title: NC15

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

data_processing:
Alignment is done by cellranger to hg38 pre-mRNA reference
Downstream differential analysis and subcluster analysis is done by Seurat
Genome_build: hg38
Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs

molecule: nuclear RNA

source_name: prefrontal cortex snRNAseq

extract_protocol:
we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.

value: prefrontal cortex

tag: diagnosis

value: healthy control


title: NC16

status: Public on Sep 28 2020

type: SRA

country: China

institute: Hong Kong University of Science and Technology

library_source: transcriptomic

organism: Homo sapiens

tag: tissue


title: NC17


title: leaf_control_rep1 (S. exigua control)

type: RNA

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

department: Biology

country: Germany

institute: Freie Universität Berlin

hyb_protocol: 600 ng of the cRNA were hybridised using the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) following the manufacturer’s protocol at 65°C for 17 h.

scan_protocol: Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron per pixel.

data_processing: Data were analyzed using the “limma” software packages from Bioconductor in “R” (R Core Team; Ritchie et al. 2015). The uploaded data were background-corrected using the “normexp” method and normalized between microarrays using the “quantile” method and Log2-transformed. For the data-upload, all raw data were background-corrected and normalized across all arrays. In the publication, a detection limitwas set at 1.5 times the 10% quantile of fluorescence signal intensity of dark corner spots on each array. All structural spots, as well as oligos that were not above this detection limit in any of the arrays, were removed from further analysis. Subsequently, the expression levels were background-corrected after removal of the non-expressed genes using the normexp method and normalized between the arrays using quantile normalisation.

molecule: total RNA

organism: Nicotiana attenuata

source_name: leaf control

label_protocol: Fluorescent cyanine 3-CTP-labelled cRNA was generated using the Low Input QuickAmp Labeling Kit (Agilent Technologies) using oligo-dT primer following the manufacture’s protocol.

growth_protocol: Nicotiana attanuata plants originated from a 15x WT inbred line collected in Utah and were grown from seed at a 16/8 h light/dark cycle and a photon irradiance between 190 - 250 µmol

extract_protocol: For each microarray sample, leaf material from three or four independent biological replicates was pooled. Leaf material was ground under liquid nitrogen and RNA was extracted with the NucleoSpin® RNA Plant kit (Macherey-Nagel GmbH & Co. KG) according to the manufacturer’s instructions using double the amount of RAP lysis buffer. RNA was DNase digested using TURBO DNA-free™ (AmbionTM) according to the manufacturer’s instructions.

treatment_protocol: Plants received oviposition by S. exigua (1-2 egg clutches). After 4 days, tissue from the next younger (systemic) leaf, or from the respective leaf position of a control plant without eggs, was harvested for RNA extraction.

tag: genotype location

value: rosette plant


title: NC14


title: iPSCs (UNC0638) rep1

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

country: USA

institute: Weill Cornell Medicine

description:
MS5
iPSCs derived MEFs with UNC0638 replicate 1 for the first 48 hours

data_processing:
Raw sequencing data were aligned to mouse genome version mm10 with the tophat algorithm (version 2.1.0)(Kim et al., 2013) and the use of «--b2-very-sensitive» parameter.
Samtools (version 1.8) (Li et al., 2009b) was used for data filtering and file format conversion
Aligned reads were assigned to exons with the use of the HT-seq count (version 0.5.4p3) algorithm (Anders et al., 2015) and the following parameters «-m intersection -nonempty». (MarkDuplicates option)
Differentially expressed genes were identified with the use of DESeq R package (R.3.4.4) (Anders and Huber, 2010), excluding  genes with RPKM<1
Genome_build: MM10
Supplementary_files_format_and_content: csv tab delimited / rna-seq raw reads

organism: Mus musculus

source_name: iPSCs derived MEFs with UNC0638 for the first 48 hours

growth_protocol: MEF cultures were established by trypsin digestion of midgestation (embryonic day (E) 13.5–E15.5) embryos and maintained in DMEM supplemented with 10% FBS, L-glutamine, penicillin/streptomycin, nonessential amino acids and β-mercaptoethanol. Reprogrammable MEFs were heterozygous Rosa26-rtTA and for Oct4-GFP and either heterozygous for a DOX-inducible OKSM allele (Stadtfeld et al., 2010b) or homozygous for an inducible OKS allele.

extract_protocol:
Total RNA was extracted from cells with the RNeasy Plus Kit (Qiagen).  Total RNA with RIN values > 8 were subjected to Automated TruSeq stranded total RNA with RiboZero Gold library preparation (Illumina).
TruSeq stranded total RNA with RiboZero Gold library preparation (Illumina).

treatment_protocol: Indicated samples were treated with 1μM UNC0638. All samples were harvested after 48h reprogramming.

tag: cell type

value: iPSC cells

tag: treatment


title: iPSCs (DMSO) rep1

description:
MS1
iPSCs derived MEFs replicate 2  with DMSO

source_name: iPSCs derived MEFs with DMSO

value: DMSO


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A2_ad004

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACB

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A2_ad002


title: H3k9me2 chip in MEF cells 48h in reprogramming (+DOX + C3 + UNC0638) - replicate2

data_processing:
Alignment was performed with Bowtie2 (2.2.6) (--very-sensitive) option
Filtering of low quality reads and multi-mapped reads was done with samtools (version 1.8)
Picard tools (version 2.12.2) was used to filter duplicate reads (MarkDuplicates option)
Enrichment was calculated with bedtools coverageBed (--mean) (version 2.26.0)
BigWig files were generated with bedGraphToBigWig (https://github.com/ENCODE-DCC/kentUtils)
Genome_build: MM10 for mouse and DM6 for spike-in genome
Supplementary_files_format_and_content: BigWig normalized to spike in reads (per million) and normalization factor based on Drosophila spike-in reads

source_name: MEF cells 48hours reprogrammed

growth_protocol: MEFs (Stadtfeld et al., 2010) were cultured and reprogrammed as described (Vidal et al., 2014)

extract_protocol:
Native ChiIP-seq was performed as previously described (Chen et al., 2018). 10 million cells were trypsinized, washed in ice-cold PBS, and flash frozen. Cell pellets were resuspended in Dounce Buffer (10mM Tris-HCl pH 7.5, 4mM MgCl2, 1mM CaCl2, protease inhibitors) with a 1:1 ratio of Drosophila Kc cells (for spike-in controls) and homogenized using 20 repetitions of a 25G syringe. Cells were treated with 150U/ml micrococcal nuclease (Worthington Biochemical) for 20 minutes at 37C and reactions were quenched with 0.5M EDTA and incubated on ice for 5 minutes. MNase-digested cells were incubated on ice for 1 hour with vortexing every 10 minutes with 1ml Hypotonic Lysis Buffer (0.2mM EDTA, 0.1mM benzamidine, 0.1mM PMSF, 1.5mM DTT, PIC) followed by a 3000g spin at 4C for 5 minutes. Supernatants were precleared by rotation for 2 hours at 4C with Protein G Dynabeads (Life Technologies) that had been washed 3x in IP Buffer (10mM Tris-HCl pH 8.0, 1% Triton X-100, 0.1% Deoxycholate, 0.1% SDS, 90mM NaCl, 2mM EDTA, PIC). Precleared chromatin was combined in 2 million cell equivalents with 5ul H3K9me2 antibody (Abcam, ab1220) and 20ul washed Protein G Dynabeads in IP Buffer and rotated at 4C overnight. Beads were then washed twice with ChIP Wash Buffer (20mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 150mM NaCl, PIC), once with Final ChIP Wash Buffer (20mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, PIC), and eluted twice 100ul Elution Buffer (100mM NaHCO3, 1% SDS) and RNase A at 68C. Input chromatin for each sample was diluted to 200ul in Elution Buffer and DNA from all samples and inputs was purified using the QIAquick PCR Purification Kit (Qiagen).
Libraries were prepared using the KAPA HyperPrep Kit (Roche)

value: mouse embryonic fibroblasts

tag: antibody

value: H3k9me2 (Abcam, ab1220)


title: γδ24+ TMREhi

city: London

first: Daniel

middle: J

last: Pennington

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

description: TMREhi CD24+ γδ24+ T cells

data_processing:
Cell Ranger v3.0 (10X Genomics) analysis pipeline was used to demultiplex sequenced libraries to generate fastq files. Subsequently, fastq files were aligned, filtered and feature-barcode matrices were generated. Fastq files were mapped to the reference mouse genome mm10 (UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: features.tsv.gz
Supplementary_files_format_and_content: matrix.mtx.gz

source_name: fetal thymic lobes

growth_protocol: Fetal thymic lobes from 15-day old C57BL/6 embryos (E15) were cultured for 2 days prior to cell isolation.

extract_protocol:
Single-cell suspensions of fetal thymocytes were obtained by gently homogenizing thymic lobes followed by straining through nylon strainers. Cells were stained for cell surface markers and mitochondria using TMRE, followed by sorting of CD24+ γδ T cells into TMREhi and TMRElo stained cells.
Single cell RNA sequencing libraries were generated using the Chromium™ Single Cell 5' Library and Gel Bead Kit (10X Genomics) according to the manufacturer's instructions. Uniquely indexed libraries were pooled for paired-end sequencing (Illumina NextSeq).

treatment_protocol: Fetal thymic lobes were cultured under control conditions and left untreated.

tag: background strain

tag: genotype

value: wild-type

value: untreated

value: fetal thymic lobes


title: γδ24+ TMRElo

description: TMRElo CD24+ γδ24+ T cells


title: H3k9me2 chip in MEF cells 48h in reprogramming (+DOX + C3 + UNC0638) - replicate1


title: NC7


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A2_ad008


title: NC18


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A12_ad012


title: AD21

value: AD


title: H3k9me2 chip in MEF cells 48h in reprogramming (+DOX + C3) - replicate2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A12_ad007


title: 2-RNA-seq_24hr

city: Nashville

first: Andrea

last: Perreault

state: TN

address: 746 Robinson Research Building

institute: Vanderbilt University

data_processing:
RNA-seq library sequence reads were aligned to the mouse mm10 reference genome using TopHat
Cufflinks was used to assemble transcripts and quantify expression of transcripts
Cuffmerge was used to merge all transcript assemblies to create a single merged transcriptome annotation for final analyses
Genome_build: mm10
Supplementary_files_format_and_content: FPKM tracking files include information about genes with reads in each file, such as gene ID, gene name, TSS, length, and coverage.

source_name: erythroid

growth_protocol: FVA-derived proerythroblasts were cultured at 10^6 cells/ml in Iscove-modified Dulbecco medium (IMDM), 30% heat-inactivated fetal bovine serum, 1% Penicillin-Streptomycin, 10% deionized BSA, and 100uM alpha-thioglycerol. Terminal erythroid differentiation of purified proerythroblasts was induced by the addition of 0.4 U/ml human recombinant Epo to media.

extract_protocol:
RNA was isolated using the Qiagen RNAeasy kit per manufacturer’s protocol. mRNA was isolated using NEBNext PolyA mRNA isolation using standard protocol. rRNA was depleted using NEBNext rRNA Depletion through standard protocol.
RNA libraries were prepared for sequencing using  NEBNext Ultra II Directional DNA library preparation kit with standard protocol. Final PCR amplified material was size selected using AMPure XP beads.

