title: normal lung rep4

city: New Haven

first: Dejian

last: Zhao

address: 333 Cedar St

institute: Yale School of Medicine

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm10) using the Tophat (v2.0.13)
Gene models of Refgene were downloaded from the UCSC genome browser on March 13, 2017. FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using the cufflinks (v2.2.1). Lowly expressed genes (mean FPKM values < 1 in both groups under comparison) were excluded from differential expression analysis.
read counts were obtained using HTSeq (v0.6.1)
DESeq2 (v1.6.3) was used to determine differentially expressed genes
genes with >2 fold change, false discovery rate (FDR) < 0.05, and FPKM>1 were identified as significantly differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited gene expression values (read counts from HTseq)

source_name: FACS sorted macrophages from lung

extract_protocol:
Lung metastases were induced by tail vein injection of 1 x 106 E0771-LG to syngenic C57BL6/J female mice (6-8 wk old). Lungs were perfused with PBS through the right ventricle, dissected and minced. Lung metastases (<1 mm in diameter) were dissected with aid of a dissection microscope and pooled from 2-4 mice. The tissues were then digested with an enzyme mix of Liberase DL (Sigma-Aldrich 5466202001, 0.52 U/mL) and TL (Sigma-Aldrich 5401020001, 0.26 U/mL) and DNase I (Sigma-Aldrich DN25, 150 µg/mL) diluted in basal DMEM medium with rotation for 30 min at 37°C and filtered (70-µm member). Transcription inhibitors alpha-amanitin (Sigma-Aldrich A2263, 5 µg/mL) and actinomycin D (Sigma-Aldrich A1410, 1 µg/mL) were also added in the digestion buffer. Red blood cells were removed by incubation with RBC lysis buffer (Biolegend, 420301) for 5 min on ice (once for tissues and twice for blood). Cells were stained with DAPI to distinguish live/dead cells and were blocked with anti-mouse CD16/CD32 antibody (BD Biosciences 553141) for 10 min on ice, followed by antibody staining. Target cells were sorted directly into the Extraction Buffer in the Picopure RNA isolation kit (Arcturus KIT0202) for isolation.
RNA sequencing of mouse total RNA was performed at Beijing Genomic Institute, using the Ovation® RNA-Seq System V2 kit for library construction, pair-end 100 bp and Hiseq 4000, which generated 60-80M reads per sample.

tag: cell type

value: Lung

value: 8-10 weeks

value: Wild type


title: Wild Type 2

status: Public on Jan 20 2021

type: SRA

city: Würzburg

first: Joachim

last: Morschhäuser

address: Josef-Schneider-Str 2, Bau D15

department: Institute for Molecular Infection Biology

country: Germany

institute: University of Würzburg

library_source: transcriptomic

data_processing:
Adapter and low quality end trimming using Trimmomatic (v0.36)
Mapping of reads to Candida albicans SC5314 genome assembly 22 using STAR (v2.6.1b) to produce BAM files
Raw read counts per feature generated using HTSeq (v0.6.1)
Normallization and determination of differentially expressed genes using DESeq2 (v1.14.1)
Genome_build: Candida albicans assembly 22
Supplementary_files_format_and_content: Processed data files for individual samples are tab delimited text files containing feature identifier (systematic orf name) and read counts

molecule: polyA RNA

organism: Candida albicans

source_name: yeast cells

growth_protocol: Strains were grown overnight in YPD shaking at 30°C. The following day they were diluted 1:100 in YPD and grown for three hours shaking at 30°C.

extract_protocol:
Cells were broken by hot phenol and RNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. Samples were treated with TURBO DNase (Invitrogen GmbH, Darmstadt, Germany) to remove any residual genomic DNA, and remaining RNA was cleaned by a second purification using the RNeasy Mini kit.
Further steps to prepare for and conduct RNA sequencing were done by Eurofins Genomics (Konstanz, Germany). Such steps included purification of poly(A) mRNA molecules, mRNA fragmentation, preparation of strand-specific cDNA libraries, adapter ligation, and Illumina (HiSeq 2500) sequencing (single reads, 1x 50 base pair length).

tag: strain

tag: genotype

value: WT


title: WT_MZ2

city: birmingham

first: Etty (Tika)

last: Benveniste

state: Alabama

address: 1918 University Blvd., MCLM 31

department: CDIB

country: USA

institute: UAB

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and demultiplexed using Illumina bcl2fastq v 2.17 program.
 After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Spleens were harvested, marginal zone B cells were flow-sorted, and RNA was extacted using Qiagen RNeasy Mini Kit. Then RNA was submitted to GENEWIZ for RNA-seq and bioinformatics analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Spleen

tag: age


title: vitro_+V_rep1

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

country: China

institute: Peking University

data_processing:
The raw sequences were cleaned using Trimmomatic (version 0.39)
Clean reads were mapped to mouse reference genome mm10 using STAR (version 2.7.3a)
High quality mapped reads were quantified using featureCounts
Raw counts were normalized to TPM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene TPM values for each sample

source_name: organoid with 8C -E condition

growth_protocol: Crypts were isolated and cultured as previously described.1 Briefly, proximal small intestine sections of approximately 20 cm were harvested, opened longitudinally, cut into 2–4mm pieces, rinsed with cold PBS and incubated in 2mM EDTA at 4 °C for 30 min with gentle shaking. Crypts were released after vigorous shaking in cold PBS and passed through a 70 μM cell strainer (BD Biosciences) for further enrichment. Approximately 500 crypts were embedded in 20 μL Matrigel (growth factor reduced; BD bioscience) and plated in 48-well plates. After Matrigel polymerization, 500 μL culture medium containing Advanced DMEM/F12 (Gibco), 10mM HEPES (Gibco), 1× GlutaMAX (Gibco), 1% penicillin/ streptomycin (Gibco), 1× N2 Supplement (Gibco), 1× B27 Supplement (Gibco), and 1mM N-Acetylcysteine (Sigma-Aldrich) was added. For ENR-organoids, culture medium containing 50 ng/mL murine EGF, 100 ng/mL murine Noggin and 500 ng/mL human R-Spondin 1 was used. For Hyper-organoids, culture medium containing 0.2 μM LDN193189, 0.1 μM GSK-3 Inhibitor XV, 1 μM Pexmetinib, 500 μM VPA, 2 μM EPZ6438, 50 ng/mL murine EGF, 10% R-Spondin 1 Conditioned Medium (Trevigen), and 20 ng/mL  FGF2 was used. The cell culture medium was changed every other day. Hyper-organoids can be generated from either ENRorganoids or primary crypts. For passage, organoids were removed from Matrigel, mechanically dissociated into singlecrypt domains and transferred to fresh Matrigel. Passage was  performed every 7 days with a 1:8 split ratio for ENR-organoids and a 1:30 split ratio for Hyper-organoids. 5% knockout serum replacement (KSR, GIBCO) was recommended to enhance expansion of Hyper-organoids after they were passaged. Six days after passage, the number of colonies containing typical organoid structures and expressing Lgr5-GFP was counted. Directed differentiation of organoid cultures was performed as previously reported.46 In brief, ENR- and Hyper-organoids were cultured under ENR conditions, supplemented with Notch inhibitor DAPT (10 μM) to induce enterocyte (alpi); with Notch inhibitor DAPT (10 μM) and Wnt inhibitor IWP2 (2 μM) to induce PC (lyz1), GC (muc2) and enteroendocrine cell (chga).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
RNA sequencing libraries were constructed using the NEBNext® Ultra RNA Library Prep Kit for Illumina® (NEB England BioLabs). Fragmented and randomly primed 2 × 150 bp paired-end libraries were sequenced using an Illumina HiSeq X Ten system.

value: organoid

tag: condition in vitro

value: organoid with 8C -E condition

tag: repeat


title: Anterior Cingulate cortex, sbb29, RNAseq

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

description:
ribosomal depletion RNA-seq
ACC_RNASeq.rawcounts.tsv.gz

data_processing:
Fastq files were aligned using TopHat
Genome_build: hg19
Supplementary_files_format_and_content: the "raw.counts" file contains counts gennerated using HTSeq-counts

organism: Homo sapiens

source_name: Brain

extract_protocol: TrueSeq Stranded Total RNA Sample Preparation + Ribo-Zero Gold kits (Illumina)

tag: group

value: Control group

value: Anterior Cingulate cortex (human brain tissue)


title: vitro_+V_rep6


title: normal lung rep2

state: CT

department: Genetics


title: normal lung rep5


title: Anterior Cingulate cortex, sbb33, RNAseq

value: Early-Life Adversity group


title: lung metastases rep5


title: Anterior Cingulate cortex, sbb31, RNAseq


title: WT_MZ1


title: vitro_+E_rep5

source_name: organoid with 8C -V condition

value: organoid with 8C -V condition


title: vitro_+V_rep4


title: vitro_+E_rep4


title: SHG_8h_2 miRNA-seq

city: Haikou

first: JunLong

last: Sun

state: Hainan

address: No.58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan University

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to pig reference genome with stringent criteria (0 mismatch in the first 18bp).
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM).
Genome_build: miRbase release 22
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

organism: Micropterus salmoides

source_name: liver

growth_protocol: To investigate the effects of hypoxia on largemouth bass, we simulated acute hypoxia caused by extreme weather, eutrophication and high-density aquaculture in actual aquaculture under laboratory conditions. At the beginning of the experiment, experimental fish were randomly distributed into 9 circulation closeness-tanks (30 fish per tank) connected with big reservoir barrel, the temperature of the tanks were still maintained at 20℃ and allowed to adapt for one day before the start of the experiment. The experiment was designed using three groups, namely severe hypoxia group (SHG) (DO: 1.2 ± 0.2 mg/L), moderate hypoxia group (MHG) (DO: 3.0 ± 0.2 mg/L) and control group (CG) (DO: 7.0 ± 0.2 mg/L), with three parallel tanks for each group. The DO treatments were regulated through the pumping of nitrogen and oxygen in the big reservoir barrel, filled with nitrogen (N2) to reduce the DO to the concentration required for the experiment within 2 h after the start of the experiment, and it was recorded as 0 h (Yang et al., 2017; Yang et al., 2019). Fish were subjected to acute hypoxic stress for 24 h (SHG and MHG) and fish in the CG were cultured simultaneously under normal oxygen conditions for 24 h, and they were recorded as 24 h. The fish were still fasted during the experiment. The DO level was monitored by measuring the water quality using the classic iodine quantity method in each experimental tank every hour (Beadle 1958) and making the appropriate adjustments.

