title: JC221_TDLEC

city: Houston

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Demultiplexed FASTQ files from each flow cell lane were downloaded from BaseSpace and were merged. Quality control of each sample was assessed using fastQC (v0.10.1) and MultiQC (v0.9)
Mate pair reads were aligned to the mouse reference genome mm10 assembly using Salmon (v1.1.0)
Transcript level quantification was then analyzed using DESeq2 (v1.20.0)  and imported using tximport (v1.14.2)
DESeq2 was used for read count normalization in RStudio (v3.5.2)
Genome_build: mm10, GRCh38
Supplementary_files_format_and_content: sf abundance quantification file: Plain-text, tab-separated file with a single header line (which names all of the columns) that contains Name, Length, EffectiveLength, TPM and NumReads

source_name: TDLEC brain cells

growth_protocol:
All mouse CRISPR-IUE GBM gliomas were generated in the CD-1 IGS mouse background. In utero electroporations (IUEs).  See supplemental materials and methods for details. CRISPR-IUE Tumors were harvest3ed at postnatal day 65 and 80.
Unique subpopulations of cells from the brain were isolated by FACS. Briefly, tumor tissue from a dissected mouse brain was dissociation with papain (10 units/ml) (Sigma Aldrich, Cat. No. P3125) with DNase I (20 units/ml) (NEB, Cat. No. M0303S) at 37°C for twenty minutes with gentle agitation. DMEM+F12 media [Thermoscientific, Cat. No. 12634010) supplemented with 10% FBS (Thermoscientific, Cat. No. 26140079] was added for neutralization, and the suspension was centrifuged at 2000 RCF for five minutes at room temperature. The pellet was resuspended in FACS buffer (Leibowitz medium (Thermoscientific, Cat. No. 21083027), supplemented with 1 mg/ml BSA (Thermoscientific, Cat. No. B14), 10 mM HEPES pH 7.05, penicillin–streptomycin (Thermoscientific, Cat. No. 15140148) and the cells were incubated with primary antibodies for 45 minutes. Primary antibodies used included anti-mouse CD31 (0.2 ug/ml) (Biolegend-102423), anti-mouse podoplanin (0.2 ug/ml) (Biolegend-127417), anti-mouse Vegfr3/Flt4 (0.2 ug/ml) (R&D Systems, Cat. No. FAB743P). Cells were then washed with PBS and suspended in FACS buffer (described above). Primary antibodies were incubated concurrently.   Acquisition and analysis were performed on a FACSAria II (BD Biosciences) using FACSDIVA software (BD Biosciences). Laser lines utilized were a Violet (407 nm) laser (450/50 nm emission filter), Blue (488 nm) laser (530/30 nm emission filter), Yellow-Green (561 nm) laser (585/15 nm emission filter), and Red (638 nm) laser (760/60nm emission filter), in addition to Forward Scatter (FSC), Forward Scatter PMT, and Side Scatter (SSC). A 100-μm/20-p.s.i. nozzle setting was utilized to accommodate for average approximate tumor cell size and viability. The gating tree was set as follows: FSC/SSC (which represents the proportion of cells in the light scatter based on size and intracellular granularity) to B: FSC/pulse width (excludes events that could represent more than 1 cell and was used to exclude potential doublets) to C: FSC/GFP positive (to identify tumor-derived cells) D: GFP/CD31-BV421 (identifies selective subsets of tumor-derived endothelium versus tumor microenvironment) or E: biexponential VEGFR3-PE/PDPN-APC-Cy7 (selects for lymphatic-like, aka TDLEC, and blood-like, aka TDBEC, subsets of endothelium). A total of 50,000 cells were analyzed; however, further cellular events were captured post-analysis in order to generate enough genetic material for sequencing. Initial SSC and FSC criterion were set utilizing fluorescent negative cells from the contralateral side of the brain. Subsequent mono-fluorescent parameters to establish further gating were determined by single color excitation channels utilizing positive controls. Cells that were positive for internal lineage dependent expression of EGFP and appropriate cell surface markers were sorted into a 1.5-ml tube containing 1x PBS for downstream analysis.

extract_protocol:
Cells were captured via FACS from bulk tumor, TAVs, and TDECs and total RNA was isolated using Trizol (Thermoscientific, Cat. No. 15596018) and the RNeasy Micro Kit (Qiagen, Cat. No. 74004). RNA quality was confirmed on a 12-Capillary Fragment Analyzer using the High Sensitivity RNA Analysis Kit (Agilent formerly AATI, Cat. No. DNF-472-0500).
Approximately 5 ng of total RNA was used for cDNA library construction using the Trio RNA-Seq System (0507-96, NuGEN). 8-bp single index libraries were quality controlled using the Standard Sensitivity NGS Fragment Analysis Kit (Agilent formerly AATI, Cat. No. DNF-473-0500,).  Samples were quantified with Quant-iT dsDNA Assay Kit, high sensitivity (Thermo Fisher, Cat. No. Q33120,) and equal concentrations (2 nM) of libraries were pooled, diluted and denatured according to the manufacture’s protocol.
Libraries were subjected to paired-end (2x75) sequencing of approximately 40 million reads per sample using the High Output v2 kit (Illumina, Cat. No. FC-404-2002) on a NextSeq500.
Ultra-Low Input Bulk RNA-Seq of Murine and Human PDX Tumor-Derived Endothelial Subpopulations: Rare, tumor-derived endothelial cells—TDLECs and TDBECs—from both our native CRISPR/Cas9 murine model and human PDOX mice, as well as PDOX bulk tumor cells, were isolated by FACS and were collected in 1x PBS (Thermoscientific, Cat. No. 10010023). Total RNA was extracted using Trizol (Thermoscientific, Cat. No. 15596018) and the RNeasy Micro Kit (Cat. No. 74004, QIAGEN). Approximately 250 pg of total RNA was isolated from 2,000 murine or human PDX-derived TDLECs and TDBECs, as well as bulk tumor PDX-derived cells. cDNA was synthesized using the SMART-Seq Ultra Low Input RNA Kit (Takara, Cat. No. 634889). cDNA concentration and quality were determined using the High Sensitivity NGS Fragment Analysis Kit (Agilent, Cat. No. DNF-474-0500) on a 12-Capillary Fragment Analyzer (Advanced Analytical Technologies Inc.). Quantification of cDNA was confirmed using the Quant-iT dsDNA Assay Kit, high sensitivity (Thermo Fisher, Cat. No. Q33120). Sequencing libraries were produced using the Nextera XT DNA Library Kit (Illumina, Cat. No. FC-131-1024) with 50 pg of cDNA input for tagmentation and ligation at ½ the manufacture recommended volumes. The resulting dual indexed Illumina sequencing libraries were validated using the Standard Sensitivity NGS Fragment Analysis Kit (DNF-473-0500, Agilent formerly AATI) and subjected to paired-end (2x75) sequencing at a depth of approximately 40 million reads per sample using a High Output v2 kit, (Illumina, Cat. No. FC-404-2002) on a NextSeq500, according to the manufacture’s protocol.

value: Brain

value: Tumor Derived Lymphatic Endothelial Cells


title: Tf2_Hippocampus_3_P14

status: Public on Jan 17 2021

type: SRA

city: Milan

first: Beatrice

last: Bodega

address: Via Francesco Sforza 35

country: Italy

institute: INGM Istituto Nazionale Genetica Molecolare

description: Bisulfite conversion based methylation analysis of L1MdTf

library_source: genomic

data_processing:
Reads were trimmed for low quality using Trimmomatic (parameters:  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15  MINLEN:75)
Paired reads were aligned to IAP and L1 consensus sequences using Bismark (parameters: --local -N 1 -L 15 --non_directional)
DNA methylation data was called was called using MethylDackel
Genome_build: Custom (IAPLTR1a_Mm and L1MdTf Mus musculus consensus sequences)
Supplementary_files_format_and_content: Per-base CpG metrics are provided in a standard bedGraph format with 4th column being the methylation percentage at a given position, 5th column the number of read pairs reporting methylated bases and 6th column the number of read pairs reporting unmethylated bases.

molecule: genomic DNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Brains were excised and cerebellum, cortex and hippocampus were isolated. Genomic DNA was extracted with phenol/chloroform. 500ng of genomic DNA were bisulfite-converted using MethylEdge Bisulfite Conversion Kit (Promega).
Targetted Bisultite-seq. Library was prepared as follows: briefly genomic DNA was bisulfite-converted and the amplified using specific primers: each organ in each developmental stage was associated to a distinct couple of Forw and Rev primers 5’-end tagged,  in order to be unambiguously identified in the sequencing analysis step. All the L1MdTf and IAPLTR1a amplicons were then pooled in equimolar quantities to obtain a final pooling concentration of 2 ng/μL. Library for DNA sequencing was produced on the pooled PCR products.

tag: strain

tag: tissue

value: Hippocampus

tag: age

value: Post natal day 14


title: JC212_TDLEC

first: Manuel

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: JC222_TDBEC

source_name: TDBEC brain cells

value: Tumor Derived Blood Endothelial Cells


title: Tf2_Hippocampus_3_P0

value: Post natal day 0


title: JC216_TDBEC


title: Tf2_Hippocampus_3_P3

value: Post natal day 3


title: Tf2_Hippocampus_3_E18.5

value: Embryonic day 18.5


title: Tf2_Hippocampus_3_E15.5

value: Embryonic day 15.5


title: Mkp-1 KO for CS

city: HANGZHOU

first: XIUWEN

last: TANG

address: YUHANGTONG ROAD

department: BIOCHEMISTRY AND GENETICS

country: China

institute: ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE

data_processing:
HTSeq v0.6.1 software used
All statistical analyses were carried out with HTSeq v0.6.1; after removing transcriptionally inactive genes (read count per million < 1) from raw RNA sequencing gene counts, we obtained high confidence gene counts
For gene expression analysis, the matched reads were calculated and then normalized to reads per kilobase of exon model per million mapped reads (FPKM)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: distal colonic epithelial tissue

growth_protocol: mice were maintained under standard conditions of ventilation, temperatures (22± 30 C), and lighting (light/dark: 13 h/11 h) and kept under observation for one week prior to experimentation. Drinking water and standard pellets diet were provided ad libitum throughout the study.

extract_protocol:
total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacture’s instruction
Illumina RNA-Seq libraries were subsequently performed  using the SMARTer Stranded RNA-Seq Kit (Clontech, Mountain View, CA) according to the manufacturer's instructions

treatment_protocol: The protocol for the induction of adenoma stage (AS) is illustrated in Fig 1. Briefly, 5–6-week-old male BALB/c mice were injected with AOM (10 mg/kg i.p.) once per week for the first 3 weeks. During this period, mice were exposed to drinking water containing 1.5% DSS and were left to drink normal water for 3 weeks. For the carcinoma stage (CS), 5–6-week-old-old male mice were also injected with AOM (10 mg/kg i.p.), exposed to drinking water containing 2% DSS for 1 week, and then left to drink normal water for 2 weeks. This treatment was repeated for three additional cycles. Finally, the mice were left to drink water containing 2% DSS for 1 week, followed by normal water for 9 weeks.

tag: background strain

tag: genotype

tag: treatment

value: untreated

tag: sample label

tag: subgroups

value: Mkp-1 KO

value: distal colonic epithelial tissue


title: Tf2_Hippocampus_2_P14


title: JC213_TDBEC


title: Mock_rep 2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: mock-overexpressing MC3T3-E1 cells

extract_protocol:
Total RNA was purified using the miRNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: For in vitro MC3T3-E1 cell analysis, subconfluent cells were digested in QIAZOL (Qiagen) to extract total RNA, in accordance with the manufacturer’s instructions.