value: BALB/cJ

value: erythroid

value: 24 hr EPO


title: H3k9me2 chip in MEF cells 48h in reprogramming (+DOX + C3) - replicate1


title: H3k9me2 chip in MEF cells 48h in reprogramming (+DOX + UNC0638) - replicate2

value: DOX & UNC0638


title: AD20

value: prefrontal cortex


title: H3k9me2 chip in MEF cells 48h in reprogramming (+DOX + UNC0638) - replicate1


title: 2-RNA-seq_4hr

value: 4 hr EPO


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A12_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A12_ad006


title: AD19


title: 2-RNA-seq_36hr

value: 36 hr EPO


title: 2-RNA-seq_1hr

value: 1 hr EPO


title: NC12

value: healthy control


title: H3k9me2 chip in MEF cells 48h in reprogramming (+DOX) - replicate2

description: DOX.bw

value: DOX


title: AD10


title: AD13


title: H3k9me2 chip in MEF cells 48h in reprogramming (+DOX) - replicate1

description: DOX.bw


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A12_ad001

value: ACB

value: male


title: NC3


title: 2-RNA-seq_0hr

value: naive


title: 1-RNA-seq_36hr


title: 2-RNA-seq_12hr

value: 12 hr EPO


title: 1-RNA-seq_24hr


title: AD9


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A11_ad007


title: H3k9me2 chip in MEF cells - replicate2

description: MEF.bw

source_name: MEF cells

value: mouse embryonic fibroblasts

value: H3k9me2 (Abcam, ab1220)


title: 1-RNA-seq_12hr


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A11_ad006


title: H3k9me2 chip in MEF cells - replicate1

description: MEF.bw


title: AD8

value: AD


title: 1-RNA-seq_4hr

value: BALB/cJ


title: AD6


title: AD5


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A11_ad004


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A11_ad002


title: 1-RNA-seq_1hr

value: erythroid


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A11_ad010


title: ATAC_ILCP_rep1

city: Chicago

first: Albert

last: Bendelac

state: IL

address: 924 E. 57th Street BSLC

department: Pathology

institute: University of Chicago

data_processing:
ATAC-seq reads were aligned to the mouse genome (mm10) with Bowtie and duplicate reads were removed using Picard Tools.
A pooled bam file was generated from all samples including replicates (n = 2) and peaks were called on the pooled bam file with MACS2 to control for type I error.
Called peaks were filtered through a modified blacklist and mitochondrial and Y chromosome peaks were removed.
ATAC-seq read counts for all samples, including replicates, were determined via bedtools multiBamCov and peaks with low read counts were removed.
Quantile-normalization, GC-content normalization, and peak length normalization were performed using the CQN R package. Peaks were filtered to select for the top peaks with the highest variance.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files and raw counts per peak
Supplementary_files_format_and_content: Generation of normalized bigWig files for data visualization was performed by first generating normalized bedGraph files with bedtools genomecov, where the sum of reads within peaks associated with transcription start sites was used as a scaling factor, followed by file conversion using the UCSC bedGraphToBigWig program.

source_name: Fetal Liver

extract_protocol:
Fetal livers were extracted with curved forceps, passed through a 70mm cell strainer, and resuspended in FACS Buffer (1X HBSS (Gibco), 0.25% BSA (Sigma-Aldrich), 50 ng/mL DNase, and 5 mM sodium azide (Sigma-Aldrich)). Fetal livers were lineage depleted using an autoMACS, stained for surface markers and viability, and individual fetal liver precursors were sorted into FACS Buffer.
Library construction was performed as described in the published Omni-ATAC protocol: Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Meth. 14, 959-962 (2017).

value: Fetal Liver

value: Embryonic Day 15


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A11_ad001


title: AD2

value: prefrontal cortex


title: AD4


title: ATAC_iILCP_rep1

value: Zbtb16-EGFP Tcf7-mCherry Rorc-Thy1.1


title: ATAC_rEILP_rep2


title: AD1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A10_ad012


title: ATAC_ILCP_rep2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A10_ad010


title: 1-HiChIP_1hr_YY1

data_processing:
Library strategy: HiChIP
HiChIP library sequence reads were aligned to the mouse mm10 reference genome using HiC-Pro
Hichipper was applied to HiC-Pro output files to identify high confidence chromatin contacts using EACH, ALL peak finding settings
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are HiC-Pro output of allValid Pairs

extract_protocol:
In situ contact libraries were generated according to the in situ Hi-C published protocol through proximity ligation with modifications. Cells are lysed and chromatin restriction digested using MboI. Biotin labeled dATP is used to fill in the restriction fragment overhangs and mark the DNA ends. Ends are then proximity ligated using DNA ligase. After proximity ligation, nuclei are pelleted and nuclei lysed. Nuclei are then sonicated to solubilize chromatin. Protein A beads are used to clarify supernatant for chromatin immunoprecipation step. Samples are incubated overnight with antibody at 4C with rotation. DNA is eluted off beads and supernatant transferred to new tubes. Crosslinks are reversed. DNA is then purified using Zymo DNA purification kit according to manufacturer’s protocol and eluted in water. Streptavidin C-1 beads are used to capture fragments with biotin-dATP labeled ends.
After capture, beads are separated with a magnet and the supernatant is discarded. Beads are then washed in several buffers. Beads are resuspended in master mix containing Tn5 Tagment DNA enzyme, which is essential for adapter ligation to samples. Beads are washed several buffers, then separated on a magnet and supernatant discarded. To generate the sequencing library, PCR amplification of the tagmented DNA is performed while the DNA is still bound to the beads. Beads are resuspended in a PCR master mix, consisting of a unique Nextera Ad2.X primer, Phusion HF 5X buffer, dNTPs, universal Nextera Ad1 primer, and Phusion DNA Polymerase. DNA is amplified with 8 cycles of PCR. After PCR, beads are separated on a magnet and the supernatant containing the PCR amplified library is transferred to a new tube, purified using the Zymo DNA Clean and Concentrator kit according to manufacturer’s protocol and eluted in water. Purified HiChIP libraries were size selected to 300-700 basepairs using a double size selection with AMPure XP beads.

value: YY1 (Abcam, Cat# ab109237)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A10_ad008


title: ATAC_rEILP_rep1


title: 2-HiChIP_0hr_YY1


title: Input

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

data_processing:
Base-calls were made with RTA 2.0, and converted to fastq files with cl2fastq2 v2.20.
ChIP-seq reads were aligned to the human hg38 genome build using the following command in bowtie2 version 2.3.4.3: bowtie2 -I 0 -X 700 --end-to-end --sensitive -x /path_to_hg38_index -1 /path_to_first_paired_read.fastq.gz -2 /path_to_second_paired_read.fastq.gz -S sample.sam
To call peaks, we used the following command from macs2 (v2.1.2): macs2 callpeak -t {IP_sample}.bam -c {Input_sample}.bam -f BAMPE -n {SAMPLE} –outdir /path_to_output_dir/ --broad -B
Genome_build: hg38
Supplementary_files_format_and_content: broadPeak files generated from macs2 (v2.1.2) indicating the location of the peak, the fold-change over input signal, and significance of the enrichment. bedGraph files were generated using deeptools (v3.2.0) indicating the number of reads that cover a 10 bp bin.

source_name: HCT-116 colorectal carcinoma cell line

growth_protocol: HCT116 colorectal carcinoma cells were grown in McCoys 5A media supplemented with 10% FBS and penicillin/streptomycin (100 units/ml) at 37°C with 5% CO2.

extract_protocol:
Approximately 10 million HCT116 cells were grown to 80% confluency in a 10 cm plates. Cells were washed in the plate with 5 mls of 1X PBS at room temperature. The 1X PBS wash was removed, and 5 mls of Fixing Buffer (50 mM HEPES-KOH pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) was added. Cells were fixed by adding 313 ul of freshly prepared 16% methanol-free formaldehyde solution (Thermo Scientific Catalog #28906) to a final concentration of 1%, and cells were incubated on a shaker at room temperature for 10 minutes. Formaldehyde was quenched by adding 266 ul of 2.5 M Glycine (final concentration 125 mM), and cells were incubated for an additional 5 minutes on the shaker at room temperature. Cells were collected from the plate by scraping the monolayer and diluting the fixation solution with 10 mls ice-cold 1X PBS. Cells were pelleted at 200 x g for 5 minutes at 4°C. Cells were washed twice more with 5 mls ice-cold 1X PBS and collected by centrifugation at 200 x g for 5 minutes at 4°C. The final PBS wash was carefully aspirated from the cell pellet, and cells were flash frozen in liquid nitrogen and stored at -80°C until use. Cells were thawed on ice for 10 minutes prior to cell lysis. Cells were lysed in 1 ml LB1 (50 mM HEPES-KOH pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, Protease inhibitor cocktail (Roche cOmplete Mini tablets, EDTA-free) and incubated for 10 minutes rotating at 4°C. Intact nuclei were collected by centrifugation at 1,700 x g for 5 minutes at 4°C. Supernatant was removed so as not to disturb the nuclei pellet, and nuclei were resuspended and washed in 1 ml LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease cocktail inhibitor) for 10 minutes rotating at 4°C. Nuclei were collected by centrifugation at 1,700 x g for 5 minutes at 4°C, and the supernatant was removed so as not to disturb the nuclei pellet. Finally, nuclei pellets were gently rinsed twice without disturbing the pellet with 1 ml LB3 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.01% NP-40, protease cocktail inhibitor) and collected at 1,700 x g for 5 minutes at 4°C. Following the two rinse steps, nuclei were resusented in 1 ml LB3 and transferred to a 1 ml milliTUBE (Covaris) for shearing. Nuclei were lysed and chromatin was sheared to range of 300-600 base-pair fragments using a Covaris E220 evolution Focused ultrasonicator with the following parameters: Peak power (140.0), Duty Factor (5.0), Cycles/Burst (200), Duration (600 seconds), Temperature (4°C). Sheared chromatin was quantified by Bradford Assay, and 300 ug of chromatin was brought to a final volume of 500 ul in LB3, and then an additional 500 ul of ChIP Cocktail Mix (40 mM Tris-HCl pH 7.6, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.5% NP-40, Protease inhibitor cocktail) was added to bring the final volume to 1 ml. Prepared chromatin was then pre-cleared by incubation with 20 ul of pre-washed Dynabeads Protein G magnetic beads (Invitrogen Catalog #:10004D) for 3 hours at 4°C with constant rotation. Prior to incubation with antibody, 10 ul of pre-cleared chromatin was removed and set aside to serve as 1% input. Pre-cleared chromatin was removed by magnetic separation, transferred to a new tube, and immunoprecipitated with 5 ul of H3K9me3 antibody (Active Motif 39161, Lot# 14418003) overnight at 4°C with constant rotation. Protein G magnetic beads (35 ul/IP) were blocked overnight in 1 ml of 1X PBS, 0.5% BSA, and 20 ug of Herring Sperm DNA (Sigma Catalog #D7290) at 4°C with constant rotation. The next morning, blocked beads were washed three times with 1X PBS + 0.5% BSA, and two times with WB1 (50 mM Tris-HCl pH 7.6, 150 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100). Immuno-chromatin complexes were incubated with blocked beads for 3 hours at 4°C with constant rotation. Unbound chromatin was then removed using magnetic separation, and the beads were washed as follows: 3 times with WB1, 3 times with WB2 (50 mM Tris-HCl pH 7.6, 500 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100), 2 times with WB1, and 1 time with Low Salt TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 50 mM NaCl). All washes require 5 minute incubations at 4°C with constant rotation followed by magnetic separation and removal of buffer. To elute DNA from the magnetic beads, 50 ul of Elution Buffer (10 mM Tris-HCl pH 8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, 1% SDS) was added to the beads and incubated at 65°C for 15 minutes. The elution step was repeated, and eluates combined. Eluents and 1% input (with 90 ul of elution buffer added) were incubated overnight at 65°C with constant shaking to reverse cross-link protein:DNA complexes. The next morning, 2 ul of DNase-free RNase A (10 mg/ml stock) was added to eluents and incubated at 37°C for 1 hour. Next, 10 ul of Proteinase K (20 mg/ml stock) was added to eluents and incubated at 37°C for 2 hours. DNA was isolated following standard KAPA Pure Beads (KAPA Biosystems Catalog# KK8000) protocol with a 1.5X ratio of beads to DNA volume as described for the Native Chromatin Immunoprecipitation. Final elution was in 20 ul of Nuclease-free water, and DNA concentration was measure by Qubit dsDNA High Sensitivity Assay kit (ThermoFisher Scientific Catalog#: Q32851). Library preparation was done as described for Native Chromatin Immunoprecipitation
Libraries were prepared according to KAPA's instructions accompanying the KAPA Hyper Prep Kit (Part# KR0961 ). Briefly, DNA was end-repaired, A-Tail extended, and KAPA adapters were ligated to DNA fragments. Adapter-ligated fragments were amplified with 11 cycles on a thermocycler, and DNA was purified using KAPA Pure Beads. Prepared libraries were submitted to the VARI Genomics Core for library QC and quantification using the Agilent 2100 Bioanalyzer and KAPA Library Quantification Kit, respectively. Libraries were sequenced on an Illumina NextSeq 500 with 2 X 75 bp paired-end reads.

