title: Bcell_RNASeq_Spt5dep3_32282

data_processing:
Adapters were trimmed from the 3' ends of the reads with cutadapt v1.10.
The trimmed reads larger than 18nt were aligned against the Fitz et al 25 rDNA of the respective organism using bowtie2 v 2.1.0 (--sensitive-local --score-min G,30,8 -N 0 --ignore-quals) to remove the rRNA reads.
rRNA cleaned reads were aligned to the genome with the TopHat splice junction mapper for RNA-seq reads v1.4.1.
Reads were quantified with featureCounts v1.5.0-p1.
Differentially expressed genes were obtained using DESeq2 v1.10.1 according to its standard comparison between two experimental conditions vignette.
Differentially expressed mRNAs were filtered for a p-adjusted value of <0.1 and a fold-change of >2.
Genome_build: NCBI mm9
Supplementary_files_format_and_content: Tab-delimited table with raw counts and DESeq2 log2-foldchanges and adjusted p-values

extract_protocol:
Cells were harvested and total RNA was extracted with Trizol reagent.
Library preparation for mRNAseq was performed using the SENSE mRNA-seq kit from Lexogen following their instructions.


title: RVI4: Vemurafenib_Ibrutinib_3

status: Public on Feb 27 2020

type: SRA

city: East Lansing

first: Sean

middle: Alexander

last: Misek

state: MI

address: 1355 Bogue Street

country: USA

institute: Michigan State University

library_source: transcriptomic

data_processing:
Basecalls performed with Illumina Real Time Analysis, RTA
Demultiplexing and FastQ conversion with Illumina Bcl2fastq
Quality Control with FastQC v0.11.5
Read Trimming with Trimmomatic v0.33
Read Mapping with HISAT2 v2.1.0
Read Counting/Analysis with HTSeq v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw HTSeq counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Human Melanoma Cells

growth_protocol: M229R cells were grown in DMEM + 1% Anti/Anti + 10% FBS which was supplemented with 2 µM vemurafenib.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit, prepared libraries were QCd and quantified using a Qubit and Labchip Bioanalyzer.

treatment_protocol: M229R cells were treated with either vemurafenib (2 µM), ibrutinib (5 µM), acalabrutinib (5 µM), or the combination of ibrutinib/acalabrutinib and vemurafenib for 24 h prior to RNA extraction.

tag: tissue

value: Human Melanoma Cells

tag: cell line


title: Bcell_4H8_Spt5dep2_40939

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

library_source: genomic

data_processing:
Adapters were trimmed from the 3' ends of the reads with cutadapt v1.10.
Trimmed reads larger than 18nt were aligned to the genome using bowtie v1.0.0 (-v 2 --best --strata --tryhard -m 1)
Genome_build: NCBI mm9
Supplementary_files_format_and_content: bigWig of rpm-normalized read densities

molecule: genomic DNA

organism: Mus musculus

source_name: primary activated splenic B lymphocytes

growth_protocol: Primary immature B cells were isolated from spleens of Supt5hFl/-Rosa26ERT2-cre/+ and Rosa26ERT2-cre/+ mice and cultured in complete RPMI medium wit IL4/LPS stimulation.

extract_protocol:
ChIPseq and ChIP-qPCR were performed as described without modifications (Pavri et al., 2010). In short, 20x10^6 cells were crosslinked with 1% HCHO for 10 min at 37 degree. After quenching with 0,125 M glycine, cells were sonicated with the Diagenode Bioruptor sonication machine.
After chromatin-immunprecipitation, samples were end-repaired with the Epicenter End-Repair Kit. After A-tailing the samples with Klenow (exo-) enzyme, NEXTflex adapters were ligated to the samples and then purified with AMPure XP beads. PCR amplification of the libraries was performed with the Phusion-HF enzyme and the NEXTflex primer mix.

treatment_protocol: Primary acttivated B cells were activated for 28h prior to the addition of 2 uM 4-HT for 32h (total of 60 h B cell activation with 32h 4-HT treatment) and then harvested for all downstream applications.

tag: antibody

value: RNA Pol II (4H8)

tag: cell type

value: Supt5hFl/- Rosa26ERT2-cre/+ primary mature B cells

tag: treatment

value: 4-hydroxy tamoxifen (4-HT)


title: Bcell_RNASeq_Spt5dep2_32279

molecule: polyA RNA


title: RVI3: Vemurafenib_Ibrutinib_2


title: 200611820005_R03C01

type: genomic

city: Exeter

first: Stefania

last: Policicchio

state: Devon

address: RILD building, BARRACK ROAD, Albion Place

country: United Kingdom

institute: University of Exeter, Medical School

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K Beadchip using standard Illumina protocol

scan_protocol: Samples were assessed using the Illumina Infinium Human Methylation850K BeadChip (Illumina) and arrays were imaged using a Illumina iScan System (Illumina).

data_processing: llumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization).   Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on   Illumina’s database and probes identified by Chen et al.* were removed. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: Cy3 and Cy5

source_name: postmortem brain

label_protocol: Samples were processed according to the Illumina Infinium Human Methylation850K BeadChip (Illumina) standard protocol.

extract_protocol: Genomic DNA was isolated from post mortem human brain using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

tag: age

tag: groupid

tag: gender

value: Female


title: Control+FMN_RNASeq 3, biological rep1

city: Göteborg

first: Xin

last: Chen

address: Kemigården 4

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

data_processing:
The raw reads from each sample were mapped to the CEN.PK 113-7D reference genome using TopHat (v 2.0.12), with 84.0—87.6% of the reads successfully mapped.
Cufflinks version 2.2.1 was used to calculate FPKM values, and the feature Counts module of the Subread package (v 1.4.6) was used to determine raw read counts.
Genome_build: CEN.PK 113-7D

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: shake flask 30 ˚C, 200rpm

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit with a FastPrep homogenizer to disrupt cells.
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.

treatment_protocol: Samples of cells were frozen rapidly in liquid nitrogen to prevent mRNA turnover.

tag: strain

value: integration of two copies of promoter+terminator sequences

tag: supplementation

value: FMN


title: Control+FMN_RNASeq 1, biological rep1


title: Control+FMN_RNASeq 2, biological rep1


title: RVI2: Vemurafenib_Ibrutinib_1


title: RA4: Acalabrutinib_3


title: Bcell_RNASeq_WT2_32280

value: Rosa26ERT2-cre/+ primary B cells


title: Bcell_RNASeq_WT3_32281


title: Control_RNASeq 4, biological rep3


title: Control_RNASeq 3, biological rep3


title: Bcell_RNASeq_WT1_32277


title: Bcell_GROSeq_Spt5dep2_24474

data_processing:
Library strategy: GRO-seq
Adapters were trimmed from the 3' ends of the reads with cutadapt (v 1.10), and a 5nt random linker was removed from the 3' end using fastx_trimmer.
Trimmed reads larger than 10nt were aligned to the genome using bowtie v1.0.0 (-v 2 --best --strata -- tryhard -m 1).
Genome_build: NCBI mm9
Supplementary_files_format_and_content: bigWig of rpm-normalized read densities

extract_protocol:
Following cell membrane lysis with hypotonic buffer, nuclei were isolated via sucrose gradient density centrifugation. GROseq was performed as described (Core & Lis, 2008). Briefly, 10 million nuclei were used per reaction, and the run-on was performed for 5 minutes with NTPs with a  limiting concentration of P32-dCTP and dBrdUTP followed by extraction of RNA with Trizol reagent (Thermo Fisher, 15596026). An updated protocol was kindly provided by Dr. John Lis (Cornell University).
After base hydrolysis and DNA end repair, Illumina compatible 3' RNA adapters were ligated to total RNA. After BrdU- incorporated RNA IP the 5' cap was removed and the 5' DNA end was repaired. Next, the 5' DNA Illumina comaptible adapters were ligated, and the library was reverse transcribed and amplified.