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by theAgilent 2100 Bioanalyzer and RNA 6000  Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.

treatment_protocol: Sampled after fasting for one days, the fish were anesthetized with MS-222. Their livers were collected from three groups in each five fish and immediately snap-frozen in liquid nitrogen, stored at -80℃ until use.

value: liver

tag: developmental stage

tag: sample group

value: severe hypoxia group (SHG) at 8h in acute hypoxic experiment


title: vitro_+V_rep3


title: normal lung rep3


title: vitro_+V_rep2


title: Anterior Cingulate cortex, sbb25, RNAseq


title: SHG_12h_1 miRNA-seq

value: severe hypoxia group (SHG) at 12h in acute hypoxic experiment


title: SHG_12h_2 miRNA-seq


title: vitro_+E_rep6


title: normal lung rep1


title: Anterior Cingulate cortex, sbb27, RNAseq


title: SHG_8h_3 miRNA-seq


title: SHG_8h_1 miRNA-seq


title: lung metastases rep2


title: Anterior Cingulate cortex, sbb23, RNAseq


title: Anterior Cingulate cortex, sbb26, RNAseq


title: Anterior Cingulate cortex, sbb30, RNAseq


title: SHG_12h_3 miRNA-seq


title: Sca1+ cells from 5-FU treated BMMNCs

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Sca1+ cells sorted from 5-FU treated BMMNCs

data_processing:
Single cell (sc) RNA-seq processing was performed with the BD Rhapsody Analysis pipeline Revision 2 (https://www.sevenbridges.com/bdgenomics/.  Refer to the BD Single Cell Genomics Bioinformatics Handbook). Firstly, the FASTQ files (Illumina Hiseq 75x 2 bp) were uploaded into the pipeline and the read quality filtering was conducted under the fixed condition determined by the manufacturer. Read1 reads were analyzed to identify cell label and Unique Molecular Index (UMI), and Read2 reads (targeted sequence reads)　were mapped  to  the reference sequences of the BD Rhapsody™ Mouse Immune Response Targeted Panel (BD BioScience) with Bowtie2 version 2.2.9. After pairing R1 reads and R2 reads, the paired sequencing reads were collapsed into raw molecule based on the UMI sequences. The raw molecule data was corrected with two UMI correction algorithms (recursive substitution error correction (RSEC) and distribution-based error correction (DBEC), and the molecule data (DBEC adjusted molecule data) was generated.  After that, the pipeline conducted cell label filtering to fix putative live cells based on number of reads in each detected cell barcode (the infraction point was basically used as a cut off value between live cells and dead cells/noise. The pipeline also ran the algorithms to recover fales negative cells and to remove fales positive cells). Finally, the pipeline generated the expression matrics data and it was used for subsequent gene expression analysis (t-Distributed Stochastic Neighbor Embedding (tSNE), Hierarchical clustering, etc) using the BD Data View software ver. 1.1 (BD BioScience).
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values of median molecules per cell; rows are genes; columns are cells with cell index

source_name: Sca1+ cells from 5-FU treated BMMNCs

extract_protocol:
Then, Sca1+ cells were sorted and targeted single-cell RNA-seq analysis was conducted using BD Rhapsody Single-Cell Analysis System (BD BioScience) following the manufacture’s protocol. In short, the single cell suspension was loaded into a BD Rhapsody cartridge with >200,000 microwells and single cell capture was achieved by random distribution and gravity precipitation.
The bead library was loaded into the microwell cartridge to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell cartridge to hybridize mRNA molecules onto barcoded capture oligos on the beads. Then, these beads were retrieved from the microwell cartridge into a single tube for the subsequent steps of cDNA synthesis, ExoI digestion and multiplex-PCR based library construction. For the library construction, we used the BD Rhapsody Immune Response Panel for mouse (BD BioScience) consisting of primer sets for 397 genes.

treatment_protocol: BMMNCs from 5-FU (200mg/kg) day 2 mice were prepared using Lymphoprep (Alere Technologies AS).

value: bone marrow mononuclear cells


title: vitro_+E_rep1


title: lung metastases rep4


title: Anterior Cingulate cortex, sbb28, RNAseq


title: lung metastases rep3


title: SHG_4h_1 miRNA-seq

value: severe hypoxia group (SHG) at 4h in acute hypoxic experiment


title: vitro_+E_rep3


title: HSAEpC_96_well_72h_CR1_S71

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

description:
HSAEpC_96_well_72h_CR1_S71
pg-2020-hsae-cov-expr.txt

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and human genome GRCm38 Ensembl version 94 annotation (Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf). Gene-level TPM values and gene annotations were computed using tximport and biomaRt R package. A custom python script was used to organize the data and log reduced using log2(TPM) if TPM > 1 and TPM - 1 if TPM <= 1.
Genome_build: Genome assembly: GRCm38 Ensembl 94, Gene annotatiopn: Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf
Supplementary_files_format_and_content: tab-delimited text files include log2(TPM) if TPM > 1 else TPM - 1 values for each Sample.

source_name: Lung

growth_protocol: Stem cells were isolated from human lung tissue and cultured as 3D organoids. The organoids were broken into single cells and seeded as a monolayer in a 384-well plate. ALI (Air-liquid interphase) model was generated from the single cells collected from the organoid. Alveolar Type 2 cells and alveolospheres were generated from iPSCs.

extract_protocol:
All cells were lysed using TRI-Reagent and RNA was isolated using Zymo Research: Direct-zol RNA MiniPrep Kit.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: The lung cells were infected by SARS-CoV2 for 48h and 72h timepoints and uninfected wells were kept as a control.

value: Small Airway epithelium

tag: agent


title: Anterior Cingulate cortex, sbb24, RNAseq


title: SHG_4h_3 miRNA-seq


title: vitro_+E_rep2


title: SHG_0h_2 miRNA-seq

value: severe hypoxia group (SHG) at 0h in acute hypoxic experiment


title: lung metastases rep1

value: Lung

value: 8-10 weeks


title: SC3, Hyper-organoids origin from Primary crypts, p3

description:
C3
sc_meta.tsv
sc_count.tsv

data_processing:
Sequences from 8 scRNA-seq samples were processed with Cellranger (v.3.0.0) software (10× Genomics)
The generated filtered cell UMI count matrixes were imported and merged using the Seurat package (version 3.1.4)
Cells with fewer than 1500 genes expressed or with more than 25% of reads from mitochondrial genes were discarded.
The Scater package (version 3.11) was used for further quality control and deconvolutionbased normalization.
For each cluster, highly expressed marker genes were identified using Wilcoxon tests and used to manually annotate cell types based on published datasets
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized UMI counts and annotations for each cell, cellranger output files for Seurat input

extract_protocol:
The sampling details for the scRNA-seq experiments are shown in Supplementary information, Table S3. To isolate single cells, Hyper-organoids and ENR-organoids were incubated with TrypLE Express at 37 °C for 20 min, after which live cells were counted using a hemocytometer. On average, ~3000 captured individual cells per sample were subjected to 10× Genomics single-cell isolation and RNA-seq following the manufacturer’s recommendations. Using single cell 3′ Library and Gel Bead Kit V3 (10× Genomics, 1000075) and Chromium Single Cell B Chip Kit (10× Genomics, 1000074), the cell suspension (300–600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10× Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 °C for 45 min, followed by 85 °C for 5 min, and hold at 4 °C. The cDNA was generated and then  amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).
According to the manufacture’s introduction, scRNA-seq libraries were constructed using Single Cell 3′ Library and Gel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

tag: condition


title: SHG_4h_2 miRNA-seq


title: SC1, ENR-organoids origin from Primary crypts, p3

description:
C1
sc_meta.tsv
sc_count.tsv


title: Anterior Cingulate cortex, sbb22, RNAseq


title: HSAEpC_72h_CR1_S65

description:
HSAEpC_72h_CR1_S65
pg-2020-hsae-cov-expr.txt


title: Anterior Cingulate cortex, sbb20, RNAseq


title: HSAEpC_48h_CR1_S63

description:
HSAEpC_48h_CR1_S63
pg-2020-hsae-cov-expr.txt


title: HSAEpC_untreated_CR1_S62

description:
HSAEpC_untreated_CR1_S62
pg-2020-hsae-cov-expr.txt


title: HSAEpC_96_well_48h_CR1_S64

description:
HSAEpC_96_well_48h_CR1_S64
pg-2020-hsae-cov-expr.txt


title: SHG_0h_1 miRNA-seq


title: MHG_24h_3 miRNA-seq

value: moderate hypoxia group (MHG) at 24h in acute hypoxic experiment


title: D2, Colonic crypts from DSS treated mice

description:
D2
sc_meta.tsv
sc_count.tsv

source_name: Colonic crypts from DSS treated mice

value: crypt

tag: treatment

value: DSS


title: S63, Hyper-organoids origin from ENR-organoids, p6

description:
6_3
sc_meta.tsv
sc_count.tsv

value: organoid


title: Anterior Cingulate cortex, sbb16, RNAseq


title: MHG_24h_2 miRNA-seq


title: Anterior Cingulate cortex, sbb21, RNAseq


title: S62, -VE-organoids origin from ENR-organoids, p6

description:
6_2
sc_meta.tsv
sc_count.tsv


title: MHG_24h_1 miRNA-seq


title: W4, Colonic crypts from normal mice

description:
W4
sc_meta.tsv
sc_count.tsv

source_name: Colonic crypts from normal mice

value: normal


title: Anterior Cingulate cortex, sbb17, RNAseq

value: Anterior Cingulate cortex (human brain tissue)


title: Cal_3_72h_S77

description:
Cal_3_72h_S77
AT2-tpm-GL-expr.txt

value: iPSC-derived Alveolar Type 2 cells


title: Anterior Cingulate cortex, sbb15, RNAseq

value: Early-Life Adversity group


title: SHG_0h_3 miRNA-seq

value: liver


title: S61, ENR-organoids, p7

description:
6_1
sc_meta.tsv
sc_count.tsv

source_name: ENR-organoids, p7

value: ENR-organoids, p7


title: Anterior Cingulate cortex, sbb19, RNAseq


title: Anterior Cingulate cortex, sbb14, RNAseq


title: Anterior Cingulate cortex, sbb18, RNAseq

value: Control group


title: Cal_2_72h_S74

description:
Cal_2_72h_S74
AT2-tpm-GL-expr.txt


title: MHG_12h_3 miRNA-seq

value: moderate hypoxia group (MHG) at 12h in acute hypoxic experiment


title: MHG_12h_2 miRNA-seq


title: Anterior Cingulate cortex, sbb13, RNAseq


title: S22, -VE-organoids origin from ENR-organoids, p1

description:
2_2
sc_meta.tsv
sc_count.tsv


title: S21, ENR-organoids, p2

description:
2_1
sc_meta.tsv
sc_count.tsv

source_name: ENR-organoids, p2

value: ENR-organoids, p2


title: Cal_2_48h_S73

description:
Cal_2_48h_S73
AT2-tpm-GL-expr.txt


title: Anterior Cingulate cortex, sbb12, RNAseq


title: MHG_12h_1 miRNA-seq


title: Cal_1_48h_S71

description:
Cal_1_48h_S71
AT2-tpm-GL-expr.txt


title: DRN-20723

city: South San Francisco

first: Thomas

last: Sandmann

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

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description:
Methoxy-positive microglia from APP-SAA homozygous animal
dst168_processed.xlsx