treatment_protocol: No treatment was perfromed on these cells.

tag: cell line

value: colorectal carcinoma cell line

tag: passages

tag: chip antibody


title: H3K9me3_R2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A10_ad007


title: H3K9me3_R1


title: 1-HiChIP_0hr_YY1


title: 2-HiChIP_1hr_H3K27ac

value: 1 hr EPO

value: H3K27ac (Abcam, Cat# ab4729)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A10_ad004

value: ACB


title: ATAC_LTiP_rep1


title: Hs31-17W3d

city: Philadelphia

first: Youngsun

last: Hwang

state: PA

address: 3800 Spruce Street Old Vet Quad 220E

institute: University of Pennsylvania

data_processing:
Raw data were demultiplexed using mkfastq command in cell Ranger (v3.1.0) to generate Fastq files.
Fastq files were trimmed using cutadapt (v.2.6). Trimmed sequence files were mapped on the reference genome for humans (GRCh38-3.0.0).
Genome_build: human (GRCh38-3.0.0)
Supplementary_files_format_and_content: Cellranger ouputs containg barcodes, features, and count matrices.

molecule: polyA RNA

source_name: human fetal testicular cells

extract_protocol:
hiPSCs and iMeLCs were harvested. The d5 floating aggregates containing hPGCLCs were incubated with 0.1% Trypsin-EDTA (Gibco) in PBS for 15 min at 37 °C with periodical pipetting. After quenching the reaction by addition of FBS and pipetting, cells were strained through a 70 µm nylon cell strainer (Thermo Fisher Scientific). The AG+ cells were sorted by FACSAria Fusion (BD Biosciences) and collected in an Eppendorf tube. xrTestes were treated with 0.1% Trypsin-EDTA in PBS for 15 min at 37 °C with periodical pipetting.  After quenching the reaction by addition of FBS and pipetting, cell suspension was washed with 0.1% BSA fraction V in PBS and strained through a 70 µm nylon cell strainer. AG+/-VT+/-PC+/- cells were sorted by FACSAria Fusion and collected in CELLOTION (Amsbio). Fetal gonads were cut into small pieces (~1mm2), then digested with collagenase type IV for 8 min at 37 ºC. Tissues were centrifuged at 200 g for 5 min and washed with Hank’s Balanced Salt Solution (Thermo Fisher Scientific). Tissues were then digested with 0.25% trypsin/EDTA and DNase I for 8 min at 37 ºC. After the digestion was quenched by adding 10% of fetal bovine serum, cells were strained through nylon cell strainer (70μm in pore size). The cells were then pelleted by centrifugation at 200 g for 5 min, which were resuspended in the MACS buffer (PBS containing 0.5% BSA and 2 mM EDTA). Dead cells were subsequently removed by Dead cell removal microbeads (Miltenyi Biotec). Flow-through cells were pelleted by centrifugation at 600 g for 15 min and resuspended in PBS containing 0.1% BSA
Cells were loaded into Chromium microfluidic chips with Chromium Single cell 3ʼ v3 chemistry and used to generate single cell gelbead emulsions (GEMs) using Chromium controller (10x Genomics) according to manufacturer’s protocol. All subsequent cDNA amplification and library construction steps were performed according to manufacturer protocol.

tag: gestational age

value: 17 weeks 3 days

value: human fetal testicular cells

tag: number of cells


title: ATAC_iLTiP_rep2


title: ATAC_iILCP_rep2


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A10_ad002

value: male


title: 2-HiChIP_1hr_YY1


title: 2-HiChIP_0hr_H3K27ac

value: naive


title: Hs27-18Wd5

value: 18 weeks 5 days


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A10_ad001


title: ATAC_RORCp_aLP_rep2


title: ATAC_LTiP_rep2


title: Hs26-18W0d

value: 18 weeks 0 days


title: 1-HiChIP_1hr_H3K27ac

value: BALB/cJ


title: ATAC_iLTiP_rep1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A1_ad012


title: ATAC_RORCp_aLP_rep1


title: 1-HiChIP_0hr_H3K27ac

value: erythroid


title: ATAC_Flt3nRORCn_aLP_rep2

value: Fetal Liver


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A1_ad007


title: Jurkat_UNC1999_rep2_1

city: Chapel Hill

first: Gang

middle: Greg

last: Wang

state: NC

address: 450 West Drive

department: BCBP

institute: UNC Lineberger Comprehensive Cancer Center

description: processed data file: RNA-seq_Jurkat_DMSO_vs_UNC1999

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed. Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

growth_protocol: Jurkat, RS4;11 and OCI-AML3 cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit.
RNA libraries were made with standard Illumina protocols or prepared by Novogene Inc.

treatment_protocol: For BAHCC1 knockdown (KD) experiments, Jurkat, RS4;11 and OCI-AML3 cells were infected with lentivirus encoding empty vector control (shEV) or sh-BAHCC1, followed by drug selection to generate stable cell lines. For compound treatment experiments, Jurkat cells were treated with 5 µM of DMSO or UNC1999 for five days and collected. For BAHCC1 gene-editing experiments, CRISPR/cas9-based genomic editing tools were used to site-specifically mutate BAHCC1 within the BAHCC1 BAH domain (Y2533A or W2554G). For RNA-seq experiments, cells were grown in regular medium and collected.

value: Jurkat cells


title: hPGCLCs-2

source_name: human primordial germ cell-like cells

value: human primordial germ cell-like cells


title: ChIP-exo_1hr_Pol2

description: Processed file is merged from two biological replicates

data_processing:
To estimate variance across biological replicates, the Pearson correlation coefficient for pairwise gene RPKM was computed using the HOMER suite (Hypergeometric Optimization of Motif EnRichment)
Biological replicates were then merged and peaks found using the HOMER suite (Hypergeometric Optimization of Motif EnRichment)
Biological replicates were also converted to bigWig files for visualization using deepTools
Genome_build: mm10
Supplementary_files_format_and_content: each bigWig and peak file is built from merged biological replicates for ChIP-exo of Pol II, CTCF, or YY1

extract_protocol:
Cells are lysed, the nuclear fraction retained, and the chromatin is fragmented by sonication to 100-500bp.
In vivo protein-DNA interactions are preserved through formaldehyde crosslinking. Cells are lysed, the nuclear fraction retained, and the chromatin is fragmented by sonication to 100-500bp. DNA fragments interacting with the protein of interest are enriched by ChIP, the important lambda exonuclease digestion effectively footprinting the left and right 5' DNA borders of the protein-DNA crosslink site, and a library is prepared by adding sequencing adapters according to manufacturer’s instructions. ChIP-exo enriched DNA fragments are sequenced from the left and right 5' DNA borders of the protein-DNA crosslink site.

value: Pol2 (Santa Cruz, Cat# sc-17798)


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A1_ad010


title: ATAC_Flt3nRORCn_aLP_rep1

value: Embryonic Day 15

value: Zbtb16-EGFP Tcf7-mCherry Rorc-Thy1.1


title: ChIP-exo_0hr_Pol2


title: Jurkat_UNC1999_rep1_1


title: Jurkat_DMSO_rep2_1

value: DMSO


title: ChIP-exo_1hr_YY1

value: 1 hr EPO

value: YY1 (Abcam, Cat# ab109237)


title: ATAC_Flt3pRORCn_aLP_rep2


title: ChIP-exo_0hr_YY1


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A1_ad002

value: ACB


title: Jurkat_DMSO_rep1_1


title: ATAC_Flt3pRORCn_aLP_rep1


title: ChIP-exo_1hr_CTCF

value: CTCF (Millipore, Cat# 07-729)


title: ATAC_CLP_rep2


title: MNC_osteoarthritis

city: New Orleans

first: Hong-Wen

last: Deng

state: Louisiana

address: 1324 Tulane Ave

institute: Tulane

data_processing:
Raw FASTQ files were mapped to the Reference genome (GRCh38/hg38) using Cell Ranger 3.0
The references were rebuilt according to instructions from 10x Genomics, which performs alignment, filtering, barcode counting and UMI counting. Following alignment, digital gene expression (DGE) matrices were generated for each sample and for all samples. Merged 10x Genomics DGE files were generated using the aggregation function of the Cell Ranger pipeline.
All the cells in different batches were merged and normalized by equalizing the read depth among libraries. Only confidently mapped, non-PCR duplicates with valid barcodes and unique molecular identifiers were used to generate the gene-barcode matrix
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Gene by cell expression matrix (raw counts)

source_name: bone marrow

extract_protocol:
Bone marrow derived mononuclear cells (BM-MNCs) were extracted from the femur head using density gradient centrifugation and then purified using CD271+ magnetic microbead
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V3 following the manufacturer’s guide. Sequencing was performed on an Illumina Novaseq6000 with a sequencing depth of at least 100,000 reads per cell for a 150bp paired end (PE150) run.