tag: cell line

value: MC3T3-E1 cells

tag: genotype/variation

value: mock-overexpressing


title: THP-1 INPUT

city: Glasgow

first: Tae Ju

last: Park

address: 21 Shelley Rd

country: United Kingdom

institute: Paul O' Gorman Leukaemia Research Centre

description: Input control

data_processing:
Quality of sequencing data was checked by FastQC
ChIP enriched regions were identified using SICER
Genome_build: hg19
Supplementary_files_format_and_content: Microsoft Excel Open XML Format Spreadsheet (xlsx) file format containing ChIP-enriched regions that feature either an increase or decrease compared to NTC for each histone modification (either increased or decreased). Changes in enrichment identified by SICER.
Supplementary_files_format_and_content: Microsoft Excel Spreadsheet (xls) file format containing KDM4A ChIP enriched regions in WT THP-1 cells. Output from SICER.
Supplementary_files_format_and_content: Wiggle (wig) file format containing sequencing depth normalised coverage files for histone modifications or KDM4A in respective conditions, window size 200bp.

growth_protocol: Cells were grown in RPMI containing 10% FBS and 2.5µM puromycin. For the determination of KDM4A binding in WT THP-1 cells, the cells were grown only in RPMI containing 10% FBS.

extract_protocol:
Genomic DNA was extracted, crosslinked, sonicated and immunoprecipitated. Following ChIP, DNA was purified using diagenode's iPure kit v2 according to the manufacturers instructions.
Library preparation using TruSeq ChIP Library Preparation Kit

treatment_protocol: To induce knockdown of KDM4A, cells were spinoculated with lentivirus targeting KDM4A. As a negative control, cells were spinoculated with lentivirus containing  a non-targeting control shRNA construct. The genomic binding sites of KDM4A were investigated in WT THP-1 cells.

value: MLL-AF9 human AML cell line

tag: knockdown

tag: chip antibody

value: none (input)


title: KDM4A_WT_THP1

description:
KDM4A IP in WT THP-1 cells
KDM4A_bound_regions.FC.xls

value: wildtype

value: A300-860A (Bethyl Laboratories, Inc.)


title: JC199_TDBEC

value: Brain


title: KDM4A_KD1_H3K9me3_ChIP

description:
KDM4A KD1 H3K9me3 IP
shKDM4A-1_H3K9me3_decrease.FC.xlsx
shKDM4A-1_H3K9me3_increase.FC.xlsx

value: C15410193 (diagenode)


title: Tf2_Hippocampus_2_P0

value: Hippocampus


title: Tf2_Hippocampus_2_E18.5


title: KDM4A_KD1_H3K27me3_ChIP

description:
KDM4A KD1 H3K27me3 IP
shKDM4A-1_H3K27me3_decrease.xlsx
shKDM4A-1_H3K27me3_increase.xlsx

value: C15410195 (diagenode)


title: KDM4A_KD1_H3K9me2_ChIP

description:
KDM4A KD1 H3K9me2 IP
shKDM4A-1_H3K9me2_decrease.FC.xlsx
shKDM4A-1_H3K9me2_increase.FC.xlsx

value: C15410060 (diagenode)


title: Tf2_Hippocampus_1_P3

value: Post natal day 3


title: Tf2_Hippocampus_2_E15.5


title: Tf2_Hippocampus_1_P14

value: Post natal day 14


title: Tf2_Hippocampus_1_P0

value: Post natal day 0


title: NTC_H3K9me2_ChIP

description:
Negative control H3K9me2 IP
shKDM4A-1_H3K9me2_decrease.FC.xlsx
shKDM4A-1_H3K9me2_increase.FC.xlsx

value: non-targeting control


title: Tf2_Hippocampus_1_E18.5

value: Embryonic day 18.5


title: NTC_H3K9me3_ChIP

description:
Negative control H3K9me3 IP
shKDM4A-1_H3K9me3_decrease.FC.xlsx
shKDM4A-1_H3K9me3_increase.FC.xlsx


title: JC219_TDBEC

value: Tumor Derived Blood Endothelial Cells


title: Tf2_Hippocampus_1_E15.5

value: Embryonic day 15.5


title: Tf2_Cortex_4_P3

value: Cortex


title: NTC_H3K27me3_ChIP

description:
Negative control H3K27me3 IP
shKDM4A-1_H3K27me3_decrease.xlsx
shKDM4A-1_H3K27me3_increase.xlsx

value: MLL-AF9 human AML cell line


title: Tf2_Cortex_4_P0


title: Tf2_Cortex_4_P14


title: KDM4A_KD2_2

description:
KDM4A KD2 rep2
KDM4-2.vs.CONTROL.Gene.ds2.csv

data_processing:
Quality of sequencing data was checked by FastQC
Kallisto was used to quantify abundances of transcripts
Differentially expressed genes were detected using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values file format containing differential gene expression analysis results from DESeq2

growth_protocol: Cells were grown in RPMI containing 10% FBS and 2.5µM puromycin

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) according to the manuafacturers instructions
Library preparation using polyA selection (TruSeq stranded mRNA kit)

treatment_protocol: To induce knockdown of KDM4A, cells were spinoculated with one of two distinct lentiviruses targeting KDM4A. As a negative control cells were spinoculated with lentivirus containing  a non-targeting control shRNA construct

value: KDM4A KD2


title: Tf2_Hippocampus_2_P3


title: Tf2_Cortex_4_E18.5


title: KDM4A_KD1_2

description:
KDM4A KD1 rep2
KDM4-1.vs.CONTROL.Gene.ds2.csv

value: KDM4A KD1


title: KDM4A_KD1_1

description:
KDM4A KD1 rep1
KDM4-1.vs.CONTROL.Gene.ds2.csv


title: Tf2_Cortex_3_P3


title: Tf2_Cortex_4_E15.5


title: NTC_2

description: Negative control rep2


title: Tf2_Cortex_3_P14


title: Tf2_Cortex_3_P0


title: Tf2_Cortex_3_E18.5


title: Tf2_Cortex_3_E15.5


title: NTC_1

description: Negative control rep1


title: Tf2_Cortex_2_P3


title: Tf2_Cortex_2_P14


title: KDM4A_KD2_3

description:
KDM4A KD2 rep3
KDM4-2.vs.CONTROL.Gene.ds2.csv


title: Tf2_Cortex_2_E18.5


title: Tf2_Cortex_2_P0


title: KDM4A_KD2_1

description:
KDM4A KD2 rep1
KDM4-2.vs.CONTROL.Gene.ds2.csv


title: KDM4A_KD1_3

description:
KDM4A KD1 rep3
KDM4-1.vs.CONTROL.Gene.ds2.csv


title: Tf2_Cortex_2_E15.5


title: Tf2_Cortex_1_P3


title: Tf2_Cortex_1_P14


title: Tf2_Cortex_1_P0


title: Tf2_Cortex_1_E18.5


title: Tf2_Cerebellum_4_P14

value: Cerebellum


title: NTC_3

description: Negative control rep3


title: Tf2_Cerebellum_4_P3


title: Tf2_Cerebellum_4_E18.5


title: Tf2_Cerebellum_4_P0


title: Tf2_Cerebellum_4_E15.5


title: Tf2_Cerebellum_3_P3


title: Tf2_Cerebellum_3_P14


title: TU4T1_PE_IVT1

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

source_name: in_vitro_ tBreg_4T1_PE

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Animal protocols were approved by the Institutional Animal Care and Use Committee review board and performed under the Guide for the Care and Use of Laboratory Animals (NIH Publication No. 86-23, 1985). Mice (5–20 weeks of age, females) were housed in a pathogen-free environment at the National Institute on Aging (NIA, Baltimore, MD). BALB/cj mice were purchased from The Jackson Laboratory, and murine breast cancer 4T1 from ATCC. Flow cytometry Antibodies were purchased from BioLegend, eBioscience, BD Biosciences, and R&D Systems.For FACS or magnetic sorting, murine B cells were predepleted of lineage-positive (Linþ) cells (Gr1/CD11b/CD3e/CD8a/TER119/ CD49b) with biotin-labeled antibody and EasySep Mouse Streptavidin RapidSpheres Isolation Kit (StemCell Technologies) or PE-labeled antibody and anti-PE microbeads (Miltenyi Biotec) following the manufacturer's instructions. B cells were positively sorted with anti-CD19-PE using AutoMACS Pro (Miltenyi Biotec) and then further enriched using relevant antibody in MoFlo XDP (Beckman Coulter, Inc.).

extract_protocol: RNA was isolated with RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer's instructions. RNA concentration and quality was assayed on an RNA6000 Bioanalyzer chip (Agilent).

value: tBreg

tag: Sex

value: Female

value: 5-20 weeks

value: BALB/cj


title: TU4T1_PE_LPS_IVT3

source_name: in_vitro_ tBreg_4T1_PE_LPS


title: TU4T1_PE_IVT3


title: Tf2_Cortex_1_E15.5


title: TU4T1_PE_IVT2


title: TU4T1_PE_LPS_IVT1


title: TU4T1_IVT3

source_name: in_vitro_ tBreg_4T1


title: TU4T1_PE_LPS_IVT2


title: TUR6_4T1_CD19pos_CD23neg_CD25neg _3

value: Tumor-bearing spleen


title: TU4T1_IVT1


title: BAF_IVT3

source_name: in_vitro_ tBreg_control

value: control


title: Tf2_Cerebellum_3_P0


title: Tf2_Cerebellum_3_E18.5


title: Tf2_Cerebellum_2_P3

value: Post natal day 3


title: TU4T1_IVT2


title: TUR7_4T1_CD19pos_CD23neg_CD25pos_3


title: BAF_IVT2


title: Tf2_Cerebellum_2_P14

value: Post natal day 14


title: TUR4_4T1_CD19pos_CD23pos_3


title: TUR7_4T1_CD19pos_CD23neg_CD25pos_2


title: TUR4_4T1_CD19pos_CD23pos_2


title: NAÏVE_CD19pos_3

value: Naive spleen


title: Tf2_Cerebellum_2_P0

value: Post natal day 0


title: PTH _rep 3

description: 7AAD-Lin-CD45-ECFP+ cells from Col2.3-ECFP mice, treated with PTH for 3 weeks

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: txt and FPKM

extract_protocol:
Total RNA was purified using the miRNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
cDNA was generated using a SMART-Seq v. 4 Ultra Low Input RNA Kit (TaKaRa Clontech, Mountain View, CA, USA). Each cDNA sample was sheared (200–500 bp) using the Covaris S220 system (Covaris, Woburn, MA, USA) and prepared using KAPA Library Preparation Kits (Kapa Biosystems, Wilmington, MA, USA) according to the manufacturer’s instructions.

treatment_protocol: AAD-Lin-CD45-ECFP+ cells from Col2.3-ECFP mice, treated with vehicle or PTH (1-34) (40 µg/kg per day, 5 days per week) for 3 weeks, were isolated using the BD FACSAria™ II instrument.