data_processing:
Sequencing adapters were trimmed from the raw reads with skewer (version 0.2.2). Reads were aligned to the mouse genome version GRCm38_p6. A STAR index (version 2.7.1a) was built with the –sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M17) were provided via the –sjdbGTFfile argument. STAR alignments were generated with the following parameters: –outFilterType BySJout, –quantMode TranscriptomeSAM, –outFilterIntronMotifs RemoveNoncanonicalUnannotated, –outSAMstrandField intronMotif, –outSAMattributes NH HI AS nM MD XS and –outSAMunmapped Within. Alignments were obtained with the following parameters: –readFilesCommand zcat –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.6 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –quantMode GeneCounts –outSAMunmapped Within –outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif –outSAMtype BAM SortedByCoordinate –outBAMcompression 6. Gene level counts were obtained using feature Counts from the subread package (version 1.6.2). Gene symbols and biotype information were extracted from the Gencode GTF file.
To calculate normalized counts per million (CPM) TMM normalization was applied across all genes annotated as protein_coding with the edgeR R package.
Genome_build: GRCm38_p6
Supplementary_files_format_and_content: Excel (XLSX) file with sample annotations, raw counts and TMM-normalized counts per million (CPM)

source_name: microglia from brain (cortex & hippocampus)

growth_protocol: Mice were maintained on the C57BL/6J genetic background and heterozygous KI mice were intercrossed to obtain homozygous KI mice and littermate controls. All mouse husbandry and experimental procedures were reviewed and approved by Denali Institutional Animal Care and Use Committee and were conducted in full compliance with regulatory statutes, Institutional Animal Care and Use Committee policies, and National Institutes of Health guidelines. Housing conditions included standard pellet food and water, a 12-h light–dark cycle at temperature of 22°C with maximal 5 mice per cage and cage replacement once per week, and regular health monitoring. At time of sacrifice, animals are deeply anesthetized via intraperitoneal (i.p.) injection of 2.5% Avertin prior to tissue collection.

extract_protocol:
Mice were perfused with cold PBS and cortical and hippocampal tissues were dissected and dissociated into a single cell suspension using the Adult Brain Dissociation Kit (Miltenyi Biotec 130-107-677), according to the manufacturer’s protocol. Cell suspensions were stained with the following antibodies in FACS buffer (1% fatty acid-free BSA + 1mM EDTA in PBS) for 25 minutes on ice: Fixable Viability Stain BV510 (BD Biosciences, 564406), CD11b-BV421 (BioLegend 101251), CD45-APC (BD Biosciences, 559864), ACSA-2-PE (Miltenyi Biotec, 130-102-365), Mouse Fc blocker (anti-mouse CD16/32, BioLegend 101320). Cells were washed twice with FACS buffer and strained through a 100 μm filter before sorting CD11b+ microglia on a FACS Aria III (BD Biosciences) with a 100 μm nozzle. For bulk RNAseq analysis, cells were sorted directly into freshly prepared RLT-plus buffer (Qiagen) containing betamercaptoethanol. Live cells were sorted directly into RLT-plus buffer (Qiagen) with 1:100 betamercaptoethanol. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) and resuspended in 14 μL nuclease-free water. RNA quantity and quality were assessed with a RNA 6000 Pico chip (Agilent) on a 2100 Bioanalyzer (Agilent).
cDNA synthesis was performed with the Clontech SMARTSeq v4 3′ DE kit (Takara Bio USA, Inc. 635040) kit from 200 microglia cells dispensed directly into 11.5 microliters of 1X Reaction Buffer. Reverse transcription was followed by 15 cycles of cDNA amplification. cDNA was purified with 0.8X volume of SPRIselect beads (Beckman Coulter B23318), quantified on a Bioanalyzer 2100 System with a High Sensitivity DNA chip (Agilent 5067-4626). 300 pg of DNA from each sample was used as input for library preparation with the Nextera XT DNA Library Prep Kit (Illumina FC-131-1096). Fragmentation and adaptors insertion were performed by tagmentation, followed by 12 cycles of PCR amplification. The final libraries were purified using 0.6X SPRIselect beads. Library quantity and quality were assessed with Qubit 4 Fluorometer with the 1X dsDNA HS Assay Kit (Invitrogen Q33231) and on a Bioanalyzer 2100 System with a High Sensitivity DNA chip. 100 bp single end reads were generated on an Illumina NovaSeq 6000 sequencer by SeqMatic (Fremont, CA, USA)

treatment_protocol: To determine microglia phagocytic activity of Aβ, mice were intraperitoneal (i.p.) injected with 10 mg/kg methoxy-X04 (R&D Systems) as reported (Wang et al., 2016). 24 hours after injection, mice were perfused with PBS and cortical and hippocampal tissues were dissected and processed into single-cell suspension for FACS and stained with Fixable/viability Dye 780 (Thermo fisher 65-0865-14), Cd11b-PE (BioLegend, 101208), CD45-APC (BD Biosciences, 559864), Mouse FC block 1:50  (BioLegend, 101320). Methoxy-X04 positive and negative microglia (CD11b+) were collected for bulk RNAseq and lipidomics analysis.

value: positive

value: months

tag: batch

value: Microglia

value: Hom

tag: region

value: cortex, hippocampus

tag: Sex

value: male


title: MHG_8h_3 miRNA-seq

value: moderate hypoxia group (MHG) at 8h in acute hypoxic experiment


title: MHG_8h_2 miRNA-seq


title: Anterior Cingulate cortex, sbb11, RNAseq


title: DRN-20722


title: CA1_3UN_S75

description:
CA1_3UN_S75
AT2-tpm-GL-expr.txt


title: CA1_1UN_S70

description:
CA1_1UN_S70
AT2-tpm-GL-expr.txt


title: Anterior Cingulate cortex, sbb10, RNAseq


title: CA1_2UN_S72

description:
CA1_2UN_S72
AT2-tpm-GL-expr.txt


title: DRN-20720


title: S23, Hyper-organoids origin from ENR-organoids, p1

description:
2_3
sc_meta.tsv
sc_count.tsv

value: organoid


title: DRN-20721


title: MHG_8h_1 miRNA-seq


title: RC_2_prime_S62

description:
RC_2_prime_S62
analysed_samples_3d_tpm-GL-expr.txt

value: Alveolosphere


title: Anterior Cingulate cortex, sbb8, RNAseq

value: Anterior Cingulate cortex (human brain tissue)


title: MHG_4h_2 miRNA-seq

value: moderate hypoxia group (MHG) at 4h in acute hypoxic experiment


title: Cal_3_48h_S76

description:
Cal_3_48h_S76
AT2-tpm-GL-expr.txt

value: iPSC-derived Alveolar Type 2 cells


title: DRN-20719


title: RC_2_S61

description:
RC_2_S61
analysed_samples_3d_tpm-GL-expr.txt


title: Anterior Cingulate cortex, sbb7, RNAseq


title: DRN-20718


title: MHG_4h_1 miRNA-seq

value: liver


title: MHG_4h_3 miRNA-seq


title: DRN-20716


title: RC_1_S59

description:
RC_1_S59
analysed_samples_3d_tpm-GL-expr.txt


title: MHG_0h_2 miRNA-seq

value: moderate hypoxia group (MHG) at 0h in acute hypoxic experiment


title: DRN-20715

value: female


title: DRN-20714


title: RC_1_prime_S60

description:
RC_1_prime_S60
analysed_samples_3d_tpm-GL-expr.txt


title: Anterior Cingulate cortex, sbb2, RNAseq

value: Early-Life Adversity group


title: MHG_0h_3 miRNA-seq


title: Anterior Cingulate cortex, sbb5, RNAseq

value: Control group


title: Anterior Cingulate cortex, sbb9, RNAseq


title: DRN-20712

description:
Methoxy-negative microglia from APP-SAA homozygous animal
dst168_processed.xlsx

value: negative


title: Anterior Cingulate cortex, sbb3, RNAseq


title: MHG_0h_1 miRNA-seq


title: Anterior Cingulate cortex, sbb6, RNAseq


title: JA1_ALI_UN_2_S77

description:
JA1_ALI_UN_2_S77
analysed_samples_tpm-GL-expr.txt

value: Lung organoid-derived ALI model


title: JA1_ALI_UN_1_S76

description:
JA1_ALI_UN_1_S76
analysed_samples_tpm-GL-expr.txt


title: DRN-20710

value: months

value: Microglia


title: LNCaP HOXD13 OE rep2

city: shanghai

first: Wei

last: Xue

state: State...

address: pujian road no.160

institute: renji hospital, school of medicine, shanghai jiao tong university

data_processing:
HCS 2.2.68 Software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using bowtie2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Gene expression level was quantified using RSEM software (http://deweylab.github.io/RSEM/).
Genome_build: hg19
Supplementary_files_format_and_content: files include FPKM values for each Sample

source_name: prostate cancer cell line

growth_protocol: LNCaP (RRID:CVCL_0395) were cultured at 37°C in a humidified incubator (5% CO2) in RPMI-1640 medium (Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and streptomycin.

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. After treating with DNaseI, mRNA was enriched by Oligo(dT) modified magnetic beads and served as templates for cDNA synthesis
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: lentivirus infection and purimycin screening

value: LNCaP

value: HOXD13 overexpression


title: JA1_monolayer_Un_S73

description:
JA1_monolayer_Un_S73
analysed_samples_tpm-GL-expr.txt

value: Lung monolayer (submerged)


title: CG_24h_1 miRNA-seq

value: control group (CG) at 24h in acute hypoxic experiment


title: CG_24h_3 miRNA-seq


title: CG_12h_3 miRNA-seq

value: control group (CG) at 12h in acute hypoxic experiment


title: JA1_2E4_UN_1_S69

description:
JA1_2E4_UN_1_S69
analysed_samples_tpm-GL-expr.txt


title: DRN-20717

value: positive

value: Hom

value: cortex, hippocampus

value: male


title: DRN-20708


title: Anterior Cingulate cortex, sbb4, RNAseq

description:
ribosomal depletion RNA-seq
ACC_RNASeq.rawcounts.tsv.gz

value: Anterior Cingulate cortex (human brain tissue)


title: JA1_1E4_UN_2_S66

description:
JA1_1E4_UN_2_S66
analysed_samples_tpm-GL-expr.txt


title: LNCaP HOXD13 OE rep1


title: DRN-20706


title: CG_12h_2 miRNA-seq

value: liver


title: CG_24h_2 miRNA-seq


title: LNCaP HOXD13 EV rep2

value: empty vehicle


title: DRN-20703


title: LNCaP HOXD13 EV rep1


title: CG_12h_1 miRNA-seq


title: JA1_2E4_UN_2_S70

description:
JA1_2E4_UN_2_S70
analysed_samples_tpm-GL-expr.txt


title: Anterior Cingulate cortex, sbb1, RNAseq

value: Early-Life Adversity group


title: JA2_P8_S69

description:
JA2_P8_S69
analysed_samples_tpm-GL-expr.txt

value: Lung organoid-ALO2


title: JA1_1E4_UN_1_S65

description:
JA1_1E4_UN_1_S65
analysed_samples_tpm-GL-expr.txt


title: DRN-20702

value: negative


title: DRN-20700

value: months


title: CG_8h_2 miRNA-seq

value: control group (CG) at 8h in acute hypoxic experiment


title: JA2_P3_D7_S67

description:
JA2_P3_D7_S67
analysed_samples_tpm-GL-expr.txt


title: CG_8h_3 miRNA-seq


title: JA1_org_P4_S84

description:
JA1_org_P4_S84
analysed_samples_tpm-GL-expr.txt

value: Lung organoid-ALO1


title: DRN-20698

value: Microglia


title: JA1_P3_D7_S66

description:
JA1_P3_D7_S66
analysed_samples_tpm-GL-expr.txt


title: CG_8h_1 miRNA-seq


title: DRN-20697

value: female


title: CG_4h_2 miRNA-seq

value: control group (CG) at 4h in acute hypoxic experiment


title: JA2_org_P1_S83

description:
JA2_org_P1_S83
analysed_samples_tpm-GL-expr.txt


title: JA1_org_P1_S82

description:
JA1_org_P1_S82
analysed_samples_tpm-GL-expr.txt


title: G1_P30_1

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

data_processing:
Illumina Casava1.7 software used for basecalling.
Mapping was done with STAR method
Quantification was done using FeatureCounts
Differential expression was calculated using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: a Mapping file with the index file
Supplementary_files_format_and_content: tab-delimited text files include feature counts for each Sample.
Supplementary_files_format_and_content: a Deseq differential expression file in csv format

source_name: Neural progenitor cells

growth_protocol: neurons were derived from iPSC cells.