tag: gender

value: male

tag: diagnosis

value: osteoarthritis

value: CD271+ BM-MNCs


title: 1-RNA-seq_0hr

value: naive


title: ChIP-exo_0hr_CTCF

value: BALB/cJ


title: ATAC_CLP_rep1

tag: tissue


title: MNC_osteoporosis

value: female

value: osteoporosis

tag: cell type


title: CEMBA181218_5F_1_CEMBA181218_5F_2_A1_ad004


title: Sample_1379: Pogz cKO-/-; Hippocampus

status: Public on Sep 27 2020

city: Jerusalem

first: Reut

last: Suliman

address: Givat ram campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Sequencing was done using Next seq 500 high output kit V2 75 cycles (illumina) on illumina’s NextSeq 500 system with 43bp paired-end reads (resulting 50-70 million reads per sample)
Reads from RNA-Seq were aligned to the mouse genome (mm9), and aligned reads were counted at the gene level using STAR aligner (v250a)
Genome_build: mm9
Supplementary_files_format_and_content: .csv files containing counts for all samplesover all genes

source_name: Hippocampus

extract_protocol:
Adult mice hippocampi and cerebella (three males and three females from each genotype) were dissected and RNA was extracted using Qiagen RNeasy lipid tissue mini kit (Qiagen 74804). The RNA integrity was measured using the Agilent BioAnalyzer machine (RNA integrity number (RIN) was above 8.5)
Libraries of mRNA for sequencing were made by pulldown of poly (A) RNA using Truseq RNA sample preparation kit (illumina). Library quantity and pooling were measured by Qubit (dsDNS HS) and quality was measured by tape station (HS)

value: Hippocampus

value: F

value: NesCre/+; Pogzfl/fl


title: Sample_1385: Pogz cKO-/-; Hippocampus


title: Sample_1433: Pogz cKO+/-; Hippocampus

value: M

value: NesCre/+; Pogzfl/+


title: ruuo mouse 10x

city: Edinburgh

first: Eoin

middle: D

last: O'Sullivan

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
10x library Sequencing was performed on a NextSeq 550 High Output Kit v2 (Illumina) for 150 cycles at 400M PE reads comprising of 2x75bp and 8bp index reads.
Using the Cell Ranger Single Cell software suite 2.1.0 by 10x Genomics the cellranger mkfastq wrapper demultiplexed the illumina output BCL files to library specific FASTQ files.  Subsequently, alignment was performed using the cellranger count function using STAR aligner 2.5.1b.1 The GRCm38 mouse reference genome, mm10 (Ensembl 93) was used.
The plate based librarys were created using the Smart-seq2 protocol for cDNA synthesis and Fluidigm protocol (PN 100-7168 M1) for tagmentation and index-PCR using Nextera chemistry to prepare single cell sequencing libraries. 8x 96-plates were pooled together and sequenced on one lane on Illumina HiSeq 4000 (50 bp, single-end reads).
Genome_build: mm10
Supplementary_files_format_and_content: genecounts are found in matrix.mtx files, cell  barcodes in barcodes.tsv and genes names in genes.tsv

source_name: Kidney

extract_protocol:
kidneys were removed, digested on ice and FACS sorted using DAPI as a live/dead gate. Libraries were constructed using the standard 10x single cell 3' V2 workflow
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney

value: 8 week

tag: condition

value: 7 days post reversal ( experimental day 14)


title: uuo7 mouse 10x

value: day 7 post uuo timepoint


title: uuo2 mouse 10x

value: day 2 post UUO timepoint


title: Sham mouse 10x

value: sham surgery/day 0 timepoint


title: Smartseq2 kidney

value: 768 wells (96*8) smartseq2 , with all timepoints represented


title: Brassica napus RNA extracted from leaves of plants infected by CaMV

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

data_processing:
Removed adaptors. Sequences without adaptor matches were discarded.
Sequences were counted and ordered
Supplementary_files_format_and_content: Tabular format. Counts of each species of sRNA in the library.
Supplementary_files_format_and_content: Canola_Turnip_cdna.tabular.xlsx includes four sheets containing the original alignment outputs with the transcriptomes of turnip and canola.

organism: Brassica napus

source_name: Brassica napus variety  "SariGol"

growth_protocol: Plants were maintained in greenhouse at 22/20 ◦C (day/night) and 16/8 h (light/dark) photoperiod.

extract_protocol:
RNAs, in three biological repeats, were extracted 20 days post-inoculation (dpi) collecting ten leaves from mock-inoculated and virus-infected plants using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Libraries were obtained using NEXTflex Small RNA-Seq Kit v3 (Bio Scientific) according to manufacturer’s instructions

treatment_protocol: Either Brassica napus or Brassica rapa were mechanically inoculated with CaMV strain NY8153 (Sample 1 and Sample 3, respectively). Phosphate buffer was used as control in mock-inoculated plants (Sample 2 and Sample 4).

tag: tissues used

value: leaves

tag: sampling

value: bulk of leaves from plant population


title: Brassica napus RNA extracted from leaves of plants mock-inoculated


title: Sample_1172: Control; Hippocampus

value: Pogzfl/fl


title: Sample_1371: Pogz cKO-/-; Hippocampus


title: Sample_1192: Control; Hippocampus


title: Sample_1189: Pogz cKO+/-; Hippocampus


title: Sample_1219: Pogz cKO-/-; Hippocampus


title: Sample_1176: Pogz cKO+/-; Hippocampus


title: Sample_1190: Control; Hippocampus


title: Sample_1155: Control; Hippocampus


title: Sample_1120: Pogz cKO+/-; Hippocampus


title: Sample_1129: Control; Hippocampus


title: Sample_1160: Pogz cKO-/-; Hippocampus


title: Sample_1170: Control; Hippocampus


title: Sample_936: Pogz cKO-/-; Hippocampus


title: Sample_938: Pogz cKO+/-; Hippocampus


title: Bewo shControl Exp B

city: Pittsburgh

first: Ofer

last: beharier

address: 204 Craft Ave

institute: MWRI

description: fer3_geo.csv: Column "shControl.B"

data_processing:
After evaluating the basecall quality and removing the adatpers, the reads were aligned to GRCh38 human genome assembly using the software STAR (version 2.5.2a).
Read count for each gene was calculated using STAR.
Additional data analysis steps: Libraries were normalized using the median of the ratios method implemented in R package DESeq2
Generalized linear model with Negative binomial distribution (implemented in DESeq2) was used to test if a gene is differentially expressed between shControl and shGPX4
P values of the tests were adjusted using the Benjamini & Hochberg's method to control the false discovery rate.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file that reports reads per gene for each sample

source_name: Bewo shControl, following ferrostatin-1 withdrawal

growth_protocol: BeWo cells were maintained in F12K Kaighn’s modified medium (Gibco) supplemented with 10% bovine growth serum and ferrostatin-1

extract_protocol:
RNA was isolated with Qiagen RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols at Novogene Corporation
The samples were sequenced using PE150 sequencing on a Novaseq 6000 with S4 flowcell.

treatment_protocol: ferroptosis activation was induced by ferrostatin-1 withdrawal

value: BeWo placental cell line

tag: treatment

value: shControl


title: Bewo shGPX4 Exp B

description: fer3_geo.csv: Column "shGPX4.B"

source_name: Bewo shGPX4, following ferrostatin-1 withdrawal


title: Bewo shGPX4 Exp A

description: fer3_geo.csv: Column "shGPX4.A"


title: H3K27ac ChIP-seq from Luminal2/BMP k.o CAF-FOXA1 o.e tumor

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

description: BMP4, 5 were knocked out in surrounding reconstituted CAF

data_processing:
FastQC-0.11.5 checked the quality of raw sequences. cutadapt-1.18 was used to detect and remove Illumina adapter sequence.
Bowtie2-2.3.4.1 aligned sequences to the Homo sapiens genome (Ensembl GRCh38 release97). QualiMap-2.2.1 checked the quality of the alignment.
Picard tools removed duplicates with parameters VALIDATION_STRINGENCY=LENIENT
MACS2-v2.1.2 was used for peak calling with default parameters and q-value < 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2; bigWig files were generated using genomeCoverageBed and bedGraphToBigWig.

source_name: Human bladder tumor organoid

growth_protocol: Maintenance of human bladder tumor assembloids were conducted in organoid media.  Organoid media: Advanced DMEM/F-12 (Gibco) supplemented with 10 mM HEPES (pH 7.4, Sigma), 10 mM Nicotinamide (Sigma), 1 mM N-acetyl-L-cysteine (Sigma), 1X Glutamax (Gibco), 1% penicillin/streptomycin (Gibco), 50 ng/ml human EGF (Peprotech), 0.5X B-27 (Gibco), 1 μM A83-01 (Tocris), and 10 μM Y-27632 (Abmole)

extract_protocol:
We crosslinked 1–2 × 106 human bladder tumor cells for 5 min at 37 °C with formaldehyde at a final 1%. We then carried out ChIP using previously described methods.80 In brief, we pre-cleared sonicated chromatin in RIPA buffer (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.01% SDS) with 2 μg of rabbit IgG (Cell Signaling Technology) and 20 μl of Protein G magnetic beads (Thermo Fisher Scientific). We then immunoprecipitated pre-cleared chromatin using 2 μg of H3K27ac antibody (Abcam) and 20 μl of Protein G magnetic beads (Thermo Fisher Scientific) overnight at 4 °C with rotation. The next day, we washed the pulled chromatin, and we reverse crosslinked it with proteinase K (20 mg/ml) and 10% SDS overnight at 65 °C. We extracted ChIPed DNA with phenol/chloroform and eluted it in 20 μl of TE.
We constructed ChIP-seq libraries using the ACCEL-NGS® 2S PLUS DNA LIBRARY KIT (Swift Bioscience), following the manufacturer’s instructions. In brief, purified ChIP DNA was subjected to end-repairing and adaptor ligation, and applied 12 cycles of PCR amplification. Amplified DNA was size selected and quantified using Bioanalyzer (Agilent). We sequenced ChIP-seq libraries using an Illumina HiSeq 2500 platform.

treatment_protocol: Human bladder tumor assembloids samples were harvested after 7 days of cultures with shaking incubation.

value: Bladder tumor

tag: chip antibodies

value: wild type


title: C. difficile R20291 smooth-rep 1

first: Rita

last: Tamayo

address: 125 Mason Farm Rd, CB# 7290

department: Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

data_processing:
HiSeq Control Software was used for basecalling. Raw sequence data files (.bcl) were converted the FASTQ format and de-multiplexed with bcl2fastq 2.17 software (Illumina). One mismatch was permitted for index sequence identification.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. difficile R20291 whole genome in CLC Genomics Workbench v20. Default settings for RNA-seq were used (allows 1 mismatch per read)
Reads Per Kilobase per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench v20
Genome_build: C. difficile R20291 reference genome, FN545816
Supplementary_files_format_and_content: Excel spreadsheet containing read information for individual samples (sheet 1), differential expression analysis (sheet 2), and list of genes >2-fold changed and p < 0.05 (sheet 3) with FDR correction
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Clostridioides difficile R20291

source_name: C. difficile R20291

growth_protocol: All steps anaerobic, 37 degrees C. Grown from freezer stocks on BHIS-agar, overnight incubation. Strain passaged on BHIS-agar, overnight incubation. Individual rough or smooth coloniy was grown overnight (14-16h) in BHIS broth. Culture (5uL) was spotted onto BHIS-agar and incubated for 24 hours.

