title: RPL34-AS1-Plasmid-1

city: nanjing

first: Hu

last: Zhang

address: gulou street

country: China

institute: southeast university

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
fresh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
After the extracted total RNA sample is subjected to agarose electrophoresis and Nanodrop quality inspection and quantification, oligo (dT) magnetic beads are used to enrich mRNA (if the RNA is a degraded sample or a prokaryotic sample, it is directly processed by rRNA removal kit); RNA sequencing The library is completed by the kit, including RNA fragmentation and inversion of random primers to generate first-strand cDNA, adding dUTP to synthesize the second-strand cDNA, double-stranded cDNA end repair plus A connected to Illumina matching adapter, PCR amplification to obtain the final library ; The constructed library is quality checked with Agilent 2100, and the library is quantified by qPCR method, and sequenced using Illumina NovaSeq 6000 sequencer
RNA libraries were prepared for sequencing using standard Illumina NovaSeq 6000.

value: Esophageal cancer cell

value: lncRPL34-AS1 plasmid


title: RPL34-AS1-Plasmid-3

status: Public on Jul 16 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype/variation


title: MPE 1

type: RNA

city: Shatin

first: Ronald

last: Wang

address: Prince of Wales Hospital

department: Obstetrics & Gynaecology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Gene expression after 3 days

hyb_protocol: Using Gene Expression Hybridiation kit (Agilent), 600 ng of Cy3-labelled cRNA (Cy3 incorporation) was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, samples were hybridized to SurePrint G3 Mouse GE microarray kit 8x60k ver 2.0 (074809, Agilent) for 17 hours at 65°C, rotating in hybridization oven (G2545A , Agilent) at 10 rpm. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner G2565BA using a setting AgilentG3_GX_1color (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Output data were further analyzed with GeneSpring GX 10.0 with a default setting, with Percentile=75, to generate values of normalized signal intensity.

organism: Mus musculus

source_name: MIN6 cells treated with Maidong polysaccharide extract (MPE) for 3 days, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mni kit purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA extracted by TRIzol reagent (Invitrogen, CA) was subjected to gene expression profiling using Agilent microarray platform (Agilent Technologies, CA). RNA was quantified using a Quantus fluorometer (Promega) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, CA).

treatment_protocol: The MIN6 cell line (passage 20-30) was cultured in DMEM medium (Invitrogen, Carlsbad, CA, USA) with 15% FBS (Gibco, USA), 1% PS (penicillin, streptomycin) (Gibco, USA) and 50 μmol/L 2-Mercaptoethanol (Gibco, USA). The cells were treated with MPE at concentrations of 0, 0.05, 0.5, 5 and 50 μg/mL or vehicle for 24, 48 and 72h for experiments. The cells treated by vehicle (PBS) or MPE for 3 days were harvested for microarray analysis.

value: MIN6 cells

tag: treatment

value: MPE

tag: day


title: Pcan16_API1

city: Göttingen

first: Victor

last: Chano

address: Buesgenweg 2

department: Forest Genetics and Forest Tree Breeding

country: Germany

institute: University of Göttingen

hyb_protocol: 600 ng of Cy3 probes were mixed and hybridized to a 60K custom microarray (Agilent Technologies) for 17 hours at 65ºC in Gex Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions, dried by centrifugation.

scan_protocol: Arrays were scanned at 3 mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and the images were analyzed with Feature Extraction software (Agilent Technologies).

data_processing: For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively (Smyth and Speed 2003).

organism: Pinus canariensis

source_name: Shoot apical meristem

label_protocol: 200 ng of total RNA was reversely transcribed using T7 promotor primer and the cDNA was converted to aRNA using T7 RNA polimerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP

growth_protocol: Pines were grown in greenhouse, using 650 ml conical containers with 3:1 (v/v) peat:vermiculite. After the first year, trees were transferred to soil in experimental garden at UPM facilities, and grown under environmental conditions. At the moment of the beginning of this experiment, trees were 5 years old, approximately 2 m high and 7-10 cm diameter at the base.

extract_protocol: Total RNA was isolated from differentiating xylem samples stored at -80ºC, using the CTAB-LiCl precipitation method (Chang et al. 1993), and purified with the RNeasy Plant Mini Kit (Qiagen, CA, USA). Quantity of total RNA for each sample was measured with Nanodrop model ND-1000 (Thermo Scientific, MA, USA), and RNA quality was checked using the Experion Bioanalyzer (Bio-Rad, CA, USA).

tag: tissue

value: Apical shoot in transition from primary to secondary growth

tag: age

value: 60 months


title: RPL34-AS1-Plasmid-2


title: COVID-19 patient3

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM21) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
Fastq reads were aligned to the genome using STARsolo with the setting ‘--outSAMattributes NH HI AS nM CR CY UR UY --readFilesCommand zcat --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outMultimapperOrder Random --runRNGseed 777 --outSAMmultNmax 1’.
Genome_build: hg38
Supplementary_files_format_and_content: expression file

molecule: polyA RNA

source_name: COVID-19 patient BALF

growth_protocol: Cells from COVID-19 patient

extract_protocol:
Cells  were collected ad resuspended in DPBS with 0.04% BSA. Then, cells suspensions (500-1000 cells per microliter) were loaded on a Chromium Single Cell Controller (10x Genomics) to obtain single-cell gel beads in emulsion (GEMs) by using Single Cell 3’ Library and Gel Bead Kit V2 (10x genomics, 120237). Captured cDNAs were lysed and the released RNA were barcoded through reverse transcription in singular GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleaned by DynaBeads® MyOne Silane Beads (Invitrogen, 37002D).
Single-cell RNA-seq libraries were prepared by Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics, 120237) following the manufacturer’s instruction. Sequencing was operated on an Illumina HiSeq X Ten

tag: subject status

value: COVID-19 patient

value: bronchoalveolar lavage fluid (BALF)


title: Patient 37 CBCS_N37

city: Houston

first: Arjun

last: Bhattacharya

state: TX

address: 1155 Pressler Street

department: Epidemiology

country: USA

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: 3 uL of Reporter CodeSet, 5 uL of hybridization buffer, up to 5 uL (25-100 ng) of sample RNA, and 2 uL of Capture ProbeSet was combined for the hybridization reaction. The reactions were incubated at 65 degrees C for at least 16 hours and at most 48 hours and temperature was ramped down to 4 degrees C for processing the following day. Hybridization was run on Prep Station Serial # 0910B0040, Prep Station Serial # 1602D0412. Details provided: https://www.nanostring.com/download_file/view/1808/3822

scan_protocol: NanoString cartridges were scanned using the nCounter MAX Analysis System (NanoString Digital Analyzer Serial # 1605C0377)

data_processing: The raw data were scaled with the geometric mean of 6 positive control genes (provided on standard NanoString nCounter chips) and geometric mean of 11 housekeeping genes (labelled as Housekeeping genes in raw data). Details provided: https://www.nanostring.com/download_file/view/1168/3779

source_name: primary breast tumor

label_protocol: NanoString nCounter technology

growth_protocol: Samples were recruited by the Carolina Breast Cancer Study, a population-based cohort of breast cancer patients from North Carolina, up-sampled for African American women (Newman et al., 1995, PMID 7612904).

extract_protocol: A study pathologist reviewed hemtoxylin and eosin for each tumor, selected a representative tumor block, and selected tumor areas for coring. Ten 10 uM sections were cut from blocks after coring, and an additional section was obtained and reviewed for tumor cellularity (Troester et al., 2018, PMID 28859290). RNA was isolated from cores using Qiagen RNeasy formalin-fixed, paraffin-embedded kit and protocol (Troester et al., 2018, PMID 28859290).

treatment_protocol: Blood samples, medical record documentation, and paraffin-embedded tumor specimens are obtained for all breast cancer patients (Newman et al., 1995, PMID 7612904).

tag: study phase

value: primary breast tumor

tag: estrogen receptor status

value: Positive

tag: pam50 molecular subtype

value: Basal


title: COVID-19 patient2


title: RPL34-AS1-NC-3

value: scramble pcDNA


title: Control 2

description: Gene expression after 3 days

source_name: MIN6 cells treated with vehicle (PBS) for 3 days, replicate 2

value: PBS


title: Control 3

description: Gene expression after 3 days

source_name: MIN6 cells treated with vehicle (PBS) for 3 days, replicate 3


title: COVID-19 patient1


title: Patient 35 CBCS_N35

value: LumA


title: Control 1

description: Gene expression after 3 days

source_name: MIN6 cells treated with vehicle (PBS) for 3 days, replicate 1


title: RPL34-AS1-NC-1


title: P15-6_scRNAseq

city: Kansas City

first: Mehmet Neset

last: Ozel

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Fastq files were generated either with Illumina "bcl2fastq" (2.18) or CellRanger (2.1.1) "mkfastq".
Alignment and counting were performed with CellRanger (2.1.1 or 3.0.1) "count".
Normalization, scaling, dimensional reduction and clustering of the single-cell transcriptomes were performed using Seurat v3 (detailed in Methods).
Pupal single-cell transcriptomes were classified with a custom neural network (detailed in Methods).
Average gene expression levels and cluster markers were calculated for each cell type at each stage using Seurat v3.
Binarized expression values for each cell type were determined using mixture modeling (Davis et al., 2018)
Genome_build: ENSEMBL-release-88-BDGP6
Supplementary_files_format_and_content: Seurat objects (.rds format) provided for each stage include raw, normalized and scaled expression values for each cell in addition to the identities determined using different methods, as detailed in the paper. Excel files are provided for average and binarized expression levels and also for the cluster markers, where each stage is in a separate type.

organism: Drosophila melanogaster

source_name: P15 optic lobe

growth_protocol: Standard Drosophila rearing protocols.

extract_protocol:
Chromium™ Single Cell 3’ Reagent Kit v2 (10X Genomics)
Chromium™ Single Cell 3’ Reagent Kit v2 (10X Genomics)

treatment_protocol: No treatments.

tag: strain

value: Canton S

tag: Sex

value: female

value: P15 optic lobe


title: Patient 34 CBCS_N34


title: Tu686_SiNC

city: Meizhou

address: Meisong Road

institute: Jiaying University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTP
mRNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using stringtie version 1.3.4b Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Genome_build: hg38
Supplementary_files_format_and_content: normalized FPKM values and raw fragment counts for each Sample

growth_protocol: All cells were incubated at 37°C in 5% CO2

extract_protocol:
Total RNA from prostate cancer cells (including PC3-NC, PC3-OE-TRIB1; DU145-NC, DU145-OE-TRIB1) were isolated by TRIzol (No.:15596026, Thermo Fisher Scientific, USA) and extracted by chloroform. RNA degradation and contamination were monitored on 1% agarose gels and purity was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer(Life Technologies, CA, USA) and integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzeer 2100 system (Agilent Technologies, CA, USA ).
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: All cells were treated with siRNA (prmt5 or negative control) for 48 h

value: Epithelial-derived  cells


title: Tu686_SiP5_2


title: P15-5_scRNAseq


title: Patient 36 CBCS_N36


title: Tu686_SiP5_1


title: P15-3_scRNAseq


title: Patient 33 CBCS_N33

value: Normal


title: fetal liver (FL), E18.5

city: Funabashi

first: Shota

last: Okuyama

state: Chiba

department: Biology

country: Japan

institute: Toho University

description: Gene expression data from E18.5 transgenic mouse fetal liver

hyb_protocol: The obtained biotin-labeled cRNAs were fragmented and hybridized to GeneChip (45 ℃, 60 r.p.m. rotation, 16 h). The arrays were stained and cleaned using an automatic staining and cleaning system, and images of the arrays were acquired using a dedicated GeneChip scanner.