extract_protocol:
neurons were collected and lysed in RLT plus buffer, RNA was extracted using the RNAeasy plus kit from quiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ES-derived neural cells

value: Healthy

tag: cell line


title: G1_P30_2

tag: cell type


title: G2_P30_1


title: A2_P30_2

value: AD


title: DRN-20713

description:
Methoxy-negative microglia from WT animal
dst168_processed.xlsx

value: WT

value: cortex, hippocampus


title: CG_4h_1 miRNA-seq


title: G2_P30_2


title: A2_P30_1


title: JA2_Tissue_b_S88

description:
JA2_Tissue_b_S88
analysed_samples_tpm-GL-expr.txt

value: Lung tissue (Lung 2)


title: JA2_Tissue_a_S87

description:
JA2_Tissue_a_S87
analysed_samples_tpm-GL-expr.txt


title: AD11-2


title: DRN-20709


title: CG_0h_2 miRNA-seq

value: liver

value: control group (CG) at 0h in acute hypoxic experiment


title: AD11-1


title: DRN-20705


title: iPSC-derived neurons, input_AD

library_source: genomic

data_processing:
Basecalls performed using Torrent_suite 5.10
ChIP-seq reads were aligned to the Hg19 genome using the Torrent_suite 5.10 with default settings
peaks were called using the easeq 1.111 peakcalling
The prediction of G4 sequences was calculated with Quadparser V2 using this code line: quadparser.py -f chr1.fa -r ([gG]{5,}\w{1,7}[gG]{5,}.  Predicted_G4 results files: HG1931733.txt and HG1931733_bedgraph.bed.
Genome_build: Hg19
Supplementary_files_format_and_content: wig files were generated using easeq 1.111 with a resolution of 100bp

molecule: genomic DNA

source_name: mature neurons derived from iPSCs

extract_protocol:
Lysates were clarified from sonicated nuclei, the chromatin was treated with pyridostatin as described in the material and methods and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to NEBNext® Fast DNA Library Prep Set for Ion Torrent™ Kit.

tag: disease state

value: iPSCs-derived neurons

tag: chip antibody


title: DRN-20707

tag: genotype


title: iPSC-derived neurons, input_Ctrl

value: control


title: CG_0h_1 miRNA-seq

tag: tissue


title: CG_4h_3 miRNA-seq


title: kpsM mt 3

city: Porto

first: Marina

middle: Patrícia

last: Santos

state: Porto

address: R. Alfredo Allen 208

department: Host Pathogen Interaction

country: Portugal

institute: i3S - Instituto de Investigação e Inovação em Saúde

description: Sample 6

data_processing:
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA)
library quality was assessed on the Agilent Bioanalyzer 2100 system. Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR).
genome build: GCF_000009725.1
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample
Supplementary_files_format_and_content: DEA between the wild type and the mutant

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis

growth_protocol: Cells were  grown in BG11 at 30 °C under a 12 h light (50 μE m−2 s−1)/12 h dark regimen, with orbital  shaking at 150 r.p.m.

extract_protocol:
For RNA extraction, the TRIzol Reagent (Ambion) was used in combination with the  PurelinkTM RNA Mini Kit (Ambion). Briefly, cells were disrupted in TRIzol containing 0.2   g of 0.2 mm-diameter glass beads (acid washed, Sigma) using a FastPrepH-24 (MP  Biomedicals) and the following extraction steps were performed according to the  manufacturer’s instructions. DNase treatment was performed according to the On-column  PureLink® DNase Treatment Protocol (Life Technologies/Invitrogen). RNA was quantified  on a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Inc.) and the quality  and integrity was checked using the ExperionTM RNA StdSens Analysis Kit (Bio-Rad).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: sp. PCC 6803

tag: optical density

value: kpsM mutant


title: kpsM mt 2

description: Sample 5


title: DRN-20695

description:
Methoxy-negative microglia from APP-SAA homozygous animal
dst168_processed.xlsx

value: negative

tag: age

value: months

value: Hom


title: DRN-20704

value: Microglia

value: male


title: DRN-20701


title: kpsM mt 1

description: Sample 4


title: iPSC-derived neurons, 1H6_Ctrl

value: 1H6 antibody (a donation from the European Research Institute for the Biology of Ageing)


title: DRN-20699

value: female


title: iPSC-derived neurons, 1H6_AD1

value: AD


title: CG_0h_3 miRNA-seq

tag: developmental stage


title: DRN-20711

value: WT


title: Experiment 1 – in vitro and transplanted hESC-myogenic progenitors

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

data_processing:
To analyze sequencing data, reads were mapped and counted using zUMIs 2.2.3 with default settings and barcodes provided as a list. zUMIs utilizes STAR (2.5.4b) to map reads to an input reference genome and feature Counts through Rsubread (1.28.1) to tabulate counts and UMI tables. We used GRCh38 from Ensembl concatenated with ERCC spike-in references for the reference genome and gene annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: For each study, we provide a counts table and well as a metadata phenotype table.

source_name: Myogenic progenitor cells

growth_protocol: hESCs (H9, WiCell) and hiPSCs were cultured using standard protocols. The hESC lines and hiPSC lines were cultured with mouse embryonic fibroblasts (MEFs) (GlobalStem, or AppliedStemCell) pre-plated at 12,000–15,000 cells/ cm2. hPSC culture medium contained DMEM/F12, 20% knockout serum replacement, 1 mM L-glutamine, 100 mM MEM non-essential amino acids, and 0.1 mM b-mercaptoethanol. 10 ng/mL of FGF-2 was added after sterile filtration, and cells were fed daily, and passaged weekly, using 6 U/mL dispase or mechanically.

extract_protocol: Pax7-GFP+ cells were sorted by Fluorescence-Activated Cell Sorting as single cells in 96-well or 384-well capture plates using MoFlo Legacy sorter. Capture plate wells contained 5 ul of capture solution (1:500 Phusion High-Fidelity Reaction Buffer, New England Biolabs; 1:250 RnaseOUT Ribonuclease Inhibitor, Invitrogen). Single cell libraries were then prepared using the previously described SCRB-seq protocol . Briefly, cells were subjected to proteinase K treatment followed by RNA desiccation to reduce the reaction volume. RNA was subsequently reverse transcribed using a custom template-switching primer as well as a barcoded adapter primer. The customized SCRB-seq barcode primers contain a unique 6 base pair cell-specific barcode as well as a 10 base pair unique molecular identifier (UMI). Transcribed products were pooled and concentrated, with unincorporated barcode primers subsequently digested using Exonuclease I treatment. cDNA was PCR-amplified using Terra PCR Direct Polymerase (Takara Bio). Final libraries were prepared using 1ng of cDNA per library with the Nextera XT kit (Ilumina) using a custom P5 primer as previously described. Pooled libraries were sequenced on two high-output lanes of the Illumina NextSeq500 with a 16 base pair barcode read, 8 base pair i7 index read, and a 66 base pair cDNA read design.

treatment_protocol: For myogenic linage derivation, hPSCs were plated as single cells on Geltrex (Gibco) treated dishes, at a density of 1.5 x 105 cells per well in a 24-well plate, in the presence of MEF-conditioned N2 media containing 10 ng/ml of FGF-2 (PeproTech) and 10 μM of Y-27632 (Cayman). The cells were induced to differentiate into myoblasts by adding CHIR99021 (3 μM, STEMCELL technologies) in N2 medium for 4 days and by DAPT (10 μM, PeproTech) for the following 8 days. Cells continued to differentiate and mature in N2 medium for the next 13 days. PAX7::GFP+ cells were isolated by FACs (FACS core at Johns Hopkins School of Public health) with GFP signal.     For transplantation: Left TA of mice were irradiated (18g) 72 hours prior to 50 µl 1.2% BaCl2 injury. 1 million PAX7::GFP MPCs were resuspended in 50 µl culture medium supplemented with rock inhibitor and injected into TA for NSG mice and TA, Gastrocnemius and Quadricep (1 million cells each) for NSG-mdx4CV.

value: hESC-myogenic progenitors


title: JA1_Tissue_a_S85

description:
JA1_Tissue_a_S85
analysed_samples_tpm-GL-expr.txt

value: Lung tissue (Lung 1)


title: Experiment 2 – Time series of transplanted hESC-myogenic progenitors


title: DRN-20696

value: cortex, hippocampus


title: wt 3

description: Sample 3

value: wild type


title: wt 2

description: Sample 2


title: DRN-20694


title: Cn_XS_10d_2A

status: Public on Jan 19 2021

city: Wenchang City

first: Yaodong

last: Yang

address: No. 496 Wenqing Av.

institute: Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAAVRAAPEI-90

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,After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences.
use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: CN-sc1
Supplementary_files_format_and_content: RPKM values for each Sample

organism: Cocos nucifera

source_name: Aromatic coconut_10 days

growth_protocol: The coconut seedling were used the experiments, the seedling is about four to five month old and 50 cm in height in a container located in the greenhouse.

extract_protocol:
RNA was isolated by modified CTAB methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A Salt stress experiment was conducted on coconut palms seedlings, weekly irrigated on Murashige and Skoog (MS) culture medium and then enriched with 200 mM NaCl  (time 0). After four hours the osmotic stress reached the leaves but not yet the cation stress; after six days the osmotic stress was still present in the leaves and the ionic stress could be felt; at seven days, a second irrigation of MS with 200 mM was performed; after ten days the osmotic and cation stresses should be present in the leaves (after two irrigation there was a NaCl accumulation).Varieties used are Hainan Tall (DB) and Aromatic Coconut (XS).