title: 200611820014_R06C01


title: RA2: Acalabrutinib_1


title: Control_RNASeq 2, biological rep3


title: Control_RNASeq 1, biological rep3


title: Bcell_GROSeq_Spt5dep1_24473


title: RI3: Ibrutinib_2


title: Control_RNASeq 4, biological rep2


title: 200611820008_R08C01

value: Male


title: RI4: Ibrutinib_3


title: 200616470004_R07C01


title: RI2: Ibrutinib_1


title: Bcell_RNASeq_Spt5dep1_32278


title: 200611820014_R05C01


title: Control_RNASeq 2, biological rep2


title: RV4: Vemurafenib_3


title: Lung Resident Cells Flu Rep2

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 10bp UMI tags were extracted from Read2.
Please note that the BAM files contain only single end reads. Though the sequence was paired, the other mate contains cell barcode information and is not present in the BAM file.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5;  Cell ranger HDF5 Feature Barcode Matrix Format, this file  contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.

source_name: Lung Resident Cells Flu

extract_protocol:
Single-cell barcoded droplets were produced using 10X Single Cell 3’ v2 chemistry. Libraries generated were sequenced using the HiSeq Rapid SBS kit.
For the heterogeneous pulmonary endothelium samples, the resulting libraries were sequenced across two lanes of an Illumina HiSeq2500 instrument in High-output mode. For the whole lung samples, the resulting libraries were sequenced across a single lane of an Illumina HiSeq2500 instrument in Rapid Run mode

tag: genotype

value: wild type

value: Adult; 6-8 weeks

value: Flu

value: CD45- Sorted lung Cells


title: RV3: Vemurafenib_2


title: Lung Resident Cells Flu Rep1


title: 200611820008_R01C01


title: Control_RNASeq 1, biological rep2


title: RV2: Vemurafenib_1


title: Lung Resident Cells Control

source_name: Lung Resident Cells Control

value: control


title: Bcell_GROSeq_WT2_24472


title: RD4: DMSO_3


title: Control_RNASeq 4, biological rep1


title: Control_RNASeq 3, biological rep1


title: RD3: DMSO_2


title: Lung Endothelial Cells Rep2

source_name: Lung Endothelial Cells control

value: CD31+/C45- Sorted Lung Cells


title: Control_RNASeq 3, biological rep2


title: 200611820039_R02C01


title: Control+FMN_RNASeq 2, biological rep2


title: RA3: Acalabrutinib_2


title: Control_RNASeq 1, biological rep1


title: RD2: DMSO_1


title: 200616470004_R08C01


title: 200611820008_R07C01


title: 200603290023_R01C01


title: Lung Endothelial Cells Rep3


title: Bcell_GROSeq_WT1_24471


title: 200611820005_R08C01


title: Control_RNASeq 2, biological rep1


title: 200603290076_R01C01


title: 200611820039_R04C01


title: 200611820014_R04C01


title: 200603220015_R04C01


title: Lung Endothelial Cells Rep1


title: Femoral bone of female 27-89

status: Public on Feb 26 2020

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

description:
Sample ID:  27-89
genomic DNA from femoral bone of female 27-89
2703.2 ng of gDNA used

hyb_protocol: Bisulfite converted DNA was amplified, fagmented and hybridised to Infinium HumanMethylation EPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were scanned with an iScan Reader (Illumina) using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v. 2011.1 (Illumina)

label: Cy5 and Cy3

source_name: femoral bone of female 27-89

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using DNA IQ system (Promega, Madison, WI, USA) or QIA symphony DNA Investor kit (Qiagen, Hilden, Germany) based on the manufacturers’ instructions

value: 89 years

tag: ethnicity

value: Korean-Asian

value: Femoral bone


title: Femoral bone of male 35-70

description:
Sample ID:  35-70
genomic DNA from femoral bone of male 35-70
61.1 ng of gDNA used

source_name: femoral bone of male 35-70

value: 70 years


title: Femoral bone of male 24-66

description:
Sample ID:  24-66
genomic DNA from femoral bone of male 24-66
912.8 ng of gDNA used

source_name: femoral bone of male 24-66

value: 66 years


title: Femoral bone of male 20-67

description:
Sample ID:  20-67
genomic DNA from femoral bone of male 20-67
1336.3 ng of gDNA used

source_name: femoral bone of male 20-67

value: 67 years


title: Femoral bone of male 31-76

description:
Sample ID:  31-76
genomic DNA from femoral bone of male 31-76
269.7 ng of gDNA used

source_name: femoral bone of male 31-76

value: 76 years


title: Femoral bone of male 22-74

description:
Sample ID:  22-74
genomic DNA from femoral bone of male 22-74
119.3 ng of gDNA used

source_name: femoral bone of male 22-74

value: 74 years


title: Femoral bone of male 34-52

description:
Sample ID:  34-52
genomic DNA from femoral bone of male 34-52
59.8 ng of gDNA used

source_name: femoral bone of male 34-52

value: 52 years


title: Femoral bone of male 11-71

description:
Sample ID:  11-71
genomic DNA from femoral bone of male 11-71
171.5 ng of gDNA used

source_name: femoral bone of male 11-71

value: 71 years


title: Femoral bone of male 18-49

description:
Sample ID:  18-49
genomic DNA from femoral bone of male 18-49
92.4 ng of gDNA used

source_name: femoral bone of male 18-49

value: 49 years

value: Male


title: Femoral bone of female 29-96

description:
Sample ID:  29-96
genomic DNA from femoral bone of female 29-96
218.1 ng of gDNA used

source_name: femoral bone of female 29-96

value: 96 years

value: Female


title: Femoral bone of male 9-59

description:
Sample ID:  9-59
genomic DNA from femoral bone of male 9-59
81.7 ng of gDNA used

source_name: femoral bone of male 9-59

value: 59 years


title: Femoral bone of male 33-87

description:
Sample ID:  33-87
genomic DNA from femoral bone of male 33-87
82.7 ng of gDNA used

source_name: femoral bone of male 33-87

value: 87 years


title: Femoral bone of female 5-58

description:
Sample ID:  5-58
genomic DNA from femoral bone of female 5-58
21.1 ng of gDNA used

source_name: femoral bone of female 5-58

value: 58 years


title: Femoral bone of male 3-37

description:
Sample ID:  3-37
genomic DNA from femoral bone of male 3-37
25.7 ng of gDNA used

source_name: femoral bone of male 3-37

value: 37 years


title: Femoral bone of male 21-50

description:
Sample ID:  21-50
genomic DNA from femoral bone of male 21-50
71.5 ng of gDNA used

source_name: femoral bone of male 21-50

value: 50 years

value: Korean-Asian


title: Femoral bone of male 26-35

description:
Sample ID:  26-35
genomic DNA from femoral bone of male 26-35
5.8 ng of gDNA used

source_name: femoral bone of male 26-35

value: 35 years

value: Femoral bone


title: Femoral bone of male 32-75

description:
Sample ID:  32-75
genomic DNA from femoral bone of male 32-75
10.3 ng of gDNA used

source_name: femoral bone of male 32-75

value: 75 years


title: Femoral bone of male 14-60

description:
Sample ID:  14-60
genomic DNA from femoral bone of male 14-60
41.5 ng of gDNA used

source_name: femoral bone of male 14-60

value: 60 years


title: Femoral bone of male 6-38

description:
Sample ID:  6-38
genomic DNA from femoral bone of male 6-38
52.1 ng of gDNA used

source_name: femoral bone of male 6-38

value: 38 years


title: Femoral bone of male 23-74

description:
Sample ID:  23-74
genomic DNA from femoral bone of male 23-74
67.7 ng of gDNA used

source_name: femoral bone of male 23-74

value: 74 years


title: Femoral bone of male 1-74

description:
Sample ID:  1-74
genomic DNA from femoral bone of male 1-74
222.1 ng of gDNA used

source_name: femoral bone of male 1-74


title: Femoral bone of male 2-55

description:
Sample ID:  2-55
genomic DNA from femoral bone of male 2-55
147.8 ng of gDNA used