scan_protocol: GeneChips were scanned using the Transcriptome Analysis Console software

data_processing: Gene Chips were analyzed with the Transcriptome Analysis Console software and normalized using the MAS5 algorithm. The expression profile was analyzed only for highly expressed genes with actual log2 values≥ 10. Genes with more than 2-fold increase or decrease in log2 values compared to other samples were considered differentially expressed genes. Heatmaps were created using R's free software, RStudio.

label: biotin

source_name: transgenic mouse FL

label_protocol: Biotin-labeled cRNA was synthesized by in vitro transcription reaction using total RNA according to the protocol recommended by Thermo Fisher Scientific.

growth_protocol: FL,AL: Chimeric mice were generated using CYP3A7R transgenic ESCs. FL and AL were extracted from mouse livers grown up to E18.5 and 6W. HLCs: HLCs were obtained by differentiating TT2F mESCs up to day-41 according to the differentiation induction conditions established in this study.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen).

value: Liver

tag: developmental stage


title: P15-2_scRNAseq


title: RPL34-AS1-NC-2

value: Esophageal cancer cell


title: Pcan16_API4

value: Apical shoot in transition from primary to secondary growth

value: 62 months and 2 weeks


title: leptomeningeal metastasis Patient_D

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB

data_processing:
Raw FASTQ files for each patient were preprocessed using the SEQC pipeline(2) using hg38 human genome and the default SEQC parameters for 10X Genomics to obtain the molecule count matrix. The SEQC pipeline aligns the reads to the genome, corrects barcode and unique molecular identifier (UMI) errors, resolves multi-mapping reads, and generates a molecule count matrix. SEQC also performs a number of filtering steps: (1) Identification of true cells from cumulative distribution of molecule counts per barcode, (2) removal of apoptotic cells identified at cells with >20% of molecules derived from the mitochondria, and (3) removal of low-complexity cells identified as cells where the detected molecules are aligned to a small subset of genes. In addition, cells with less than 800-1,000 molecules detected were filtered out. After the filtering, we have retained ~19,000 cells with a median molecule count of ~4,100 and median gene count of ~1,200, indicating the high quality of the data. Each patient contributed from 1,800 to 5,000 single-cells to this dataset.
Cell doublets are a characteristic error source in droplet-based single-cell sequencing data where two cells are randomly co-encapsulated with the same barcode. To remove likely doublet cells we have employed unsupervised machine learning classifier (3). This classifier operates on a count matrix and leverages the creation of in silico synthetic doublets to determine which cells in the input count matrix have gene expression that is best explained by the combination of distinct cell types in the matrix. Each patient was processed separately, cells with p-values <1e-7 were identified as doublets and removed. In total, we have removed ~1,300 cells.
Filtered count matrices for each patient were median size normalized. To avoid numerical issues counts were multiplied by 10,000 and log transformed with pseudo count of 1 using SCANPY package (4). After normalization, count matrices were concatenated and batch effect corrected with mnnCorrect (5, 6). As a reference, we selected the patient with the most cells (patient E) and to facilitate identification of mutual nearest neighbors we used top 3,000 highly variable genes (HVGs) identified from all patients and opted for non-cosine normalized batch effect corrected output for downstream analyses.
Using earlier selected top 3,000 HVGs, batch effect corrected gene expression matrix was decomposed using randomized principal component analysis (PCA). We selected to retain 12 principal components using the knee point (minimum radius of curvature in eigenvalues). We clustered the PCA-reduced matrix was using PhenoGraph (69) resulting in 18 clusters. The same principal components were used to construct a k-nearest-neighbor (kNN) graph based on Euclidian distance. This kNN graph was used to generate UMAP projections (66) using the SCANPY package. In addition, we applied MAGIC (7) to the PCA-reduced matrix to denoise the data and impute missing values. Note, all UMAP plots show post-MAGIC expression values.
Genome_build: hg38
Supplementary_files_format_and_content: count matrices in comma separated value format

source_name: CSF cell fraction isolated from a patient with newly diagnosed leptomeningeal metastasis

extract_protocol: CSF, collected with informed consent from patients under protocol IRB 13-039, was processed to isolate the sample into cell-free CSF and the cellular contents of the CSF:  The whole CSF sample was centrifuged at 600 x g for 5 minutes without brake at 4 ºC to pellet the cells, and the supernatant was saved as cell-free CSF. The pellet was resuspended, washed with PBS supplemented with 0.4% BSA twice and processed immediatelly. The cells were manually counted with a hematocytometer. scRNA-Seq was performed with 10X genomics system using Chromium Single Cell 3’ Library and Gel Bead Kit V2 (catalog no. 120234). Briefly, 8,700 cells (viability 70-80%) were processed per sample, targeting recovery of ~5,000 cells with 3.9% multiplet rate. In cases, where cell count was too low to target 5,000 cells, maximum volume (34 µl) was loaded in the microfluidic droplet generation device. After reverse transcription reaction emulsions were broken, barcoded cDNA was purified with DynaBeads, followed by 12-cycles of PCR amplification. The resulting amplified barcoded-cDNA library was fragmented to ~400-600 bp, ligated to sequencing adapter and PCR-amplified to obtain sufficient amount of material for next-generation sequencing. The final libraries were sequenced on an Illumina NovaSeq 6000 system (Read 1 – 28 cycles, Index Read – 8 cycles, and Read 2 – 96 cycles).

tag: disease state

value: leptomeningeal metastasis

tag: metastatic site

value: leptomeninges/CSF


title: leptomeningeal metastasis Patient_E


title: SiNC_P5

description: R19027653-SiNC-P5-JZ201904152023_combined


title: leptomeningeal metastasis Patient_A


title: Patient 32 CBCS_N32

value: primary breast tumor


title: P30-5_scRNAseq

source_name: P30 optic lobe

value: P30 optic lobe


title: C33_I_10x_TCR

city: La Jolla

first: John

last: Chang

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: UCSD

description:
TCR RNA
5' VDJ sequencing (10X genomics)

data_processing:
Library strategy: VDJ-seq
data were processed by cellranger 2.1.0 with default parameter, using mm10 as reference.
Raw cell-reads were then loaded to R using the cellrangerRkit package. The pre-filtered VDJ information table (all_contig_annotations.csv, output by cellranger) were loaded at the same time. A cell was considered “valid” if it satisfied the following criteria: (1) Cell has enough RNA reads to pass the Cell Ranger threshold. (2) Cell has productive full-length BCR or TCR detected. Only valid cells were kept for downstream analysis in both the scRNA-seq and scTCR-seq/scBCR-seq datasets. The scRNA-seq dataset was then further filtered based on gene numbers and mitochondria gene counts tototal counts ratio. Only cells with > 400 genes,UMI > 0,and 0.5% ~ 30% of their UMIs mappingto mitochondria genes were kept for downstream analysis.
All the VDJ data that don't have the following flag of cellranger were filtered: 1. the is_cell flag, 2. the full-length flag and 3. the productive flag.
For the 5' scRNA-seq and 5' VDJ-seq, the first 16 bp of R1 is the cell barcode and the next 10bp (17-26bp) is the UMI.
Genome_build: hg38
Supplementary_files_format_and_content: cell-gene UMI table: UMI table with each row represent a cell and each column represent a gene.   BCR table: table containing BCR information, including V/D/J/C genes and CDR3  TCR table:  table containing TCR information, including V/D/J/C genes and CDR3

source_name: Ileum immune cell

growth_protocol: No growth procedure was required.

extract_protocol:
Human Peripheral Blood Mononuclear Cell Isolation  Blood was collected in BD Vacutainer CPT tube and centrifuged at 400 x g for 25 minutes. The buffy coat layer was removed, washed, and counted. Cells were resuspended in freezing buffer (10%(v/v) DMSO, 40%(v/v) complete RPMI [RPMI +10%(v/v) fetal bovine serum (FBS) +100 U/mL penicillin/100 μg/mL streptomycin], 50%(v/v) FBS), placed into a freezing container (Mr. Frosty), and stored at -80°C. Cells were recovered, washed, and filtered, and labeled with anti-human CD45. CD45+ immune cells were sorted on a FACSAria2 (BD Biosciences).     Human Intestinal Cell Isolation  Four intestinal biopsies were obtained with endoscopic biopsy forceps from the rectum or ileum and collected in a conical tube with Hank’s buffered saline solution (HBSS). Intestinal biopsies were transferred into freezing buffer (10%(v/v) DMSO, 40%(v/v) complete RPMI, 50%(v/v) FBS) and stored at -80°C. Biopsies were recovered, incubated in HBSS on a shaker, then incubated twice in HBSS + 5 mM dithiothreitol (DTT) with shaking, then washed in HBSS. Intestinal biopsies were mechanically dissociated, then placed into 10 mL of digestion mixture (complete RPMI + 1.5 mg/mL Collagenase type VIII + 50 µg/mL DNase I) on a rocker at 37°C for 20 minutes, filtered and stained with anti-human CD45. CD45+ immune cells were sorted on a FACSAria2 (BD Biosciences).
Single cell libraries were prepared according to the protocol for 10X Genomics for Single Cell V(D)J + 5’ Gene Expression. Approximately 20,000 sorted CD45+ cells were loaded and partitioned into Gel Bead In-Emulsions (GEM). scRNA libraries were sequenced on a HiSeq4000 (Illumina). The B and T cell receptor libraries were amplified according to the manufacturer’s protocol and sequenced on a NovaSeqS4 (Illumina).

treatment_protocol: These details are included in extraction protocol.

tag: subject #

value: control

value: ileum

tag: cell subtype surface markers

tag: cell subtype

value: immune cells


title: PITRM1-WT iPSCs

city: Paris

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, INSERM UMR1163

data_processing:
Demultiplexing of bcl to fastq file occured via bcl2fastq v2.19.1.403
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count (v3.1.0, default settings) to generate filtered gene-barcode matrices. Matrices from same samples but sequenced on different flow cells were combined with cellranger aggr v3.1.0 (default settings).
R package Seurat v3.1.3 was used to merge data, perform quality control and filter data to exclude cells with UMI <2500,  UMI > 15000 and detected genes <500 as well as genes expressed in less than 10 cells.
Seurat v3.1.3 function NormalizeData was run to normalize counts for visualization, followed by CellCycleScoring to visualize cell cycle phases. Function SCTransform was used to normalize single cell counts for data integration. Data integration was performed running SelectIntegrationFeatures with nfeatures = 3000, PrepSCTIntegration, FindIntegrationAnchors and IntegrateData.
Seurat v3.1.3 function FindNeigbors with dims = 1:40 and FindClusters with resolution = 0.8  were used to perform graph-based clustering.
Seurat v3.1.3 function FindConservedMarkers was run to identify conserved markers in each cluster and FindMarkers (min.pct=0.1, logfc.threshold=0.1) to identify differentially expressed genes between KO and WT samples for each cluster.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: cellranger output files for filtered gene-barcode matrix (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz)

source_name: Cerebral organoid

growth_protocol: Cerebral organoids were generated and maintained using the protocol described by Lancaster et al. 2014 (Nature Protocols)

extract_protocol:
RNA libraries were prepared using standard 10X Genomics 3' Single Cell v2 protocol.
scRNA-seq libraries were generated using the 10X Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Cat. 1000128) according to manufacturer’s instructions. Approximately 18000 cells per sample were loaded on the Chromium Next GEM Chip G, which was subsequently run on the Chromium Controller (10X Genomics) to partition cells into gel beads-in-emulsion (GEMs). Cell lysis and reverse transcription of poly-adenylated mRNA occurred within the GEMs and resulted in cDNA with GEM-specific barcodes and transcript-specific unique molecular identifiers (UMIs). After breaking the emulsion, cDNA was amplified (11 cycles), enzymatically fragmented, end-repaired, extended with 3’ A-overhangs and ligated to adapters. P5 and P7 sequences as well as sample indices (Chromium i7 Multiplex kit) were added during the final PCR amplification step (7 cycles). The fragment size of the final libraries was determined using the Bioanalyzer High Sensitivity DNA Kit (Agilent). Their concentration was determined using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). scRNA libraries were pooled and paired-end sequenced on the Illumina NovaSeq 6000 platform.