tag: cultivar

value: Aromatic Coconut (XS)

tag: time

value: 10 days

value: leaves


title: Atg5 KO_1

type: RNA

city: Kanazawa

first: Atsushi

last: Hirao

state: Ishikawa

address: Kakuma-machi

department: Cancer Research Institute

institute: Kanazawa University

description: Gene expression in Atg5KO LSK at around P7

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacturer's protocol. The slides were washed using Gene Expression Wash Buffer (Agilent Technologies).

scan_protocol: Images were scanned using Agilent Technologies Microarray Scanner (Scan Resolution; 3μm, TIFF file dynamic range; 20bit).

data_processing: The scanned images of the microarray were digitalized using Agilent Feature Extraction 12.0.3.1. The raw digitalized signal values were imported into GeneSpring GX software (Agilent Technologies) and normalized to shift to the 75th percentile.

source_name: Mouse bone marrow

label_protocol: The RNA samples were labeled using Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: LSK cells were sorted directly into TRIzol Reagent (Invitrogen) and total RNA was isolated according to the manufacturer’s protocol. RNA quality was confirmed using Nanodrop (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Bone marrow

value: Atg5 Knock out (Atg5f/f;VaviCre+)

value: HSCs/progenitor cells

tag: cell markers

value: LSK (Lineage marker-/Sca1+/cKit+)

tag: background strain


title: Atg5 KO_3


title: Cn_XS_10d_1A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAANRAAPEI-47


title: Atg5 KO_2


title: M2_24hrs_snATACseq

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences III

institute: UC Irvine

data_processing:
RNA-seq: Raw data was converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
RNA-seq: Reads were mapped to hg38 by STAR (version 2.5.1b) using defaults except with a maximum of 10 mismatches per pair, a ratio of mismatches to read length of 0.07, and a maximum of 10 multiple alignments.
RNA-seq: Quantitation was performed using RSEM (version 1.2.25) by defaults with gene annotations from GENCODE v29, and results were output in transcripts per million (TPM).
RNA-seq: Genes were TMM normalized using edgeR (version 3.28.1) and log2-transformed.
ATAC-seq:  Raw data was converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
ATAC-seq:  Reads were mapped to hg38 by Bowtie2 (version 2.2.7); mismatches were not allowed. Reads mapped to mitochondrial chromossome were discarded.
ATAC-seq: PCR duplicates were removed using Picard (version 2.18.4).
ATAC-seq: Peaks were called using HOMER (version 4.7).
ATAC-seq: Biologically reproducible regions across replicates were identified by irreproducible discovery rate analysis (IDR), then ENCODE ÒblacklistÓ regions were removed in order to generate the final set of open regions.
ATAC-seq: Peaks were annotated using HOMER (version 4.7). Counts were TMM normalized using edgeR (version 3.28.1).
scRNA-seq: Raw data was converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
scRNA-seq: Reads were demultiplexed using ddSeeker.
scRNA-seq: Reads were mapped to hg38 by STAR  (version 2.5.1b).
scRNA-seq: Quantification was performed using RSEM (version 1.2.25)  by defaults with gene annotations from GENCODE v29 and spliced and unspliced reads were calculated using velocyto (version 0.17.16).
snATAC-seq: Raw data was converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
snATAC-seq: Raw sequencing data were primarily processed using the Bio-Rad ATAC-seq Analysis Toolkit that performed fastq QC, debarcoding of fastq files, alignment to hg38 using BWA with blacklist regions removed, and alignment QC using Picard Tools.
snATAC-seq:  Bio-Rad Toolkit mapped reads for UMI-passing cells.
snATAC-seq: Peaks were called using MACS2 and these peaks were used in a custom python script to generate peaks-by-cells counts matrices for each sample.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq: RSEM outputs are tab-delimited text files with abundance measures in counts and TPM; Supplementary file is a comma-separated file that contains compiled expression values in TPM; scRNA-seq: comma-separated files contain compiled (per cell) abundance measures in counts; scATAC-seq: comma-separated files contain compiled (per cell) peaks annotated in counts.

source_name: Macrophage

growth_protocol: HL-60 cells (ATCC) were grown in Modified Dulbecco's Medium in a final concentration of 20% FBS with penicillin antibiotics (1%). Cells were routinely cultured at a density of 1,000,000 cells/ml.

extract_protocol:
snATAC-seq protocol; SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) for the ddSEQ system (20014279, Illumina).
Approximately 60,000 HL-60, macrophages and activated macrophages nuclei were collected for snATAC-seq. Briefly, cellular viability was assessed and cells were subsequently washed with PBS and nuclei was extracted prior to library preparation. snATAC-seq protocol was performed as previously described (Lareau et al., 2019; Corces, et al., 2017)
Cells were lifted using trypsin. Total RNA was extracted by using the RNeasy kit (QIAGEN).

treatment_protocol:
Differentiation of HL-60 cells into M0 macrophages (Murao et al., 1983). Aditionally, M0 cells were polarized into M1 and M2 macrophages (Huang et al., 2018) as previously described. Lastly, M2 cells were repolarized towards M1.
Differentiation of HL-60 cells into M0 macrophages was performed as described (Murao et al., 1983). Aditionally, M0 cells were polarized into M1 and M2 macrophages (Huang et al., 2018) as previously described. Lastly, M2 cells were repolarized towards M1.

tag: induction

tag: differentiation time


title: Mac_0hrs_snATACseq

value: PMA


title: M2M1_repolarized_scRNAseq

extract_protocol:
scRNA-seq protocol; SureCell WTA 3_ Library Prep Kit for the ddSEQ System (20014279, Illumina).
Approximately 15,000 HL-60, macrophages and activated macrophages were collected for scRNA-seq. Briefly, cellular viability was assessed and cells were subsequently washed with PBS prior to library preparation. scRNA-seq protocol was performed as previously described Illumina 2016).
Cells were lifted using trypsin. Total RNA was extracted by using the RNeasy kit (QIAGEN).

value: LPS + IFN-Gamma


title: M2M1_repolarized_snATACseq


title: M2_24hrs_sorted_scRNAseq


title: M2_24hrs_scRNAseq


title: Atg5 WT_2

description: Gene expression in WT LSK at around P7

value: Wild type (Atg5w/w;VaviCre+)


title: Atg5 WT_3

description: Gene expression in WT LSK at around P7


title: Atg5 WT_1

description: Gene expression in WT LSK at around P7


title: Cn_XS_6d_2A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAATRAAPEI-88

source_name: Aromatic coconut_6 days

value: 6 days


title: wt 1

description: Sample 1

value: sp. PCC 6803


title: M1_24hrs_snATACseq


title: Cn_XS_6d_3A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAALRAAPEI-45


title: Cn_XS_6d_1A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAAKRAAPEI-44


title: M2_12hrs_scRNAseq


title: M2_3hrs_scRNAseq


title: M1_12hrs_scRNAseq


title: Cn_XS_0_3A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAAERAAPEI-35

source_name: Aromatic coconut_0h


title: Cn_XS_4h_2A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAARRAAPEI-84

source_name: Aromatic coconut_4 hours

value: 4 hours


title: M2_6hrs_scRNAseq


title: M1_6hrs_scRNAseq


title: Cn_XS_4h_1A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAAQRAAPEI-75


title: Cn_XS_4h_3A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAAHRAAPEI-39


title: M1_24hrs_scRNAseq


title: Cn_XS_0_2A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAADRAAPEI-34


title: Cn_BD_10d_1A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAAURAAPEI-89

source_name: Hainan Tall_10 days

value: Hainan Tall (DB)


title: Cn_BD_10d_2A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAAMRAAPEI-46


title: HL60_scRNAseq


title: Cn_BD_4h_3A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAAPRAAPEI-56

source_name: Hainan Tall_4 hours


title: M2_ID2_KD_Rep1_bATACseq

extract_protocol:
Omni ATAC protocol(Corces et al., 2017) as previously described.
Approximately 50,000 HL-60, macrophages and activated macrophages were collected for bulk ATAC-seq. Briefly, cellular viability was assessed and cells were subsequently washed with PBS prior to library preparation. Bulk ATAC-seq protocol was performed as previously described (Corces et al., 2017) with an added size selection step to enrich for DNA fragments ranging from 150 to 500bp.
Cells were lifted using trypsin. Total RNA was extracted by using the RNeasy kit (QIAGEN).


title: M1_3hrs_scRNAseq


title: Cn_BD_6d_3A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAASRAAPEI-87

source_name: Hainan Tall_6 days


title: M2_ID2_KD_Rep2_bATACseq

extract_protocol:
Omni ATAC protocol(Corces et al., 2017) as previously described.
Approximately 15,000 HL-60, macrophages and activated macrophages were collected for scRNA-seq. Briefly, cellular viability was assessed and cells were subsequently washed with PBS prior to library preparation. scRNA-seq protocol was performed as previously described Illumina 2016).
Cells were lifted using trypsin. Total RNA was extracted by using the RNeasy kit (QIAGEN).


title: Cn_BD_4h_1A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAAFRAAPEI-36


title: M2_IRF7_KD_Rep2_bATACseq


title: M2_IRF7_KD_Rep1_bATACseq


title: Mac_0hrs_scRNAseq


title: Cn_XS_0_1A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAACRAAPEI-33


title: Cn_BD_0_2A

description: 150712_I649_FCC7AWTACXX_L1_WHCOCrqgRAAORAAPEI-53

source_name: Hainan Tall_0h


title: M2_IRF9_KD_Rep2_bATACseq


title: Cn_BD_6d_2A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAAJRAAPEI-43


title: M2_Pos_Ctrl_KD_Rep2_bATACseq

description: M2_Pos_Ctrl_KD_bATACseq_IDRoutput.bed.gz


title: Cn_BD_6d_1A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAAIRAAPEI-41


title: M2_IRF9_KD_Rep1_bATACseq


title: Cn_BD_0_1A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAAARBAPEI-30


title: M2_Neg_Ctrl_KD_Rep2_bATACseq

description: M2_Neg_Ctrl_KD_bATACseq_IDRoutput.bed.gz


title: M2_Neg_Ctrl_KD_Rep1_bATACseq


title: 22629_4h_rep3

city: Berkeley

first: Amy

middle: Moreda

last: Tresenrider

address: 628 Barker Hall

department: Molecular and Cell Biology

institute: UC Berkeley

data_processing:
the proccessing steps for each type of data is outlined in our methods section
salmon quant.sf
DESeq2_normalized_counts
Supplementary_files_format_and_content: sf, counts, bw

organism: Saccharomyces cerevisiae

source_name: SPO 4h

growth_protocol: Yeast cells were prepared for meiosis as described in our methods section

extract_protocol: Cells were collected by filtration and then flash frozen in liquid nitrogen. RNA was extracted by AcidPhenol:Chloroform:Isoamyl alchohol isolation. PolyA selection was performed with 100 ug of RNA and oligo-dT DynaBeads.

treatment_protocol: To induce entry into meiosis, after 2 hours in SPO, cells were treated with 50 𝜇M CuSO4.