value: 7AAD-Lin-CD45-ECFP+ cells

tag: mice


title: Tf2_Cerebellum_2_E18.5

value: Embryonic day 18.5


title: PTH _rep 1


title: PTH _rep 2


title: Tf2_Cerebellum_2_E15.5

value: Embryonic day 15.5


title: PBS _rep 3

description: 7AAD-Lin-CD45-ECFP+ cells from Col2.3-ECFP mice, treated with vehicle for 3 weeks


title: Tf2_Cerebellum_1_P3


title: PBS _rep 2


title: PBS _rep 1


title: Tf2_Cerebellum_3_E15.5


title: Tf2_Cerebellum_1_P0


title: Tf2_Cerebellum_1_E18.5


title: Tf2_Cerebellum_1_E15.5


title: BAF_IVT1


title: NAÏVE_CD19pos_2


title: TUR4_4T1_CD19pos_CD23pos_1


title: NAÏVE_CD19pos_1


title: TUR6_4T1_CD19pos_CD23neg_CD25neg _2


title: RC8h QuantSeq REV

city: Piscataway

first: Wei Vivian

last: Li

address: 683 Hoes Lane West

department: Biostatistics and Epidemiology

institute: Rutgers, The State University of New Jersey

data_processing:
Sequencing reads were aligned to the reference genome using the STAR software version 2.5.2a.
APA profiles were obtained using the MAAPER package version 1.0.0.
Genome_build: mm9
Supplementary_files_format_and_content: txt files were generated by applying MAAPER to the QuantSeq FWD data. The AS, RC4h, and RD8h samples were compared with the NT sample. For each comparison, the gene.txt file contains the number of predicted PASs and calculated APA statistics for each gene, and the pas.txt file contains the proportions  of each PAS in the two samples used for the comparison.

source_name: NIH3T3 cells

extract_protocol:
3' mRNA-Seq libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina or QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina
QuantSeq FWD or QuantSeq REV

tag: growth medium

value: DMEM supplemented with 10% calf serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Proliferating

value: 250 µM of sodium arsenite (NaASO2) for 1 hour then 8 hours of recovery in normal medium

tag: fraction

value: Total

tag: extraction protocol

value: TRIZol

tag: library protocol

value: QuantSeq REV


title: IAP_Hippocampus_4_P3

description: Bisulfite conversion based methylation analysis of IAPLTR1a

tag: strain

tag: tissue

value: Hippocampus

tag: age


title: RC4h QuantSeq REV

tag: cell type

tag: treatment

value: 250 µM of sodium arsenite (NaASO2) for 1 hour then 4 hours of recovery in normal medium


title: TUR7_4T1_CD19pos_CD23neg_CD25pos_1

value: Tumor-bearing spleen

value: Female

value: 5-20 weeks

value: BALB/cj


title: TUR6_4T1_CD19pos_CD23neg_CD25neg _1


title: AS QuantSeq REV

value: 250 µM of Sodium Arsenite for 1 hour


title: RC8h QuantSeq FWD

value: QuantSeq FWD


title: NT QuantSeq REV

value: Control


title: IAP_Hippocampus_4_P14

value: Post natal day 14


title: IAP_Hippocampus_4_P0

value: Post natal day 0


title: IAP_Hippocampus_4_E18.5

value: Embryonic day 18.5


title: IAP_Hippocampus_3_P3

value: Post natal day 3


title: IAP_Hippocampus_3_P14


title: CD31_Enriched_Tumor_SC

description: Single Cell RNA Sequencing

source_name: Enriched TAV

extract_protocol:
Processing of tumor tissue for MACS was virtually identical to tissue preparation for FACS until the step of papain neutralization. At this point, the cell suspension was pelleted, the pellet was washed two times with PBS and then resuspended in 180 uL MACS PEB buffer (phosphate-buffered saline (PBS), pH 7.2, 0.5% bovine serum albumin (BSA), and 2 mM EDTA by diluting MACS BSA Stock Solution (Miltenyi Biotec, Cat. No. 130-091-376) 1:20 with autoMACS Rinsing Solution (Miltenyi Biotec, Cat. No. 130-091-222). The cell suspension was then incubated for 15 minutes with 20 uL of anti-CD31 MicroBeads (Miltenyibiotec, Cat. No. 130-097-418) at 4°C. Cells were then washed with 1 mL of PEB buffer, centrifuged at 300 xg for 5 minutes, and applied to an MS Column (Miltenyi Biotec, Cat. No. 130-042-201) on a magnetic stand. Cells were collected after three consecutive washes with 0.5 mL of PEB. These cells were then pelleted at 300 xg for 10 minutes at 4°C, then resuspended in 1x PBS at a concentration of 50,000 cells per 50 uL in a total of 50 uL with a viability ≥ 90% and then used for downstream applications. Using the Single Cell Genomics Core at Baylor College of Medicine, single cells were isolated using the10x Genomics Chromium Controller Instrument within a Chromium Next GEM Chip G (10X Genomics, Cat. No. PN-1000120) platform, and the resulting libraries were created with a Chromium Next GEM Single 3’ GEM, Library and Gel Bead Kit v3.1 (10X Genomics, Cat. No. PN-1000121). Samples were then indexed using a Chromium i7 Multiplex Kit (10X Genomics, PN-120262). Raw sequencing data were handled using the 10x Genomics Cell Ranger software (www.10xgenomics.com). Fastq files were mapped to the mm10 genome, and gene counts were quantified using the Cellranger count function. Expression counts were imported into Seurat (version 3.2.0, https://satijalab.org/seurat/) and count matrix was exported from the seurat object into a text file.
Cells were captured via FACS from bulk tumor, TAVs, and TDECs and total RNA was isolated using Trizol (Thermoscientific, Cat. No. 15596018) and the RNeasy Micro Kit (Qiagen, Cat. No. 74004). RNA quality was confirmed on a 12-Capillary Fragment Analyzer using the High Sensitivity RNA Analysis Kit (Agilent formerly AATI, Cat. No. DNF-472-0500).
Approximately 5 ng of total RNA was used for cDNA library construction using the Trio RNA-Seq System (0507-96, NuGEN). 8-bp single index libraries were quality controlled using the Standard Sensitivity NGS Fragment Analysis Kit (Agilent formerly AATI, Cat. No. DNF-473-0500,).  Samples were quantified with Quant-iT dsDNA Assay Kit, high sensitivity (Thermo Fisher, Cat. No. Q33120,) and equal concentrations (2 nM) of libraries were pooled, diluted and denatured according to the manufacture’s protocol.
Libraries were subjected to paired-end (2x75) sequencing of approximately 40 million reads per sample using the High Output v2 kit (Illumina, Cat. No. FC-404-2002) on a NextSeq500.
Ultra-Low Input Bulk RNA-Seq of Murine and Human PDX Tumor-Derived Endothelial Subpopulations: Rare, tumor-derived endothelial cells—TDLECs and TDBECs—from both our native CRISPR/Cas9 murine model and human PDOX mice, as well as PDOX bulk tumor cells, were isolated by FACS and were collected in 1x PBS (Thermoscientific, Cat. No. 10010023). Total RNA was extracted using Trizol (Thermoscientific, Cat. No. 15596018) and the RNeasy Micro Kit (Cat. No. 74004, QIAGEN). Approximately 250 pg of total RNA was isolated from 2,000 murine or human PDX-derived TDLECs and TDBECs, as well as bulk tumor PDX-derived cells. cDNA was synthesized using the SMART-Seq Ultra Low Input RNA Kit (Takara, Cat. No. 634889). cDNA concentration and quality were determined using the High Sensitivity NGS Fragment Analysis Kit (Agilent, Cat. No. DNF-474-0500) on a 12-Capillary Fragment Analyzer (Advanced Analytical Technologies Inc.). Quantification of cDNA was confirmed using the Quant-iT dsDNA Assay Kit, high sensitivity (Thermo Fisher, Cat. No. Q33120). Sequencing libraries were produced using the Nextera XT DNA Library Kit (Illumina, Cat. No. FC-131-1024) with 50 pg of cDNA input for tagmentation and ligation at ½ the manufacture recommended volumes. The resulting dual indexed Illumina sequencing libraries were validated using the Standard Sensitivity NGS Fragment Analysis Kit (DNF-473-0500, Agilent formerly AATI) and subjected to paired-end (2x75) sequencing at a depth of approximately 40 million reads per sample using a High Output v2 kit, (Illumina, Cat. No. FC-404-2002) on a NextSeq500, according to the manufacture’s protocol.

value: Brain

value: Tumor Associated Endothelial Cells


title: IAP_Hippocampus_4_E15.5

value: Embryonic day 15.5


title: IAP_Hippocampus_3_P0


title: AS QuantSeq FWD

value: DMEM supplemented with 10% calf serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

value: Proliferating

value: Total

value: TRIZol


title: NT QuantSeq FWD


title: Tf2_Cerebellum_1_P14

description: Bisulfite conversion based methylation analysis of L1MdTf

value: Cerebellum


title: Bulk_Tumor_SC

description: Single Cell RNA Sequencing

source_name: Bulk tumor brain cells

value: Bulk brain cells


title: IAP_Hippocampus_3_E18.5

value: Hippocampus


title: JC113_TDLEC_P80

value: Tumor Derived Lymphatic Endothelial Cells


title: IAP_Hippocampus_2_P3


title: IAP_Hippocampus_2_P14


title: RC4h QuantSeq FWD

value: 250 µM of sodium arsenite (NaASO2) for 1 hour then 4 hours of recovery in normal medium

value: QuantSeq FWD


title: IAP_Hippocampus_2_E18.5


title: IAP_Hippocampus_2_P0


title: JC105_TDLEC_P80


title: JC111_TDLEC_P80


title: JC108_TDLEC_P80


title: JC102_TDLEC_P80


title: IAP_Hippocampus_2_E15.5


title: IAP_Hippocampus_1_P3


title: JC114_TDBEC_P65

value: Tumor Derived Blood Endothelial Cells


title: IAP_Hippocampus_1_P14

value: Post natal day 14


title: IAP_Hippocampus_1_P0

value: Post natal day 0


title: IAP_Hippocampus_1_E18.5

value: Embryonic day 18.5


title: JC106_TDBEC_P80

value: Brain


title: JC103_TDBEC_P80


title: J25_TDEC_P65

source_name: TDEC brain cells

value: Tumor Derived Endothelial Cells


title: IAP_Hippocampus_1_E15.5

value: Embryonic day 15.5


title: IAP_Cortex_4_P0

value: Cortex


title: IAP_Cortex_4_P3

value: Post natal day 3


title: J24_TDEC_P65


title: IAP_Hippocampus_3_E15.5


title: J20_TDEC_P80


title: J19_TDEC_P80


title: J18_TDEC_P80


title: IAP_Cortex_4_E18.5


title: JC101_TDLEC_P80


title: IAP_Cortex_4_E15.5


title: IAP_Cortex_3_P3


title: J02_TDEC_P65


title: J04_TDEC_P65


title: JC104_TDBEC_P80


title: J27_TAV_P80

source_name: TAV brain cells

value: Tumor Associated Endothelial Cells


title: J22_TAV_P65


title: IAP_Cortex_3_E18.5


title: IAP_Cortex_3_P14


title: IAP_Cortex_3_E15.5


title: IAP_Cortex_4_P14


title: IAP_Cortex_2_P3


title: J06_TAV_P65


title: IAP_Cortex_2_P14


title: J05_TAV_P65


title: IAP_Cortex_3_P0


title: J21_TAV_P65


title: J01_TDEC_P65


title: IAP_Cortex_2_P0


title: J47_Bulk_P65

source_name: Bulk brain cells


title: IAP_Cortex_2_E18.5


title: J28_Bulk_P80


title: J17_Bulk_P80


title: J45_Bulk_P65


title: IAP_Cortex_2_E15.5


title: J16_Bulk_P80


title: IAP_Cortex_1_P3


title: IAP_Cortex_1_P0


title: IAP_Cortex_1_E15.5


title: IAP_Cortex_1_E18.5


title: IAP_Cerebellum_4_P3


title: T22

city: Nanning

first: Fu

middle: hua

last: Zhou

state: Guangxi

address: No. 6 Shuangyong Road, Qingxiu District

department: Department of Cardio-Thoracic Surgery,

institute: The First Affiliated Hospital of Guangxi Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using STAR_2.4.2a with default parameters.
The expression level of transcript per million (TPM) reads were quantified using RNA-Seq by Expectation-Maximization algorithm (RSEM v1.2.29).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: mRNA_Expression_Summary.txt: Tab-delimited text file includes TPM values for each Sample.