treatment_protocol: Cerebral organoids were dissociated into single-cell suspension following the Worthington Papain Dissociation System kit instructions (Worthington Biochemical) with intermittent trituration steps. The final solution was centrifuge 300g per 7 min, cell pellet were resuspended in PBS-0,5% BSA and filtered twice (40um, 30um) to obtain single-cell suspensions.

value: iPSC-derived cerebral organoids

tag: day of differentiation

tag: genotype

value: Wild Type


title: PITRM1-KO iPSCs

value: PITRM1 Knock Out


title: Patient 31 CBCS_N31

value: Positive

value: Basal


title: P30-4_scRNAseq

value: Canton S

value: female


title: C21_I_10x_TCR


title: Patient 29 CBCS_N29

value: LumA


title: C33_PBMC_10x_TCR

source_name: Blood immune cell

value: PBMC


title: Patient 30 CBCS_N30


title: P30-3_scRNAseq


title: Patient 28 CBCS_N28


title: leptomeningeal metastasis Patient_B


title: C21_PBMC_10x_TCR


title: C30_PBMC_10x_TCR


title: P30-2_scRNAseq


title: P15-1_scRNAseq

value: P15 optic lobe


title: P30-1_scRNAseq


title: U41_PBMC_10x_TCR

value: UC


title: leptomeningeal metastasis Patient_C

value: leptomeningeal metastasis

value: leptomeninges/CSF


title: U35_PBMC_10x_TCR


title: P40-4_scRNAseq

source_name: P40 optic lobe

value: P40 optic lobe


title: U45_PBMC_10x_TCR


title: Patient 27 CBCS_N27

value: primary breast tumor


title: C30_I_10x_TCR

value: control

value: ileum


title: Pcan1_API1

value: Apical shoot in transition from primary to secondary growth

value: 60 months


title: Pcan1_API3

value: 61 months and 1 week


title: U44_PBMC_10x_TCR

value: immune cells


title: U5_PBMC_10x_TCR


title: Patient 25 CBCS_N25

value: Positive


title: Patient 26 CBCS_N26


title: U4_PBMC_10x_TCR


title: Patient 3 CBCS_N3

value: Negative

value: Basal


title: C16_PBMC_10x_TCR


title: P40-2_scRNAseq

value: Canton S

value: female


title: C30_R_10x_TCR

source_name: Rectum immune cell

value: rectum


title: Patient 22 CBCS_N22


title: C21_R_10x_TCR


title: P40-1_scRNAseq


title: U45_R_10x_TCR

value: UC


title: Patient 18 CBCS_N18


title: P50-4_scRNAseq

source_name: P50 optic lobe

value: P50 optic lobe


title: C19_R_10x_TCR


title: U34_PBMC_10x_TCR

value: PBMC


title: P50-3_scRNAseq


title: U44_R_10x_TCR


title: U35_R_10x_TCR


title: P40-3_scRNAseq

value: P40 optic lobe


title: U34_R_10x_TCR


title: U41_R_10x_TCR


title: P50-2_scRNAseq


title: P70-9_scRNAseq

source_name: P70 optic lobe

value: P70 optic lobe


title: Patient 19 CBCS_N19

value: primary breast tumor


title: U5_R_10x_TCR


title: Patient 2 CBCS_N2


title: U4_R_10x_TCR


title: Patient 21 CBCS_N21


title: C33_I_10x_BCR

description:
BCR RNA
5' VDJ sequencing (10X genomics)

value: control

value: ileum


title: CBE-KO-enhancer-capture-C-Rep3

city: Tianjin

first: Niannian

last: Li

state: Tianjin

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

department: college of Life Sciences

institute: Nankai University

description: Capture-C  of  RA induced differentiation CBE-KO Embryonic stem cells

library_source: genomic

data_processing:
Library strategy: Capture-C
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were count.txted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Capture-C were cut into two pieces in the DpnII sites
All the reads were mapped to mm10 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes count.txts values for each Sample, Capture-C signal peaks for three Baits

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: Mouse ESCs E14 was cultured as the previous scheme with a few modifications. ESCs were grown in culture dishes coated with 0.1% gelatin (Sigma, Lot # SLBQ9498V) in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, Lot # 8119213) supplemented with 15% fetal bovine serum (FBS, AusGeneX, Lot # FBS00717-1), 100 nM nonessential amino acids (100x, Gibco, Lot # 2027433), 200 mM L-Glutamate (100x, Gibco, Lot # 2085472), 1% Penicillin-streptomycin (Gibco, Lot # 2029632), 50 μM β-mercaptoethanol (Sigma, Cas # 60-24-2), 10 ng/mL LIF (ESGRO, Lot # ESG1107), 1 μM PD0325901 (a MEK inhibitor, MedChemExpress, Lot # HY-10254) and 3 μM CHIR99021 (a GSK inhibitor, MedChemExpress, Lot # HY-10182). The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
1. For RNA -seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions. 2. For Capture-C：Briefly, cells were fixed with 1% (vol/vol) formaldehyde for 10 min at room temperature, quenched with 125 mM glycine in PBS, and then lysed in cold lysis buffer (10 mM Tris–HCl, pH7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.2% NP-40, 1× complete protease inhibitor cocktail (Roche)). Chromatin was digested with DpnII (New England Biolabs) at 37°C overnight. Fragments were then diluted and ligated with T4 DNA ligase (Takara) at 16°C overnight. Cross-linking was reversed by overnight incubation at 60°C with proteinase K (Bioline). Then 3C libraries were purified by phenol-chloroform followed by chloroform extraction and ethanol-precipitated at −80°C overnight. Sequencing libraries were prepared from 10μg of the 3C library by sonication to an average size of 200 ~300 bp and indexed using NEBnext reagents (New England Biolabs), according to the manufacturer's protocol. Enrichment of 2μg of an indexed library incubated with 3uM of a pool of biotinylated oligonucleotides (probe sequences are listed in Supplementary Table 7) was performed using the SeqCap EZ Hybridization reagent kit (#05634261001, Roche/NimbleGen), following the manufacturer's instructions. Two rounds of capture employing 48~72 and 24 hr hybridizations, respectively, were used. Correct library size was confirmed by agarose gel electrophoresis, and DNA concentrations were determined using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). All sequencing was performed on Hi-Seq 2500 platforms using paired 150 bp protocols (Illumina).
The Capture-C libraray was constructed with NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).

treatment_protocol: To induce ESCs differentiation, cells were gently washed with 1x phosphate buffer saline solution (PBS), dissociated and replanted at an appropriate density on gelatin-coated plates in LIF/2i withdrawal medium supplemented with 2µm RA (Solarbio®, Lot # 1108F031). The culture medium was replaced at the given point-in-time.

tag: cell line

value: embryo, blastocyst embryo, blastocyst

tag: treatment

value: RA induced differentiation

value: CBE-KO


title: C30_I_10x_BCR

tag: tissue

value: immune cells


title: P70-7_scRNAseq

tag: age


title: P70-8_scRNAseq


title: CBE-KO-enhancer-capture-C-Rep2


title: Patient 17 CBCS_N17

tag: study phase

value: Negative


title: C21_I_10x_BCR

tag: subject status


title: CBE-KO-enhancer-capture-C-Rep1


title: C33_PBMC_10x_BCR


title: Patient 15 CBCS_N15

tag: estrogen receptor status

tag: pam50 molecular subtype

value: Basal


title: Patient 20 CBCS_N20


title: P70-5_scRNAseq

tag: strain

value: Canton S

tag: Sex


title: WT-enhancer-capture-C-Rep2

description: Capture-C  of  RA induced differentiation  Embryonic stem cells

value: WT


title: Patient 14 CBCS_N14


title: C21_PBMC_10x_BCR


title: C16_R_10x_TCR

value: rectum


title: Adult8_scRNAseq

source_name: adult optic lobe

value: female

value: 1-3 days old

value: adult optic lobe


title: C30_PBMC_10x_BCR

value: PBMC


title: WT-enhancer-capture-C-Rep3


title: WT-enhancer-capture-C-Rep1


title: Patient 13 CBCS_N13

source_name: primary breast tumor


title: Adult6_scRNAseq


title: Adult7_scRNAseq


title: Patient 16 CBCS_N16


title: Patient 10 CBCS_N10


title: Adult5_scRNAseq


title: P70-6_scRNAseq

value: P70 optic lobe


title: U44_PBMC_10x_BCR

value: UC


title: Patient 11 CBCS_N11

value: primary breast tumor


title: Adult4_scRNAseq


title: Patient 1 CBCS_N1


title: C4_1_1

city: Galveston

first: Yingzi

last: Cong

address: 301 University Boulevard

institute: University of Texas Medical Branch at Galveston

data_processing:
Raw data processing and quality assessment: 1. Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). 2.Base Quality and Phred score relationship in illumina Casava 1.8. 3.GC-content is used to detect potential AT/GC separation. 4. Raw reads filtering conditions are as follows:(1) Remove reads containing adaptors;(2) Remove reads containing N > 10% (N represents base that could not be determined);(3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Aligment: 1. Mapping reads to reference genome. 2.Reads is mapped to exon, intron and intergenic. 3. Distribution of mapped reads on chromosome.
Gene expression level analysis: The abundance of transcript reflects gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008)
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: CD4+ T cells

growth_protocol: 1 × 106 Cells were cultured in 1640 RPMI medium supplemented with 10% FBS, 1 mM sodium pyruvate, and 0.05mM 2-ME.

extract_protocol:
mRNA from T cells is isolated by using Trizol reagent. All samples need to pass through the following three steps before library construction: (1) Nanodrop: for RNA purity (OD260/OD280). (2) Agarose gel electrophoresis: for RNA integrity and potential contamination. (3) Agilent 2100: check RNA integrity again.
1 µg of RNA was used for cDNA library constuction at Novogene using an NEBNext@ Utra RNA library Prep Kit for Illumina@ (cat# E7420S, New England Biolabs, lpswich, MA, USA) according to the manufacturer's protocol.

treatment_protocol: Cells were activated with antiCD3 and antiCD28 treated with or without butyrate for 2 days in the presence or absence of IL-12 for 2 days

value: Spleen

tag: cell type

value: CD4+ T cells

value: 10 ng IL-12 + 0.5 mM butyrate


title: C4_1_2


title: NT_1_3


title: Adult3_scRNAseq


title: Patient 12 CBCS_N12


title: Adult2_scRNAseq


title: U5_PBMC_10x_BCR


title: U34_PBMC_10x_BCR


title: Adult1_scRNAseq


title: U35_PBMC_10x_BCR


title: NT_1_2


title: U45_PBMC_10x_BCR


title: NT_1_1


title: C4_1_3


title: Patient 7 CBCS_N7


title: Adult_3d_N_scRNAseq


title: U4_PBMC_10x_BCR


title: Patient 6 CBCS_N6


title: Adult_3d_F_2nd_scRNAseq


title: C4_0_3

value: 0.5 mM butyrate


title: U41_PBMC_10x_BCR

value: immune cells


title: Patient 9 CBCS_N9

value: Negative


title: C4_0_2


title: Patient 4 CBCS_N4

value: Basal


title: C30_R_10x_BCR

value: control


title: G6P+Q rep3

city: Wuerzburg

first: Thomas

last: Rudel

state: Bavaria

address: Am Hubland

department: Chair of Microbiology

institute: University of Wuerzburg

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT2 (Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019)).
Measure gene expression in RNA-Seq experiments
Genome_build: AE001273.1 Chlamydia trachomatis D/UW-3/CX, complete genome
Supplementary_files_format_and_content: Gene expression with treatment.