source_name: femoral bone of male 2-55

value: 55 years


title: Femoral bone of male 25-38

description:
Sample ID:  25-38
genomic DNA from femoral bone of male 25-38
50.4 ng of gDNA used

source_name: femoral bone of male 25-38


title: Femoral bone of male 30-36

description:
Sample ID:  30-36
genomic DNA from femoral bone of male 30-36
4.5 ng of gDNA used

source_name: femoral bone of male 30-36

value: 36 years


title: Femoral bone of male 17-43

description:
Sample ID:  17-43
genomic DNA from femoral bone of male 17-43
32.9 ng of gDNA used

source_name: femoral bone of male 17-43

value: 43 years

value: Male


title: MB-CN-12_S12: KO2

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: tumor cell line

growth_protocol: McCoy's 5A 10% FBS

extract_protocol:
Qiagen Rneasy protocol
Oligo-dT Library
200 bp Paired-end

value: cell Renal Carcinoma (ccRCC)

tag: genotype/variation


title: MB-CN-09_S9: KO2


title: MB-CN-10_S10: KO2


title: MB-CN-08_S8: KO1


title: Femoral bone of male 16-79

description:
Sample ID:  16-79
genomic DNA from femoral bone of male 16-79
100 ng of gDNA used

source_name: femoral bone of male 16-79

value: 79 years


title: Femoral bone of male 4-57

description:
Sample ID:  4-57
genomic DNA from femoral bone of male 4-57
109 ng of gDNA used

source_name: femoral bone of male 4-57

value: 57 years


title: Femoral bone of male 8-66

description:
Sample ID:  8-66
genomic DNA from femoral bone of male 8-66
607.1 ng of gDNA used

source_name: femoral bone of male 8-66

value: 66 years


title: MB-CN-07_S7: KO1


title: MB-CN-06_S6: KO1


title: Femoral bone of male 13-42

description:
Sample ID:  13-42
genomic DNA from femoral bone of male 13-42
84 ng of gDNA used

source_name: femoral bone of male 13-42

value: 42 years


title: MB-CN-05_S5: KO1


title: Femoral bone of male 12-47

description:
Sample ID:  12-47
genomic DNA from femoral bone of male 12-47
326.9 ng of gDNA used

source_name: femoral bone of male 12-47

value: 47 years


title: MB-CN-11_S11: KO2


title: MB-CN-04_S4: WT

value: WT


title: Femoral bone of male 19-37

description:
Sample ID:  19-37
genomic DNA from femoral bone of male 19-37
42.9 ng of gDNA used

source_name: femoral bone of male 19-37

value: 37 years

value: Korean-Asian


title: MB-CN-02_S2: WT


title: MB-CN-01_S1: WT


title: grhZwt_11-12hr

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

data_processing:
To remove adapter and low-quality sequences, raw ATAC-seq reads were trimmed using Trimmomatic v0.36 (Bolger et al., 2014).
Reads from single and paired-end libraries were aligned to the BDGP D. melanogaster genome release 6 (dm6) using bowtie 2 (Langmead et al., 2012). Single end libraries were aligned using default parameters, paired-end used parameters: -dovetail -k 2 -p 4 -N 1 -R 3
Reads that were unmapped, multiply aligning, aligned to mitochondia, and aligned to scaffolds were discarded.
MACS version 2 (Zhang, et al., 2008) was used with default parameters to identify any regions of open chromatin in all datasets, grouping replicates when available.
Bedtools genomecov (Quinlan and Hall, 2010) was used to generage bedgraphs.
Genome_build: dm6
Supplementary_files_format_and_content: BEDGRAPH, TEXT

organism: Drosophila melanogaster

growth_protocol: All stocks were grown on molasses food at 25°C

extract_protocol:
After collection, dechorionation, and staging embryos were homogenized in ATAC lysis buffer as described in Blythe and Wieschaus (2016).
Library preparation was performed using the Illumina Nextera DNA library preperation kit according to manufacturer instructions. Resultant tagmented DNA was purified with a Qiagen Minelute Cleanup Kit. Libraries were size-selected using a 1.2x ratio of Axygen Axyprep Mag PCR Cleanup beads.

treatment_protocol: Maternal depletion embryos were examined under a fluorescence microsocope to identify embryos depleted of maternal GRH and wild-type siblings. These embryos were then dechorionated. Zygotic depletion embryos were first dechorionated, then examined under a fluorescence microscope to identify embryos depleted of zygotic GRH and wild-type siblings. After separation of embryos and dechorionation, embryos were precisely staged under a light microscope

tag: developmental stage

value: 11-12hr after egg laying


title: grhZ-_11-12hr


title: G0161_1

city: Atlanta

first: Anna

middle: K

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University

description: Infinium MethylationEPIC BeadChip- standard protocol

hyb_protocol: MethylationEPIC

scan_protocol: BeadStudio

label: biotin

source_name: PBMC

label_protocol: MethylationEPIC

extract_protocol: AllPrep RNA/DNA Mini Kit (Qiagen)

tag: Sex

value: Female

tag: race

value: African American

tag: visit

value: PBMC

tag: sample group

value: Case


title: G0160_2


title: JunB_ERT2cre_PP_KO1

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

data_processing:
Raw sequencing reads were trimmed to remove low quality bases (Q<20) and sequencing adapters using TrimGalore!, and reads having less than 20 bp remaining after trimming were removed.
Trimmed reads were aligned to the mm10 genome using STAR.
Aligned reads were counted within features specified by the GENCODE vM22 annotation using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts output from featureCounts.

source_name: CD25- Tregs from Peyer's patch

extract_protocol:
Single cell suspensions were obtained from Peyer's patches or colon lamina propria by digestion with collagenase, DNAse I, and Dispase (colon only), followed by FACS to purify the indicated populations. Sorted cells were lysed in Trizol, followed by hybrid extraction from the aqueous phase using the Qiagen RNeasy Micro Kit.
Low-input library construction was performed by the Duke Sequencing and Genomic Technologies Shared Resource using the Clontech SMARTer v4 kit.

value: JunB F/F Foxp3ERT2cre+ Rosa26-tdTomato+

value: male

value: 3 doses of 8mg tamoxifen in olive oil by oral gavage (days 0,1,3), collection on day 7.


title: G0148_2


title: JunB_ERT2cre_PP_KO2

value: JunB F/F Foxp3ERT2cre+/+ Rosa26-tdTomato+

value: female


title: E0512_2

value: Control


title: G0165_1


title: MB-CN-03_S3: WT

tag: cell line

value: cell Renal Carcinoma (ccRCC)


title: JunB_ERT2cre_coLP_KO2

source_name: Tregs from colon lamina propria


title: G0155_2


title: G0138_2


title: G0165_2


title: JunB_ERT2cre_PP_HET1

value: JunB F/+ Foxp3ERT2cre+ Rosa26-tdTomato+


title: JunB_ERT2cre_PP_HET2

value: JunB F/+ Foxp3ERT2cre+/+ Rosa26-tdTomato+


title: G0138_1


title: G0161_2


title: G0139_1


title: JunB_ERT2cre_coLP_HET3


title: G0132_2


title: G0134_1


title: G0148_1


title: G0134_2


title: G0151_2


title: G0130_2


title: G0155_1


title: JunB_ERT2cre_coLP_HET2


title: JunB_ERT2cre_coLP_KO3


title: G0151_1


title: JunB_ERT2cre_coLP_KO1


title: JunB_ERT2cre_coLP_HET1


title: Femoral bone of female 15-31

description:
Sample ID:  15-31
genomic DNA from femoral bone of female 15-31
22.4 ng of gDNA used