source_name: ESCC tissue

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: patient

value: esophageal squamous cell carcinoma

value: without preoperative chemotherapy or radiotherapy

tag: gender

value: Male

tag: t

tag: n

tag: grade

tag: Stage

value: IIA


title: T21


title: IAP_Cerebellum_4_P14

value: Cerebellum


title: T19

value: IIB


title: T13


title: T5

value: IIIA


title: T3


title: IAP_Cerebellum_4_E18.5


title: IAP_Cerebellum_4_E15.5


title: IAP_Cerebellum_3_P3


title: IAP_Cerebellum_4_P0


title: IAP_Cerebellum_3_P14


title: T4

value: Female


title: 231 CELLS-si-NC

city: Jinan

first: Haiting

last: Liu

address: West Wenhua Road 44

institute: Shandong University

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

source_name: human breast cancer cells

growth_protocol: Cells were cultured L15 culture medium with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THAP7-AS1 was knocked down by transfection with THAP7-AS1 Smart Silencer in 231 cells

tag: cell line

value: breaste cancer cell line

tag: genotype/variation

value: transfection with Si-NC

tag: morphology

value: epithelioid


title: N22

source_name: Adjacent normal tissue

value: normal esophageal


title: IAP_Cerebellum_3_E18.5

source_name: Brain

value: Embryonic day 18.5


title: IAP_Cerebellum_2_P3


title: IAP_Cerebellum_3_E15.5

value: Embryonic day 15.5


title: N19


title: N21


title: IAP_Cerebellum_2_P14

value: Post natal day 14


title: IAP_Cerebellum_2_E18.5

value: Embryoinic day 18.5


title: IAP_Cerebellum_2_E15.5


title: IAP_Cortex_1_P14

value: Cortex


title: N5


title: N13


title: IAP_Cerebellum_1_P3

value: Post natal day 3


title: P. tomentosa dormant stage rep1

city: Xinxiang

first: Qiu

last: Zongbo

state: Henan

address: 147 Jianshe Road

department: College of Life Science

institute: Henan Normal University

data_processing:
Basecalls performed using illumina Casava 1.8 version
(1) Removal of low quality reads (reads with mass sQ <= 5 bases representing more than 50% of the entire read);  (2) remove the reads whose proportion of N (N indicates that the base information can not be determined) is more than 10%  (3) remove reads contaminated with 5 'linkers;  (4) Remove reads without 3 'linker sequence and insert;  (5) Trim 3 'linker sequence;  (6) Remove the reads of polyA / T / G / C
the clean reads were mapped to the P. tomentosa mRNA transcriptome database by using Bowtie software
The criteria of |log2 fold change| ≥ 2 and P ≤ 0.01 was set as the threshold for defining significantly different expression
Genome_build: P. tomentosa mRNA
Supplementary_files_format_and_content: xls file was generated using TPM expression level normalized and contains the readcount of various periods(AC、DC and RC)

organism: Paulownia tomentosa

source_name: cambial tissues

extract_protocol:
total RNAs from dormant, reactivating, and active cambium meristem were isolated using the Trizol reagent
The library was constructed using Small RNA Sample Pre Kit. Based on the 3 'and 5' special structures of Small RNA (complete phosphate groups on the 5 'end and hydroxyl groups on the 3' end), total RNA was used as a starting sample and Small Both ends of the RNA were spliced and cDNA was reverse transcribed. Followed by PCR amplification, PAGE gel electrophoresis separation of the target DNA fragment, gel recovery obtained is the cDNA library

value: 20 years

tag: developmental stage

value: dormant stage

value: cambial tissues


title: P. tomentosa reactivating stage rep1

value: reactivating stage


title: 231 CELLS-si-THAP7-AS1

value: transfection with THAP7-AS1 Smart Silencer


title: N4

value: without preoperative chemotherapy or radiotherapy


title: P. tomentosa active stage rep1

value: active stage


title: IAP_Cerebellum_3_P0

value: Cerebellum

value: Post natal day 0


title: IAP_Cerebellum_1_P14


title: N3

value: Male


title: IAP_Cerebellum_1_E18.5


title: T17

value: esophageal squamous cell carcinoma

value: Female

value: IIB


title: N17

value: normal esophageal


title: IAP_Cerebellum_2_P0


title: chipseq-donor-921-alwayson

status: Public on Jan 16 2021

city: Stanford

first: Evan

middle: W

last: Weber

state: California

address: 265 Campus Drive, SIM1, Room G2105

department: Stanford Cancer Institute

institute: Stanford University

data_processing:
Reads were trimmed and quality filtered using fastp.
Reads were aligned to hg38 using hisat2
Aligned reads were de-duplicated using Picard
Mitochondrial reads and Y chromosome reads were removed
Peaks were called for each sample using MACS2, merged into a union peak set, and the peak by count matrix was loaded into DESeq2 for differential analysis
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files contain the reads quantified against the merged peak set, representing the raw reads-in-peaks for each sample.

source_name: Cultured CAR-T cells

extract_protocol:
Samples were processed using the Omni-ATAC protocol or standard chip-seq protocols. For details, see Methods.
Library construction for ATACseq and chipseq is detailed in Methods.

tag: individual

value: donor 921

value: Cultured CAR-T cells

value: alwayson

tag: culture conditions

value: Shield-1 D1-15 + vehicle + complete medium

tag: chip antibody

value: Anti-H3K27me3, Diagenode, C15410069, 2ug/sample


title: chipseq-donor-921-rested

value: rested

value: Shield-1 D1-11 + vehicle + complete medium


title: chipseq-donor-921-alwaysoff-ezhi

value: alwaysoff-ezhi

value: 1uM tazemetostat D11-15 + complete medium


title: chipseq-donor-921-alwayson-ezhi

value: alwayson-ezhi

value: Shield-1 D1-15 + 1uM tazemetostat D11-15 + complete medium


title: IAP_Cerebellum_1_E15.5

tag: strain

tag: tissue

value: Cerebellum

value: Embryonic day 15.5


title: chipseq-donor-916-alwayson

value: donor 916

tag: cell type


title: chipseq-donor-921-alwaysoff

tag: treatment

value: alwaysoff

value: Vehicle + complete medium


title: IAP_Cerebellum_1_P0

tag: age

value: Post natal day 0


title: chipseq-donor-916-rested


title: chipseq-donor-914-alwayson-ezhi

value: donor 914


title: chipseq-donor-916-rested-ezhi

value: Cultured CAR-T cells

value: rested-ezhi

value: Shield-1 D1-11 + 1uM tazemetostat D11-15 + complete medium


title: chipseq-donor-914-rested-ezhi

value: Anti-H3K27me3, Diagenode, C15410069, 2ug/sample


title: chipseq-donor-914-alwaysoff


title: chipseq-donor-916-alwaysoff


title: chipseq-donor-916-alwaysoff-ezhi


title: chipseq-donor-921-rested-ezhi

value: donor 921


title: ATAC-donor-8-stim

value: donor 8

value: stim

value: Complete medium + immobilized anti-FMC63 idiotype antibody from D15-16


title: ATAC-donor-24-stim

value: donor 24


title: chipseq-donor-914-rested

value: rested

value: Shield-1 D1-11 + vehicle + complete medium


title: PDLGO

city: Tokyo

first: Asakawa

last: Takeyoshi

state: Ota-ku

address: 2-1-1 Kitasenzoku

department: Pediatric

institute: Showa university

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hrs at 45˚C on Clariom S Array, Human. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4.1 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

label: biotin

source_name: PDLGO

label_protocol: Biotinylated cDNA was prepared from 100 ng of total RNA using GeneChip WT PLUS Reagent Kit（Thermo Fisher Scientific).

growth_protocol: Both PDLGO and PDLDS were cultured in the presence of 10% FBS.

extract_protocol: Extract protocol not provided

value: periodontal ligament cells

tag: patient diagnosis

value: healthy control


title: ATAC-donor-7-naïve

value: donor 7

value: naïve

value: Complete medium


title: ATAC-donor-23-naïve

value: donor 23


title: nkx3.2 mutant cartilage

city: New York

first: Joanna

last: Smeeton

state: NY

address: 650 W 168TH ST, ROOM 1103A, William Black Building

department: Rehabilitation and Regenerative Medicine

institute: Columbia University Irving Medical Center

description: 10X Genomics single cell barcoding

data_processing:
Reads were aligned to z11 genome using Cell Ranger 3.
Genome_build: z11
Supplementary_files_format_and_content: barcode, gene and matrix files from Cell Ranger alignment and trimming

organism: Danio rerio

source_name: cartilage

extract_protocol:
Cells were dissociated from 21dpf zebrafish and FACS sorted for fli1a:eGFP;sox10:DsRed double positive live cells. Single cells were processed through the 10X chromium controller
Barcoded cDNA libraries were generated using 10X Genomics standard scRNAseq protocol using 3' Gene Expression v2 Library kit.

tag: genotype

value: 22 days post fertilization

value: cartilage


title: ATAC-donor-15-naïve

value: donor 15

value: Cultured CAR-T cells


title: chipseq-donor-914-alwayson

value: donor 914

value: alwayson

value: Shield-1 D1-15 + vehicle + complete medium

value: Anti-H3K27me3, Diagenode, C15410069, 2ug/sample


title: ATAC-donor-921-always-on

value: donor 921

value: always-on

value: Shield-1 D1-15 + complete medium


title: WT cartilage

description: 10X Genomics single cell barcoding

value: WT

value: 21 days post fertilization


title: ATAC-donor-914-always-on


title: ATAC-donor-916-always-on

value: donor 916


title: Probe6_A_375RR

city: Leipzig

first: Maria

last: Schmidt

address: Haertelstraße 16-18

country: Germany

institute: IZBI

data_processing:
Demultiplexing was done using bcl2fastq v2.20.0.422 (Illumina®).
For further analysis and read alignment CellRanger software was used with default settings suggested by 10x Genomics.
Genome_build: GRCh38
Supplementary_files_format_and_content: 4 matrix tables with raw gene counts for every gene and every sample (CellRanger output)

source_name: Melanoma

growth_protocol: The commercially available BRAF V600E mutant melanoma cell line A375 was used for the inhibitor experiments. Cells were kept under standard conditions in RPMI medium with 10% fetal calf serum and 1% penicillin/streptomycin.