organism: Chlamydia trachomatis

source_name: Chlamydia trachomatis D seovar

extract_protocol:
Total RNA was isolated from Chlamydia trachomatis D serovar grown in axenic culture either with G6P or G6P and glutamine and was used for RNA sequencing (RNA seq). Libraries for RNA Seq were generated using NEBNext® Ultra™
RNA Library Prep Kit for Illumina® with 12 PCR cycles for amplification.

value: Chlamydia trachomatis D seovar


title: MB12

city: Chicago

first: Daniel

last: Foltz

address: 303 E Superior St

institute: Northwestern University

data_processing:
Raw BCL output files were processed using bclfastq (Illumina, version 2.17.1.14)
Raw BCL output files were quality trimmed with trimmomatic
Trimmed reads were aligned to the human genome (UCSC hg19) with TopHat (version 2.1.0) 95 with gene annotations sourced from Ensembl release 72 assigned using Phython package HTSeq 0.6.1
Differential gene expression was calculated using EdgeR.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files including normalized counts for each sample and log2FC differential gene expression of EYFP CENP-A +DOX (MB10-12) versus -DOX (MB07-09)

source_name: DLD-1 cells

growth_protocol: 1-2e6 EYFP-CENP-A DLD-1 cells per condition and per replicate cultured in RPMI media supplemented with 10% fetal calf serum (FSC) (Sigma-F6178-500ml), penicillin/streptomycin (15140122), fungizone (15290018) and L-glutamine (A2916801)s in a 5% CO2 37 °C incubator

extract_protocol:
RNA was isolated from cells with the RNeasy Plus Mini Kit (Qiagen;74134) according to manufacturer protocol
One microgram (1 µg) of total RNA was used as input for RNA-seq libraries, prepared according to the Low Sample (LS) protocol for Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion (Illumina;RS-122-2201)

treatment_protocol: EYFP-CENP-A were left untreated as control (MB07-MB09) or treated with 0.1ug/mL doxycycline in culture medium for 30m, washed 3x5m with PBS, then incubated overnight in fresh culture medium for >20h before collection

value: DLD-1 colorectal cells

tag: disease state

value: cancer

tag: genotype (transduced)

value: EYFP-CENP-A

value: 0.1u/gmL DOX 30m, 20-30h washout


title: Patient 8 CBCS_N8


title: C4_0_1


title: C21_R_10x_BCR

tag: subject #

value: rectum

tag: cell subtype surface markers


title: Patient 5 CBCS_N5


title: MB11


title: NT_0_3

value: Medium aone


title: G6P+Q rep2


title: NT_0_1

value: Medium alone


title: NT_0_2


title: U45_R_10x_BCR

value: UC

tag: cell subtype


title: MB09

value: untreated


title: G6P+Q rep1


title: MB08


title: MB10


title: U41_R_10x_BCR


title: G6P rep2


title: C16_PBMC_10x_BCR

value: PBMC


title: U35_R_10x_BCR


title: G6P rep3


title: G6P rep1


title: U34_R_10x_BCR


title: Renal progenitor cells (index 4)

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

description:
processed data file: barcodes.tsv
processed data file: features.tsv
processed data file: matrix.mtx

data_processing:
Basecall performed with cellranger mkfastq v3.0.1.
Single cell feature counts performed with cellranger count v.3.0.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx (filtered count matrix), barcodes.tsv, and features.tsv files generated through cellranger count.

source_name: renal progenitor cells

growth_protocol: Renal progenitor cells were generated by plating processed human kidney (typically 2–3 × 10^6 cells into a T75 flask) on coated plastic in EGM-MV media (Lonza) supplemented with 20% FBS (Hyclone).

extract_protocol:
The single cell suspension with 98% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following manufacturer’s instructions.
3’ gene expression libraries were constructed following 10x Genomics's instructions. Four libraries, all from the same sample, were constructed; each library was linked to a different 10X Genomics index.
Libraries were sequenced on an Illumina NextSeq550 (Illumina Inc., San Diego, CA).

value: Primary cell culture of renal progenitor from kidney

tag: passage

tag: development stage

value: Adult


title: Renal progenitor cells (index 3)


title: Control rep2


title: Renal progenitor cells (index 2)


title: Control rep3


title: U4_R_10x_BCR

value: immune cells


title: MB07

tag: treatment


title: U5_R_10x_BCR

tag: tissue


title: Sperm low fertile bulls 1

city: Bangalore

first: Arumugam

last: Kumaresan

state: Karnataka

address: Hosur Road

department: Veterinary Gynaecology and Obstetrics

country: India

institute: National Dairy Research Institute

description: Gene expression in spermatozoa – buffalo low fertile

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method

organism: Bos taurus

source_name: Sperm

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA was extracted using Qiagen Rneasy mini kit with Dnase treatment as per the manufacturer’s protocol.

value: Male

tag: status

value: Breeding bull

tag: fertility

value: low


title: C16_R_10x_BCR

tag: subject status

value: control


title: C19_R_10x_BCR


title: Renal progenitor cells (index 1)


title: Sperm low fertile bulls 2


title: Sperm high fertile bulls 1

description: Gene expression in spermatozoa – buffalo high fertile

value: high


title: Sperm low fertile bulls

description: Gene expression in spermatozoa – Crossbred low fertile

value: spermatozoa


title: Sperm high fertile bulls

description: Gene expression in spermatozoa – Crossbred high fertile


title: Sperm high fertile bulls 2


title: Control rep1

value: Chlamydia trachomatis D seovar


title: Input_Me31B_oocyte

status: Public on Jul 15 2020

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

institute: University of Colorado Denver

data_processing:
Libraries were pooled and sequenced on an Illumina HiSeq 2500 by The Centre for Applied Genomics at The Hospital for Sick Children. 50 base-pair single-end reads were demultiplexed and converted to FASTQ format using bcl2fastq2 v2.17 (Illumina)
Reads were trimmed for quality and clipped for Illumina adaptors using TrimmomaticSE version 0.36
Surviving reads were mapped by STAR 2.5.2a (Dobin et al., 2013) to the D. melanogaster genome obtained from UCSC on 7 August 2016
Genes were quantified using Cufflinks 2.2.1
Downstream analyses were then performed with R version 3.1.2, using in-house scripts.
To calculate occupancy values for each gene, the IP FPKM was divided by the unnormalized input FPKM.
Genome_build: dm6
Supplementary_files_format_and_content: Comma separated values file contains FPKMs for each gene in each sample

source_name: Oocyte

growth_protocol: Fly stocks were maintained in a 25°C room with 65% humidity according to standard protocols.

extract_protocol:
RNA was extracted from immunoprecipitates and input lysate using TRI-reagent.
RNA was subjected to Ribo-Zero Gold rRNA depletion according to the manufacturer’s protocol. Libraries were then generated using Illumina’s TruSeq stranded mRNA library preparation kit according to the manufacturer’s protocol and sequenced at The Center for Applied Genetics (SickKids).

treatment_protocol: Stage 14 oocytes were isolated from a large-scale Drosophila culture established with w1118;eGFP-Me31B flies, and were homogenized in lysis buffer B (150 mM KCl, 20 mM HEPES-KOH pH 7.4, 1 mM MgCl2, 1 mM DTT) (with protease inhibitor cocktail (BioShop, Canada) and additional freshly added protease inhibitors [100 µM Leupeptin, 100 µM Chymostatin, 4 mM Benzamidine HCl, 3 µM Pepstatin; Sigma] and SUPERase-In RNase inhibitors). The homogenized lysates were clarified at 15,000 rpm, 4°C for 15 min, and the supernatant was stored at –80°C. Prior to the IP anti-GFP or IgG antibodies were conjugated to protein G beads overnight at 4°C. The beads were also blocked with salmon ssDNA. Lysates were diluted to 1.1 mg/ml, and then incubated with conjugated beads for 2–3 hr, rotating at 4°C. Beads were washed six times with lysis buffer.

tag: developmental stage

value: Stage 14

value: oocyte

tag: rip antibody


title: Me31B_oocyte

tag: strain


title: SCC_Metastastic [D681]

city: Omaha

first: Marissa

last: Lobl

state: NE

address: 4014 Leavenworth St.

institute: UNMC

description:
D681
tumor DNA
Instrument model: Sentosa SQ301

data_processing:
Library strategy: DNA-Seq
Base-calling and signal processing were done using the Sentosa SQ Suite software.
Alignment was done according to manufacturer instructions using the Sentosa instrument to a minimum quality control level of 85%.
Filtering was done to 0.05 variant allele frequency and above.
Genome_build: hg19
Supplementary_files_format_and_content: *.copy.xlsx: Excel files with sample id and mutation details.

source_name: Human SCC cells

extract_protocol:
Macro-dissections were made on unstained tissue sections and genomic DNA was isolated using the Maxwell FFPE DNA isolation KIT (Promega Corp).
Libraries were prepared using the automated setting on the Sentosa SX101 instrument.

value: Cutaneous squamous cell carcinoma

tag: tumor location

value: Metastatic


title: SCC_Metastastic [D683]

description:
D683
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_Metastastic [D679]

description:
D679
tumor DNA
Instrument model: Sentosa SQ301


title: Methionine pup brain 7

city: Irvine, CA

first: Amal

last: Alachkar

address: 355 Med Surge II

institute: University of California Irvine

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Following fragmentation, 1 ug of ss-cDNA were hybridized for 20 hr at 48C on GeneChip MoGene-2.1-ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) software (Affymetrix) using Tukey's Biweight Average algorithm and default settings

source_name: pup brain harvested at 24 hours of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Genechip WT Expression Array Manual, 2018).

growth_protocol: Pregnant mice were administered treatments at gestational day 14 until delivery

extract_protocol: Extraction of total RNA was performed according to Qiagen RNeasy kit manufacturer's instructions.

treatment_protocol: Pup brain tissue collected at 24-hours old

value: 24-hour old

tag: agent

value: Mother administered methionine


title: Methionine pup brain 1


title: Saline pup brain 6

value: Mother administered saline


title: Methionine pup brain 2


title: SCC_Metastastic [D758]

description:
D758
tumor DNA
Instrument model: Sentosa SQ301


title: Ctbp1/2 DKO d2 strip2

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

institute: Kwansei Gakuin University

description: Gene expression data of mESCs

hyb_protocol: The labelled single-strand cDNA was hybridized to the GeneChiPTM Mouse Gene 2.1 ST Array Strip (Thermo Fisher Scientific).

scan_protocol: The signal intensities of microarray probes were scanned and quantitated using the GeneAtlas Personal Microarray System (Thermo Fisher Scientific).

data_processing: CELL files of Gene ChiP data were normalized using the Robust Multi-array Average program with the default settings in Affymetrix Expression ConsoleTM.

label_protocol: Total RNA was labelled using the GeneChiPTM WT Terminal Labeling and Control Kit (Thermo Fisher Scientific).

growth_protocol: mESCs are cultured under serum plus LIF condition.

extract_protocol: Total RNA was purified using the PureLink RNA Mini Kit (Thermo Fisher Scientific).