source_name: femoral bone of female 15-31

value: 31 years

tag: tissue

value: Femoral bone


title: G0129_2

tag: cell type


title: JunB_Foxp3YFPcre_PP_KO1

source_name: Tregs from Peyer's patch

value: JunB F/F Foxp3YFPcre

tag: treatment


title: G0129_1


title: JunB_Foxp3YFPcre_PP_HET2

value: JunB F/+ Foxp3YFPcre


title: G0130_1

value: Female


title: JunB_Foxp3YFPcre_PP_KO2


title: G0132_1

value: African American


title: G0139_2

value: PBMC


title: pituitary gland, Hesx1Cre

city: Stony Brook

first: Leonard

middle: YM

last: Cheung

state: New York

address: 101 Nicolls Road

institute: Stony Brook University

description: single-cell RNAseq on 10x Genomics Chromium platform of pituitary cells from one P4 female Hesx1Cre/+ mouse

data_processing:
Illumina BCL file unpacked and demultiplexed using 10x Genomics Cellranger 3.0.2 mkfastq command.
Fastq files analyzed by self-contained Cellranger count software 3.0.2 from 10x Genomics.  Cellranger performs barcode processing, alignment to mm10 transcriptome using STAR, and transcript counting.
Processed gene counts per cell are loaded into Seurat 3.0.2 for further computational analyses, including cell filtering, sample integration, uniform manifold approximation and projection (UMAP), and gene expression visualization.
Genome_build: modified UCSC mm10 chromosome 11: 50,948,572-50,949,192 amended as extended unannotated 3' UTR of Prop1
Supplementary_files_format_and_content: The *matrix.mtx is the processed matrix for the transcript counts of each of the samples.  It uses the row number from genes.tsv as the gene number in column 1, and the row number from barcodes.tsv as the cell number in column 2.  Column 3 is the count. Direct output from Cell Ranger 3.0.2 are zipped files and Seurat 3.0.2 loads those in directly.

source_name: Pituitary gland from a P4 female mouse carrying the Hesx1Cre/+ knock-in allele

extract_protocol:
Pituitary cells were dissociated as previously described in Cheung et al. 2018 Endocrinology 159(12):3910-3924.  The pituitary glands were dissected and the tissue dispersed as previously described.  Briefly, the dissected tissue is placed into an enzyme mix containing 0.5% w/v collagenase type 2 (Lorne Laboratories, UK), 0.1x trypsin (Invitrogen), 50 mg/ml DNase I (Worthington Biochemical, USA), and 2.5 mg/ml Fungizone (Invitrogen) in Hank’s balanced salt solution (HBSS) (Invitrogen) for 4 hrs at 37°C.  The tissue and cells are gently triturated, counted on a hemocytometer, pelleted at 200g for 5 min, and resuspended at ~1000 cells per ml in 0.4% bovine serum albumin (BSA)/HBSS.
Single-cell libraries were constructed as previously described in Cheung et al. 2018 Endocrinology 159(12):3910-3924.  From that article: Single-cell 3′ library generation was performed on the 10x Genomics Chromium Controller following the manufacturer’s protocol for the v2 reagent kit (10x Genomics) (10). Cell suspensions were loaded onto a Chromium Single Cell A Chip along with reverse transcription master mix and single-cell 3′ gel beads, aiming for 10,000 cells per channel. For each pool, 17,400 cells with 71% to 82% viability were encapsulated into emulsion droplets at a concentration of 700 to 1200 cells per μL, which targets 10,000 single cells with an expected multiple cell rate of 7.6%. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed and the resulting post-GEM reverse transcription product was cleaned up using DynaBeads MyOne silane beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA) cleaned and quantified, and then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup was performed after end repair and A-tailing. Another single-sided cleanup was done after adapter ligation. Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by KAPA quantitative PCR for Illumina adapters (Roche, Pleasanton, CA) and size was determined by Agilent TapeStation D1000 tapes. Read 1 primer sequences were added to the molecules during GEM incubation. P5, P7, and sample index and read 2 primer sequences were added during library construction via end repair, A-tailing, adaptor ligation, and PCR. Libraries were generated with unique sample indices for each sample. Libraries were sequenced on a HiSeq 4000 (Illumina, San Diego, CA) using a HiSeq 4000 paired-end cluster kit with HiSeq 4000 sequencing by synthesis kit (100 cycles, reagents, loaded at 200 pM) following Illumina’s denaturing and dilution recommendations. PhiX was spiked into the load at 1%. The run configuration was 26 × 8 × 98 (115) cycles for read 1, index, and read 2, respectively.

value: pituitary gland

value: Hesx1Cre/+ mouse

tag: age


title: pituitary gland, Hesx1Cre_dnRAR

description: single-cell RNAseq on 10x Genomics Chromium platform of pituitary cells from one P4 female Hesx1Cre/+; R26 dnRAR/dnRAR mouse

source_name: Pituitary gland from a P4 female mouse carrying the Hesx1Cre/+ knock-in allele and homozygous for a Rosa26 allele overexpressing a truncated dominant-negative human retinoic acid receptor alpha (dnRAR).

value: Hesx1Cre/+; R26 dnRAR/dnRAR mouse


title: 266649_D1

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of read counts for each sample

source_name: B cells

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® UltraII RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

tag: b cell subset

value: B1 B cell

tag: donor

tag: replicate


title: E0564_1


title: 266649_C3

value: MZ B cell


title: 266649_C2


title: 266649_C1


title: 266649_B3

value: Follicular


title: 266649_B2


title: JunB_Foxp3YFPcre_PP_HET1

value: male


title: 266649_B1


title: 266649_A2

value: Anergic


title: 266649_A3


title: 266649_A1


title: G0160_1

value: Case


title: G0110_2


title: 265823_D1


title: 265823_C3


title: G0125_1


title: G0110_1


title: 265823_C2


title: G0125_2


title: 265823_C1


title: 265823_B3


title: G0107_1


title: G0108_1


title: 265823_B1


title: G0108_2


title: 265823_A3


title: G0106_2


title: 265823_A2


title: 265823_B2


title: G0104_2


title: G0104_1


title: G0106_1


title: G0103_2


title: 265823_A1


title: G0105_1


title: G0100_1


title: BM3W_R3

value: Bone marrow

tag: harvest time

value: 3 weeks

value: IgHEL transgenic


title: BM3W_R2

tag: genotype


title: G0101_2


title: G0103_1


title: G0105_2


title: BM3W_R1


title: G0107_2


title: BM10W_R3

value: 10 weeks


title: G0100_2


title: G0092_1


title: 151379_NL3

value: Neonatal liver

tag: batch

value: B cells


title: BM10W_R1


title: 151379_NL2


title: G0102_1

value: Female

value: African American


title: 151379_NL1


title: 151379_BM3


title: G0092_2

value: PBMC


title: 151379_BM2


title: G0098_1


title: G0102_2


title: BM10W_R2


title: G0093_2


title: G0093_1


title: G0099_2


title: 151378_NL3


title: G0099_1


title: 151378_NL2


title: 151378_BM1


title: 151378_BM2


title: G0090_1


title: 151378_BM3


title: 151378_NL1


title: G0091_2


title: G0101_1


title: G0091_1


title: G0088_1


title: G0088_2


title: G0089_2


title: G0086_1


title: KO Input

first: Patrick

last: Seale

address: Smilow Center for Translational Research, 12th Floor 3400 Civic Center Blvd. Bldg 421

department: Institute for Diabetes, Obesity & Metabolism

institute: University of Pennsylvania

data_processing:
ChIP-seq sequencing reads were aligned to UCSC mm9 using STAR aligner. Each aligned reads were de-duplicated and pooled for each group or condition. Prdm16 peaks were called using Control Prdm16 against KO. Peaks located within ENCODE blacklist regions were discarded and > 1RPM cutoff was further applied before downstream analysis. BigWig files were generated for the pooled samples using "makeUCSCfile" command in Homer and bedGraphToBigWig command in bedtools.
Genome_build: mm9
Supplementary_files_format_and_content: Peak bed file & bigWig file