extract_protocol:
Cell suspensions were generated by washing melanoma cells from different cultures with PBS followed by trypsinizing with TripLE Xpress (Invitrogen, Darmstadt, Germany) for 5 minutes. The reaction was stopped by adding media containing FCS. The number of dead cells was counted by Trypan blue staining (Sigma Aldrich, Munich) and did not exceed 5% of cells. Single melanoma cells from short-term cultures were captured on 10x Genomics Chromium Controller® according to the manufacturer’s specifications. 10,000 cells were used in these experiments. Overall, 10,000 cells were loaded into one channel of the Chromium system using the v2 single cell reagent kit (10x Genomics®). Following capture and lysis, cDNA was synthesized and amplified for 12 cycles.
The amplified cDNA was used to construct Illumina sequencing libraries according to the instruction of the Chromium Used Guide (10x Genomics). Briefly, blunt end repair was followed by adapter ligation. Finally, during PCR amplification sample indexes were added. The barcoded libraries were purified with SPRI beads and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. Correct size distribution of the library DNA was analyzed using the Fragment Analyzer (Agilent). A pool of up to 4 libraries was used for cluster generation.

treatment_protocol: Cells were made resistant to vemurafenib or a combination of vemurafenib and cobimetinib or trametinib (MEK1/2 inhibitor) by keeping cells for 10-14 days under half IC50 concentrations of inhibitors, which had been determined in earlier experiments. Inhibitors were removed 24h before start of single-cell analyses in order to avoid direct toxic effects of substances on cell cultures. Chemical inhibitors were purchased from Biozol, Munich, Germany (vemurafenib, SEL-S1267; cobimetinib, SEL-S8041; trametinib, SEL-S2673).

value: Melanoma cells

value: vemurafenib + trametinib


title: ATAC-seq_patient-812_time-D15_D7OFF

data_processing:
Cells were processed using the Pepatac pipeline (http://pepatac.databio.org/en/latest/), aligned against hg19, using default settings unless otherwise noted.
Briefly, all samples were first trimmed to remove Illumina adapter sequences, then checked using FastQC.
Bowtie2 was used to pre-align reads to remove any reads aligning to the mitochondrial genome or other repeat regions in the rCRSd human_repeats dataset.
Bowtie2 was then used to align to the hg19 human reference genome.
Non-uniquely mapped reads were filtered out using Samtools, and Picard was used to remove duplicate reads to generate the final de-duplicated BAM file for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file contains the reads quantified against the merged peak set, representing the raw reads-in-peaks for each sample.

extract_protocol:
Samples were processed following the Omni-ATAC protocol (Corces et al., Nature Methods, 2017).  Briefly, cells were pelletted, resuspended in ATAC resuspension buffer with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin, and incubated on ice for 3 minutes; prior to washing out with ATAC resuspension buffer containing only 0.1% Tween-20.  These cells were pelletted and resuspended in transposition mixture containing Tn5, then incubated at 37 degrees for 30 minutes on a thermomixer at 1000 RPM.  The resulting DNA was eluted using a Zymo Clean and Concentrator 5 kit.
Libraries were prepared following the Omni-ATAC protocol.  Briefly, 5 initial cycles of PCR were performed.  Then, 10% of this mixture was used for a subsequent qPCR to identify the number of remaining cycles needed for sufficient amplification, which generally ranged from 1-5 additional cycles.  For those additional cycles of PCR, indexing primers were used to label each sample with dual indexes for sequencing.

value: Shield-1 D1-7 + complete medium


title: ATAC-donor-16-stim

value: donor 16

value: stim

value: Complete medium + immobilized anti-FMC63 idiotype antibody from D15-16


title: ATAC-seq_patient-812_time-D15_D11OFF

value: Cultured CAR-T cells

value: Shield-1 D1-11 + complete medium


title: ATAC-seq_patient-812_time-D15_ON


title: Probe4_A_375S

value: untreated


title: ATAC-seq_patient-812_time-D15_ON_Nivo

value: Shield-1 D1-15 + anti-PD-1 D7-15 + complete medium


title: Probe3_A_375R

value: vemurafenib


title: RNA-seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, 5. Replicate, Batch two

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
Random UMI barcodes were extracted and removed using UMI-Tools v.1.0.1 .
Adaptors, low quality reads and specific UMIs were removed using Trim Galore v.0.6.5.
Processed fastq files were aligned using Hisat2 v.2.2.1.
Count tables were generated from BAM files using the summarizeOverlaps function from the GenomicAlignments BioConductor package.
Normalization of read counts and detection of differentially expressed genes was done using DESeq2 v.1.28.1 with batches and conditions as design variables.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized read count tables per gene in csv format.

source_name: HeLa Kyoto cells

growth_protocol: HeLa Kyoto cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo Fisher Scientific) supplemented with 10% heat inactivated fetal bovine serum (FBS, Thermo Fisher Scientific) and 1% penicillin/streptomycin (Thermo Fisher Scientific) in a humidified atmosphere at +37 °C and 5% CO2.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) and on-column DNase digestion (RNase-Free DNase Set, QIAGEN) was performed according to the manufacturer’s instructions.
RNA libraries were generated with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen) according to the manufacturer’s instructions.
RNA-seq (75 bp read length, single-read) on the Illumina NextSeq550 platform

treatment_protocol: HeLa Kyoto cells were transfected with control or JAZF1 siRNA pools using oligofectamine (Invitrogen) according to the manufacturer’s instructions and harvested after two days incubation.

value: HeLa Kyoto

value: Cervix carcinoma cells

value: JAZF1 siRNA pool

value: JAZF1 knockdown


title: ATAC-seq_patient-812_time-D15_OFF

value: Complete medium


title: PDLDS

source_name: PDLDS

value: periodontal ligament cells

value: Down syndrome


title: Bile duct ligation (BDL)-3

city: Nanjing

first: Li

last: jie

address: No. 24, Tong Jia Lane

institute: China Pharmaceutical University

description: Biological replicate 2 of 3.The common bile duct was ligated twice in mice and cut open between ligations.

hyb_protocol: After purification the labeled RNAs were hybridized onto the microarray. After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

scan_protocol: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.

data_processing:
Genespring software (version 14.8, Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in "Detected" were chosen for further data analysis.
Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05.

source_name: Liver

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP.

growth_protocol: Livers were harvested and  frozen in liquid nitrogen further analysis.

extract_protocol: Total RNA of the samples was quantified by Nanodrop ND-2000 (Thermo Scientific) and RNA integrity was detected by Agilent BioAnalyzer 2100(Agilent Technologies).

tag: gender

value: male


title: chipseq-donor-916-alwayson-ezhi

value: donor 916

value: alwayson-ezhi

value: Shield-1 D1-15 + 1uM tazemetostat D11-15 + complete medium

value: Anti-H3K27me3, Diagenode, C15410069, 2ug/sample


title: ATAC-seq_patient-352_time-D15_D11OFF

value: Cultured CAR-T cells


title: Control-1

description: Biological replicate 1 of 2. Sham-operated mice were subjected to laparotomy without BDL.


title: LIX1L-Knockout-Bile duct ligation (BDL)-5

description: Biological replicate 3 of 3.The common bile duct was ligated twice in LIX1L-KO mice and cut open between ligations.


title: LIX1L-Knockout-Bile duct ligation (BDL)-3

description: Biological replicate 2 of 3.The common bile duct was ligated twice in LIX1L-KO mice and cut open between ligations.


title: RNA-seq of HeLa Kyoto cells treated with control siRNA pool, 5. Replicate, Batch two

value: control siRNA pool

value: control


title: RNA-seq of HeLa Kyoto cells treated with control siRNA pool, 4. Replicate, Batch two


title: RNA-seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, 4. Replicate, Batch two


title: Bile duct ligation (BDL)-4

description: Biological replicate 3 of 3.The common bile duct was ligated twice in mice and cut open between ligations.


title: Control-2

description: Biological replicate 2of 2. Sham-operated mice were subjected to laparotomy without BDL.


title: Bile duct ligation (BDL)-1

description: Biological replicate 1 of 3.The common bile duct was ligated twice in mice and cut open between ligations.


title: LIX1L-Knockout-Bile duct ligation (BDL)-2

description: Biological replicate 1 of 3.The common bile duct was ligated twice in LIX1L-KO mice and cut open between ligations.


title: Probe5_A_375RR

value: Melanoma cells

value: vemurafenib + cobimetinib


title: RNA-seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, 3. Replicate, Batch two

value: HeLa Kyoto


title: ATAC-seq_patient-352_time-D15_D7OFF

value: Shield-1 D1-7 + complete medium


title: ATAC-seq_patient-352_time-D15_ON_Nivo

value: Shield-1 D1-15 + anti-PD-1 D7-15 + complete medium


title: RNA-seq of HeLa Kyoto cells treated with control siRNA pool, 3. Replicate, Batch two

value: Cervix carcinoma cells


title: ATAC-seq_patient-352_time-D15_ON

value: Shield-1 D1-15 + complete medium


title: ATAC-seq_patient-352_time-D15_OFF

value: Complete medium


title: RNA-seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, 2. Replicate, Batch one

value: JAZF1 siRNA pool

value: JAZF1 knockdown


title: ATAC-seq_patient-176_time-D15_D7OFF


title: RNA-seq of HeLa Kyoto cells treated with control siRNA pool, 1. Replicate, Batch one


title: RNA-seq of HeLa Kyoto cells treated with JAZF1 siRNA pool, 1. Replicate, Batch one


title: RNA-seq of HeLa Kyoto cells treated with control siRNA pool, 2. Replicate, Batch one


title: chipseq-donor-914-alwaysoff-ezhi

value: donor 914

value: alwaysoff-ezhi

value: 1uM tazemetostat D11-15 + complete medium


title: ATAC-seq_patient-812_time-D11_D7OFF

value: Shield-1 D1-D7 + complete medium


title: ATAC-seq_patient-176_time-D15_ON_Nivo

value: Cultured CAR-T cells


title: ATAC-seq_patient-176_time-D15_OFF


title: ATAC-seq_patient-812_time-D11_ON_Nivo

value: Shield-1 D1-11 + anti-PD-1 D7-11 + complete medium


title: ATAC-seq_patient-176_time-D15_ON


title: ATAC-seq_patient-812_time-D11_ON

value: Shield-1 D1-11 + complete medium


title: ATAC-seq_patient-812_time-D11_OFF


title: ATAC-seq_patient-352_time-D11_D7OFF


title: ATAC-seq_patient-352_time-D11_ON_Nivo


title: ATAC-seq_patient-352_time-D11_ON


title: ATAC-seq_patient-352_time-D11_OFF


title: ATAC-seq_patient-176_time-D11_ON


title: ATAC-seq_patient-176_time-D11_OFF


title: ATAC-seq_patient-176_time-D11_D7OFF


title: ATAC-seq_patient-176_time-D11_ON_Nivo


title: ATAC-seq_patient-176_time-D15_D11OFF


title: ML171612 Thermal neutrality

city: Parkville

first: Peter

middle: John

last: Houweling

state: Does Not Apply

address: Flemington Road

department: Cell Biology

country: Australia

institute: Murdoch Childrens Research Institute

description: Total gene counts before processing

data_processing:
Raw read data was processed using the Illumina BaseSpace RNA Express application (Illumina Inc. 2016)
Sequencing reads were aligned using STAR ultrafast RNA seq aligner in the SAM file format
Reads were counted using HTSeq
genewise count data was analyzed using the R (3.6.0) statistical programming language
Differential expression (DE) was conducted using the voom precision weights approach in the limma (3.40.6) package from the Bioconductor (3.9) project
Genome_build: mm10
Supplementary_files_format_and_content: text

source_name: Brown adipose tissue

extract_protocol:
Brown adipose tissue was removed and weighed, then flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA was purified using Qiagen RNA columns and Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols on a Illumina HiSeq 2500

value: Female

value: KO

value: Brown adipose tissue

value: Thermal neutrality


title: ML171611 Thermal neutrality

description: Total gene counts before processing


title: ML171609 Thermal neutrality

description: Total gene counts before processing

value: WT


title: ATAC-seq_patient-812_time-D7_ON

value: Shield-1 D1-7 + complete medium


title: ML171608 Thermal neutrality

description: Total gene counts before processing


title: ML171607 Thermal neutrality

description: Total gene counts before processing


title: ML171606 Thermal neutrality

description: Total gene counts before processing


title: GLA9_1

city: Seoul

first: Hae Jin

last: Cho

address: 222, Banpo-daero, Seocho-gu

country: South Korea

institute: Catholic university

description: GLA knockout kidney organoid

hyb_protocol: cDNA was hybridized to the arrays for 16 hours at 45°C, the chips were processed in a Genechip Fluidics Station 450 (Affymetrix).