tag: cell type

value: mESCs

tag: genotype/variation

value: Ctbp1/2 DKO


title: SCC_Metastastic [D677]

description:
D677
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_Metastastic [D718]

description:
D718
tumor DNA
Instrument model: Sentosa SQ301


title: WT_d2 strip2

description: Gene expression data of mESCs

value: wild type


title: WT_d0 strip2

description: Gene expression data of mESCs


title: Suz12 KO d2 strip1

description: Gene expression data of mESCs

value: Suz12 KO


title: Saline pup brain 5


title: Ctbp1/2 DKO d0 strip2

description: Gene expression data of mESCs


title: Saline pup brain 2


title: WT_d2 strip1

description: Gene expression data of mESCs


title: Methionine pup brain 5


title: SCC_Metastastic [D673]

description:
D673
tumor DNA
Instrument model: Sentosa SQ301


title: Saline pup brain 4


title: SCC_Metastastic [D675]

description:
D675
tumor DNA
Instrument model: Sentosa SQ301


title: Saline pup brain 3


title: Saline pup brain 1


title: Methionine pup brain 4


title: Suz12 KO d0 strip1

description: Gene expression data of mESCs


title: SCC_Metastastic [D713]

description:
D713
tumor DNA
Instrument model: Sentosa SQ301


title: Methionine pup brain 3


title: SCC_Localized [D691]

description:
D691
tumor DNA
Instrument model: Sentosa SQ301

value: Localized


title: SCC_Localized [D692]

description:
D692
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_Metastastic [D671]

description:
D671
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_Localized [D732]

description:
D732
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_Localized [D722]

description:
D722
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_Localized [D715]

description:
D715
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_Localized [D720]

description:
D720
tumor DNA
Instrument model: Sentosa SQ301


title: WT_d0 strip1

description: Gene expression data of mESCs


title: SCC_Localized [D686]

description:
D686
tumor DNA
Instrument model: Sentosa SQ301


title: SCC_Localized [D721]

description:
D721
tumor DNA
Instrument model: Sentosa SQ301


title: HUVECs, W-4-1_RNA-seq

city: Beijing

first: Jingxue

last: Xin

address: 55 Zhong Guan Cun East Road

department: Academy of Mathematics and Systems Science

institute: Chinese Academy of Sciences

description: Han-4 normoxia 0h

data_processing:
We used TopHat to map sequencing reads to human reference genome hg19.
We used Cufflinks to call FPKM values as gene expression measurement.
ATAC-seq pair-end reads were trimmed for Illumina adaptor sequences and transposase sequences.
We mapped the reads to reference human genome hg19 with Bowtie v1.0.0. Duplicate reads were removed with Samtools.v0.1.19.  Only uniquely aligned reads were used for peak calling with Hotspot using default parameters
HiC-Pro was used to process Hi-C data from raw sequencing reads to normalized contact matrix.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Peaks calling by hotspot. The score in the 5th column of the hotspot files are the z-scores that come from the binomial model for scoring hotspots.

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs were cultured on flasks coated with 0.1% gelatin. The cells were grown in complete medium (Medium199 supplemented with 10% FBS, 20 mmol/l HEPES (pH 7.4), 1 ng/ml recombinant human fibroblast growth factor (bFGF), 1 ng/ml endothelial growth factors (EGF), and 100 units/ml penicillin, 0.1 mg/ml streptomycin) (Gibco) at 37C in 5% CO2, and the medium was changed every 2–3 days. About 7 to 10 days, the primary culture cells were confluent in the flask. For subculture, cells were detached and harvested with 0.05% trypsin-EDTA solution, then neutralized with FBS (Gibco). When the cells were cultured to passage-3, they were cryopreserved with cell freezing medium (NCS + 10% DMSO) in liquid nitrogen.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Ambion).
Libraries from the resulting total RNA were prepared using the TruSeq paired-end mRNASeq kit.
We used the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) to prepare the ready-to-use DNA library for ATAC-Seq
Hi-C library was performed as described in Belaghzal H et al, 2017.

treatment_protocol: Cells were placed in a conventional 37° C humidified incubator (Thermo-Forma, Model 3141) with automated gas control of 1% O2, 5% CO2, balanced with N2. The oxygen concentration of the hypoxic incubator was constantly monitored by a real-time O2 sensor with 0.1% sensitivity.

value: HUVEC

tag: individual

tag: stress

value: normoxia

tag: time


title: HUVECs, W-3-5_RNA-seq

description: Han-3 hypoxia 5d

value: hypoxia


title: HUVECs, W-3-2_RNA-seq

description: Han-3 hypoxia 6h


title: HUVECs, W-5-4_RNA-seq

description: Han-5 hypoxia 3d


title: HUVECs, W-3-3_RNA-seq

description: Han-3 hypoxia 1d


title: HUVECs, W-4-3_RNA-seq

description: Han-4 hypoxia 1d


title: HUVECs, W-4-5_RNA-seq

description: Han-4 hypoxia 5d


title: HUVECs, W-5-2_RNA-seq

description: Han-5 hypoxia 6h


title: HUVECs, W-4-4_RNA-seq

description: Han-4 hypoxia 3d


title: HUVECs, W-3-4_RNA-seq

description: Han-3 hypoxia 3d


title: HUVECs, W-5-1_RNA-seq

description: Han-5 normoxia 0h


title: HUVECs, W-4-2_RNA-seq

description: Han-4 hypoxia 6h


title: HUVECs, W-3-1_RNA-seq

description: Han-3 normoxia 0h


title: HUVECs, W-2-5_RNA-seq

description: Han-2 hypoxia 5d


title: HUVECs, W-5-5_RNA-seq

description: Han-5 hypoxia 5d


title: HUVECs, W-2-2_RNA-seq

description: Han-2 hypoxia 6h


title: HUVECs, W-2-3_RNA-seq

description: Han-2 hypoxia 1d


title: HUVECs, W-2-4_RNA-seq

description: Han-2 hypoxia 3d


title: HUVECs, W-2-1_RNA-seq

description: Han-2 normoxia 0h


title: SCC_Localized [D690]

description:
D690
tumor DNA
Instrument model: Sentosa SQ301


title: HUVECs, W-1-5_RNA-seq

description: Han-1 hypoxia 5d


title: SCC_Localized [D685]