extract_protocol:
Growth was collected from plates and suspended in 1:1 ethanol:acetone. Cell pellets collected by centrifugation. RNA extraction with TriSure and chloroform, beadbeating, and isopropanol/ethanol precipitation. Quality verified with Bioanalyzer Assay.
Ribozero rRNA Removal Kit, NEBNext Ultra RNA Library Prep Kit for Illumina, Illumina HiSeq 2500 instrument

value: bacterial culture

tag: isolate

value: smooth colony isolate

tag: culture

value: grown on BHIS-agar


title: C. difficile R20291 rough-rep 2

value: rough colony isolate


title: C. difficile R20291 smooth-rep 2


title: C. difficile R20291 rough-rep 1


title: Bewo shControl Exp A

description: fer3_geo.csv: Column "shControl.A"


title: H3K27ac ChIP-seq from Luminal2/BMP k.o CAF

tag: genotype


title: H3K27ac ChIP-seq from Luminal1/BMP k.o CAF-FOXA1 o.e tumor


title: Sample_933: Pogz cKO+/-; Hippocampus

value: Hippocampus

tag: strain

value: M

value: NesCre/+; Pogzfl/+


title: H3K27ac ChIP-seq from Luminal2/FOXA1 k.o tumor

description: FOXA1 was knocked out in luminal tumor organoid 2

tag: passages


title: Sample_1385: Pogz cKO-/-; Cerebellum

source_name: Cerebellum

value: Cerebellum

value: F

value: NesCre/+; Pogzfl/fl


title: Sample_1371: Pogz cKO-/-; Cerebellum


title: Sample_1433: Pogz cKO+/-; Cerebellum


title: H3K27ac ChIP-seq from Luminal1/FOXA1 k.o tumor

description: FOXA1 was knocked out in luminal tumor organoid 1


title: H3K27ac ChIP-seq from Luminal1/BMP k.o CAF


title: Sample_1219: Pogz cKO-/-; Cerebellum


title: Sample_1379: Pogz cKO-/-; Cerebellum


title: H3K27ac ChIP-seq from Luminal2

description: control


title: H3K27ac ChIP-seq from Luminal1

description: control


title: H3K27ac ChIP-seq from Luminal1_input

description: input control


title: Sample_1172: Control; Cerebellum


title: Sample_1189: Pogz cKO+/-; Cerebellum


title: Sample_1190: Control; Cerebellum


title: Sample_1160: Pogz cKO-/-; Cerebellum


title: Sample_1170: Control; Cerebellum


title: Sample_1176: Pogz cKO+/-; Cerebellum


title: H3K27ac ChIP-seq from Basal2/BMP o.e CAF

description: BMP4, 5 were overexpressed in surrounding reconstituted CAF


title: H3K27ac ChIP-seq from Basal1/BMP o.e CAF-FOXA1 k.o tumor


title: H3K27ac ChIP-seq from Basal1/BMP o.e CAF


title: H3K27ac ChIP-seq from Basal1/FOXA1 o.e tumor

description: FOXA1 was overexpressed in basal tumor organoid 1


title: H3K27ac ChIP-seq from Basal2/BMP o.e CAF-FOXA1 k.o tumor


title: H3K27ac ChIP-seq from Basal2

description: control


title: Sample_1129: Control; Cerebellum


title: Sample_1155: Control; Cerebellum


title: Sample_1192: Control; Cerebellum


title: H3K27ac ChIP-seq from Basal2/FOXA1 o.e tumor

description: FOXA1 was overexpressed in basal tumor organoid 2


title: Sample_938: Pogz cKO+/-; Cerebellum


title: H3K27ac ChIP-seq from Basal1_input

description: input control


title: H3K27ac ChIP-seq from Basal1

description: control


title: Sample_936: Pogz cKO-/-; Cerebellum


title: FOXA1 ChIP-seq from Luminal1/BMP k.o CAF-FOXA1 o.e tumor

extract_protocol:
We crosslinked 1–2 × 106 human bladder tumor cells for 5 min at 37 °C with formaldehyde at a final 1%. We then carried out ChIP using previously described methods.80 In brief, we pre-cleared sonicated chromatin in RIPA buffer (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.01% SDS) with 2 μg of rabbit IgG (Cell Signaling Technology) and 20 μl of Protein G magnetic beads (Thermo Fisher Scientific). We then immunoprecipitated pre-cleared chromatin using 2 μg of FOXA1 antibody (Abcam) and 20 μl of Protein G magnetic beads (Thermo Fisher Scientific) overnight at 4 °C with rotation. The next day, we washed the pulled chromatin, and we reverse crosslinked it with proteinase K (20 mg/ml) and 10% SDS overnight at 65 °C. We extracted ChIPed DNA with phenol/chloroform and eluted it in 20 μl of TE.
We constructed ChIP-seq libraries using the ACCEL-NGS® 2S PLUS DNA LIBRARY KIT (Swift Bioscience), following the manufacturer’s instructions. In brief, purified ChIP DNA was subjected to end-repairing and adaptor ligation, and applied 12 cycles of PCR amplification. Amplified DNA was size selected and quantified using Bioanalyzer (Agilent). We sequenced ChIP-seq libraries using an Illumina HiSeq 2500 platform.

tag: subtype

value: luminal

tag: description

value: BMP4, 5 were knocked out in surrounding reconstituted CAF


title: Brassica rapa RNA extracted from leaves of plants infected by CaMV

organism: Brassica rapa

source_name: Brassica rapa variety "Purple To White Globe"

value: leaves

value: bulk of leaves from plant population


title: Brassica rapa RNA extracted from leaves of plants mock-inoculated


title: DTC2_negative_2

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

data_processing:
Data was separated by barcode and aligned using Tophat version 2.0.10 (Kim et al. 2013) with default settings.
Transcripts were quantified by the Broad Technology Labs computational pipeline using Cuffquant version 2.2.1 (Trapnell et al. 2012).
Data were processed through CuffNorm if 50% of the reads aligned and if at least 100,000 pairs were aligned per sample. Normalization used the default settings, including “geometric” normalization, and expression level information as FPKM (Fragments per kilobase of transcript per million mapped fragments) are provided.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including FPKM for each sample

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained after Ficoll density centrifugation (Sigma-Aldrich, St Louis, MO). B cells were purified from PBMC by negative selection on magnetic columns according to the manufacturer’s instructions (B cell isolation Kit II, Miltenyi Biotech, Gladbach, Germany) with a purity >95%. B cells were stimulated at 1.106cells/ml for 3 days in complet RPMI 1640 (Sigma-Aldrich, St Louis, USA) containing L-glutamine, penicillin/streptomycin (Life technologies, Carlsbad, USA), and 10% FCS (Lonza, Verviers, Belgium) in 24-well plates (Nunc, Langenselbold, Germany) at 37°C, 5% CO2. Stimulation was performed using 1μg/ml CpG oligonucleotide (ODN 2006, Invivogen, San Diego, USA), 50ng/ml recombinant human soluble CD40L (R&D Systems, Minneapolis, USA), 5μg/ml F(ab’)2 Fragment Goat anti-Human IgA+IgG+IgM+ (H+L) (Jackson ImmunoResearch Laboratories, West Grove, PA), 50U/ml recombinant IL-2 (Novartis) and 10ng/ml recombinant IL-21 (Miltenyi Biotech, Gladbach, Germany).

extract_protocol:
After sorting, total RNA was extracted using the RecoverAll Total Nucleic Acid Isolation Kit (Ambion). RNA quantity was measured with a Nanodrop ND1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was assessed using an Agilent 2100 Bioanalyser.
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform according to the SmartSeq2 protocol (Picelli et al, 2013, 2014) with some modifications (Trombetta et al, 2014). Briefly, total RNA was purified using RNA-SPRI beads, polyA mRNA was converted to cDNA and amplified cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Sequencing was carried out as paired-end 2x25bp with an additional 8 cycles for each index.

treatment_protocol: After 3 days enrichment, B cells were permeabilized, fixed and marked with anti-GZMB-Alexa645 (BD biosciences) 30 minutes at 4°C, and GZMB+i B cells and GzmB- B cells were sorted on the FACs ARIA II (BD biosciences) using FACSDiva software. Because of permeabilization, we followed a Method for Analyzing RNA following Intracellular Sorting (MARIS) described by Hrvatin et al. (Hrvatin et al, PLosOne 2014) in order to preserve the RNA.

tag: volunteer

value: Purified B cells

tag: gzmb secretion

value: negative

tag: rin


title: FOXA1 ChIP-seq from Luminal2/FOXA1 k.o tumor

tag: tissue

value: Bladder tumor

value: FOXA1 was knocked out in luminal tumor organoid


title: Sample_1120: Pogz cKO+/-; Cerebellum

tag: gender


title: FOXA1 ChIP-seq from Luminal1/BMP k.o CAF

value: wild type


title: DTC2_negative_1

source_name: Peripheral blood mononuclear cells (PBMC)


title: H3K27ac ChIP-seq from Basal2_input

description: input control


title: FOXA1 ChIP-seq from Luminal1/FOXA1 k.o tumor


title: DTC1_negative_2


title: FOXA1 ChIP-seq from Luminal1

value: control


title: FOXA1 ChIP-seq from Basal2/BMP o.e CAF-FOXA1 k.o tumor

value: basal

value: BMP4, 5 were overexpressed in surrounding reconstituted CAF


title: FOXA1 ChIP-seq from Luminal1_input

value: input control


title: FOXA1 ChIP-seq from Luminal2/BMP k.o CAF-FOXA1 o.e tumor


title: AK32_negative_1


title: AK30_negative_2


title: AK30_negative_1


title: DTC1_negative_1


title: AK22_negative_1


title: FOXA1 ChIP-seq from Basal1/BMP o.e CAF-FOXA1 k.o tumor


title: FOXA1 ChIP-seq from Luminal2/BMP k.o CAF


title: Sample_933: Pogz cKO+/-; Cerebellum

value: M

value: NesCre/+; Pogzfl/+


title: FOXA1 ChIP-seq from Basal2/BMP o.e CAF


title: FOXA1 ChIP-seq from Luminal2


title: DTC3_negative_1


title: FOXA1 ChIP-seq from Basal2/FOXA1 o.e tumor

value: FOXA1 was overexpressed in basal tumor organoid


title: FOXA1 ChIP-seq from Basal1/BMP o.e CAF


title: AK21_negative_1


title: AK16_negative_2


title: AK18_negative_1


title: FOXA1 ChIP-seq from Basal2


title: DTC3_positive_1

value: positive


title: FOXA1 ChIP-seq from Basal1


title: AK16_negative_1


title: FOXA1 ChIP-seq from Luminal2_input

value: luminal


title: FOXA1 ChIP-seq from Basal2_input


title: DTC2_positive_2


title: AK30_positive_1


title: ATAC-seq from Luminal2/BMP k.o CAF-FOXA1 o.e tumor

data_processing:
FastQC-0.11.5 checked the quality of raw sequences. cutadapt-1.18 was used to detect and remove Illumina adapter sequence.
Bowtie2-2.3.4.1 aligned sequences to the Homo sapiens genome (Ensembl GRCh38 release97). QualiMap-2.2.1 checked the quality of the alignment.
Picard tools removed duplicates with parameters "VALIDATION_STRINGENCY=LENIENT".
The reads were offset by +4 bases for the + strand and -5 bases for the - strand.
MACS2-v2.1.2 was used for peak calling with parameters "--nomodel --shift -100 --extsize 200" and q-value < 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2; bigWig files were generated using genomeCoverageBed and bedGraphToBigWig.