tag: ploidy

value: diploid


title: 22629_4h_rep1


title: Cn_BD_4h_2A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAAGRAAPEI-37


title: M2_IRF1_KD_Rep2_bATACseq


title: 22629_4h_rep2


title: M2_IRF1_KD_Rep1_bATACseq


title: M2_Pos_Ctrl_KD_Rep1_bATACseq


title: Cn_BD_0_3A

description: 150717_I806_FCC7AVTACXX_L1_WHCOCrqgRAABRBAPEI-31


title: M2_ID2_KD_Rep2_bRNAseq

extract_protocol:
Smart-seq2 protocol (Picelli et al., 2013); Nextera DNA Flex Library Prep Kit (20018704, Illumina)
Approximately ~1 million HL-60, macrophages and activated macrophages were collected for bulk RNA-seq. Briefly, cellular viability was assessed and cells were subsequently washed with PBS prior to library preparation. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al., 2008).
Cells were lifted using trypsin. Total RNA was extracted by using the RNeasy kit (QIAGEN).


title: M2_IRF9_KD_Rep2_bRNAseq


title: M2_ID2_KD_Rep1_bRNAseq


title: 22629_3h_rep3

source_name: SPO 3h


title: 22629_3h_rep1


title: 22629_3h_rep2


title: M2_IRF9_KD_Rep1_bRNAseq


title: 22629_2h_rep3

source_name: SPO 2h


title: M2_IRF7_KD_Rep2_bRNAseq


title: 22629_2h_rep1


title: 22629_2h_rep2


title: M2_IRF1_KD_Rep2_bRNAseq


title: M2_Pos_Ctrl_KD_Rep2_bRNAseq


title: 22629_0h_rep1

source_name: SPO 0h


title: M2_IRF1_KD_Rep1_bRNAseq


title: 20649_4h_rep3


title: M2_Neg_Ctrl_KD_Rep2_bRNAseq


title: 22629_0h_rep3


title: M2_Neg_Ctrl_KD_Rep1_bRNAseq


title: 22629_0h_rep2


title: 20649_4h_rep2


title: 20649_4h_rep1


title: 20649_3h_rep3


title: M2_24hrs_Rep1_bATACseq


title: M2_24hrs_Rep2_bATACseq


title: M2_12hrs_Rep2_bATACseq


title: 20649_3h_rep1


title: 20649_3h_rep2


title: M2_12hrs_Rep1_bATACseq


title: M2_IRF7_KD_Rep1_bRNAseq


title: M2_6hrs_Rep1_bATACseq


title: M2_6hrs_Rep2_bATACseq


title: 20649_2h_rep3


title: 20649_2h_rep1


title: 20649_0h_rep3


title: M2_3hrs_Rep1_bATACseq


title: 20649_0h_rep2


title: M2_Pos_Ctrl_KD_Rep1_bRNAseq


title: 20649_0h_rep1


title: M1_24hrs_Rep1_bATACseq


title: M1_24hrs_Rep2_bATACseq


title: M1_12hrs_Rep2_bATACseq


title: M1_12hrs_Rep1_bATACseq


title: M1_6hrs_Rep2_bATACseq


title: M1_6hrs_Rep1_bATACseq


title: ZT-WT1-GC1-A1-R1-T1

city: Worcester

first: Anne-Laure

last: Valton

state: MA

address: 368 Plantation St

institute: University of Massachusetts Medical School

description: WT

data_processing:
Fastq files were mapped to the hg19 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019).
WT replicates and STAG2 knockouts were combined into two multires.cool file
Genome_build: hg19 human genome
Supplementary_files_format_and_content: Multiresolution cooler files (multires.cool) containing pairwise interactions

source_name: AML U937 cell line WT

growth_protocol: Cells were grown in RPMI (Invitrogen) and supplemented with 10% fetal calf serum (Sigma) and 100u/mL penicillin and 100ug/mL streptomycin (Invitrogen)

extract_protocol:
10M formaldehyde cross-linked cells were lysed and digested overnight at 37°C with 400 units of DpnII (NEB). Next, the DNA ends were marked with biotin-14-dATP (Thermo Fisher Scientific #19524016) for 4 hours at 23°C and ligated for 4 hours at 16°C. To remove proteins and reverse crosslink, DNA was treated with proteinase K overnight at 65°C. DNA was then purified using phenol:chloroform and biotin was removed from unligated ends. Ligation products were fragmented by sonication to an average size of 200bp and size selected with Ampure XP beads (Beckman Coulter, # A63880) to fragments ranging from 100 to 350 bp.
End repair was performed on the DNA fragments to obtain blunt ends and biotinylated ligation products were purified using streptavidin beads (Thermo Fisher Scientific #65001). dA-tailing was then performed and the TrueSeq DNA LT kits Set A (Illumina, #15041757) was used for adapter ligation and PCR amplification. PCR primers were removed using Ampure XP beads.
The Hi-C libraries were sequenced using 50 bp paired end reads on Illumina HiSeq4000.

tag: enzyme

value: DpnII

tag: cell line


title: ZT-WT2-GC3-E1-R1-T1

description: WT


title: ZT-KO1-STAG2-A2-F11-R1-T1

description: STAG2 KO

source_name: AML U937 cell line STAG2 KO


title: 20649_2h_rep2


title: M1_3hrs_Rep1_bATACseq

tag: cell type


title: ZT-KO1-STAG2-A2-F11-R2-T1

description: STAG2 KO


title: ZT-KO2-STAG2-A2-H4-R2-T1

description: STAG2 KO


title: ZT-WT2-GC3-E1-R2-T1

description: WT


title: M2_3hrs_Rep2_bATACseq


title: Mac_0hrs_Rep1_bATACseq


title: Mac_0hrs_Rep2_bATACseq


title: ZT-WT1-GC1-A1-R2-T1

description: WT


title: HL60_Rep2_bATACseq


title: M2_24hrs_Rep1_bRNAseq


title: GBM11_IDHMT_snRNA

first: Ramya

last: Raviram

address: 9500 Gilman Drive

institute: University of California San Diego

description: nuclear RNA

data_processing:
Reads from snRNA-seq were mapped to the hg38 genome using STAR. Clustering analysis was performed using Seurat V3 on cells that had greater than 200 reads and less than 5% mitochondrial reads.
Read from snATAC-seq were mapped to the hg38 genome using bowtie2. Snaptools was used to generate binary count matrices in 5kb genomic bins. Clustering analysis was performed using SnapATAC for cells with greater than 1000 reads and percentage of reads in promoters greater than 20%.
Genome_build: hg38
Supplementary_files_format_and_content: RDS

source_name: glioblastoma

extract_protocol:
Ground frozen tumor tissue was resuspended in nuclei buffer (2% BSA, 0.2% Triton-X,  cOmplete Protease Inhibitors (Roche), 1 mM DTT, 0.2 U/µl RNAsin (Promega) in PBS). After spind down, nuclei were resuspnded in sort buffer, filtered and sorted using a SH800 sorter (Sony).
Nuclei were loaded on a 10x Chromium controller and libraries were generated using the Chromium™ Single Cell 3’ v2 Library kit (10x Genomics) according to manufacturer descriptions and sequenced on a Hiseq4000 or NextSeq500 (Illumina)

value: glioblastoma

tag: protocol

value: snRNA

tag: idh mutation

value: IDH1 MT

tag: sample id


title: GBM12_IDHWT_snRNA

description: nuclear RNA

tag: tissue

value: IDH WT


title: Non_tumor_brain_snRNA

extract_protocol:
Ground frozen brain tissue was resuspended in nuclei buffer (2% BSA, 0.2% Triton-X,  cOmplete Protease Inhibitors (Roche), 1 mM DTT, 0.2 U/µl RNAsin (Promega) in PBS). After spind down, nuclei were resuspnded in sort buffer, filtered and sorted using a SH800 sorter (Sony).
Nuclei were loaded on a 10x Chromium controller and libraries were generated using the Chromium™ Single Cell 3’ v2 Library kit (10x Genomics) according to manufacturer descriptions and sequenced on a Hiseq4000 or NextSeq500 (Illumina)

value: brain

value: Non-tumor


title: HL60_Rep1_bATACseq


title: GBM1_IDHMT_snRNA

description: nuclear RNA


title: M2_24hrs_Rep2_bRNAseq


title: M2_12hrs_Rep2_bRNAseq


title: GBM9_IDHWT_snRNA

description: nuclear RNA


title: M2_12hrs_Rep1_bRNAseq


title: GBM4_IDHWT_snRNA

description: nuclear RNA


title: 76N

city: Guangzhou

first: Fang

last: Zheng

address: 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

description: lncRNA expression data

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer.

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

source_name: breast cancer cell line

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of cyanine-3-CTP.

growth_protocol: The breast cancer cell lines 76N and MBA-MD-231 were cultured under normoxia (20%) or hypoxia (0.6%) conditions.

extract_protocol: Hypoxic cell lines 76N and MBA-MD-231 and 4 pairs of ground breast cancer and adjacent normal tissues were stored in TRIZOL, then were extracted according to protocol.

treatment_protocol: Hypoxic cell lines 76N and MBA-MD-231 were harvested.

value: Breast cancer cell line

tag: condition

value: Normoxia


title: Non_tumor_brain_snATAC

extract_protocol:
Nuclei were isolated from ground frozen brain tissue and permeabilized using NPB (5% BSA, 0.2% IGEPAL-CA630, cOmplete Protease Inhibitors, 1 mM DTT in PBS).
Nuclei were tagmented with Tn5 in 96 wells to introduce a first barcode. After pooling, 20-25 nuclei were sorted into 768 wells and a second barcode was introduced by PCR. Libraries were purified and sequenced on a HiSeq2500, HiSeq4000 or NextSeq500 (Illumina).

value: snATAC


title: M2_6hrs_Rep1_bRNAseq


title: GBM11_IDHMT_snATAC

extract_protocol:
Nuclei were isolated from ground frozen tumor tissue and permeabilized using NPB (5% BSA, 0.2% IGEPAL-CA630, cOmplete Protease Inhibitors, 1 mM DTT in PBS).
Nuclei were tagmented with Tn5 in 96 wells to introduce a first barcode. After pooling, 20-25 nuclei were sorted into 768 wells and a second barcode was introduced by PCR. Libraries were purified and sequenced on a HiSeq2500, HiSeq4000 or NextSeq500 (Illumina).