description:
D685
tumor DNA
Instrument model: Sentosa SQ301


title: HUVECs, W-1-4_RNA-seq

description: Han-1 hypoxia 3d


title: HUVECs, W-5-3_RNA-seq

description: Han-5 hypoxia 1d


title: HUVECs, W-1-2_RNA-seq

description: Han-1 hypoxia 6h


title: HUVECs, W-1-3_RNA-seq

description: Han-1 hypoxia 1d


title: HUVECs, A-5-5_RNA-seq

description: Tibetan-5 hypoxia 5d


title: HUVECs, W-1-1_RNA-seq

description: Han-1 normoxia 0h


title: HUVECs, A-5-2_RNA-seq

description: Tibetan-5 hypoxia 6h


title: HUVECs, A-5-4_RNA-seq

description: Tibetan-5 hypoxia 3d


title: HUVECs, A-5-1_RNA-seq

description: Tibetan-5 normoxia 0h


title: HUVECs, A-5-3_RNA-seq

description: Tibetan-5 hypoxia 1d


title: HUVECs, A-4-3_RNA-seq

description: Tibetan-4 hypoxia 1d


title: HUVECs, A-2-5_RNA-seq

description: Tibetan-2 hypoxia 5d


title: HUVECs, A-4-1_RNA-seq

description: Tibetan-4 normoxia 0h


title: HUVECs, A-4-5_RNA-seq

description: Tibetan-4 hypoxia 5d


title: HUVECs, A-2-2_RNA-seq

description: Tibetan-2 hypoxia 6h


title: HUVECs, A-3-3_RNA-seq

description: Tibetan-3 hypoxia 1d


title: HUVECs, A-2-3_RNA-seq

description: Tibetan-2 hypoxia 1d


title: HUVECs, A-4-2_RNA-seq

description: Tibetan-4 hypoxia 6h


title: HUVECs, A-3-5_RNA-seq

description: Tibetan-3 hypoxia 5d


title: HUVECs, A-1-4_RNA-seq

description: Tibetan-1 hypoxia 3d


title: HUVECs, A-3-4_RNA-seq

description: Tibetan-3 hypoxia 3d


title: HUVECs, A-3-2_RNA-seq

description: Tibetan-3 hypoxia 6h


title: HUVECs, A-2-1_RNA-seq

description: Tibetan-2 normoxia 0h


title: HUVECs, A-1-5_RNA-seq

description: Tibetan-1 hypoxia 5d


title: HUVECs, A-1-3_RNA-seq

description: Tibetan-1 hypoxia 1d


title: HUVECs, A-1-1_RNA-seq

description: Tibetan-1 normoxia 0h


title: HUVECs, W-5-3_ATAC-seq

description: Han-5 hypoxia 1d


title: HUVECs, W-5-2_ATAC-seq

description: Han-5 hypoxia 6h


title: HUVECs, W-5-5_ATAC-seq

description: Han-5 hypoxia 5d


title: HUVECs, W-5-4_ATAC-seq

description: Han-5 hypoxia 3d


title: HUVECs, W-5-1_ATAC-seq

description: Han-5 normoxia 0h


title: HUVECs, W-4-5_ATAC-seq

description: Han-4 hypoxia 5d


title: HUVECs, A-4-4_RNA-seq

description: Tibetan-4 hypoxia 3d


title: HUVECs, A-3-1_RNA-seq

description: Tibetan-3 normoxia 0h


title: HUVECs, A-2-4_RNA-seq

description: Tibetan-2 hypoxia 3d


title: HUVECs, A-1-2_RNA-seq

description: Tibetan-1 hypoxia 6h


title: HUVECs, W-3-4_ATAC-seq

description: Han-3 hypoxia 3d


title: HUVECs, W-4-4_ATAC-seq

description: Han-4 hypoxia 3d


title: HUVECs, W-4-1_ATAC-seq

description: Han-4 normoxia 0h


title: HUVECs, W-3-3_ATAC-seq

description: Han-3 hypoxia 1d


title: HUVECs, W-3-2_ATAC-seq

description: Han-3 hypoxia 6h


title: HUVECs, W-3-1_ATAC-seq

description: Han-3 normoxia 0h


title: HUVECs, W-2-5_ATAC-seq

description: Han-2 hypoxia 5d


title: HUVECs, W-4-3_ATAC-seq

description: Han-4 hypoxia 1d


title: HUVECs, W-2-2_ATAC-seq

description: Han-2 hypoxia 6h


title: HUVECs, W-2-3_ATAC-seq

description: Han-2 hypoxia 1d


title: HUVECs, W-3-5_ATAC-seq

description: Han-3 hypoxia 5d


title: HUVECs, W-2-1_ATAC-seq

description: Han-2 normoxia 0h


title: HUVECs, W-1-3_ATAC-seq

description: Han-1 hypoxia 1d


title: HUVECs, W-1-5_ATAC-seq

description: Han-1 hypoxia 5d


title: HUVECs, W-1-4_ATAC-seq

description: Han-1 hypoxia 3d


title: HUVECs, W-1-2_ATAC-seq

description: Han-1 hypoxia 6h


title: HUVECs, W-1-1_ATAC-seq

description: Han-1 normoxia 0h


title: HUVECs, A-5-5_ATAC-seq

description: Tibetan-5 hypoxia 5d


title: HUVECs, A-5-4_ATAC-seq

description: Tibetan-5 hypoxia 3d


title: HUVECs, A-5-2_ATAC-seq

description: Tibetan-5 hypoxia 6h


title: HUVECs, A-5-3_ATAC-seq

description: Tibetan-5 hypoxia 1d


title: HUVECs, A-4-4_ATAC-seq

description: Tibetan-4 hypoxia 3d


title: HUVECs, A-4-5_ATAC-seq

description: Tibetan-4 hypoxia 5d


title: HUVECs, A-5-1_ATAC-seq

description: Tibetan-5 normoxia 0h


title: HUVECs, W-4-2_ATAC-seq

description: Han-4 hypoxia 6h


title: HUVECs, A-4-2_ATAC-seq

description: Tibetan-4 hypoxia 6h


title: HUVECs, A-4-3_ATAC-seq

description: Tibetan-4 hypoxia 1d


title: HUVECs, W-2-4_ATAC-seq

description: Han-2 hypoxia 3d


title: HUVECs, A-4-1_ATAC-seq

description: Tibetan-4 normoxia 0h


title: HUVECs, A-3-5_ATAC-seq

description: Tibetan-3 hypoxia 5d


title: HUVECs, A-3-4_ATAC-seq

description: Tibetan-3 hypoxia 3d


title: HUVECs, A-3-2_ATAC-seq

description: Tibetan-3 hypoxia 6h


title: HUVECs, A-2-2_ATAC-seq

description: Tibetan-2 hypoxia 6h


title: HUVECs, A-3-1_ATAC-seq

description: Tibetan-3 normoxia 0h


title: HUVECs, A-1-4_ATAC-seq

description: Tibetan-1 hypoxia 3d


title: HUVECs, A-1-2_ATAC-seq

description: Tibetan-1 hypoxia 6h


title: HUVECs, A-2-3_ATAC-seq

description: Tibetan-2 hypoxia 1d


title: HUVECs, A-2-4_ATAC-seq

description: Tibetan-2 hypoxia 3d


title: HUVECs, A-2-5_ATAC-seq

description: Tibetan-2 hypoxia 5d


title: HUVECs, A-3-3_ATAC-seq

description: Tibetan-3 hypoxia 1d


title: HUVECs, A-1-1_ATAC-seq

description: Tibetan-1 normoxia 0h


title: HUVECs, A-1-3_ATAC-seq

description: Tibetan-1 hypoxia 1d


title: Sample 8: IPAHCC014

first: Paul

middle: A

last: Insel

department: Pharmacology

institute: UC San Diego

data_processing:
FASTQC to inspect quality of sequencing.
Kallisto v0.43.1 on rat reference transcriptome, ensembl release 79, yielding transcript-level TPM and counts estimates.
Transcript-level expression was converted to gene-level expression using tximport.
Differential expression analysis was performed using gene-level counts estimates as input for edgeR
Sets of differentially expressed genes were subsequently analyzed via tools such as Enrichr, GSEA and STRING
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: excel files with gene expression in TPM and estimated counts, obtained from tximport

source_name: IPAH PASMC

growth_protocol: Cells were cultured in Smooth muscle cell culture media (SCM): Dulbecco’s Modified Eagle’s Medium with 1 g/L glucose, 5% fetal bovine serum, 5 ng/mL fibroblast growth factor, 5 μg/mL insulin, 50 μg/mL ascorbic acid, and 5 ng/mL epidermal growth factor.

extract_protocol:
Cultured cells were homogenized in RLT Lysis buffer (Qiagen). RNA from this lysate was extracted using the RNeasy mini kit (Qiagen) with on-column DNase-1 digestion.
Libraries were constructed at the UCSD IGM core using the Illumina Truseq stranded mRNA protocol, using ~0.5-1 ug of total RNA as input.
RNA-sequencing on a Hiseq-4000, 12 samples multiplexed on a single lane (~25-30 million single reads per sample)

value: human pulmonary artery smooth muscle cells

tag: disease state

value: idiopathic pulmonary hypertension

tag: age (yrs)

tag: Sex

value: Male


title: Sample 7: IPAH908


title: HUVECs, A-2-1_ATAC-seq

description: Tibetan-2 normoxia 0h


title: Sample 5: IPAH4

value: Female


title: Sample 6: IPAH1028


title: Sample 2: PA1189

source_name: Control PASMC

value: healthy


title: Sample 3: CHPT1


title: Sample 4: CHLONZA


title: Sample 1: PA1217


title: MEIS1_ChIP_in_HOXB13ko-LV-MEIS1

first: Donald

middle: J

last: Vander Griend

state: IL

address: 909 S Wolcott Ave., RM5051

department: Pathology

institute: University of Illinois at Chicago

data_processing:
Basecalling was performed using Illumina CASAVA version 1.8.
Adapter sequences and low quality reads were trimmed using Trimmomatic v0.38.
Duplicate reads were marked and removed using Picard Tools (v2.18.10).
Processed reads were then aligned to human reference genome hg38 (ENSEMBL release 93, GRCh38.p12) using Bowtie2 with default settings. Samtools was then used to change .sam files to .bam files, sort, and index the .bam files.
Peaks were called against sequenced input chromatin using MACS2 and pooling immunoprecipitated samples for either LV-MEIS1 or HOXB13ko-LV-MEIS1 cells. Called peaks were then annotated to hg38 using the annotatePeaks.pl command in HOMER (v4.9.1).
Genome_build: hg38
Supplementary_files_format_and_content: MEIS1_ChIP_in_LV-MEIS1_peaks.txt: peak file with quantitative data for MEIS1 peaks called in the LV-MEIS1 cell line vs input DNA; annotated_MEIS1_ChIP_in_LV-MEIS1_peaks.txt: HOMER annotation of MEIS1 peaks called in LV-MEIS1 cells, annotated to hg38.; MEIS1_ChIP_in_HOXB13ko-LV-MEIS1_peaks.txt:  peak file with quantitative data for MEIS1 peaks called in the HOXB13ko-LV-MEIS1 cell line vs input DNA.; annotated_MEIS1_ChIP_in_HOXB13ko-LV-MEIS1_peaks.txt: HOMER annotation of MEIS1 peaks called in HOXB13ko-LV-MEIS1 cells, annotated to hg38.

source_name: prostate carcinoma cell line

growth_protocol: 22Rv1 cells were grown in RPMI medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml), and puromycin (1 ug/mL).

extract_protocol:
Chromatin was harvested, sonicated, and immunoprecipitated (or not immunoprecipitated in the case of input DNA control) according to manufacturer protocol for Diagenode iDeal ChIP-seq kit for Transcription Factors (Cat# C01010055). Briefly, 25 million cells per replicate were fixed with formaldehyde at room temp for 15 mins before stopping fixation with glycine. Cells were then lysed and chromatin was harvestd and sonicated with a Diagenode Biorupter Pico for 5 cycles of 30 seconds on, 30 seconds off. Sheared chromatin size was checked with agarose gel electrophoresis and shown to be ~200 bp. MEIS1 bound chromatin was immunoprecipitated with MEIS1 ChIP-grade antibody (Cat# ab19867) at 4C overnight before being washed, eluted, and quantified with high sensitivity Qubit. IPs were performed in triplicate for LV-MEIS1 condition and in duplicate for HOXB13ko-LV-MEIS1 condition. Effective pulldown of MEIS1 was validated by western blot before library construction.
5ng of ChIP'd DNA (or of input DNA) was used as starting material for library construction using the KAPA LTP Library prep kit (Roche Cat# 07961863001) following manufacturer protocol for chromatin sheared to 175 bp. Briefly, end repair was performed on fragmented DNA, followed by A-tailing and Illumina TruSeq adapter ligation. Each library was then amplified with 13 cycles of PCR. Final library quality was assessed on an Agilent TapeStation 2200. Libraries were quantified using KAPA Universal Library Quantification Kit (Roche Cat# 07960140001) before pooling libraries in equamolar concentrations. Sequencing was performed on Illumina HiSeq 4000 using single end, 50bp reads.

treatment_protocol: All lines were seeded at 5 x 10^6 cells per dish in 15 cm dishes and were incubated at 37°C in 5% CO2 for 48 hrs prior to fixing and harvesting chromatin.

tag: cell line

value: prostate carcinoma epithelial cell line derived from a xenograft that was serially propagated in mice after castration-induced regression and relapse of the parental, androgen-dependent CWR22 xenograft

tag: treatment

value: Knockout of HOXB13 by CRISPR and exogenous expression of MEIS1

tag: antibody used for chip

value: MEIS1 ChIP-grade (ab19867)


title: MEIS1_ChIP_in_LV-MEIS1

value: Exogenous expression of MEIS1


title: CWR-22Rv1 input DNA

description: input chromatin that was used as control for calling peaks against


title: HOXB13ko-LV-MEIS1_2

data_processing:
Basecalling was performed using Illumina CASAVA version 1.8.
Adapter sequences and low quality reads were trimmed using Trimmomatic v0.38.
All reads were pseudo-aligned to the human transcriptome built from ENSEMBL Human GRCh38.p12 cDNA and ncRNA using kallisto (v0.43.1) with default settings for single-end reads with fragment length of 180 and standard deviation of 20.
Estimated transcript counts were summarized to the gene level using tximport (v1.8.0).
Filtering of lowly-expressed genes (<1 count per million in 6 of the 12 libraries), library normalization, and differential expression analysis was carried out in edgeR (v3.22.2) using the glmTreat method with a log fold change threshold of log2(1.5) and FDR < 0.05.
Genome_build: hg38 transcriptome
Supplementary_files_format_and_content: All processed data files are Tab-delimited text files with the final count per million (cpm) value from edgeR for every gene in each of the replicates for the condition specified by the filename.

extract_protocol:
total RNA was harvested using a Qiagen Rneasy mini kit (Cat# 74106) following the manufacturer protocol and including the on-column DNA digestion.
2 ug of total RNA was used as starting material for library construction using the KAPA Stranded mRNA Seq Kit (Roche Cat# 07962193001) following manufacturer protocol for a desired insert size of 100-200 bp. Briefly RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina TruSeq adapters/indexes prior to 9 cycles of PCR. Final library quality was assessed on an Agilent TapeStation 2200. Libraries were quantified using KAPA Universal Library Quantification Kit (Roche Cat# 07960140001) before pooling libraries in equamolar concentrations. Sequencing was performed on Illumina HiSeq 4000 using single end, 50bp reads.

treatment_protocol: All lines were seeded at 1 x 10^6 cells per dish in 10 cm dishes and were incubated at 37°C in 5% CO2 for 48 hrs prior to harvesting RNA.


title: HOXB13ko-LV-MEIS1_1


title: HOXB13ko-LV-MEIS1_3


title: HUVECs, A-1-5_ATAC-seq

description: Tibetan-1 hypoxia 5d


title: HOXB13ko_2

value: Knockout of HOXB13 by CRISPR


title: HOXB13ko_3


title: HOXB13ko_1


title: LV-MEIS1_3


title: LV-MEIS1_2


title: Control_3

value: Exogenous expression of Cas9, no gRNA provided


title: Control_2


title: Control_1


title: N619

city: Taipei

first: Hsing-Chen

last: Tsai

address: No.1 Jen Ai road section 1

department: Medicine

country: Taiwan

institute: National Taiwan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v2.2.6 with parameters --forward-prob 0 --output-genome-bam for both cell ine and clinical samples
Each cell line bam files were splig to two files using Python
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library using DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: normalized_count.txt: normalized count of clinical samples using DESeq2 of 81 tumor and 19 adjacent tissues
Supplementary_files_format_and_content: FPKM_A549_CL10.csv: FPKM of FUT4 overexpressed cell lines

source_name: adjacent lung

growth_protocol: Lung cancer cell lines were cultured in RPMI-1640 medium with 10% FBS and 1% antibiotics.

extract_protocol:
Lung cancer cell lines, frozen tumor or adjacent tissue were harvested for RNA  using Trizol reagent. Invitrogen PureLink RNA Mini Kit (Cat#12183018A) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lung cancer cell lines were transfected with FUT4 overexpression plasmid using Lipofectamine3000 reagent.