source_name: Duodenal crypts

extract_protocol:
Wt and KO Crypts were isolated from 3 mice each, pooled, and fixed with 1.1% formaldehyde for 15 min at room temperature and then quenched  with 2.5 M glycine for 5 mins at room temperature. Samples were washed with PBS, pelleted and resuspended in ChIP lysis buffer (0.6% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris at pH 8) with protease inhibitors (Roche) and 1 mM PMSF. Crypts were sonicated to shear chromatin using an Active Motif EpiShear platform (8 minutes active time, 30 sec on, 20 sec off, amplitude 25%). To a achieve a final concentration of 0.1% SDS, chromatin was diluted 1:6 with ChIP dilution buffer (1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris at pH 8).  Inputs were removed.  Chromatin was split into 1 ml samples and primary antibody was added for overnight incubation at 4°C with rotation with 3ug anti Prdm16 (Peptide Ab against AA 1-240, originally published in PMC2564846). Protein A Sepharose beads (GE healthcare) were then added for 4 hours at 4°C. Samples were washed twice with wash buffer 1 (0.1% SDS, 0.1% NaDOC, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris at pH 8), once with wash buffer 2 (0.1% SDS, 0.1% NaDOC, 1% Triton X-100, 0.5 M NaCl, 1 mM EDTA, 20 mM Tris at pH 8), once with wash buffer 3 (0.25 M LiCl, 0.5% NaDOC, 0.5% NP-40, 1 mM EDTA, 20 mM Tris at pH 8), and twice with wash buffer 4 (1 mM EDTA, 20 mM Tris at pH 8).  Samples were then eluted from beads with warm 100 mM NaHCO3/1% SDS buffer. Samples were reverse cross-linked overnight at 65°C with RNase A and then treated with proteinase K and column purified (Clontech NucleoSpin). ChIP enrichment was calculated as percent of input. PRDM16 ChIP WT and KO samples were prepared as ChIPseq libraries and sequenced using a HiSeq 4000 high output sequencer.
NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: Control and R26R-CreERT2; Prdm16 loxp/loxp mice were injected with tamoxifen 3 days before crypt extraction

value: knock out

value: 6-8 weeks old

tag: strain

value: Mixed

tag: antibody


title: G0087_2

tag: Sex


title: miR-200 induced with Doxycycline 2

city: Boulder

first: Glen

last: Bjerke

state: CO

address: 347 UCB

department: MCDB

institute: University of Colorado

description:
HM_C3_Ind2
MiSeq and HiSeq 4000

data_processing:
Aligned with Bowtie2
Genes counted with Htseq against mm10
For miR-200 samples the Hiseq and Miseq counts were combined
Htseq was loaded into DESeq2 for differential analysis using the default settings
Genome_build: mm10
Supplementary_files_format_and_content: Htseq count files and DESeq output for each experiment

source_name: Keratinocytes

extract_protocol:
RNA extracted with Trizol
Poly A selected and then NEB Next Ultra Directional kit

treatment_protocol: Treated with vehicle or 3 ug/ml doxycycline

tag: agent

value: Doxycycline

value: Keratinocytes


title: G0087_1

tag: race

tag: visit


title: 151379_BM1


title: G0089_1

tag: sample group


title: G0083_2


title: G0086_2


title: Prdm16 KO Prdm16  ChipSeq 1

value: Rb anti Prdm16 (Peptide Ab against AA 1-240)


title: G0084_1


title: miR-200 induced with Doxycycline 1

description:
HM_C3_Ind1
MiSeq and HiSeq 4000


title: G0080_1


title: Control Prdm16 ChipSeq 2

description:
Intestine_Prdm16_WT_pool.res1.bw
Intestine_Prdm16_WT_pool.homer.200bp.exBL.1rpm.bed

value: control


title: miR-200 Control 1 - Vehicle

description:
HM_C3_Control1
MiSeq and HiSeq 4000

value: Vehicle


title: AI002_MSC_336_EP_TPA

first: Seema

middle: Ahsan

last: Khan

address: 303 E. Superior Street, 4-111

data_processing:
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the mm9 genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: mm9
Supplementary_files_format_and_content: AI002_ReadCounts.csv

source_name: Mammary Stem Cell

extract_protocol:
FACS sorted luminal and basal cell subpopulation from mouse mammary tissue
Total RNA was first evaluated for its quantity, and quality, using Agilent Bioanalyzer 2100. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control. One to two nanograms of total RNA per sample were used for library preparation. cDNA was first synthesized using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.). Dual indexed cDNA library was then prepared using Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. Average size of library insert was about 150b. Five microliters of 2 nM pooled libraries per lane were then denatured, neutralized and applied to the cBot for flow cell deposition and cluster amplification, before loading on to HiSeq 4000 for 75b paired-end sequencing (Illumina, Inc.). Each lane generated approximately 300-350 million reads. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

treatment_protocol:
Protocol name: PR blocakade in ovariectomized mice
AntiPR in ovariectomized mice

tag: tissue

value: Mammary Stem Cell

tag: mouse id

value: FVB


title: G0083_1

tag: cell type

value: Case


title: G0079_1


title: Control Input

tag: age


title: G0081_1


title: G0079_2


title: G0081_2


title: AI002_MSC_334_sham

tag: treatment

value: sham


title: G0080_2


title: Control Prdm16 ChipSeq 1


title: G0078_2


title: miR-200 Control 2 - Vehicle

description:
HM_C3_Control2
MiSeq and HiSeq 4000


title: AI002_MSC_329_EP_RU486


title: AI002_MSC_328_EP_TPA


title: Prdm16 KO  Prdm16  ChipSeq 2


title: AI002_MSC_322_EP


title: AI002_MSC_313_EP_RU486


title: AI002_MSC_324_EP_RU486


title: G0077_1


title: AI002_MSC_327_EP


title: AI002_MSC_312_EP_TPA


title: G0098_2


title: G0076_2


title: G0078_1


title: AI002_MSC_311_EP


title: AI002_MSC_310_sham


title: G0090_2


title: AI002_MSC_323_EP_TPA


title: AI002_MSC_326_sham


title: AI002_MSC_306_EP


title: AI002_MSC_305_sham


title: G0076_1


title: AI002_MSC_308_EP_RU486


title: AI002_LP_336_EP_TPA

source_name: Luminal Progenitor

value: Luminal Progenitor


title: G0071_2


title: AI002_LP_328_EP_TPA


title: AI002_LP_329_EP_RU486


title: G0077_2


title: AI002_LP_327_EP


title: G0084_2


title: G0071_1


title: AI002_LP_326_sham


title: G0072_1


title: AI002_LP_324_EP_RU486


title: AI002_LP_323_EP_TPA


title: AI002_LP_322_EP


title: G0073_1


title: AI002_LP_312_EP_TPA


title: G0070_2


title: G0065_1


title: G0068_2


title: AI002_LP_311_EP


title: G0066_2


title: AI002_LP_310_sham


title: G0070_1


title: AI002_LP_308_EP_RU486


title: G0068_1


title: AI002_LP_305_sham


title: AI002_LP_304_EP_RU486


title: G0073_2


title: G0072_2


title: AI002_LP_306_EP


title: G0062_1


title: AI002_LP_301_sham


title: G0064_2


title: AI002_LM_336_EP_TPA

source_name: Luminal Mature

value: Luminal Mature


title: AI002_LM_333_EP_RU486


title: G0063_1

value: Female


title: AI002_LM_332_EP_TPA


title: G0065_2

value: African American


title: AI002_LM_329_EP_RU486


title: AI002_LM_328_EP_TPA


title: G0066_1

value: PBMC


title: G0063_2


title: G0058_1


title: G0062_2


title: G0056_2


title: AI002_LM_327_EP


title: G0064_1


title: G0058_2


title: AI002_LM_326_sham


title: AI002_LM_313_EP_RU486


title: AI002_LM_312_EP_TPA


title: G0051_2


title: AI002_LM_311_EP


title: G0050_2


title: AI002_LM_310_sham


title: AI002_LM_308_EP_RU486


title: G0050_1


title: G0056_1


title: AI002_LM_301_sham


title: AI002_LM_306_EP

value: E2+Progesterone (E2+Progesterone)


title: G0051_1


title: G0049_1


title: G0049_2


title: G0048_2


title: AI002_LM_305_sham


title: G0046_1


title: G0048_1


title: G0046_2


title: G0038_2


title: Hypoxia 1

type: RNA

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description:
4_24HA7
Gene expression data from human astrocytes.
Human astrocytes from ScienCell Research laboratories (Carlsbad CA USA).

hyb_protocol: 12µg of cRNA molecules were heat fragmented and applied to the Human U133 Plus 2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix Fluidics Station again following the protocol outlined in the Affymetrix instructions.

