maturation Medium (STEMCELL Technologies, Catalog No. 100-0020). More than 90% of the iMG were double positive for CD45 and CD11b, and were plated for experiments between 31 days and 39 days.

extract_protocol:
Cells were lysed with Qiagen RLT-plus buffer containing β -mercaptoethanol. Samples were stored at -80°C until cell lysates from all individual experiments were collected. ERRC control RNA that was pre-diluted at 1:10,000 and spiked into each sample at a volume  proportional to the cell count determined by microscopy. RNA extraction was performed using the RNeasy Plus Micro Kit (Qiagen, 74034).
For each of the 12 independent biological samples, two replicate sequencing libraries were prepared from 10-60 ng of total RNA each using the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173). The UMI second strand synthesis module was used to introduce unique molecular identifiers. Library quantity and quality were assessed with the High Sensitivity D1000 ScreenTape (Agilent 5067-5584). Libraries were pooled in equimolar ratios and the sequencing pool was purified with magnetic beads to remove residual adaptor dimers.

treatment_protocol: LPS-stimulated APOE KO iMG were treated with ApoE isoforms (ApoE2/E3/E4) pre-complexed with BODIPY-CE and HDL -/+ recombinant LDLR ECD for 1 day prior to RNA harvest.

tag: experiment id

tag: group

value: Human Episomal iPSC Line A18968

value: iPSC-derived microglia

tag: technical replicate

tag: qc pass

value: TRUE

value: C

tag: ldlr ecd_treated


title: scRNA_Fosl2 cko_Rep2


title: DEX-25169, APOE4, no_LDLR, batch_C, tech_replicate_2

source_name: Human Episomal iPSC Line A18967

value: Human Episomal iPSC Line A18967

value: FALSE


title: RWPE1_rep1, PCHI-C


title: DEX-25168, APOE3, no_LDLR, batch_C, tech_replicate_2

source_name: Human Episomal iPSC Line A18966

value: Human Episomal iPSC Line A18966


title: OVCAR4_rep2, PCHI-C

value: OVCAR4 cell line

value: Ovarian cancer cell line


title: DEX-25166, APOE4, LDLR, batch_B, tech_replicate_2

source_name: Human Episomal iPSC Line A18964

value: Human Episomal iPSC Line A18964

value: B


title: FT282_rep2, PCHI-C

value: FT282 cell line

value: Fallopian tube cell line