tag: tissue

value: adjacent lung

tag: histology

value: adjacent tissue


title: N536


title: N575


title: N532


title: N515


title: N494


title: N580


title: N581


title: N573


title: N531


title: N527


title: N520


title: N519


title: N504


title: N467


title: S789

source_name: lung cancer

value: lung cancer

tag: gender

value: F

tag: t

tag: n

tag: m

tag: Stage

value: squamous cell carcinoma


title: LV-MEIS1_1

tag: cell type


title: S667

value: M


title: N160


title: S666


title: S637


title: S646


title: S662


title: S614


title: S584


title: S636


title: S601


title: N471


title: S602


title: N538


title: S612


title: N534


title: S564


title: S582


title: S540


title: S543


title: S545


title: S551


title: S521


title: S518


title: S517


title: S496

value: squamous cell carcinoma, keratinizing


title: S495

value: squamous cell carcinoma, non-keratinizing


title: S476


title: S462


title: S463


title: S622


title: S458


title: S455


title: S447


title: S413


title: S427


title: S310

value: squamous cell carcinoma,keratinizing


title: S176

value: Squamous cell carcinoma


title: A669

value: adenocarcinoma


title: A696


title: S268


title: A654


title: A665


title: A656


title: A653


title: A651


title: A631


title: A644


title: A652


title: A619


title: A613


title: A611


title: A610


title: S441


title: A576


title: A595


title: A591


title: A581


title: A572


title: A588


title: A562


title: A559


title: S293


title: A627


title: A624


title: A513


title: A537


title: A531


title: A547


title: A526


title: A621


title: A534


title: A479


title: A468


title: A459


title: A473


title: A457


title: A442


title: A438

value: adenocarcinoma, BAC


title: A306


title: A272

value: Adenocarcinoma


title: A271


title: YTHDF2-7 crispr-3

city: Riverside

first: Weifeng

last: Gu

state: California

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

description: Bisulfite-converted RNA from YTHDF2 knockout cells, rep 3

data_processing:
After de-multiplexing, the samples were processed to remove the partial 3' linkers if the sequences are shorter than 50 nts. And inserts less than 30 nts were discarded.
The C in the transcriptome was converted to T. Then the reads were mapped to the human transcriptome using Bowtie 0.12.7 with parametes  using '-n 3 -e 180 -m 4000', which allow a maximum of 3 mismatches in the seed region, 6 mismatches for the whole size, and 4000 hits for each read.
And then for each read, only the mapped loci with the minimum mismatches were selected for further analysis. To minimize non-specific matches, we allow a maximum of 6 mismatches for reads 45-50 nts long, 5 for reads 41-44 nts long, 4 for reads 38-40 nts long, 3 for reads 35-37 nts long, 2 for 32-34 nts long, and 1 for 30 nts long.
We then identified C to T mutations, and converted the transcript nt position to genomic nt position. Our analysis also allowed the analysis of reads spanning exon-exon junctions.
We only considered any C position with at least 10 total reads including converted T read. We discarded C positions with C-A or C-G mutation number more than C-T conversion since these C's may represent hot spots with more sequencing errors as indicated by C-A or C-G mutations. We then calculated the C-T conversion rate for each C position in each sample.
Genome_build: human genome Ensembl GRCh37 release 71
Supplementary_files_format_and_content: tab-delimited txt file containing the sequences and read number used for the analysis

source_name: Human Embryonic Kidney 293T cells

growth_protocol: HEK293T cells (American Type Culture Collection, ATCC) were cultured at 37°C in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (Invitrogen) and 100 IUml−1penicillin (ATCC) in an incubator containing 5% CO2.

extract_protocol:
RNAs were extracted with TRIzol. mRNA was isolated using PolyATract kit and Ribominus kit. The samples were subject to bisulfite conversion.
Fragmented RNAs were linked with Truseq LT/V1/V2 linkers using the standard 5' and 3' ligation methods. Amplicons with 50-100 nt inserts were selected for sequencing. The samples were multiplexed with 8 nt indexes in the 3' linker.

treatment_protocol: CRISPR-Cas9-mediated knockout of YTHDF2 gene

tag: genotype/variation

value: YTHDF2 knockout


title: YTHDF2-7 crispr-1

description: Bisulfite-converted RNA from YTHDF2 knockout cells, rep 1


title: 293T-3

description: Bisulfite-converted RNA from HEK293T cells, rep 3

value: wild type


title: A557


title: 293T-2

description: Bisulfite-converted RNA from HEK293T cells, rep 2


title: YTHDF2-7 crispr-2

description: Bisulfite-converted RNA from YTHDF2 knockout cells, rep 2


title: 293T-1

description: Bisulfite-converted RNA from HEK293T cells, rep 1


title: A503


title: T111d_5month_DEHP_M_Heart

city: Ann Arbor

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

institute: University of Michigan

data_processing:
The sample quality was first assessed with FastQC (v0.11.3), then Trim Galore! (v0.4.5) was used for adapter and quality trimming. More specifically, low-quality bases (quality score lower than 20), adapter sequences (required overlap of 6bp), and end-repair bases from the 3’ end of reads were trimmed, and all reads shorter than 20bp after trimming were discarded.
Bismark was used for alignment and methylation calling, where reads were aligned to mm10 genome using Bowtie2 and methylation calls were reported for all nucleotides with a read depth of at least 5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_R1_trimmed_bismark_bt2.bismark.cov.gz: Bismark coverage files including the percentage of methylation at each position, the number of C bases that are methylated and the number of C bases that are unmethylated.

source_name: heart

extract_protocol:
Upon euthanasia at 5 months of age, heart were collected. Briefly, blood was removed by cardiac puncture (to be used in another study) and organs were perfused with PBS. Heart tissue was snap frozen in liquid nitrogen and stored at -80 deg C. Heart DNA extraction was performed using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen #80224).
A total of 50 ng of genomic DNA was digested using restriction enzyme Mspl, and the digested DNA was then purified using phenol:chloroform extraction and ethanol precipitation in the presence of glycogen, before blunt-ending and phosphorylation. A single adenine nucleotide was next added to the 3′ end of the fragments in preparation for the ligation of the adapter duplex with a thymine overhang. The ligated fragments were cleaned, then processed for size selection on agarose gel. Selected fragments were treated with sodium bisulfite to convert unmethylated cytosines to uracils, which are then replaced with thymines during PCR amplification. These libraries were next cleaned up with AMPure XP beads (Product #A63880; Beckman Coulter), quantified using the Agilent TapeStation genomic DNA kit (Catalog #G2991AA; Agilent) and Qubit High Sensitivity dsDNA (Catalog #Q32850; Invitrogen).

value: Heart

value: Male

tag: age

value: 5 months

value: DEHP


title: T101c_5month_Ctrl_F_Heart

value: Female

value: Ctrl


title: T118h_5month_Ctrl_M_Heart


title: A474

value: lung cancer


title: T108d_5month_Ctrl_M_Heart


title: T114d_5month_DEHP_M_Heart


title: T113c_5month_Ctrl_F_Heart


title: T109d_5month_Ctrl_M_Heart


title: T117h_5month_DEHP_M_Heart


title: T101d_5month_Ctrl_M_Heart


title: T115c_5month_DEHP_F_Heart


title: T104c_5month_DEHP_F_Heart


title: T118c_5month_Ctrl_F_Heart


title: T110c_5month_DEHP_F_Heart


title: T118d_5month_Ctrl_M_Heart


title: T119e_5month_Ctrl_F_Heart


title: T115d_5month_DEHP_M_Heart


title: T119g_5month_Ctrl_F_Heart


title: T109c_5month_Ctrl_F_Heart


title: T114c_5month_DEHP_F_Heart


title: T111g_5month_DEHP_F_Heart


title: T117d_5month_DEHP_M_Heart


title: 24h.IR.PGE.Female-3

city: Indianapolis

first: Andrea

middle: Marie

last: Patterson

state: IN

address: 980 W. Walnut St.

institute: Indiana University School of Medicine

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC mm10
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

source_name: Hematopoietic stem cells

growth_protocol: All cells direct ex vivo (taken from mouse bone marrow and immediately sorted/RNA-extracted)

extract_protocol:
RNeasy Plus Micro Kit (Qiagen, Hilden, Germany)
Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Cat# 634889), 24 rxns; Illumina Nextera XT DNA Lib Kit. Nextera XT dual-index (8b).

treatment_protocol: DmPGE2 in methyl acetate was purchased from Cayman Chemicals (Ann Arbor, MI) and stored at -20 oC. Prior to use, dmPGE2 was evaporated to dryness on ice under N2 and reconstituted in 100% EtOH at 0.1 mg/ml. Mice received a single subcutaneous injection containing 3.5 µL (35 ug) dmPGE2 or EtOH in a volume of 100 µL saline 30 min prior to irradiation.

tag: time point

tag: irradiation

value: Irradiated


title: 24h.IR.PGE.Female-4


title: T113d_5month_Ctrl_M_Heart


title: 24h.IR.PGE.Female-2


title: 24h.IR.PGE.Female-1


title: T104d_5month_DEHP_M_Heart


title: T104j_5month_DEHP_M_Heart


title: 24h.IR.PGE.Male-2


title: 24h.IR.PGE.Male-1


title: 24h.IR.VEH.Female-4

value: Vehicle


title: 24h.IR.PGE.Male-3


title: 24h.IR.VEH.Female-3


title: 24h.IR.VEH.Female-1


title: 24h.IR.VEH.Male-3


title: 24h.IR.VEH.Male-1


title: 24h.NI.VEH.Female-3

value: Non-irradiated


title: 24h.IR.VEH.Male-4


title: 24h.IR.PGE.Male-4


title: 24h.NI.VEH.Female-2


title: 24h.NI.VEH.Female-1


title: 24h.NI.VEH.Male-4


title: 24h.NI.VEH.Male-1


title: 24h.NI.VEH.Male-2


title: 1h.IR.PGE.Female-4

value: 1 h


title: 1h.IR.PGE.Female-3


title: 24h.NI.VEH.Male-3


title: 1h.IR.PGE.Female-2


title: 1h.IR.PGE.Male-3


title: 1h.IR.PGE.Male-2


title: 1h.IR.PGE.Male-4


title: 1h.IR.PGE.Female-1


title: 1h.IR.VEH.Female-3


title: 1h.IR.VEH.Female-4


title: 24h.IR.VEH.Female-2


title: 24h.IR.VEH.Male-2


title: 1h.IR.PGE.Male-1


title: 1h.IR.VEH.Female-2


title: 1h.IR.VEH.Male-4


title: 1h.IR.VEH.Male-3


title: 1h.NI.PGE.Female-4


title: KO_cort3

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

data_processing:
Fastq formatted read files were preprocessed with Trimmomatic version 0.38 with default options.
Fastq files were then aligned to the Zebrafish genome version 11, as presented in Ensembl version 93, using the STAR aligner version 2.6.1b.
The Ensembl transcriptome was preprocessed with a splice junction overhang of 100nt.
Following alignment, the resulting BAM files were preprocessed with RSEM version 1.3.0 for isoform and gene-level expression estimates.
The resulting gene-level expression values were merged into a single expression matrix with an in-house python script.
Further normalization was achieved using EDAseq version 2.18.0 using GC content data downloaded from Ensembl version 98 with EDAs built in scripts.
Counts were normalized with the data-within function using GC content and full normalization.
Additional normalization was accomplished with EDAseq using the following two commands: dataNorm <- betweenLaneNormalization(dataWithin, which=“full”) dataWithin <- withinLaneNormalization(edaData,“gc”, which=“full”)
Differential expression analysis was carried out in R version 3.6.1 with the DESeq2 version 1.24.0.  DESeq2 was also used to generate an rlog-matrix which was Z-transformed to normalize each gene across all samples.
The Z-transformed rlog matrix was then loaded into JMP version 13 and used for PCA after thresholding to an average rlog expression value of 7.5
DESeq2 output tables were filtered with the following restrictions for the identification of statistically significant differentially expressed genes: BaseMean >= 75 (average of 5 counts per sample), padj <= 0.05, |log2foldchange| >= 0.5, estimated standard error of the log2foldchange < 1.0.
GOrilla algorithm was used for Gene Ontology term enrichment analysis, data was visualized using REVIGO.  Venn diagrams were generated using Venny 2.1
Genome_build: GRCz11 Genome Reference Consortium Zebrafish Build 11
Supplementary_files_format_and_content: Tab-delimited text file includes normalized log2counts for each sample

organism: Danio rerio

source_name: Whole embryo

growth_protocol: The AB wild-type strain was used for all genetic modifications. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of the MDI Biological Laboratory. Embryo culture and cortisol treatments were performed as previously described, with one difference: embryos were cultured in a diurnal light-dark cycle (14 hours light – 10 hours dark). Briefly, fertilized eggs were collected in the morning, disinfected and at ~4 hours post fertilization placed in dishes with either 1uM cortisol or vehicle (DMSO) added to embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.