extract_protocol:
We lysed 50,000 cells with 50 μl of Lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Triton X-100) and incubated them for 5 min on ice . Following centrifuging at 1,000 g for 10 min at 4 °C, we resuspended the nuclei pellets with 50 μl of transposition mix (25 μl 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, and 20% Dimethyl Formamide in sterile water) and 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.01% Triton X-100, 0.1% Tween-20, and 5 μl H2O) and incubated the mixture with shaking for 1 h at 55 °C in a thermomixer. We purified transposed DNA using DNA Clean and the Concentrator-5 Kit (Zymo Research).
We amplified the transposed DNA using the NEBNext® High-Fidelity 2X PCR Master Mix for 10 cycles. We then performed ATAC-Seq using the Illumina HiSeq 2500 platform.

value: BMP4, 5 were knocked out in surrounding reconstituted CAF


title: FOXA1 ChIP-seq from Basal1_input


title: DTC2_positive_1


title: AK30_positive_2


title: ATAC-seq from Luminal1/BMP k.o CAF-FOXA1 o.e tumor


title: FOXA1 ChIP-seq from Basal1/FOXA1 o.e tumor


title: AK25_positive_2


title: AK29_positive_1


title: ATAC-seq from Luminal2/BMP k.o CAF


title: ATAC-seq from Luminal1/BMP k.o CAF


title: AK24_positive_2


title: ATAC-seq from Luminal2/FOXA1 k.o tumor


title: AK24_positive_1


title: AK22_positive_1


title: ATAC-seq from Luminal1


title: ATAC-seq from Luminal2


title: ATAC-seq from Basal2/BMP o.e CAF-FOXA1 k.o tumor


title: ATAC-seq from Basal1/BMP o.e CAF-FOXA1 k.o tumor


title: H3K27ac ChIP-seq from Luminal2_input

description: input control


title: Decato-2018-Human_SmallAirway_expression [SA_AGTCAA_L007]

city: Los Angeles

first: Benjamin

middle: E

last: Decato

address: 1050 Childs Way

department: Molecular and Computational Biology

institute: University of Southern California

description:
SmallAirway
SA_AGTCAA_L007Aligned

data_processing:
Reads aligned to hg19 or mm10 reference genome using WALT (https://github.com/smithlabcode/walt)
Methylation levels computed from reads using methpipe v3.4.2
Genome_build: hg19, mm10
Supplementary_files_format_and_content: All processed data files are methcounts format which includes, for each CpG site, the chromosome, position, strand, context, methylation level, and sequencing depth.
Supplementary_files_format_and_content: plain text of raw counts

source_name: Lung

extract_protocol: Illumina Truseq stranded RNA seq kit with Ribo minus depletion.

value: Lung


title: Decato-2018-Human_BronchialAirway_expression [BE_GTCCGC_L004]

description:
BronchialAirway
BE_GTCCGC_L004Aligned


title: Decato-2018-Human_M3Lung_expression [M3_ATGTCA_L007]

description:
ATCC M3 lung cancer cell line.
M3_ATGTCA_L007Aligned

tag: cell line


title: Decato-2018-Human_BronchialAirway_expression [BE_GTCCGC_L007]

description:
BronchialAirway
BE_GTCCGC_L007Aligned


title: Decato-2018-Human_SmallAirway_expression [SA_AGTCAA_L004]

description:
SmallAirway
SA_AGTCAA_L004Aligned


title: ATAC-seq from Luminal1/FOXA1 k.o tumor


title: ATAC-seq from Basal2/FOXA1 o.e tumor


title: ATAC-seq from Basal1/BMP o.e CAF


title: HT19111002_CM1

city: San Antonio

first: Tim

middle: Hui-Ming

last: Huang

state: TX

address: 7703 Floyd Curl Dr

institute: University of Texas Health at San Antonio

data_processing:
Illumina Real-Time Analysis software used for basecalling.
Stand-alone API script (Fluidigm) for demultiplexing row barcodes of column sample using R1 reads
Trim and align R2 reads to reference genome
Sequenced reads were mapped to GRCh38 human genome using STAR-2.5.3a
Fragments Per Kilobase of transcript per Million mapped reads were calculated for each sample using RSEM software
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include expected counts, TPM and FPKM values for each Sample

growth_protocol: EM-E6/E7/TERT-1 endometrial epithelial cell line was culture in DMEM/F-12 medium with 10%FBS and 1% penicillin/streptomycin aired with 5%CO2 at 37oC

extract_protocol:
single cell cDNA generation with Fluidigm C1 Single-Cell Auto Prep System
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Prep Kit with Nextera XT Index Kit v2 Set A and B index primers.

treatment_protocol: EME6/7t cells were treated with condition medium of ASCs or plus 50 μM tiplaxtinin for 24 hr

value: ASC-CM


title: Decato-2018-Human_Calu1Lung_expression [Calu1_GTGAAA_L007]

description:
Cell line derived from metastatic cancer cell lines from pleural effusion of epidermoid carcinoma (https://www.atcc.org/Products/All/HTB-54)
Calu1_GTGAAA_L007Aligned


title: AK25_positive_1

value: Purified B cells


title: ATAC-seq from Basal2


title: ATAC-seq from Basal1


title: Decato-2018-Human_441NSCLC_expression [s441_CCGTCC_L007]

description:
Cell line derived from human papillary adenocarcinoma (https://www.atcc.org/products/all/HTB-174.aspx)
s441_CCGTCC_L007Aligned


title: Decato-2018-Human_M3Lung_expression [M3_ATGTCA_L004]

description:
ATCC M3 lung cancer cell line.
M3_ATGTCA_L004Aligned


title: Decato-2018-Human_Calu1Lung_expression [Calu1_GTGAAA_L004]

description:
Cell line derived from metastatic cancer cell lines from pleural effusion of epidermoid carcinoma (https://www.atcc.org/Products/All/HTB-54)
Calu1_GTGAAA_L004Aligned


title: Decato-2018-Human_441NSCLC_expression [s441_CCGTCC_L004]

description:
Cell line derived from human papillary adenocarcinoma (https://www.atcc.org/products/all/HTB-174.aspx)
s441_CCGTCC_L004Aligned


title: RNA-seq from Luminal2/BMP k.o CAF-FOXA1 o.e tumor

data_processing:
Reads were mapped to the genome (Ensembl GRCh38 release97) using STAR-v2.7.2b with ENCODE option.
RSEM-v1.2.31 was used to calculate read counts and normalization.
Genome_build: hg38
Supplementary_files_format_and_content: tab separated RSEM results:

extract_protocol:
We extracted total RNA from 1.5 × 106 tumor cells using TRIzol reagent (Thermo Fisher Scientific), following the manufacturer’s instructions, and treated DNaseI.
We constructed RNA-seq libraries using the NEXTflex™ Rapid Directional RNA-Seq Kit (Perkin Elmer), following the manufacturer’s instructions. In brief, we selected and fragmented poly-A-tailed mRNA ligated double-stranded cDNA fragments with adapters and amplified them for 9 cycles of PCR. We then performed RNA-seq using the Illumina HiSeq 2500 platform.


title: Decato-2018-Human_1650Lung_expression [s1650_AGTTCC_L004]

description:
Cell line derived from stage 3 bronchoalveolar carcinoma (https://www.atcc.org/products/all/CRL-5883.aspx)
s1650_AGTTCC_L004Aligned


title: NC11

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

data_processing:
Alignment is done by cellranger to hg38 pre-mRNA reference
Downstream differential analysis and subcluster analysis is done by Seurat
Genome_build: hg38
Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs

source_name: prefrontal cortex snRNAseq

extract_protocol:
we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.

value: prefrontal cortex

tag: diagnosis

value: healthy control


title: Decato-2018-Human_1650Lung_expression [s1650_AGTTCC_L007]

description:
Cell line derived from stage 3 bronchoalveolar carcinoma (https://www.atcc.org/products/all/CRL-5883.aspx)
s1650_AGTTCC_L007Aligned


title: ATAC-seq from Basal2/BMP o.e CAF

value: Bladder tumor


title: Decato-2018-Human_M3Lung

description: ATCC M3 lung cancer cell line.

extract_protocol: The parental mouse mammary tumor cell line 4T1 (ATCC) and the derived clonal cell lines were cultured as described in \cite{wagenblast2015model}. Genomic DNA was extracted using the QIAmp DNA Blood Mini Kit (Qiagen). Bisulfite sequencing libraries were generated as previously described \cite{hodges2011primaryBloodMeth} In short, genomic DNA was fragmented using the Covaris LE220 sonicator to a target fragment size of 200bp. DNA fragments were repaired and ends blunted and phosphorylated. Then, adenylated fragments were ligated to Illumina-compatible paired-end adapters. Subsequently, DNA fragments were purified using the MinElute PCR Purification Kit (Qiagen). Fragments were then denatured and treated with sodium bisulfite using the EZ DNA Methylation-Gold Kit (Zymo Research). Then, the sample was desulfonated and PCR amplified with High Fidelity Expand Plus (Roche) using paired-end adapter-compatible primers. Illumnia sequencing was performed, generating 76-nucleotide paired-end reads.


title: RNA-seq from Luminal1/BMP k.o CAF

value: wild type


title: RNA-seq from Luminal2/FOXA1 k.o tumor

value: FOXA1 was knocked out in luminal tumor organoid


title: ATAC-seq from Basal1/FOXA1 o.e tumor

value: basal


title: Decato-2018-Human_441NSCLC

description: Cell line derived from human papillary adenocarcinoma (https://www.atcc.org/products/all/HTB-174.aspx)


title: RNA-seq from Luminal1/FOXA1 k.o tumor


title: Decato-2018-Human_Calu1Lung

description: Cell line derived from metastatic cancer cell lines from pleural effusion of epidermoid carcinoma (https://www.atcc.org/Products/All/HTB-54)


title: Decato-2018-Human_1650Lung

description: Cell line derived from stage 3 bronchoalveolar carcinoma (https://www.atcc.org/products/all/CRL-5883.aspx)


title: UUO-2 4

first: Laura

last: Denby

state: Midlothian

address: Queen's Medical Research Institute, 47 Little France Cres

data_processing:
RNA library preparation via polyA selection, multiplexing, High Output mode sequencing was performed.High Output Kit v4 (Illumina) with  2x100bp PE reads. GENEWIZ multiplexed 20 standard RNA libraries across 3 lanes of sequencing in 2x100bp PE configuration.  Run on Illumina HiSeq2500
FastQC was used for initial quality control, reads were mapped to the mm10 transcriptome using RSEM and Bowtie2, while DESeq2 was used for differential gene expression analysis

extract_protocol:
Kidneys were removed.  Libraries were constructed using polyA pulldown.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney

tag: age

value: 8 week

value: UUO-2 Animal culled at 2 days post UUO.


title: HT19111003_CMI1

source_name: EME6/7t_ASC-CM + PAI-039

value: EM-E6/E7/TERT-1 endometrial epithelial cell line

tag: treatment

value: ASC-CM + PAI-039


title: RNA-seq from Luminal1

value: control


title: RNA-seq from Basal2/BMP o.e CAF-FOXA1 k.o tumor

value: BMP4, 5 were overexpressed in surrounding reconstituted CAF


title: RNA-seq from Luminal2

value: luminal


title: UUO-2 2


title: RNA-seq from Basal1/BMP o.e CAF-FOXA1 k.o tumor


title: RNA-seq from Luminal1/BMP k.o CAF-FOXA1 o.e tumor

value: BMP4, 5 were knocked out in surrounding reconstituted CAF


title: UUO-2 3


title: RNA-seq from Basal2/BMP o.e CAF


title: UUO R4W 4

value: UUO R 4W - 7 day UUO reversed for 4 weeks.