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the AGCC software package to prepare the .CEL files.

data_processing: The data were analyzed with Transcriptome Analysis Console v4 using RMA as normalization method.

source_name: Hypoxia astrocytes

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix IVT protocol.

growth_protocol: Astrocytes were cultured in Human Astrocyte media supplemented with 2% fetal bovine serum (FBS), 1% penicillin streptomycin and 1% Astrocyte Growth Supplement (ScienCell Research Laboratories). To characterize the effect of hypoxia on the astrocyte transcriptome, astrocytes were cultured under normoxic (5% CO2, 95% air) or hypoxic conditions (1% O2, 5% CO2, 94% N2) for 24h.

extract_protocol: Directzol RNA Extraction kit was used according to manufacturer's instructions.

treatment_protocol: Human astrocytes were cultured under normoxic (5% CO2, 95% air) or hypoxic conditions (1% O2, 5% CO2, 94% N2) for 24h, and the gene expression profile assessed by microarray analysis.

value: Astrocytes

tag: condition

value: Hypoxic


title: G0038_1


title: G0037_1


title: Hypoxia 3

description:
6_24HA12
Gene expression data from human astrocytes.
Human astrocytes from ScienCell Research laboratories (Carlsbad CA USA).


title: G0011_2


title: G0037_2


title: Hypoxia 2

description:
5_24HA10
Gene expression data from human astrocytes.
Human astrocytes from ScienCell Research laboratories (Carlsbad CA USA).


title: Control 3

description:
3_24NA12
Gene expression data from human astrocytes.
Human astrocytes from ScienCell Research laboratories (Carlsbad CA USA).

source_name: Control astrocytes

value: Normoxic


title: E0688_1


title: Control 1

description:
1_24NA1
Gene expression data from human astrocytes.
Human astrocytes from ScienCell Research laboratories (Carlsbad CA USA).


title: E0633_2


title: Control 2

description:
2_24NA7
Gene expression data from human astrocytes.
Human astrocytes from ScienCell Research laboratories (Carlsbad CA USA).


title: G0011_1


title: E0688_2


title: U87_siSETX1

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

hyb_protocol: RNA was hybridized to GeneChip Exon 1.0 ST Arrays (Affymetrix) according to standard protocols.

scan_protocol: Standard Affymetrix protocol

data_processing:
Raw data from the Affymetrix GeneChip Human Exon 1.0 ST Array were normalized by the RMA method in the Affymetrix Power Tools (APT) program and probe sets with detection above background (DABG) P value < 0.05 in at least one sample group were used for further analysis.
Summarization Method: Gene Level - Extended: RMA-Sketch
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label_protocol: The GeneChip WT Terminal Labeling and Controls Kit, combined with the Ambion WT Expression Kit were then used.

extract_protocol: RNA was purified using the RNeasy kit (Qiagen) followed by on column DNAse treatment (Qiagen).

treatment_protocol: 20nM SETX siRNA or control siRNA was transfected in U87 cells with RNAimax (Invitrogen) for 72 hrs.

tag: cell line

value: SETX siRNA


title: U87_siSETX3


title: E0596_2


title: U87_siSETX2


title: E0615_2


title: E0594_1


title: E0601_1


title: E0615_1


title: U87_siCtrl1

value: control siRNA


title: U87_siCtrl3


title: U87_siCtrl2


title: E0671_2


title: LA_STS-Rep4: HT-29 with LA + STS Replicate 4

city: Oshawa

middle: P

last: Jeffrey

state: Ontario

address: 2000 Simcoe St N

department: Faculty of Science

country: Canada

institute: Ontario Tech University

description: Biological Replicate 4 of 4

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50C for 18h on the Agilent whole human gene expression microarray (GE 4x44K; GPL10332).

scan_protocol: Each array was scanned with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with ImaGene® microarray analysis software.

data_processing: Global LOWESS normalization was conducted with ImaGene® microarray analysis software.

source_name: HT-29 Control Rep 4

label_protocol: Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript IV (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).

extract_protocol: Total RNA was extracted by using TRIzol Reagent (ThermoFisher Scientific, MA, USA) following manufacturer's protocol with PhaseLock tubes (5 Prime, MD). Total extracted RNA was then purified using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). The purity and quality of RNA was determined using both the ND100 NanoDrop and an Agilent 2000 Bioanalyzer, respectively. Only samples with an RNA Integrity Number (RIN) greater than 9.0 were used for microarray analysis.

treatment_protocol: HT-29 cells were incubated for 3 h with with either the Lactobacillus rhamnosus R0011 secretome (LrS) (40% v/v), a matched L-lactic acid control (LA), TNF-α (50ng/mL), Salmonella enterica subsp. enterica serovar Typimurium secretome (STS) (1% v/v), or a combination of the treatments