scan_protocol: Microarray images were collected with the GCS3000 Scanner (Affymetrix)

data_processing: Data were extracted using Affymetrix® GeneChip Command Console® Software (AGCC).

source_name: CMC11 cell line, GLA knockout kidney organoid by CRISPR-Cas9 genome-editing system

label_protocol: Gene expression studies were performed using the Affymetrix One Cycle labeling kit. The data were summarized and normalized using the robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT).

growth_protocol: The CMC11 iPSC cell line was obtained from The Catholic University of Korea (male donor). Cells were used between passages 30 and 60. Kidney organoid differentiation was performed as previously described (Freedman et al., 2015). In brief, hPSCs were plated at a density of 5,000 cells/well in a 24-well plate in mTeSR1 medium (Stem Cell Technologies) + 10 µM Y27632 (LC Laboratories) on glass plates (LabTek) coated with 3% GelTrex (Thermo Fisher Scientific) (day -3). The medium was exchanged with 1.5% GelTrex in mTeSR1 (day -2), mTeSR1 (day -1), RPMI (Thermo Fisher Scientific) + 12 µM CHIR99021 (Tocris) (day 0), or RPMI + B27 supplement (Thermo Fisher Scientific) (day 1.5) and cells were fed every 2–3 days to promote kidney organoid differentiation. Organoids were fixed on day 18.

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

treatment_protocol: Total RNA was prepared from the kidney organoids and GLA knockout kidney organoids using TRIzol (Invitrogen)

value: Human inducible pluripotent stem cell line

tag: derived cell type

value: kidney organoid

value: GLA knockout


title: GLA9_3

description: GLA knockout kidney organoid


title: ATAC-seq_patient-176_time-D7_ON


title: CMC11_2

description: Human iPSC derived kidney organoid

source_name: CMC11 cell line, Human iPSC derived kidney organoid

value: wildtype


title: ATAC-seq_patient-352_time-D7_ON


title: CMC11_1

description: Human iPSC derived kidney organoid


title: ML171610 Thermal neutrality

description: Total gene counts before processing


title: ML171602 Thermal neutrality

description: Total gene counts before processing


title: ML171601 Cold exposure

description: Total gene counts before processing

value: Cold exposure


title: ATAC-seq_patient-812_time-D0_naive


title: GLA9_2

description: GLA knockout kidney organoid


title: ML171599 Cold exposure

description: Total gene counts before processing


title: ATAC-seq_patient-352_time-D7_OFF

value: Complete medium


title: ATAC-seq_patient-176_time-D7_OFF


title: ATAC-seq_patient-352_time-D0_naive


title: ATAC-seq_patient-812_time-D7_OFF


title: ML171598 Room temperature

description: Total gene counts before processing

value: Room temperature


title: ML171595 Cold exposure

description: Total gene counts before processing


title: ML171597 Thermal neutrality

description: Total gene counts before processing


title: ML171596 Thermal neutrality

description: Total gene counts before processing


title: TG6C-2

city: Berkeley

first: Zoë

last: Steier

state: CA

address: 378 Stanley Hall

institute: UC Berkeley

description: TG6 biological replicate 2

data_processing:
Sequencing reads were processed with Trimmomatic (v0.32) to remove adapter sequences and trim low-quality bases. Reads were aligned to the mm10 genome using Bowtie2 (v2.3.2) and transcripts were quantified using RSEM (v1.2.31).
Genome_build: mm10
Supplementary_files_format_and_content: txi_rsem_transcript_counts.rds: R object including transcript counts, abundance, and gene lengths as quantified by RSEM for all genes and for each sample.
Supplementary_files_format_and_content: normalized_counts.csv: Matrix of normalized counts for all genes and for each sample (normalized by DESeq2 median of ratios method).

source_name: thymus

extract_protocol:
RNA was harvested using a Quick-RNA Microprep Kit from Zymo Research (Cat. No. R1050) according to the manufacturer’s instructions. RNA integrity was confirmed via Bioanalyzer and Qbit.
RNA was sent to BGI Genomics for library generation and RNA sequencing. RNA was sequenced on an Illumina-HiSeq2500/4000 to a depth of 20 million reads.

treatment_protocol: Thymuses were removed and thymocytes were dissociated into single cell suspensions into RPMI. Thymocytes were surface stained with CD4, CD8, CXCR4 and CCR7 antibodies and then sorted into CD4+CD8+CXCR4+CCR7- (early positive selection), CD4+CD8+CXCR4-CCR7+ (late positive selection), and CD4-CD8+CXCR4-CCR7+ (Mature CD8SP) populations using a BD Influx or BD FACSAria Fusion sorter.

value: TG6tg H2b/d

value: C57/BL6 x B6.C-H2d/bByJ

tag: sort population

value: early positive selection


title: ML171604 Thermal neutrality

description: Total gene counts before processing


title: TG6C-3

description: TG6 biological replicate 3


title: ATAC-seq_patient-176_time-D0_naive

value: Cultured CAR-T cells


title: ML171603 Thermal neutrality

description: Total gene counts before processing

value: Female


title: TG62B-2

description: TG6 biological replicate 2

value: late positive selection


title: TG6C-1

description: TG6 biological replicate 1


title: ML171605 Thermal neutrality

description: Total gene counts before processing

value: Brown adipose tissue


title: ML171593 Cold exposure

description: Total gene counts before processing

value: KO


title: ML171594 Cold exposure

description: Total gene counts before processing

value: WT


title: TG6A-2

description: TG6 biological replicate 2

value: mature single positive


title: ML171591 Cold exposure

description: Total gene counts before processing


title: TG62B-1

description: TG6 biological replicate 1


title: TG6A-1

description: TG6 biological replicate 1


title: OTIC-3

description: OT-1 biological replicate 3

value: OT-1tg Rag2KO


title: ML171587 Thermal neutrality

description: Total gene counts before processing

value: Thermal neutrality


title: ML171586 Thermal neutrality

description: Total gene counts before processing


title: TG6A-3

description: TG6 biological replicate 3


title: ML171585 Cold exposure

description: Total gene counts before processing


title: OTIC-1

description: OT-1 biological replicate 1


title: OTIC-2

description: OT-1 biological replicate 2


title: OTIB-3

description: OT-1 biological replicate 3


title: ML171584 Cold exposure

description: Total gene counts before processing


title: ML171590 Cold exposure

description: Total gene counts before processing


title: ML171583 Cold exposure

description: Total gene counts before processing


title: OTIB-2

description: OT-1 biological replicate 2


title: ML171580 Room temperature

description: Total gene counts before processing


title: ML171581 Room temperature

description: Total gene counts before processing


title: ML171592 Cold exposure

description: Total gene counts before processing


title: ML171577 Room temperature

description: Total gene counts before processing


title: ML171579 Room temperature

description: Total gene counts before processing


title: OTIA-1

description: OT-1 biological replicate 1


title: OTIA-2

description: OT-1 biological replicate 2


title: ML171578 Room temperature

description: Total gene counts before processing


title: ML171576 Room temperature

description: Total gene counts before processing


title: OTIA-3

description: OT-1 biological replicate 3


title: F5C-3

description: F5 biological replicate 3

value: F5tg Rag1KO


title: ML171575 Room temperature

description: Total gene counts before processing


title: ML171574 Room temperature

description: Total gene counts before processing


title: F5B-3

description: F5 biological replicate 3


title: BMDM_Ctrl-3

first: Varshini

last: Vasudevaraja

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38, respectively) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Heatmaps and other statistics was performed using R3.2
Genome_build: mm10
Supplementary_files_format_and_content: csv files include raw read counts table for genomic features and Transcript FPKM counts.

source_name: Bone marrow

growth_protocol: Bone marrow derived macrophages (BMDMs) were isolated and plated with cRPMI and GM-CSF in a standard cell incubator

extract_protocol:
Bone marrow derived macrophages were collected and flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Piceatannol or vehicle were added to day 7 BMDM cultures overnight

value: Bone marrow derived macrophage

tag: agent

value: control


title: F5A-2

description: F5 biological replicate 2


title: F5A-3

description: F5 biological replicate 3


title: BMDM_Ctrl-1


title: BMDM_Ctrl-2


title: OTIB-1

description: OT-1 biological replicate 1


title: RNA-Seq drddDD7 pro-Rep3

city: Shanghai

first: Huang

last: Huan

address: No. 3888 Chenhua Road

institute: Chinese Academy of Sciences

description: drddDD7 pro-Rep3

data_processing:
Low-quality sequences (q < 20) were trimmed using trimmomatic(v0.36).And adapters were removed by cutadapt.
Reads were mapped to TAIR10 using STAR(v2.5.3)
Differetial gene expresssion was analysed by DESeq
RSEM(v2.3.0) was used to estimate gene expression from RNA-Seq data
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: 10-days-old Col-0 plants grown in 1/2MS plates

extract_protocol:
Total RNAs were extracted using the RNeasy Plant (Qiagen, Hilden, Germany).
Total RNAs were sent to the Genomics Core Facility at the Shanghai Center for Plant Stress Biology (Shanghai, China) for library preparation and sequencing using standard Illumina protocols.

value: mutant


title: BMDM_Piceatannol-3

value: Piceatannol


title: F5A-1

description: F5 biological replicate 1


title: BMDM_Piceatannol-1


title: F5C-1

description: F5 biological replicate 1


title: F5C-2

description: F5 biological replicate 2


title: RNA-Seq dmeDD7 pro-Rep1

department: Shanghai Center for Plant Stress  Biology

description: dmeDD7 pro-Rep1


title: F5B-1

description: F5 biological replicate 1


title: RNA-Seq drddDD7 pro-Rep2

description: drddDD7 pro-Rep2


title: BMDM_Piceatannol-2


title: RNA-Seq dmeDD7 pro-Rep2

description: dmeDD7 pro-Rep2


title: RNA-Seq drdd+395 pro

description: drdd+395 pro


title: F5B-2

description: F5 biological replicate 2


title: RNA-Seq rdd-2-Rep2


title: RNA-Seq Col-0-Rep2

value: wild type


title: RNA-Seq rdd-2-Rep3


title: RNA-Seq Col-0-Rep3


title: RNA-Seq drddDD7 pro-Rep1

description: drddDD7 pro-Rep1


title: RNA-Seq Col-0-Rep1


title: BS-Seq drddDD7 pro-Rep2-BS

description:
drddDD7 pro-Rep2-BS
treated with bisulfite

data_processing:
Low-quality sequences (q < 20) were trimmed using trimmomatic(v0.36).And adapters were removed by cutadapt.
Reads were mapped to TAIR10 using BSMAP 2.90
methratio.py python script of BSMAP was used to extract metylation ratios from BSMAP results with parameters -z and -r
Genome_build: TAIR10

growth_protocol: 10-days-old plants grown in 1/2MS plates

extract_protocol:
Total DNAs were extracted using the DNeasy Plant (Qiagen, Hilden, Germany).
Genomic DNA was extracted from 10-d-old seedlings and sent to  the Genomics Core Facility at the Shanghai Center for Plant Stress Biology  (Shanghai, China)  for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.


title: BS-Seq drddDD7 pro-Rep3-BS

description:
drddDD7 pro-Rep3-BS
treated with bisulfite


title: BS-Seq drddDD7 pro-Rep1-BS

description:
drddDD7 pro-Rep1-BS
treated with bisulfite


title: BS-Seq drdd+395 pro-BS

description:
drdd+395 pro-BS
treated with bisulfite


title: BS-Seq dmeDD7 pro-Rep2-BS

description:
dmeDD7 pro-Rep2-BS
treated with bisulfite


title: RNA-Seq rdd-2-Rep1


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P16

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.54.1).