title: RNA-seq from Luminal2/BMP k.o CAF


title: UUO-2 1


title: RNA-seq from Basal2/FOXA1 o.e tumor

value: FOXA1 was overexpressed in basal tumor organoid


title: RNA-seq from Basal1/FOXA1 o.e tumor


title: UUO R4W 3

description: Sample 16


title: RNA-seq from Basal2


title: UUO R2W 4

description: Sample 38

value: UUO R 2W -  7 day UUO reversed for 2 weeks


title: RNA-seq from Basal1


title: UUO R2W 3

description: Sample 37


title: P4-BSAdEnSC_rep3

city: Valencia

first: Francisco

last: Domínguez

state: SPAIN

address: Avenida Fernando Abril Martorell, 106

country: Spain

institute: IVI Foundation

hyb_protocol: 1,65µg of labeled cRNA were hybridized to an Agilent Human Gene Expression 4x44K v2 Microarray (Part Number G4845A) for 17 h at 65°C in a rotating hybridization chamber. Arrays were washed in 6 x saline sodium phosphate–EDTA (SSPE)/0.005% N-lauroylsarcosine (Sigma-Aldrich, Spain) for 1 min, then in 0.06 x SSPE/0.005% N-lauroylsarcosine for 1 min, and finally in acetonitrile (Sigma-Aldrich) for 30 sec, followed by drying in a nitrogen flow

scan_protocol: Slides were scanned immediately after washing on the Axon 4100A scanner (Molecular Devices).

data_processing: The scanned images were analyzed with GenePix Pro-6.0 software (Molecular Devices) using default parameters. Intensity backgrounds were corrected by RMA and normalized by quantiles. Normalization consists on isolating the statistical error in repeated easured data. This correction is required so that multiple chips can be compared to each other and analyzed together.

source_name: P4-BSA decidual Endometrial Stromal cell Replicate 3

label_protocol: The Quick-AMP labeling kit (Agilent Technologies) was used for sample amplification and fluorescent labeling according to manufacturer’s instructions. 200 ng experimental RNA input and 50 ng reference pool RNA input was used for linear amplification and fluorescent labeling. Experimental samples were labeled with Cy3-CTP, and the reference pool was labeled with Cy5-CTP.

growth_protocol: Primary EnSC were grown in DMEM/F12 (Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham, Sigma-Aldrich, Spain) media containing 10% fetal bovine serum and 0.1% antibiotics.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) method according to the manufacturer's recommendations.

treatment_protocol: At 70%–80% confluence, media was replaced with fresh media containing 2% fetal bovine serum, and in vitro decidualization was induced. We established four conditions, including three different decidualization groups in our experiments. Firstly, a group of EnSC was maintained in culture without hormones (ndEnSC). For control decidualized stromal cells (dEnSC), cells were exposed to a decidualization cocktail containing Progesterone (P4) (1 µM; Sigma-Aldrich, Munich, Germany) and Estradiol (E2) (10 nM; Sigma-Aldrich, Munich, Germany) for 8 days. In the second group, a specific PGRMC1 inhibitor, AG-205 (50uM), which blocks specifically its activation, was added to P4/E2 (AG205dEnSC). Finally, to better understand membrane receptors involvement during endometrial decidualization, we used a membrane-impermeable P4 (P4-BSA, 1uM) in combination with E2 (P4BSAdEnSC), which avoids P4 entering the cell, thereby activating only the receptors located in the plasmatic membrane

tag: cell type

value: Primary Endometrial Stromal Cell

value: Female

value: after 8d of decidualization stimuli by membrane impermeable P4-BSA/E2


title: P4-BSAdEnSC_rep4

source_name: P4-BSA decidual Endometrial Stromal cell Replicate 4


title: UUO R2W 2

description: Sample 36


title: P4-BSAdEnSC_rep1

source_name: P4-BSA decidual Endometrial Stromal cell Replicate 1


title: RNA-seq from Basal1/BMP o.e CAF

value: Bladder tumor

value: wild type


title: UUO R2W 1

description: Sample 27

value: Kidney


title: P4-BSAdEnSC_rep2

source_name: P4-BSA decidual Endometrial Stromal cell Replicate 2


title: AG205dEnsC_rep3

source_name: AG-205 decidual Endometrial Stromal cell Replicate 3

value: after 8d of decidualization stimuli by P4/E2 plus PGRMC1 inhibitor AG205


title: AG205dEnsC_rep1

source_name: AG-205 decidual Endometrial Stromal cell Replicate 1


title: dEnSC_rep4

source_name: decidual Endometrial Stromal cell Replicate 4

value: after 8d of decidualization stimuli by P4/E2


title: UUO R1W 3

description: Sample 22

source_name: Kidney

value: 8 week

value: UUO R 1W -  7 day UUO reversed for 1 week


title: UUO R1W 1

description: Sample 18


title: UUO R4W 2

description: Sample 14

value: UUO R 2W - 7 day UUO reversed for 2 weeks.


title: UUO R1W 2

description: Sample 19


title: UUO R1W 4

description: Sample 24


title: AG205dEnsC_rep2

source_name: AG-205 decidual Endometrial Stromal cell Replicate 2


title: UUO R4W 1

description: Sample 13


title: dEnSC_rep3

source_name: decidual Endometrial Stromal cell Replicate 3


title: dEnSC_rep2

source_name: decidual Endometrial Stromal cell Replicate 2


title: dEnSC_rep1

source_name: decidual Endometrial Stromal cell Replicate 1


title: UUO-7 4

description: Sample 2

value: UUO-7 Animal culled at 7 days post UUO


title: UUO-7 2

description: Sample 8


title: UUO-7 1

description: Sample 7


title: ndEnSC_rep4

source_name: non-decidual Endometrial Stromal cell Replicate 4

value: after 8d whitout decidualization stimuli


title: Sham mouse 3

description: Sample 4

value: sham surgery


title: ndEnSC_rep2

source_name: non-decidual Endometrial Stromal cell Replicate 2


title: Sham mouse 2

description: Sample 3


title: Sham mouse 4

description: Sample 5


title: AG205dEnsC_rep4

source_name: AG-205 decidual Endometrial Stromal cell Replicate 4


title: Sham mouse 1

description: Sample 12


title: ndEnSC_rep1

source_name: non-decidual Endometrial Stromal cell Replicate 1


title: 7-days bladder assembloid

description: bladder assembloids after 7 days of reconstitution

data_processing:
The Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing, barcode processing, and single cell 3' gene counting.
The reads were aligned to GRCh38 and mm10 reference (v3.1.0) provided by 10X Genomics.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: barcodes.tsv: barcode ids for each sample; features.tsv: gene ids for each sample; mtx: count matrix in a sparse matrix format

source_name: Bladder assembloid

extract_protocol:
RNA from was extracted using the 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3 following the manufacturer’s instructions.
Dissociated single cell suspension was loaded on Chromium Single Cell Chips.   We constructed single-cell RNA-seq libraries using the 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3.

treatment_protocol: Mouse bladder and bladder assembloids were enzymatically dissociated into single cell and cells were resuspended at 1,000 cells/µl.

value: Bladder assembloid

value: 7 days


title: Decato-2018-Mouse_4T1-P

description: Mouse mammary gland tumor clonal population.

organism: Mus musculus musculus

source_name: 4T1 Breast tumor

value: Breast tumor


title: 1-day bladder assembloid

description: bladder assembloids after 1 day of reconstitution

value: 1 day


title: UUO-7 3

description: Sample 10


title: wt mouse bladder

description: wild-type mouse bladders

source_name: Bladder

value: Bladder

value: 8-9 weeks


title: Decato-2018-Mouse_4T1-T


title: ko_del_R3

city: Mainz

first: Ari

last: Waisman

address: Obere Zahlbacher Straße 67

institute: Institute for Molecular Medicine

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0j)
The ENSEMBL Mus_musculus.GRCm38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v76) was used.
Exploratory data analysis was performed with the pcaExplorer package (version version 2.8.0, Marini et al., 2016)
Differential expression analysis was performed with DESeq2 (version 1.22.1), setting the False Discovery Rate to 0.05
Accurate estimation of the effect sizes (in terms of log fold change) is performed using the apeglm shrinkage estimator (version 1.4.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts as input matrix to DESeq2

source_name: Brain microglia

growth_protocol: C57Bl/6 background, housed under specific-pathogen-free conditions

extract_protocol:
Papain digestion and sorting for eYFP-positive cells
Sorted microglia were processed for RNA extraction using the Qiagen RNeasy Plus mini kit according to manufacturer’s instructions.
RNA quality and concentration were measured using a NanoDropTM (Thermo Fisher Scientific). For sequencing, RNA quality and integrity was determined using a Qbit and Bioanalyzer. Only samples with a RIN value of 7.0 and above were taken for further processing.
cDNA libraries were prepared with 10ng from each sample using the NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: 2mg Tamoxifen at P14 and P16

tag: condition

value: 4 weeks


title: ko_del_R2


title: ndEnSC_rep3

source_name: non-decidual Endometrial Stromal cell Replicate 3

value: Primary Endometrial Stromal Cell

value: Female


title: ko_del_R1


title: Decato-2018-Mouse_4T1-L


title: wt H2O2 rep2

city: Vienna

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

country: Austria

institute: Max Perutz Labs

data_processing:
Reads were trimmed via cutadapt with a quality score threshold of 30.
Reads were mapped onto the Assembly 22 of the haploid C. albicans genome using NextGenMap (Sedlazeck, Bioinfromatics, 2013) with only keeping aligned reads with a mapping quality higher than 30.
Optical read duplicates were removed using the Picard tool and mitochondrial reads were removed with BEDtools intersect.
Aligned bam files were split according to the fragment length of sequencing read pairs as in Buenrostro et al., Nature Methods, 2013. Read fragments below 100 bp were considered as nucleosome-free fragments and used for further analysis.
Peaks were called using MACS2 call peak function using merged gDNA samples as background control and the -f BAMPE setting. Reads in peaks were counted using htseq count (AndersS, Bioinformatics, 2014) and a reference annotation (C_albicans_SC5314_version_A22-s07-m01-r88; http://www.candidagenome.org) and used for differential peak analysis with edgeR (RobinsonMD, Bioinformatics, 2010).
Genome_build: Assembly 22
Supplementary_files_format_and_content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)
Supplementary_files_format_and_content: raw counts of sequencing reads per peak and genomic annotation for each sample: wt rep1, wt H2O2 rep1, wt rep2, wt H2O2 rep2, wt 3, wt H2O2 rep3

organism: Candida albicans

source_name: fungal cells

growth_protocol: Cells were grown in YPD to the logarithmic growth phase at 30 °C in an orbital shaker set at 200 rpm. When indiciated, cells were treated with 1.6 mM hydrogen peroxide (H2O2) or left untreated and further cultured for 15 minutes at 30 °C with 200 rpm shaking. For gDNA extraction, cell were grown overnight in YPD at 30 °C with 200 rpm shaking

extract_protocol:
Spheroblasts were generated by Zymolase treatment in Sorbitol buffer plus DTT for 5 minutes at 30 °C and then subjected to tagmentation by directly lysing the cell pellet in the tagmentation mix
Tagmented samples were subjected to ATAC-seq library prep based on the published protocol from the Greenleaf lab. Additionally, PCR-amplified libraires were purified with SPRI beads.