value: Colonic adenocarcinoma cells

source_name: HT-29 with LA + STS Rep4


title: LA_STS-Rep2: HT-29 with LA + STS Replicate 2

description: Biological Replicate 2 of 4

source_name: HT-29 with LA + STS Rep2

source_name: HT-29 Control Rep 2


title: E0671_1

source_name: PBMC


title: E0591_2


title: E0596_1


title: E0592_2


title: LA_STS-Rep3: HT-29 with LA + STS Replicate 3

description: Biological Replicate 3 of 4

source_name: HT-29 Control Rep 3

source_name: HT-29 with LA + STS Rep3


title: LA_STS-Rep1: HT-29 with LA + STS Replicate 1

description: Biological Replicate 1 of 4

source_name: HT-29 with LA + STS Rep1

source_name: HT-29 Control Rep 1


title: LrS_STS-Rep3: HT-29 with LrS + STS Replicate 3

description: Biological Replicate 3 of 4

source_name: HT-29 with LrS + STS Rep3


title: LrS_STS-Rep2: HT-29 with LrS + STS Replicate 2

description: Biological Replicate 2 of 4

source_name: HT-29 with LrS + STS Rep2


title: LrS_STS-Rep1: HT-29 with LrS + STS Replicate 1

description: Biological Replicate 1 of 4

source_name: HT-29 with LrS + STS Rep1


title: LrS_STS-Rep4: HT-29 with LrS + STS Replicate 4

description: Biological Replicate 4 of 4

source_name: HT-29 with LrS + STS Rep4


title: E0601_2


title: STS-Rep4: HT-29 with STS Only Replicate 4

description: Biological Replicate 4 of 4

source_name: HT-29 with STS Rep 4


title: E0633_1


title: STS-Rep2: HT-29 with STS Only Replicate 2

description: Biological Replicate 2 of 4

source_name: HT-29 with STS Rep 2


title: E0594_2


title: E0586_1


title: STS-Rep1: HT-29 with STS Only Replicate 1

description: Biological Replicate 1 of 4

source_name: HT-29 with STS Rep 1


title: E0591_1


title: E0584_2


title: E0583_2


title: STS-Rep3: HT-29 with STS Only Replicate 3

description: Biological Replicate 3 of 4

source_name: HT-29 with STS Rep 3


title: LA_TNFa-Rep2: HT-29 with LA + TNF-α-Replicate 2

description: Biological Replicate 2 of 4

source_name: HT-29 with LA + TNF-α Rep 2


title: LA_TNFa-Rep3: HT-29 with LA + TNF-α-Replicate 3

description: Biological Replicate 3 of 4

source_name: HT-29 with LA + TNF-α Rep 3


title: LA_TNFa-Rep1: HT-29 with LA + TNF-α-Replicate 1

description: Biological Replicate 1 of 4

source_name: HT-29 with LA + TNF-α Rep 1


title: E0583_1


title: LA_TNFa-Rep4: HT-29 with LA + TNF-α-Replicate 4

description: Biological Replicate 4 of 4

source_name: HT-29 Control Rep 4

source_name: HT-29 with LA + TNF-α Rep 4


title: E0584_1

source_name: PBMC


title: E0586_2


title: E0592_1


title: LrS_TNFa-Rep4: HT-29 with LrS + TNF-α-Replicate 4

description: Biological Replicate 4 of 4

source_name: HT-29 with LrS + TNF-α Rep 4


title: E0580_2


title: E0582_2


title: LrS_TNFa-Rep2: HT-29 with LrS + TNF-α-Replicate 2

description: Biological Replicate 2 of 4

source_name: HT-29 with LrS + TNF-α Rep 2

source_name: HT-29 Control Rep 2


title: E0580_1


title: E0582_1


title: LA-Rep3: HT-29 with LA Only Replicate 3

description: Biological Replicate 3 of 4

source_name: HT-29 Control Rep 3

source_name: HT-29 with LA Rep 3


title: LrS_TNFa-Rep1: HT-29 with LrS + TNF-α-Replicate 1

description: Biological Replicate 1 of 4

source_name: HT-29 with LrS + TNF-α Rep 1

source_name: HT-29 Control Rep 1


title: E0576_2


title: E0579_1


title: LA-Rep4: HT-29 with LA Only Replicate 4

description: Biological Replicate 4 of 4

source_name: HT-29 with LA Rep 4


title: LA-Rep1: HT-29 with LA Only Replicate 1

description: Biological Replicate 1 of 4

source_name: HT-29 with LA Rep 1


title: LA-Rep2: HT-29 with LA Only Replicate 2

description: Biological Replicate 2 of 4

source_name: HT-29 with LA Rep 2


title: TNFa-Rep4: HT-29 with TNF-α Only Replicate 4

description: Biological Replicate 4 of 4

source_name: HT-29 with TNF-α Rep 4


title: E0579_2


title: E0574_2


title: TNFa-Rep3: HT-29 with TNF-α Only Replicate 3

description: Biological Replicate 3 of 4

source_name: HT-29 with TNF-α Rep 3


title: E0576_1


title: TNFa-Rep2: HT-29 with TNF-α Only Replicate 2

description: Biological Replicate 2 of 4

source_name: HT-29 with TNF-α Rep 2


title: TNFa-Rep1: HT-29 with TNF-α Only Replicate 1

description: Biological Replicate 1 of 4

source_name: HT-29 with TNF-α Rep 1


title: LrS_TNFa-Rep3: HT-29 with LrS + TNF-α-Replicate 3

description: Biological Replicate 3 of 4

source_name: HT-29 with LrS + TNF-α Rep 3


title: E0572_2


title: E0574_1


title: LrS-Rep3: HT-29 with LrS Only Replicate 3

description: Biological Replicate 3 of 4

source_name: HT-29 with LrS Rep 3


title: LrS-Rep2: HT-29 with LrS Only Replicate 2

description: Biological Replicate 2 of 4

source_name: HT-29 with LrS Rep 2


title: E0575_2

source_name: PBMC


title: E0575_1


title: R_120

first: David

last: Pincus

institute: University of Chicago

data_processing:
bases called by Illumina software
aligned to sacCer3 by bowtie
quantified by htseq-count
Genome_build: saccer3
Supplementary_files_format_and_content: .txt files with normalized counts

growth_protocol: YPD

extract_protocol:
phenol chloroform total RNA prep
NEB next ultra RNA library prep; multiplex barcoded

treatment_protocol: heat shock at 39C or 1 µM rapamycin

tag: perturbation

value: 120 min 1 µM rapamycin


title: E0570_2


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-6F

city: La Jolla

first: Christopher

middle: Jen-Yue

last: Wei

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

data_processing:
base-callingwith bcl2fastq with barcode-mismatch=0
methylpy on paired-end reads with min-qual-score=30
Genome_build: hg19
Supplementary_files_format_and_content: methylpy tsv file output (column 1=chromosome; column 2=position; column 3=strand; column 4=sequence context; column 5=number methylated reads; column 6=read coverage)

source_name: U87MG likely glioblastoma cell line

extract_protocol:
SDS cell lysis
RETrace methylation post-processing

value: U87MG likely glioblastoma cell line


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-6G


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-6E


title: E0572_1


title: LrS-Rep1: HT-29 with LrS Only Replicate 1

description: Biological Replicate 1 of 4

source_name: HT-29 with LrS Rep 1


title: R_90

value: 90 min 1 µM rapamycin


title: R_30

value: 30 min 1 µM rapamycin


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-6D


title: E0568_1

value: Case


title: R_60

value: 60 min 1 µM rapamycin


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-6B


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-6C


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-5G


title: HS_120

value: 120 min HS 39ºC


title: R_15

value: 15 min 1 µM rapamycin


title: E0570_1

value: Female

value: African American


title: HS_90

value: 90 min HS 39ºC


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-5F


title: LrS-Rep4: HT-29 with LrS Only Replicate 4

description: Biological Replicate 4 of 4

source_name: HT-29 Control Rep 4

source_name: HT-29 with LrS Rep 4


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-5E


title: E0562_2

value: PBMC


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-5D


title: HS_30

value: 30 min HS 39ºC


title: E0563_1


title: E0565_1


title: E0567_1


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-5C


title: R_0

value: control - rapamycin


title: HS_0

value: control 30ºC


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-4G


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-4F


title: E0568_2


title: E0563_2


title: S5_p3c0: p3c0-1

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

data_processing:
RNA-Seq reads were aligned to S.cerevisiae S288C reference using STAR version 2.5.3a in 2Pass mode
resulted sequence alignment map file (SAM) were filtered on ambigious alignments and sorted with samtools to sorted binary alignement file (BAM)
The sorted BAM file was processed with htseq-count from the HTSeq framework version 0.9.1 with -m union and -stranded reverse to calculate the transcript counts
The raw transcript counts were normalized on fragments per kilobase million (FPKM) by applying rpkm module from edgeR package
Genome_build: S288C_reference_genome_R64-2-1_20150113
Supplementary_files_format_and_content: Comma delimited file, normalized transcript counts

growth_protocol:
S. cerevisiae CEN.PK113-7D was grown in bioreactors sparged with  compressed air, resulting in a 50% CO2 in the inflowing gas, in synthetic medium (SM) containing 3.0 g L-1 KH2PO4, 5.0 g L-1 (NH4)2SO4, 0.5 g L-1 MgSO4, 7 H2O, 1.5 mL L-1 trace element solution, and 2 mL L-1 vitamin solution, and a final concentration of iron sulfate in EDTA (7.5 mg/L final concentration) and biotin (1.1 mg/L  final concentration) . The dilution rate was 0.025 h-1 the pH was kept constant at pH 3 by the automatic addition of (NH4)2OH (12.5%). The medium was autoclaved for 20 minutes at 120 °C. Vitamin solutions (Verduyn et al. 1992) were sterilized by filtration and added to the sterile medium. Concentrated sugar solutions were autoclaved at 110 °C for 20 min and added to the sterile flasks to give a final concentration of 20 g L-1 carbon source during chemostat and retentostat cultivation.
S. cerevisiae CEN.PK113-7D was grown as indicated in the growth condition column on synthetic medium.