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Nineteen overweight (BMI>27 kg/m2) male and postmenopausal female subjects between 50-70 years old with an impaired glucose tolerance were recruited. Impaired glucose tolerance was determined by either a 75g two-hour OGTT with glucose levels >7.8 mmol/L and/or a fasting glucose > 6.1 mmol/L. All subjects were non-smoking, had a stable body weight and were not diagnosed with a chronic medical condition or high blood pressure (systolic> 160mmHg and/or diastolic > 100mmHg). Subjects were not allowed to use any medication or food supplements known to interfere with glucose homeostasis. Subjects were not allowed to participate if they used medication, known to interact with Hypericum perforatum (St. John’s Wort). Female participants were not allowed to use any hormone treatment and the menstrual cycle had to be absent for more than one year. The study was conducted according to the principles of the Declaration of Helsinki, in accordance with the Medical Research Involving Human Subjects Act (WMO) and registered at Clinical Trials.gov (identifier NCT NCT02065271).

extract_protocol: Total RNA was prepared from the adipose tissue biopsies  using TRIzol reagent, whereafter purified total RNA was isolated using and RNeasy Mini Spin columns (RNeasy mini kit, Qiagen, Venlo, the Netherlands). RNA was quantified (Nanodrop ND 1000, Nanodrop technologies, Wilmington, Delaware USA) and integrity was checked by an Agilent 2100 Bioanalyser with RNA 6000 nanochips (Agilent Technologies, South Queensferry, UK). Samples passed the RNA quality control if RIN>7.

treatment_protocol: The study was a randomised, double blind, placebo controlled cross-over intervention trial in which subjects received two interventions, e.g. an intervention with a herbal mixture and an intervention with a placebo supplement. During the 4 week intervention, subjects consumed three times a day one capsule with either the herbal supplement or the placebo before a meal. Subjects received both interventions in a random order with a wash-out period of 4-weeks between both interventions. The herbal preparation contained some common herbs, like mint leaves, coriander, oregano, rosemary and some are less common like kodra millet, buckbean and siam pumpkin (see paper). Placebo contained 500mg microcrystalline cellulose. Capsules were matched in size and colour for blinding.

value: adipose tissue

tag: Sex

value: female

tag: subjectid

tag: bmi

tag: intervention name

value: placebo preparation


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P21

value: male

value: herbal preparation


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P08


title: BS-Seq rdd-2-Rep3-BS

description:
rdd-2-Rep3-BS
treated with bisulfite


title: BS-Seq dmeDD7 pro-Rep1-BS

description:
dmeDD7 pro-Rep1-BS
treated with bisulfite


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P18


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P04


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P04


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P21


title: BS-Seq rdd-2-Rep2-BS

description:
rdd-2-Rep2-BS
treated with bisulfite


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P16


title: BS-Seq rdd-2-Rep1-BS

description:
rdd-2-Rep1-BS
treated with bisulfite


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P14


title: BS-Seq Col-0-Rep3-BS

description:
Col-0-Rep3-BS
treated with bisulfite


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P08


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P03


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P18


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P07


title: BS-Seq Col-0-Rep2-BS

description:
Col-0-Rep2-BS
treated with bisulfite


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P14


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P03


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P17


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P22


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P07


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P05


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P22


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P02


title: adipose tissue biopsy, after 4 wks supplementation with herbal preparation, subject P09


title: BS-Seq dme-3-In-Rep3-BS

description:
dme-3-In-Rep3-BS
treated with bisulfite


title: BS-Seq Col-0-Rep1-BS

description:
Col-0-Rep1-BS
treated with bisulfite


title: BS-Seq dme-3-In-Rep1-BS

description:
dme-3-In-Rep1-BS
treated with bisulfite


title: BS-Seq dme-T-In-Rep3-BS

description:
dme-T-In-Rep3-BS
treated with bisulfite


title: BS-Seq dme-T-In-Rep2-BS

description:
dme-T-In-Rep2-BS
treated with bisulfite


title: BS-Seq dme-T-In-Rep1-BS

description:
dme-T-In-Rep1-BS
treated with bisulfite


title: BS-Seq dme-A-del-BS

description:
dme-A-del-BS
treated with bisulfite


title: BS-Seq rdd-2-weak-Rep3-BS

description:
rdd-2-weak-Rep3-BS
treated with bisulfite


title: BS-Seq rdd-2-weak-Rep2-BS

description:
rdd-2-weak-Rep2-BS
treated with bisulfite


title: BS-Seq rdd-2-weak-Rep1-BS

description:
rdd-2-weak-Rep1-BS
treated with bisulfite


title: BS-Seq dme-3-In-Rep2-BS

description:
dme-3-In-Rep2-BS
treated with bisulfite


title: DN614-EW6

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D11_OFF_D7

data_processing:
Expression levels of genes were quantified using Kallisto 0.44.0 , with Gencode v27 reference transcriptome , and hg38 as the reference human genome
TPMs were summed for transcript-level quantification
TPM
Genome_build: hg38
Supplementary_files_format_and_content: TPM

source_name: CAR T CELLS

extract_protocol:
Cryopreserved T cells were thawed and activated on day 0 with Human T-Expander αCD3/CD28 Dynabeads (Gibco) at 3:1 bead:cell ratio in T cell media (AIMV supplemented with 5% FBS, 10mM HEPES, 2mM GlutaMAX, 100 U/mL penicillin, and 100ug/mL streptomycin (Gibco). Recombinant human IL-2 (Peprotech) was provided at 100 U/mL. Lentiviral transduction was done on day 1 and retroviral transductions were done on days 2 and 3 post-bead activation. Magnetic beads were removed on day 4, and T cells were fed with fresh culture medium every 2-3 days and normalized to 0.5 x 106 cells/mL. For culture conditions requiring αPD-1, 5ug/mL nivolumab was added on D7 and supplemented every 2-3 days. For culture conditions requiring shield-1 (1uM unless otherwise noted), trimethoprim (1uM unless otherwise noted), dasatinib (1uM), or tazemetostat (1uM), freshly thawed drug was mixed with T cell culture medium and supplemented every 2-3d ays. HA.28ζ.FKBP CAR-T cells were rested via removal of either shield-1 or trimethoprim from the culture medium, whereby cells were washed 2X in PBS (changing conicals in between washes to ensure complete drug washout) and resuspended in fresh T cell culture medium lacking shield-1/trimethoprim. On days 7, 11, and 15 of culture, RNA was isolated using Qiagen mRNEasy kit.
Samples library prep and sequencing was performed by BGI America (Cambridge, MA)

tag: individual

value: CAR T CELLS

tag: culture conditions

value: Shield-1 D1-D7 + complete medium

tag: timepoint

value: Day 11


title: BS-Seq Col-0-weak-Rep2-BS

description:
Col-0-weak-Rep2-BS
treated with bisulfite


title: DN614-EW4

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D11_A_ON

value: Shield-1 D1-11 + complete medium


title: BS-Seq Col-0-weak-Rep1-BS

description:
Col-0-weak-Rep1-BS
treated with bisulfite


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P17

tag: tissue


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P02


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P05


title: DN614-EW5

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D11_A_ON_Nivo

tag: cell type

value: Shield-1 D1-11 + anti-PD-1 D7-11 + complete medium


title: DN614-EW2

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D7_A_ON

tag: treatment

value: Shield-1 D1-7 + complete medium

value: Day 7


title: adipose tissue biopsy, after 4 wks supplementation with placebo preparation, subject P09


title: DN614-EW1

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D7_A_OFF

value: Complete medium


title: C_MCF10DCIS-sh:p53_RMF_3D_rep2

city: Chapel Hill

first: Melissa

middle: A

last: Troester

state: NC

address: 135 Dauer Dr

institute: University of North Carolina

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: Microarray data were Lowess-normalized, and probes with signal >10 dpi in both channels and data present in at least 80% of samples were selected for further analysis. During data pre-processing, we: 1) eliminated probes without corresponding ENTREZ Gene IDs; 2) collapsed duplicate probes corresponding to the same ENTREZ Gene ID by averaging; and 3) imputed missing data using the k-nearest neighbors’ imputation with k = 10.

source_name: MCF10DCIS-sh:p53 3D co-culture

label_protocol: Samples were labeled and amplified using the Agilent Low Input Two-Color, QuickAmp Labeling kit (#5190-2306). Cy-5-labeled cDNAs were generated from all experimental samples, and reference RNA (Stratagene Universal Human Reference spiked 1:1000 with MCF-7 RNA and 1:1000 ME16C RNA to increase expression of breast cancer genes) was labeled with Cy-3.

growth_protocol: MCF10 series cells were maintained in Dulbecco’s modified Eagle’s medium/F12 nutrient mix (DMEM/F12, Gibco, Life Technologies, Carlsbad, CA) supplemented with 5% horse serum (Gibco), 20 ng/mL epidermal growth factor (Invitrogen, Life Technologies, Carlsbad, CA), 0.5 μg/mL hydrocortisone (Sigma-Aldrich, St. Louis, MO), 10 μg/mL insulin (Gibco), and 0.1 μg/mL cholera toxin (Millipore Sigma, Burlington, MA). RMFs were maintained in RPMI1640 medium with 10% fetal bovine serum prior to use in co-cultures. All cells were grown in a humidified incubator at 37°C and 5% CO2, and propagated for <6 months (breast cells) or <1 month (RMFs) prior to use in experiments.

extract_protocol: Cultures were rinsed with cold PBS, and technical replicates (2 cultures per independent experiment) were transferred into a single conical tube containing 800 μL of Cell Recovery Solution (#354253; Corning) on ice. Each well was rinsed with additional Cell Recovery Solution to ensure complete sample transfer. Phenol-chloroform RNA extraction was then performed using QIAzol lysis reagent (QIAGEN) according to the manufacturer’s instructions, with modifications: following centrifugal separation of the organic and aqueous phases, the aqueous phase was mixed with 100% ethanol at a ratio of 1:1 v/v and applied to a QIAGEN RNeasy column. RNA concentrations were determined using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA). Samples were further purified with the RNA Clean and Concentrator Kit (Zymo Research, Irvine, CA) as needed.