treatment_protocol: When indicated, cells were treated with 1.6 mM hydrogen peroxide (H2O2) for 15 minutes while shaking at 30 °C in YPD and additionally 1.6 mM H2O2 was added during spheroblasting (30 °C 5 minutes)

value: log-phase cells

tag: strain background

value: 1.6 mM hydrogen peroxide for 20 minutes


title: Decato-2018-Mouse_4T1K


title: control_R2

value: partially deficient (control)

tag: genotype

value: eYFP-A20fl/wt Cx3cr1-CreERT2/+


title: wt rep2

value: no treatment


title: wt H2O2 rep1


title: wt rep3


title: wt rep1


title: gDNA rep1

value: stationary phase cell


title: Decato-2018-Mouse_4T1-E


title: Ly6Clo macrophages RNA-seq

city: Chiba City

first: Akihiko

last: Kubota

state: Chiba

address: 1-8-1 Inohana

department: Department of Cardiovascular Medicine

country: Japan

institute: Graduate School of Medicine, Chiba University

data_processing:
Illumina CASAVA ver 1.8.2  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat.
Then, we got WAD ranking list from BAM files.
Data are normalized by using TCC (an acronym for Tag Count Comparison) of R package (PMID 23837715) , and then differentially expressed genes (DEGs) were analysed by weighted average difference method (WAD) (PMID 18578891).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include WAD ranking for each Sample. G1_rep1 denotes FPKM of Ly6Chi macrophages, G2_rep1 denotes FPKM of Ly6Clo macrophages.

source_name: Ly6Clo macrophages

extract_protocol:
Total RNA of Ly6Chi and Ly6Clo macrophage were purified using a ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 J mice were subjected to ligation of the left anterior descending coronary artery.

tag: strain

value: infarcted heart

value: Ly6Clo macrophages

tag: day of collection

value: at 3 days after MI


title: wt H2O2 rep3


title: Decato-2018-Mouse_4T1parent

description: Mouse mammary gland tumor parental population.


title: Ly6Chi macrophages RNA-seq

source_name: Ly6Chi macrophages

value: Ly6Chi macrophages


title: control_R1


title: gDNA rep2


title: Decato-2018-Mouse_4T1-I

value: Breast tumor


title: FPP-1746-Omomyc 6hours, biological rep2

status: Public on Sep 26 2020

city: Nedlands

first: Pilar

last: Blancafort

state: WA

address: 6 Verdun Street

department: Cancer and Cell Biology

country: Australia

institute: Harry Perkins Institute of Medical Research

description: Expressing luciferase gene

data_processing:
Image analysis and base-calling was perfromed by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. Sequence data are generated by bcl2fastq 2.17.1.14 pipeline.
Sequence data were aligned to the mm9(NCBIv37) genome build using STAR (v2.1.3)
Expression at the gene level (FPKM values) was estimated and normalized by Cufflinks (v2.2.1), Cuffmerge (v1.0.0) and Cuffnorm (v2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include average RPKM values for each replicate sample

growth_protocol: 150,000 cells were seeded in a p6-well plate in complete media (RPMI supplemented in 1% FBS and 1% antibiotic/antimicotic). Cells were allowed to grow for three days

extract_protocol:
Total RNA was extracted following the manufacturer´s kit, RNeasy Mini Kit from Qiagen. An additional step of genomic DNA elimination was included before the RNA elution using the RNase-Free DNase set (Qiagen). Eluted RNA samples were assayed with an absorbance at 260/280 nm between 1.8 and 2.0 and were subjected to a strict quality control at the Australian Genomic Research Facility (AGRF) in Perth before proceeding to library preparation and RNA Sequencing at the AGRF in Melbourne. All submitted samples had RNA integrity number (RIN) of 10.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with PBS, Omomyc, FPP-1746 and FPP-1746-Omomyc at 5µM for 3 and 6 hours.

tag: genotype/variation

value: FPP-1746-Omomyc for 3 hours


title: FPP-1746-Omomyc 6hours, biological rep3

description: Expressing luciferase gene


title: FPP-1746-Omomyc 6hours, biological rep1

description: Expressing luciferase gene


title: FPP-1746 6hours, biological rep3

description: Expressing luciferase gene

value: FPP-1746 for 6 hours


title: FPP-1746 6hours, biological rep1

description: Expressing luciferase gene


title: FPP-1746 6hours, biological rep2

description: Expressing luciferase gene


title: Omomyc 6hours, biological rep3

description: Expressing luciferase gene

value: Omomyc for 6 hours


title: Omomyc 6hours, biological rep2

description: Expressing luciferase gene


title: PBS 6hours, biological rep3

description: Expressing luciferase gene

value: PBS for 6 hrs


title: Omomyc 6hours, biological rep1

description: Expressing luciferase gene


title: PBS 6hours, biological rep2

description: Expressing luciferase gene


title: FPP-1746-Omomyc 3hours, biological rep3

description: Expressing luciferase gene


title: CYTO_minus_Rep3

city: Buffalo

first: Laurie

last: Read

state: NY

address: 955 Main St

institute: Jacobs School of Medicine and Biomedical Sciences

data_processing:
Aligned to Trypanosoma brucei TREU927 reference genome with STAR 2.7.1
Transcript abundances estimated with RSEM 1.3.1
Genome_build: TriTrypDB v41 Trypanosoma brucei TREU927
Supplementary_files_format_and_content: RSEM isform abundance tsv files

organism: Trypanosoma brucei

source_name: Fractionated cells

growth_protocol: Procyclic form T. brucei strain 29-13 was grown at 27 degrees C in SM media plus 10% FBS, 50 micrograms/ml hygromycin, and 15 micrograms/ml G418.

extract_protocol:
RNA was isolated using Trizol reagent.
RNA libraries were prepared following the New England Biolabs NEXT UltraII Directional RNA library kit using polyA+ magnetic beads.
Final libraries were pooled to 10 nM and the concentration of the pool was determined using the Kapa Biosystems Universal qPCR kit. After dilution and denaturing, the pooled library was loaded onto a NextSeq 500 high output flow cell (PE75) for sequencing.

treatment_protocol: Cells were either untreated or treated with 4 micrograms/ml doxycycline for 23 hours.  For cytoplasmic RNA, nuclear cytoplasmic fractionation was performed by the method of Dostalova, et al, 2013 (Mol Micro 88:728).

tag: rna fraction

value: Cytoplasm

value: -Doxycycline


title: CYTO_plus_Rep3

value: +Doxycycline


title: WC_plus_Rep3

value: Whole cell


title: PBS 6hours, biological rep1

description: Expressing luciferase gene


title: FPP-1746-Omomyc 3hours, biological rep2

description: Expressing luciferase gene


title: CYTO_plus_Rep1


title: WC_plus_Rep2


title: WC_minus_Rep3


title: CYTO_minus_Rep2


title: WC_minus_Rep2


title: WC_plus_Rep1


title: CYTO_minus_Rep1


title: FPP-1746 3hours, biological rep2

description: Expressing luciferase gene

value: FPP-1746 for 3 hours


title: HT19111001_Con1

value: EM-E6/E7/TERT-1 endometrial epithelial cell line

value: Ctrl


title: FPP-1746 3hours, biological rep3

description: Expressing luciferase gene


title: CYTO_plus_Rep2


title: WC_minus_Rep1


title: FPP-1746 3hours, biological rep1

description: Expressing luciferase gene


title: Omomyc 3hours, biological rep3

description: Expressing luciferase gene

value: Omomyc for 3 hours


title: H460 3D

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: Gene expression data

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C.  GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: The data were analyzed with Genespring GX 7.3.1 using Affymetrix default analysis settings and normalized to day1 control

label: biotin

source_name: H460 cells on Matrigel

label_protocol: This project used the Affymetrix Human Genome U133 Plus 2.0 GeneChip 200 ng of total RNA was used as input

growth_protocol: lung cancer cell lines were grown either on tissue culture plastic (2D) or in 3D culture on a thin layer of Matrigel covered with 2 % Matrigel dissolved in media (‘on top’ method).

extract_protocol: Phenol/cholorofom

treatment_protocol: grown on 2D or 3D

value: lung cancer cell

tag: protocol

value: matrigel (3D)


title: H661 3D

description: Gene expression data

source_name: H661 cells on Matrigel


title: H1703 3D

description: Gene expression data

source_name: H1703 cells on Matrigel


title: H1437 3D

description: Gene expression data

source_name: H1437 cells on Matrigel


title: H23 3D

description: Gene expression data

source_name: H23 cells on Matrigel


title: A549 3D

description: Gene expression data

source_name: A549 cells on Matrigel


title: Omomyc 3hours, biological rep1

description: Expressing luciferase gene


title: Phf8-KO1

city: Chongqing

first: Jun

last: Jiang

state: Chongqing

address: 10#, Changjiang Zhilu, Yuzhong District

department: Department of Urology

institute: Daping Hospital, Army Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

source_name: tumor tissue

extract_protocol:
Total RNA was extracted from cell  by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 4200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TRAMP

value: prostate

value: 37 weeks post natal

value: PHF8 knockout


title: SAM24331843 Female WT GMP 2 Bone Marrow

city: South San Francisco

first: Luz

last: Orozco

address: 1 DNA Way

department: Bioinformatics

institute: Genentech Inc.

description: SAM24331843 Female WT GMP 2 Bone Marrow SAM24331843 WT GMP 2 R3722 1,2,3,4,5,6,7,8 LIB339346 POOL8637 NXG422890 TCCGGAGA D702 CCTATCCT D503 WT GMP 1.6733006891862

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Ensembl IDs, counts and nRPKM statistics.

source_name: bone marrow

extract_protocol: Cells were centrifuged at 2,600 rcf for 7 minutes (neurons) or 6,600 rcf for 7 minutes (other cell types) and the supernatant was discarded. RNA was extracted from the cell pellet using Qiagen RNeasy Plus Micro kit in a final volume of 25 μl. We typically obtained 200-300 ng RNA from neurons, 10-20 ng from microglia, and 2-5 ng from astrocytes. RNA quality was quantified using the Bioanalyzer.

value: Female

value: WT GMP 2

value: Bone Marrow

value: TCCGGAGA

value: CCTATCCT

value: WT

value: GMP


title: TRAMP

value: PHF8 wild-type


title: PBS 3hours, biological rep3

description: Expressing luciferase gene

value: PBS for 3 hrs


title: Phf8-KO2


title: H358 3D

description: Gene expression data

source_name: H358 cells on Matrigel


description: SAM24331847 Female NSP4 KO CMP 2 Bone Marrow SAM24331847 NSP4 KO CMP 2 R3722 1,2,3,4,5,6,7,8 LIB339350 POOL8637 NXG422892 TCCGGAGA D702 CAGGACGT D507 NSP4.KO CMP 0.775959978920463

value: NSP4 KO CMP 2

value: SAM24331847 NSP4 KO CMP 2

value: CAGGACGT

value: CMP


title: H1703 2D

description: Gene expression data

source_name: untreated H1703 cells

value: lung cancer cell

value: culture plastic (2D)


title: H661 2D

description: Gene expression data

source_name: untreated H661 cells


title: H1437 2D

description: Gene expression data

source_name: untreated H1437 cells


title: PBS 3hours, biological rep2

description: Expressing luciferase gene