extract_protocol:
At 3 hours zeitgeber time (post lights-on) on day 5 post-fertilization four biological replicates of cortisol-treated and control embryos were collected as follows.  For the first RNA-seq experiment, one by one, a dish of larvae corresponding to a single condition was removed from the incubator, and 8 larvae per replicate (4 replicates) were collected in a 1.5 mL tube with minimal water and immediately snap frozen in liquid nitrogen. All replicates from one condition were collected sequentially before moving on to the next condition. Total RNA was extracted using the Qiagen RNA-Easy Plus mini kit (Qiagen). For the second RNA-seq experiment, four replicates of n=10 larvae were collected from a single dish for each condition and immediately snap frozen in liquid nitrogen. Collection of 16 samples occurred over 22 minutes. RNA was prepared as described above on two different days. On the first day (experimental replicates 1 and 2) the lysis buffer was added to all 8 frozen samples before homogenization, while on the second day the lysis buffer was added to each sample which was then immediately homogenized. This difference in sample preparation likely accounts for the large variance between samples prepared on day 1 and day 2. RNA was sent to the Oklahoma State Genomics Facility for Illumina library preparation and single-end sequencing.
RNA libraries were prepared for sequencing using KAPA Library Kits compatible with Illumina RNA (polyA-selected) sequencing platform

treatment_protocol: To mutate nr3c1 and klf9 we used CRISPR-Cas9, injecting zygotes with multiple guide RNAs for each gene and mRNA encoding Cas9. Guide RNAs were designed using the CHOP-CHOP algorithm. To generate the GR369- mutant line fertilized wild-type AB embryos were injected at the 1 cell stage with 1-2 nL of a gRNA cocktail targeting nr3c1 exons 2 and 3 (final concentration 40 ng/µL for each gRNA, 230 ng/µL Cas9 mRNA, 0.1 M KCl, and 0.01% phenol red indicator dye). Individual whole injected larvae were screened for mutations of the targeted regions by high resolution melt analysis (HRMA) of PCR amplicons containing those regions43. Detected mutations were then verified by Sanger sequencing of a PCR amplicon containing the targeted region. F0 adults bearing mutations were identified by HRMA of DNA extracted from tailfin clips, and germline mutations were then identified by PCR and HRMA/sequencing of sperm. F0 males with germline mutations were outcrossed to AB females, and heterozygous progeny were screened via sequencing from tailfin clips. The GR369- mutation was identified and selected for by breeding over 2 additional generations to yield F3 homozygous progeny. Subsequent generations were maintained as heterozygotes for health and breeding purposes. To generate the klf9-/- mutant line fertilized wild-type AB embryos were injected at the 1-cell stage with <20% cell volume of injection mix consisting of 200ng/ul Cas9 mRNA, 100ng/ul guide RNA, 0.05% phenol red dye, and 0.2M KCl. Individual F0 larvae were screened with HRMA to confirm CRISPR efficacy. Larvae were placed into system and raised. Young adult fish were genotyped via HRMA using DNA extracted from fin clips, and mutations were confirmed by Sanger sequencing. F0 fish positive for mutation were outcrossed to wild-type (AB) fish. F1 offspring of this cross were screened by HRMA to confirm germline transmission, and Sanger sequencing identified the 2bp frame-shift mutation in one female founder. This female was out crossed with WT AB males. The resulting F2 fish were screened as young adults via fin clip and HRMA, and males positive for mutation were back crossed to the F1 founder female. Resulting F3 generation fish were screened via fin clip HRMA and sequenced to identify homozygous mutants as well as homozygous wild-type siblings. F3 generation was Mendelian 1:2:1 wild-type:heterozygote:homozygous-mutant ratio.

value: whole embryo

tag: genotype

value: CRISPR-Cas9-mediated mutation of klf9

tag: agent

value: Cortisol


title: KO_cort4


title: KO_cort1


title: 1h.IR.VEH.Male-2

tag: Sex


title: KO_cort2


title: 1h.NI.PGE.Female-3

tag: treatment


title: 1h.IR.VEH.Male-1


title: KO_veh4

value: DMSO


title: 1h.NI.PGE.Female-2


title: 1h.NI.PGE.Male-3


title: 1h.NI.VEH.Female-3


title: 1h.NI.PGE.Male-1


title: 1h.IR.VEH.Female-1


title: 1h.NI.VEH.Female-4


title: KO_veh3


title: 1h.NI.PGE.Male-2


title: WT_cort4

value: wildtype


title: 1h.NI.VEH.Female-2


title: KO_veh2


title: 1h.NI.VEH.Female-1


title: WT_cort3


title: 1h.NI.VEH.Male-4


title: KO_veh1


title: WT_cort1


title: 1h.NI.PGE.Female-1


title: WT_cort2


title: 1h.NI.VEH.Male-3


title: WT_veh4


title: WT_veh3


title: 1h.NI.VEH.Male-1


title: 1h.NI.VEH.Male-2


title: 1GRKO_4_S24

data_processing:
Fastq formatted read files were preprocessed with Trimmomatic version 0.36 with default options.
Fastq files were then aligned to the Zebrafish genome version 11, as presented in Ensembl version 93, using the STAR aligner version 2.6.1b.
The Ensembl transcriptome was preprocessed with a splice junction overhang of 100nt.
Following alignment, the resulting BAM files were preprocessed with RSEM version 1.3.0 for isoform and gene-level expression estimates.
The resulting gene-level expression values were merged into a single expression matrix with an in-house python script.
Further normalization was achieved using EDAseq version 2.18.0 using GC content data downloaded from Ensembl version 98 with EDAs built in scripts.
Counts were normalized with the data-within function using GC content and full normalization.
Additional normalization was accomplished with EDAseq using the following two commands: dataNorm <- betweenLaneNormalization(dataWithin, which=“full”) dataWithin <- withinLaneNormalization(edaData,“gc”, which=“full”)
Differential expression analysis was carried out in R version 3.6.1 with the DESeq2 version 1.24.0.  DESeq2 was also used to generate an rlog-matrix which was Z-transformed to normalize each gene across all samples.
The Z-transformed rlog matrix was then loaded into JMP version 13 and used for PCA after thresholding to an average rlog expression value of 7.5
DESeq2 output tables were filtered with the following restrictions for the identification of statistically significant differentially expressed genes: BaseMean >= 75 (average of 5 counts per sample), padj <= 0.05, |log2foldchange| >= 0.5, estimated standard error of the log2foldchange < 1.0.
GOrilla algorithm was used for Gene Ontology term enrichment analysis, data was visualized using REVIGO.  Venn diagrams were generated using Venny 2.1
Genome_build: GRCz11 Genome Reference Consortium Zebrafish Build 11
Supplementary_files_format_and_content: Tab-delimited text file includes normalized log2counts for each sample

value: VBA minus


title: 1GRKO4_S16

value: VBA plus


title: EEC BR#1

city: Irvine

first: Amber

middle: Nicole

last: Habowski

address: 240 Sprague Hall

department: MMG

institute: University of California, Irvine

description:
SE.MATS.JCEC_StemVEEC.txt
DaPars_Output_StemVEEC_All_Prediction_Results.txt
MAJIQ_StemVEEC.txt

data_processing:
Paired-end sequencing reads were trimmed of adapter sequences and analyzed for quality using Fastqc (version 0.11.7).
Data was aligned to the mouse genome (UCSC mm10 from Illumina iGenome) using STAR (version 2.5.2a), converted to bam files and merged (samtools 1.3)
Read counts were generated using HTSeq (version 0.6.1p1, with enthought_python version 7.3.2; option -s no).
Differential gene expression analysis was done in R studios (version 1.0.153) using DESeq2 (version 1.16.1; with cooksCutoff = FALSE option).
For Splicing: Merged bam files were sorted and indexed (samtools 1.3) for downstream analysis. Alternative splicing was investigated using rMATS Turbo was run (rMATS.4.0.1) with STAR 2.5.2a, Samtool 1.3, and enthought_python 7.3.2 comparing two cell types at a time using UCSC mm10 gtf. MAJIQ (v1.1) was also run for alternative splicing with anaconda 3-2.0.1 and recommended mm10 ensembl gff3 reference with type=strand-specific followed by VIOLA for visualization
For APA: DaPars (v0.9.1) was used for alternative polyadenylation analysis with recommended mm10 UCSC reference files and python 2.7.15, bedtools 2.25.0, R 3.4.1, and the following settings (Num_least_in_group1=1, Num_least_in_group2=1, Coverage_cutoff=30, FDR_cutoff=0.05, PDUI_cutoff=0.15, Fold_change_cutoff=0.32).
Genome_build: mm10
Supplementary_files_format_and_content: Counts files for Gene Expression; Splicing data from rMATS - SE only for cell type comparisons with stem; Alternative Polyadenylation data from DaPars - for cell comparison with stem.

source_name: EEC BR_colon

extract_protocol:
Mouse colons (caecum to rectum) were removed, flushed, and linearized and then dissociated with EDTA and mechanical force. Populations of Epcam+ cells (See manuscript for details) were bulk sorted on a BD FACS Aria Fusion using a 100 µm nozzle (20 PSI) at a flow rate of 2.0 with a maximum threshold of 5000 events/sec. The sample chamber and collection tubes were kept at 4 °C. Following exclusion of debris and singlet/doublet discrimination, cells were gated as demonstrated in the paper supplement. Populations were sorted into TRIzol (Invitrogen # 15-596-018) for downstream RNA isolation and sequencing. RNA was extracted from TRIzol samples using a Direct-zol RNA Micro-Prep kit (Zymo #11-330M) and associated guidelines. Sorted samples of each cell type were pooled as needed at the start of RNA preparations to ensure a minimum of 2,500 cells per sample. RNA sample quality and concentration was evaluated using an Aligent Bioanalyzer on an RNA high sensitivity pico chip.
RNA samples were then pooled as needed to allow 1 ng library preps with Clontech Low Input Pico Kit (Takara #634940)

treatment_protocol: Wild Type mice - no treatment. Aged 5-7 weeks, Male.

tag: strain background

value: wild type

value: 5-7 weeks

value: male

value: Colon

value: Sorted colon EEC:Cd31-, Cd45-, Epcam+, Cd44low/-, Cd24+, live


title: 1GRKO_3_S23

tag: tissue


title: EEC BR#2