treatment_protocol: Cells were suspended in a biologically derived matrix comprised of 50% phenol red-free Matrigel (#356237; Corning, Corning, NY) and 50% rat-tail collagen I (#354236; Corning) diluted to a final concentration of 1 mg/mL as previously described [8, 9, 22, 23]. Suspended cells were then seeded into tissue culture plates pre-coated with the same matrix, and growth medium was dispensed to the apical side of each culture after 30-60 minutes. Cultures were constructed with the same total starting cell number (30,000 cells/mL for mono-cultures; 15,000 breast cells/mL + 15,000 RMFs/mL for co-cultures), rather than the same starting number of breast cells, to reduce the potential for nutrient deprivation in co-cultures. RMF mono-cultures (30,000 cells/mL) were generated as normalization controls for gene expression microarray analyses (see below). Cultures were refreshed with MCF10 growth medium every 2-3 days, and maintained for 14 days.

tag: cell line

value: MCF10DCIS + reduction mammoplasty fibroblast

tag: epithelial p53 status

value: p53-deficient (knock-down)

tag: sample type

value: reference


title: DN0022-EW6

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D11_OFF_D7


title: C_MCF10AT1-sh:p53_RMF_3D_rep1

source_name: MCF10AT1-sh:p53 3D co-culture

value: MCF10AT1 + reduction mammoplasty fibroblast

source_name: Stratagene Universal Human Reference spiked 1:1000 with MCF-7 RNA and 1:1000 ME16C RNA


title: C_MCF10DCIS-sh:GFP_RMF_3D_rep2

source_name: MCF10DCIS-sh:GFP 3D co-culture

value: p53-sufficient (wild-type)


title: DN614-EW3

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D11_A_OFF


title: polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 3

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_36_72h_S2_200nM17AAG-3

data_processing:
Sequencing reads were aligned to the human genome (version hg19) using hisat2 (Kim et al., 2015, doi: 10.1038/s41587-019-0201-4), and reads counted using quasR (Gaidatzis et al., 2015, doi: 10.1093/bioinformatics/btu781)
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values; readcounts

molecule: polyA RNA

source_name: AEC

growth_protocol: Airway epithelial cells (AEC) were prepared as described previously (Imai-Matsushima et al., 2018, doi: 10.1016/j.ebiom.2018.05.032)

extract_protocol:
For polyA/total/small RNA-seq, cells were lysed in Trizol and RNA extracted using standard methods.
RNA was extracted using the RNA clean and concentrator kit (Zymo) and subjected to bulk polyA RNA-sequencing using the NebNext Ultra II Directional RNA Library (New England Biolabs).

treatment_protocol: Infections were done by adding the appropriate amount of virus stock solution (produced in Vero E6 cells) at an MOI of 0.5 directly to the cells. For mock infections, supernatant from non-infected Vero E6 cells was used. Two hours after adding the virus, growth mediu was supplemented with DMSO (solvent control) or 17-AAG as indicated.

tag: infection

tag: moi

tag: time point


title: DN0022-EW5

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D11_A_ON_Nivo


title: DN0022-EW4

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D11_A_ON


title: polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_35_72h_S2_200nM17AAG-2


title: C_MCF10DCIS-sh:GFP_RMF_3D_rep1


title: DN0022-EW3

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D11_A_OFF


title: C_MCF10AT1-sh:GFP_RMF_3D_rep2

source_name: MCF10AT1-sh:GFP 3D co-culture


title: C_MCF10AT1-sh:GFP_RMF_3D_rep1


title: C_MCF10A-sh:p53_RMF_3D_rep1

source_name: MCF10A-sh:p53 3D co-culture

value: MCF10A + reduction mammoplasty fibroblast


title: polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_34_72h_S2_200nM17AAG-1


title: DN0022-EW1

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D7_A_OFF


title: DN0022-EW2

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D7_A_ON


title: DN614-EW7

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D15_A_OFF

value: Day 15


title: polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_33_72h_S2_DMSO-3


title: C_MCF10DCIS-sh:p53_RMF_3D_rep1


title: DN614-EW9

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D15_A_ON_Nivo

value: Shield-1 D1-15 + anti-PD-1 D7-15 + complete medium


title: polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_32_72h_S2_DMSO-2


title: BS-Seq Col-0-weak-Rep3-BS

description:
Col-0-weak-Rep3-BS
treated with bisulfite

tag: genotype

value: wild type


title: polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_31_72h_S2_DMSO-1


title: DN614-EW11

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D15_OFF_D11

value: CAR T CELLS


title: C_MCF10A-sh:GFP_RMF_3D_rep2

source_name: MCF10A-sh:GFP 3D co-culture


title: polyA RNA from AEC, harvested at 72hpi, mock infected, 17-AAG (200 nM) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_30_72h_200nM17AAG-3

value: mock


title: DN0022-EW7

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D15_A_OFF


title: DN0022-EW8

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D15_A_ON

value: Shield-1 D1-15 + complete medium


title: Culture media, blank, 17 hours

type: other

city: London

first: Dean

middle: Harvey

last: Betts

state: Ontario

address: 1151 Richmond St.

department: Department of Physiology and Pharmacology

country: Canada

institute: Western University

description: Control

data_processing:
The array data was normalized to the endogenous control (U6) signals on each plate. Caution: Since these arrays were used as a discovery tool to identify new mature microRNAs in conditioned culture media, this typical normalization regime is less meaningful in this context. Notably, the U6 RNA in the blank negative control microdroplets originated from a non-murine origin.
Fold-change matrix reflects the fold change increase in the normalized conditioned sample compared to the normalized blank, calculated when possible.

label: FAM

organism: other sequences

source_name: Culture media (KSOM, BSA-free, 0.1% polyvinylacetate), no blastocysts, cultured for 17 hours

label_protocol: A TaqMan MicroRNA Cells-to-Ct Kit was used to lyse and digest the samples. Reverse transcription of microRNA target cDNA was generated using TaqMan MicroRNA Reverse Transcription Kit followed by preamplification using TaqMan Megaplex Preamp Primers (12 cycles). qPCR amplification was performed using a Viia7 instrument equipped with an adapter block for compatibility with TaqMan MicroRNA Rodent v3.0 A + B Cards.

growth_protocol: 3 wk. old female mice were superovulated, mated with male CD1 mice, euthanized and the zygotes collected. Zygotes were collected and cultured (5% O2, 5% CO2, 37C) until 99 hours post-hCG, at which point 25 blastocysts were selected and cultured separately under this atmosphere in an 8 uL microdroplet until 116 hours post-hCG.

extract_protocol: No RNA extraction was performed; instead, a TaqMan 'Cells-to-Ct' kit was used. 6 µL of whole conditioned media was mixed with equal parts 'Lysis Solution' containing 1:100 DNase I, followed by 'Stop Solution' after 8 minutes. RT/qPCR was performed directly on this.

tag: culture

value: No blastocysts

tag: sample

value: Culture media


title: DN614-EW8

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D15_A_ON


title: DN0022-EW9

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D15_A_ON_Nivo


title: polyA RNA from AEC, harvested at 72hpi, mock infected, 17-AAG (200 nM) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_29_72h_200nM17AAG-2


title: C_MCF10A-sh:p53_RMF_3D_rep2


title: C_MCF10A-sh:GFP_RMF_3D_rep1


title: DN0022-EW11

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D15_OFF_D11

value: Shield-1 D1-11 + complete medium


title: C_MCF10AT1-sh:p53_RMF_3D_rep2


title: DN0022-EW10

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0022_D15_OFF_D7

value: Shield-1 D1-7 + complete medium


title: DN614-EW10

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor0614_D15_OFF_D7


title: M_RMF_DMEM/F12_3D_rep4

source_name: RMF mono-culture

value: Reduction mammoplasty fibroblast


title: D7_A_ON

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D7_A_ON

value: Day 7


title: M_RMF_DMEM/F12_3D_rep1


title: polyA RNA from AEC, harvested at 72hpi, mock infected, DMSO (solvent) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_26_72h_DMSO-2


title: M_RMF_DMEM/F12_3D_rep2


title: polyA RNA from AEC, harvested at 72hpi, mock infected, DMSO (solvent) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_25_72h_DMSO-1


title: D15_OFF_D7

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D15_OFF_D7


title: M_MCF10DCIS-sh:p53_3D_rep1

source_name: MCF10DCIS-sh:p53 3D mono-culture

value: p53-deficient (knock-down)


title: M_MCF10DCIS-sh:p53_3D_rep2

value: reference


title: polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 3

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_24_48h_S2_200nM17AAG-3


title: D15_OFF_D11

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D15_OFF_D11


title: polyA RNA from AEC, harvested at 72hpi, mock infected, 17-AAG (200 nM) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_28_72h_200nM17AAG-1


title: D7_A_OFF

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D7_A_OFF

value: Complete medium


title: D15_A_ON_Nivo

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D15_A_ON_Nivo


title: PP_16: Postpartum cow 4 d100

city: Aichi-gun

first: Shuichi

last: Matsuyama

address: 94 Hatajiri, Morowa

institute: Nagoya University

hyb_protocol: For microarray hybridization, 1650 ng of Cy3-labeled cRNA was fragmented and hybridized on a slide of bovine 4 × 44K microarray (Agilent Technologies; 023647) at 65°C for 17 hours.

scan_protocol: Slides were scanned on the Agilent G2505C DNA microarray scanner.

data_processing: Background correction of the Cy3 raw signals was performed using the Agilent Feature Extraction software (version 10.5.1.1). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Bos taurus

source_name: Endometrial tissue in fertile cow_4

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction. Labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from the endometrial samples using RNeasy Plus Universal Mini kit (Qiagen) according to the manufacturer’s instructions. Total RNA quality and quantity were confirmed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.

tag: animal no.

tag: days after parturition

value: endometrium


title: M_MCF10AT1-sh:GFP_3D_rep2

source_name: MCF10AT1-sh:GFP 3D mono-culture

value: p53-sufficient (wild-type)


title: polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 1

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_22_48h_S2_200nM17AAG-1


title: M_MCF10AT1-sh:p53_3D_rep2

source_name: MCF10AT1-sh:p53 3D mono-culture


title: M_MCF10DCIS-sh:GFP_3D_rep2

source_name: MCF10DCIS-sh:GFP 3D mono-culture


title: M_MCF10AT1-sh:GFP_3D_rep1


title: M_MCF10DCIS-sh:GFP_3D_rep1


title: D15_A_ON

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D15_A_ON

tag: individual

value: Day 15


title: PP_14: Postpartum cow 4 d30


title: polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_23_48h_S2_200nM17AAG-2


title: PP_15: Postpartum cow 4 d50


title: D15_A_OFF

description:
Processed_log2TPM_Tuning-CAR-dataset.csv
Donor3047_D15_A_OFF

tag: culture conditions


title: polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 2

description:
polyA RNA extracted from whole cells
AEC_SARSCoV2_17AAG_readcounts.tsv.gz
AECII_20_48h_S2_DMSO-2


title: M_MCF10AT1-sh:p53_3D_rep1