title: 76H

description: lncRNA expression data

value: Hypoxia


title: M2_3hrs_Rep2_bRNAseq


title: GBM4_IDHWT_snATAC


title: GBM12_IDHWT_snATAC


title: M1_24hrs_Rep2_bRNAseq

value: LPS + IFN-Gamma


title: GBM9_IDHWT_snATAC


title: M1_12hrs_Rep1_bRNAseq


title: M1_3hrs_Rep2_bATACseq


title: M1_12hrs_Rep2_bRNAseq


title: M2_3hrs_Rep1_bRNAseq


title: M1_6hrs_Rep2_bRNAseq


title: M1_6hrs_Rep1_bRNAseq


title: COMP_KD_2_l1

city: Shenzhen

first: Ruilin

last: Tian

address: 1088 Xueyuan Avenue

institute: SUSTech

description:
Quant-seq
COMP_2

data_processing:
Raw sequencing reads from QuantSeq were trimmed using Trimmomatic (v0.39)
Salmon v1.3.0 was used to obtain transcript abundance counts
Gene-level count estimates were obtained using tximport  (v1.18.0) with default settings
differential gene-expression analyses were performed using the glmQLFTest method implemented in the edgeR package(v3.28.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files are in "CSV(Comma-separated values)" format. Each row is a gene and each column is a sample. Values are normalzied counts

extract_protocol:
RNA was extracted from cells using the Quick-RNA Miniprep Kit (Zymo; Cat. No. R1054)
Libraries were generated according to the Quantseq protocol

tag: genotype/variation

value: COMP knockdown


title: Mac_0hrs_Rep2_bRNAseq

value: PMA


title: ACE2_KD_1_l1

description:
Quant-seq
ACE2_1

value: ACE2 knockdownn


title: M1_3hrs_Rep2_bRNAseq


title: COMP_KD_1_l1

description:
Quant-seq
COMP_1


title: M2_6hrs_Rep2_bRNAseq


title: GBM1_IDHMT_snATAC


title: Mac_0hrs_Rep1_bRNAseq


title: ABBV_2_l1

description:
Quant-seq
ABBV744_72_hour_2

value: 10uM ABBV-744

value: wildtype


title: ABBV_1_l1

description:
Quant-seq
ABBV744_72_hour_1


title: JQ1_2_l1

description:
Quant-seq
JQ1_72_hour_2

value: 10uM JQ1


title: HL60_Rep2_bRNAseq


title: HL60_Rep1_bRNAseq


title: M1_24hrs_Rep1_bRNAseq


title: JQ1_1_l1

description:
Quant-seq
JQ1_72_hour_1


title: untreated_2_l1

description:
Quant-seq
nosgRNA_2

value: untreated


title: untreated_1_l1

description:
Quant-seq
nosgRNA_1


title: ACE2_KD_2_l1

description:
Quant-seq
ACE2_2


title: Breast biopsy UVABC5 10-cell sample 28

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

description:
BCC9.Sample28
2020_02_06_breastcancer_allcompiled.csv

data_processing:
Adapters were trimmed using fastq-mcf with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to the human (GRCh38.p12)  transcriptome using RSEM. Reference ERCC sequences were also provided for the alignment.
RSEM options  --bowtie2 --single-cell-prior --paired-end (Bowtie2 transcriptome aligner, single-cell prior to account for dropouts)
Comma separated file includes read counts from RSEM
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: 2020_02_06_breastcancer_allcompiled.csv (read counts)

source_name: Breast tumor

extract_protocol:
All samples were cryoembedded and sectioned on to glass slides (8µm sections). Cell samples were isolated with laser capture microdissection and poly(A) RNA extracted, reverse transcribed and poly(A) PCR amplified prior to library preparation
Amplified cDNA samples were diluted to 0.2 µg/ml for tagmentation with the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s earlier recommendation to purify libraries with 180% (vol/vol) SPRI beads

tag: tumor

tag: sample type

value: 10-cell sample

tag: stage/grade

value: Stage 1 Grade 1


title: Breast biopsy UVABC5 10-cell sample 27

description:
BCC9.Sample27
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 26

description:
BCC9.Sample26
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 25

description:
BCC9.Sample25
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 24

description:
BCC9.Sample24
2020_02_06_breastcancer_allcompiled.csv


title: BRD2

description: CUT & RUN

data_processing:
Library strategy: CUT & RUN
Paired-end reads were mapped to the human genome GRCh38 using Bowtie2 (v2.3.4.1) with options: --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 1000.
Sparse Enrichment Analysis for CUT&RUN (SEACR, https://seacr.fredhutch.org/) was used for peak calling
Genome_build: GRCh38
Supplementary_files_format_and_content: Peaks calling data files are in bed format. Raw singal files are in bedgraph format

extract_protocol:
CUT&RUN was performed with 1 million Calu-3 cells. Cells were removed from the plate by treatment with Versene (Life Technologies 15040066) for 20 minutes and resuspended in fresh media. They were spun down and washed twice with DPBS before proceeding with the CUTANA CUT&RUN kit (Epicypher 14-0050)
The experiment was performed with the included IgG and H3K4Me control antibodies and the BRD2 antibody (abcam 197865) as well as E.coli spike-in DNA according to the kit protocol.

tag: antibody


title: Breast biopsy UVABC5 10-cell sample 23

description:
BCC9.Sample23
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 21

description:
BCC9.Sample21
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 22

description:
BCC9.Sample22
2020_02_06_breastcancer_allcompiled.csv


title: B-97 (miRNA)

city: Amsterdam

first: Giulia

last: Mantini

address: De Boelelaan

country: Netherlands

institute: Amsterdam UMC

description:
miRNA.canonical.rawcounts.txt
isomiRs.rawcounts.txt

data_processing:
Intron-spanning reads were detected using the ThromboSeq pipeline while gene counts were detected using STAR and HTSeq counts
filtering steps are described in the material and methods section
Genome_build: Homo_sapiens.GRCh38.77.gtf
Supplementary_files_format_and_content: txt files were rows are intron-reads / genes and columns are the samples.
intron.spanning.rawcounts.txt:  raw counts on intron spanning reads
mRNA.raw_counts.txt:  raw counts on mRNA
miRNA.canonical.rawcounts.txt:  raw counts on canonical miRNAs
isomiRs.rawcounts.txt:  raw counts on isomiRs

source_name: Blood Platelets

extract_protocol:
Total RNA was extracted from platelets using the MiRVAna kit (Ambion) while the protein fraction was stored for proteomics analysis after removal of RNA
thromboSeq protocol described previously (Best et al. Nature Protocols 2019)

tag: disease type

value: Benign

tag: gender

value: F

tag: age at biopsy

value: platelets


title: Breast biopsy UVABC5 10-cell sample 20

description:
BCC9.Sample20
2020_02_06_breastcancer_allcompiled.csv


title: B-71 (miRNA)


title: B-82 (miRNA)


title: B-98 (miRNA)


title: B-40 (miRNA)

value: M


title: B-10 (miRNA)


title: Breast biopsy UVABC5 10-cell sample 18

description:
BCC9.Sample18
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 16

description:
BCC9.Sample16
2020_02_06_breastcancer_allcompiled.csv


title: B-35 (miRNA)


title: Breast biopsy UVABC5 10-cell sample 15

description:
BCC9.Sample15
2020_02_06_breastcancer_allcompiled.csv


title: H3K4me3

description: CUT & RUN


title: B-2 (miRNA)


title: IgG

description: CUT & RUN

value: IgG


title: Breast biopsy UVABC5 10-cell sample 14

description:
BCC9.Sample14
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 13

description:
BCC9.Sample13
2020_02_06_breastcancer_allcompiled.csv


title: B-118 (miRNA)


title: B-127 (miRNA)


title: PDAC-26 (miRNA)

value: PDAC

tag: Stage

value: IIB


title: Breast biopsy UVABC5 10-cell sample 12

description:
BCC9.Sample12
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 11

description:
BCC9.Sample11
2020_02_06_breastcancer_allcompiled.csv


title: PDAC-22 (miRNA)


title: Breast biopsy UVABC5 10-cell sample 19

description:
BCC9.Sample19
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 17

description:
BCC9.Sample17
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 9

description:
BCC9.Sample09
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 8

description:
BCC9.Sample08
2020_02_06_breastcancer_allcompiled.csv


title: PDAC-91 (miRNA)

value: IIA


title: Breast biopsy UVABC5 10-cell sample 7

description:
BCC9.Sample07
2020_02_06_breastcancer_allcompiled.csv


title: PDAC-17 (miRNA)

value: IA


title: Breast biopsy UVABC5 10-cell sample 6

description:
BCC9.Sample06
2020_02_06_breastcancer_allcompiled.csv


title: PDAC-18 (miRNA)


title: PDAC-11 (miRNA)


title: Breast biopsy UVABC5 10-cell sample 10

description:
BCC9.Sample10
2020_02_06_breastcancer_allcompiled.csv


title: PDAC-95 (miRNA)


title: Breast biopsy UVABC5 10-cell sample 5

description:
BCC9.Sample05
2020_02_06_breastcancer_allcompiled.csv


title: B-1 (miRNA)

description:
miRNA.canonical.rawcounts.txt
isomiRs.rawcounts.txt


title: PDAC-4 (miRNA)


title: PDAC-94 (miRNA)


title: Breast biopsy UVABC5 10-cell sample 4

description:
BCC9.Sample04
2020_02_06_breastcancer_allcompiled.csv


title: PDAC-8 (miRNA)


title: Breast biopsy UVABC5 10-cell sample 3

description:
BCC9.Sample03
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 1

description:
BCC9.Sample01
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell sample 2

description:
BCC9.Sample02
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 20

description:
BCC9.Control20
2020_02_06_breastcancer_allcompiled.csv

value: Pool-and-split control


title: Cyt49_PP2.ATAC-Seq.replicate.1.merged

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

data_processing:
For ATAC-seq: adaptors were trimmed from ATAC-Seq reads using the trim_galore package. Reads were mapped to human reference genome hg19 using bwa. Mapped reads were filtered by Samtools, skipping alignment for reads with MAPQ smaller than 30, removing duplicate and mitochondrial reads. Peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Fragments were normalized to 1e7 bases of library size using Homer
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated

source_name: Cyt49 Control

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012).

extract_protocol:
Genomic DNA was extracted using Dneasy Blood and Tissue Kit from Qiagen.
Cells were collected and lysed using spin lysis buffer mix. Next, transposition reaction was performed using reaction mix and then DNA was purified using Zymo DNA clean and concentrator. Lastly, DNA product was amplified by PCR and then gel purified for tapestation analysis.
Cells were collected and lysed using spin lysis buffer mix. Next, transposition reaction was performed using reaction mix and then DNA was purified using Zymo DNA clean and concentrator. Lastly, DNA product was amplified by PCR and then gel purified for tapestation analysis.

value: differentiated hESCs

tag: development stage

value: Late pancreatic progenitor cells


title: Cyt49_PP1.ATAC-Seq.replicate.1.merged

value: Early pancreatic progenitor cells


title: Cyt49_PP1.ATAC-Seq.replicate.2.merged


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 19

description:
BCC9.Control19
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_GT.ATAC-Seq.replicate.2.merged

value: Gut tube cells


title: Cyt49_ES.ATAC-Seq.replicate.2.merged

value: Embyonic stem cells


title: Cyt49_ES.ATAC-Seq.replicate.1.merged


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 16

description:
BCC9.Control16
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_DE.ATAC-Seq.replicate.2.merged

value: Definitive endoderm cells


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 12

description:
BCC9.Control12
2020_02_06_breastcancer_allcompiled.csv

value: Stage 1 Grade 1


title: Cyt49_DE.ATAC-Seq.replicate.1.merged


title: PDAC-9 (miRNA)


title: K562/G01_shTCF7_Imatinib

city: Chongqing

first: Hui

last: Zhang

state: Chongqing

address: Yixueyuan road 1#

department: School of Laboratory Medicine

institute: Chongqing Medical University

description:
Imatinib-resistant cell
processed data file: Gene.count.fpkm.txt

data_processing:
The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DEGseq R package (1.28.0). Pvalue <0.05 and |FoldChange|>1.5 were set as the threshold for significantly differential expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene.count.fpkm.txt: Tab-delimited text file includes count and FPKM values for each Sample.

source_name: leukocyte

growth_protocol: Seed out at ca. 1.0 x 10e6 cells/ml; split saturated culture 1:3 every 2-3 days; maintain at ca 0.4-2.0 x 10e6 cells/ml.

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: K562/G01 cells were infected with recombinant lentivirus of LV-Scramble and LV-TCF7-RNAi, and set as control group (Scramble) and experimental group (TCF7_KD). Subsequently, imatinib was used to treat or not treat the two groups cells at a concentration of 1 μM for 48 hours.

value: chronic myeloid leukemia cell

tag: cell line

tag: treatment

value: TCF7 knockdown + imatinib


title: K562/G01_shNC_Imatinib

tag: cell type

value: Scramble + imatinib


title: K562/G01_shNC

value: Scramble


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 10

description:
BCC9.Control10
2020_02_06_breastcancer_allcompiled.csv


title: K562/G01_shTCF7

value: TCF7 knockdown


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 9

description:
BCC9.Control09
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP2.ChIP-Seq.H3K4me3.replicate.2

description: Histone Modification

data_processing:
For RNA-seq: Sequence fragments were aligned to the hg19 genome build with STAR using the parameters: --runThreadN 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragment per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build using bwa. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragments were normalized to 1e7 bases of library size using Homer.
For ATAC-seq: adaptors were trimmed from ATAC-Seq reads using the trim_galore package. Reads were mapped to human reference genome hg19 using bwa. Mapped reads were filtered by Samtools, skipping alignment for reads with MAPQ smaller than 30, removing duplicate and mitochondrial reads. Peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Fragments were normalized to 1e7 bases of library size using Homer
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012). H1 cells were maintained and differentiated as previously described (Jin et al. 2019).

extract_protocol:
ChIP-seq was performed using the ChIP-IT High-Sensitivity kit (Active Motif) according to the manufacturer’s instructions. Briefly, for each cell stage and condition analyzed, 5-10 x 10e6 cells were harvested and fixed for 15 min in an 11.1% formaldehyde solution. Cells were lysed and homogenised using a Dounce homogeniser and the lysate was sonicated in a Bioruptor® Plus (Diagenode), on high for 3 x 5 min (30 sec on, 30 sec off). Between 10 and 30 µg of the resulting sheared chromatin was used for each immunoprecipitation.
Libraries were prepared using the KAPA DNA Library Preparation Kits for Illumina® Kit

tag: developmental stage

tag: chip antibody


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 7

description:
BCC9.Control07
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 6

description:
BCC9.Control06
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP1.ChIP-Seq.H3K4me3.replicate.2

description: Histone Modification


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 8

description:
BCC9.Control08
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 15

description:
BCC9.Control15
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 17

description:
BCC9.Control17
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 5

description:
BCC9.Control05
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_GT.ATAC-Seq.replicate.1.merged


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 14

description:
BCC9.Control14
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP1.ChIP-Seq.H3K27me3.replicate.2

description: Histone Modification


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 13

description:
BCC9.Control13
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 11

description:
BCC9.Control11
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP2.ChIP-Seq.H3K27me3.replicate.2

description: Histone Modification


title: Cyt49_ES.ChIP-Seq.H3K4me3.replicate.2

description: Histone Modification


title: Cyt49_GT.ChIP-Seq.H3K4me3.replicate.2

description: Histone Modification


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 4

description:
BCC9.Control04
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 3

description:
BCC9.Control03
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 1

description:
BCC9.Control01
2020_02_06_breastcancer_allcompiled.csv


title: BRD2_KD_2_l1

description:
Quant-seq
BRD2_KD_2

value: BRD2 knockdown


title: BRD2_KD_1_l1

description:
Quant-seq
BRD2_KD_1


title: Cyt49_DE.ChIP-Seq.H3K27me3.replicate.2

description: Histone Modification


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 2

description:
BCC9.Control02
2020_02_06_breastcancer_allcompiled.csv


title: HEK293 PDPK1 clone RNA-seq R3A rep2 [C6-R3A-2]

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description:
C6-R3A-2
processed data file: HEK293-PDK1-count.txt

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each Sample

source_name: HEK293 PDPK1 clone RNA-seq R3A

growth_protocol: All cells were grown in DMEM with 10% FBS and 10 U/ml Penicillin-Streptomycin. All cells were cultured at 37˚C and 5% CO2.

extract_protocol:
Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment. RNA was submitted to GENEWIZ or the Vanderbilt Technologies for Advanced Genomics Core Laboratory for rRNA reduction, library preparation, and deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: engineered genotype

value: PDPK1 R3A point mutant + R3A PDPK1 retroviral expression


title: M1_3hrs_Rep1_bRNAseq

source_name: Macrophage

tag: induction

value: LPS + IFN-Gamma

tag: differentiation time


title: Breast biopsy UVABC4 10-cell sample 24

description:
BCC6.Sample24
2020_02_06_breastcancer_allcompiled.csv

tag: tumor

value: 10-cell sample

value: Stage 1 Grade 2


title: Breast biopsy UVABC4 10-cell sample 28

description:
BCC6.Sample28
2020_02_06_breastcancer_allcompiled.csv

tag: sample type


title: HEK293 PDPK1 clone RNA-seq R3A rep1 [C6-R3A-1]

description:
C6-R3A-1
processed data file: HEK293-PDK1-count.txt


title: Cyt49_GT.ChIP-Seq.H3K27me3.replicate.2

city: La Jolla

description: Histone Modification

value: differentiated hESCs


title: Breast biopsy UVABC4 10-cell sample 27

description:
BCC6.Sample27
2020_02_06_breastcancer_allcompiled.csv

tag: stage/grade


title: Breast biopsy UVABC5 10-cell pool-and-split control replicate 18

description:
BCC9.Control18
2020_02_06_breastcancer_allcompiled.csv

value: Pool-and-split control


title: Breast biopsy UVABC4 10-cell sample 25

description:
BCC6.Sample25
2020_02_06_breastcancer_allcompiled.csv


title: HEK293 PDPK1 clone RNA-seq Vector rep1 [C6-vector-1]

description:
C6-vector-1
processed data file: HEK293-PDK1-count.txt

source_name: HEK293 PDPK1 clone RNA-seq Vector

value: PDPK1 R3A point mutant + empty vector retroviral expression


title: Cyt49_DE.ChIP-Seq.H3K4me3.replicate.2

description: Histone Modification


title: HEK293 PDPK1 clone RNA-seq WT rep1 [C6-WT-1]

description:
C6-WT-1
processed data file: HEK293-PDK1-count.txt

source_name: HEK293 PDPK1 clone RNA-seq WT

value: PDPK1 R3A point mutant + WT PDPK1 retroviral expression


title: Breast biopsy UVABC4 10-cell sample 26

description:
BCC6.Sample26
2020_02_06_breastcancer_allcompiled.csv


title: HEK293 PDPK1 clone RNA-seq Vector rep2 [C6-vector-2]

description:
C6-vector-2
processed data file: HEK293-PDK1-count.txt


title: U2OS PDPK1-FKBP(F36V) RNA-seq dTAG 24hr rep3 [dTAG-24hr-3]

description:
24hr-dTAG-3
processed data file: U2OS-PDK1-count.txt

source_name: U2OS PDPK1-FKBP(F36V) RNA-seq dTAG 24hr

value: endogenous C-terminal tag on PDPK1, FKBP(F36V)-2xHA

value: 500 nM dTAG47 for 24 hours


title: Cyt49_ES.ChIP-Seq.H3K27me3.replicate.2

description: Histone Modification

value: Embyonic stem cells


title: Breast biopsy UVABC4 10-cell sample 21

description:
BCC6.Sample21
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 23

description:
BCC6.Sample23
2020_02_06_breastcancer_allcompiled.csv


title: HEK293 PDPK1 clone RNA-seq WT rep2 [C6-WT-2]

description:
C6-WT-2
processed data file: HEK293-PDK1-count.txt


title: Breast biopsy UVABC4 10-cell sample 20

description:
BCC6.Sample20
2020_02_06_breastcancer_allcompiled.csv


title: U2OS PDPK1-FKBP(F36V) RNA-seq dTAG 24hr rep1 [dTAG-24hr-1]

description:
24hr-dTAG-1
processed data file: U2OS-PDK1-count.txt


title: Breast biopsy UVABC4 10-cell sample 16

description:
BCC6.Sample16
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 19

description:
BCC6.Sample19
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 17

description:
BCC6.Sample17
2020_02_06_breastcancer_allcompiled.csv


title: U2OS PDPK1-FKBP(F36V) RNA-seq DMSO rep1 [DMSO-1]

description:
DMSO-1
processed data file: U2OS-PDK1-count.txt

source_name: U2OS PDPK1-FKBP(F36V) RNA-seq DMSO

value: 0.01% DMSO for 24 hours


title: Breast biopsy UVABC4 10-cell sample 14

description:
BCC6.Sample14
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 11

description:
BCC6.Sample11
2020_02_06_breastcancer_allcompiled.csv


title: hip joint synovial tissues, T3

city: Shenyang

first: Lei

last: Guo

state: Liaoning

address: Nanjing North Street

institute: First Affiliated Hospital, China Medical University

description: circRNA

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)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplice junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: Expression_circRNA.xlsx

source_name: hip joint synovial tissues

growth_protocol: The experimental tissues were obtained from the patients, who received revision operations for aseptic loosening after total hip arthroplasty. The control specimens were obtained from the patients, who received primary total hip arthroplasty after femoral neck fracture.

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: tissue

value: synovial tissues of hip joint

tag: condition


title: Breast biopsy UVABC4 10-cell sample 18

description:
BCC6.Sample18
2020_02_06_breastcancer_allcompiled.csv


title: U2OS PDPK1-FKBP(F36V) RNA-seq dTAG 24hr rep2 [dTAG-24hr-2]

description:
24hr-dTAG-2
processed data file: U2OS-PDK1-count.txt


title: hip joint synovial tissues, N3

description: circRNA

value: femoral neck fracture during their primary total hip arthroplasty


title: Breast biopsy UVABC4 10-cell sample 9

description:
BCC6.Sample09
2020_02_06_breastcancer_allcompiled.csv


title: hip joint synovial tissues, T1

description: circRNA

value: aseptic loosening after total hip arthroplasty


title: U2OS PDPK1-FKBP(F36V) RNA-seq DMSO rep3 [DMSO-3]

description:
DMSO-3
processed data file: U2OS-PDK1-count.txt


title: hip joint synovial tissues, N2

description: circRNA


title: Breast biopsy UVABC4 10-cell sample 10

description:
BCC6.Sample10
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 12

description:
BCC6.Sample12
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 8

description:
BCC6.Sample08
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 7

description:
BCC6.Sample07
2020_02_06_breastcancer_allcompiled.csv


title: hip joint synovial tissues, N1

description: circRNA