extract_protocol:
The resulting ice pellet was gently thawed on ice and spun down at 4700 x g for 5 min at 0 o C. Pellets were then resuspended in 1.2 mL of ice-cold AE buffer (50 mM sodium acetate and 10 mM EDTA, pH 5.0), followed by addition of 1.2 mL of acid phenol/chloroform/isoamyl alcohol mix and 0.12 mL 10 % sodium dodecyl sulfate. The resulting mix was vortexed for 30 s and incubated for 5 min at 65 °C. After homogenizing for 30 sec by vortexing, 800 µL aliquots were distributed in RNase-free screw-cap tubes (Tai et al. 2005). After centrifugation (15 min at 10,000 x g), the aqueous phase was transferred to a new tube containing 0.4 mL of acid phenol/chloroform. The mix was vortexed for 30 seconds, centrifuged (15 min at 10,000 x g) and the aqueous phase was again transferred to a new tube. RNA was then ethanol precipitated and re-suspended in RNAse-free water. Prior to cDNA synthesis, purity, concentration and integrity of the RNA in the samples was assessed with the Nanodrop (Thermo Fisher Scientific), Qubit (Thermo Fisher Scientific) and Tapestation 220 with RNA Screen Tape (Agilent Technologies), respectively, according the manufacturers’ recommendations.
cDNA libraries were prepared using the TruSeq RNA V2 kit (Illumina)and sequenced on HISeq 2500 (Illumina) at Novogene (HK) Company Ltd (Hong Kong, China).

treatment_protocol: S. cerevisiae CEN.PK113-7D was grown as indicated in the growth condition column on synthetic medium. Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

tag: carbon source

value: Glucose

tag: cultivation condition

value: Chemostat pH3 0.04% CO2


title: S9_p3c0: p3c0-2

tag: strain


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-4E


title: S6_p5c5: p5c5-2

growth_protocol:
S. cerevisiae CEN.PK113-7D was grown in bioreactors sparged with a 50:50 mix of compressed air and pure CO2, resulting in a 50% CO2 in the inflowing gas, in synthetic medium (SM) containing 3.0 g L-1 KH2PO4, 5.0 g L-1 (NH4)2SO4, 0.5 g L-1 MgSO4, 7 H2O, 1.5 mL L-1 trace element solution, and 2 mL L-1 vitamin solution, and a final concentration of iron sulfate in EDTA (7.5 mg/L final concentration) and biotin (1.1 mg/L  final concentration) . The dilution rate was 0.025 h-1 the pH was kept constant at pH 5 by the automatic addition of (NH4)2OH (12.5%). The medium was autoclaved for 20 minutes at 120 °C. Vitamin solutions (Verduyn et al. 1992) were sterilized by filtration and added to the sterile medium. Concentrated sugar solutions were autoclaved at 110 °C for 20 min and added to the sterile flasks to give a final concentration of 20 g L-1 carbon source during chemostat and retentostat cultivation.
S. cerevisiae CEN.PK113-7D was grown as indicated in the growth condition column on synthetic medium.

value: Chemostat pH5 50% CO2


title: S7_p5c5: p5c5-3


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-4D

value: U87MG likely glioblastoma cell line


title: E0567_2


title: E0565_2


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-4C


title: S14_p5c5: p5c5-1


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-12F


title: E0561_1


title: E0561_2


title: E0554_1


title: S13_p5c0: p5c0-3

growth_protocol:
S. cerevisiae CEN.PK113-7D was grown in bioreactors sparged with  compressed air, resulting in a 50% CO2 in the inflowing gas, in synthetic medium (SM) containing 3.0 g L-1 KH2PO4, 5.0 g L-1 (NH4)2SO4, 0.5 g L-1 MgSO4, 7 H2O, 1.5 mL L-1 trace element solution, and 2 mL L-1 vitamin solution, and a final concentration of iron sulfate in EDTA (7.5 mg/L final concentration) and biotin (1.1 mg/L  final concentration) . The dilution rate was 0.025 h-1 the pH was kept constant at pH 5 by the automatic addition of (NH4)2OH (12.5%). The medium was autoclaved for 20 minutes at 120 °C. Vitamin solutions (Verduyn et al. 1992) were sterilized by filtration and added to the sterile medium. Concentrated sugar solutions were autoclaved at 110 °C for 20 min and added to the sterile flasks to give a final concentration of 20 g L-1 carbon source during chemostat and retentostat cultivation.
S. cerevisiae CEN.PK113-7D was grown as indicated in the growth condition column on synthetic medium.

value: Chemostat pH5 0.04% CO2


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-12D


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-12G


title: S8_p5c0: p5c0-1


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-12C


title: S12_p5c0: p5c0-2


title: S11_p3c50: p3c5-3

growth_protocol:
S. cerevisiae CEN.PK113-7D was grown in bioreactors sparged with a 50:50 mix of compressed air and pure CO2, resulting in a 50% CO2 in the inflowing gas, in synthetic medium (SM) containing 3.0 g L-1 KH2PO4, 5.0 g L-1 (NH4)2SO4, 0.5 g L-1 MgSO4, 7 H2O, 1.5 mL L-1 trace element solution, and 2 mL L-1 vitamin solution, and a final concentration of iron sulfate in EDTA (7.5 mg/L final concentration) and biotin (1.1 mg/L  final concentration) . The dilution rate was 0.025 h-1 the pH was kept constant at pH 3 by the automatic addition of (NH4)2OH (12.5%). The medium was autoclaved for 20 minutes at 120 °C. Vitamin solutions (Verduyn et al. 1992) were sterilized by filtration and added to the sterile medium. Concentrated sugar solutions were autoclaved at 110 °C for 20 min and added to the sterile flasks to give a final concentration of 20 g L-1 carbon source during chemostat and retentostat cultivation.
S. cerevisiae CEN.PK113-7D was grown as indicated in the growth condition column on synthetic medium.

value: Chemostat pH3 50% CO2


title: E0562_1

value: Case


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-12B


title: S4_R3: ind ret 4-2

source_name: industrial conditions retentostat S4-2

value: retentostat pH3 50% CO2


title: U87MG_SC_2-1-3C_3-1-8E_20190922-Plate2-5B


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-11G


title: HS_60

value: 60 min HS 39ºC


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-11D


title: S3_R3: ind ret 4-1

source_name: industrial conditions retentostat S4-1


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-11F


title: S4_R1: ind ret 2-2

source_name: industrial conditions retentostat S2_2


title: S4_R2: ind ret 3-2

source_name: industrial conditions retentostat S3_2


title: S3_R2: ind ret 3-1

source_name: industrial conditions retentostat S3_1


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-11C


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-11B


title: S3_R1: ind ret 2-1

source_name: industrial conditions retentostat S2_1


title: S4_SS: ind ret 1-2

source_name: industrial conditions retnetostat S1_2


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-10G


title: E0545_2


title: E0545_1


title: S3_SS: ind ret 1-1

source_name: industrial conditions retentostat S1_1


title: E0554_2


title: S2_R5: aer ret 3-2

source_name: laboratory conditions retentostat S3_2

growth_protocol:
S. cerevisiae CEN.PK113-7D was grown in bioreactors sparged with compressed air in synthetic medium (SM) containing 3.0 g L-1 KH2PO4, 5.0 g L-1 (NH4)2SO4, 0.5 g L-1 MgSO4, 7 H2O, 1.5 mL L-1 trace element solution, and 2 mL L-1 vitamin solution. The dilution rate was 0.025 h-1 the pH was kept constant at pH 5.0 by the automatic addition of (NH4)2OH (12,5%). The medium was autoclaved for 20 minutes at 120 °C. Vitamin solutions (Verduyn et al. 1992) were sterilized by filtration and added to the sterile medium. Concentrated sugar solutions were autoclaved at 110 °C for 20 min and added to the sterile flasks to give a final concentration of 20 g L-1 carbon source during chemostat cultivation prior to the start of the retentostat and at 7.5 g L-1 after the start of the retentostat.
S. cerevisiae CEN.PK113-7D was grown as indicated in the growth condition column on synthetic medium.

value: retentostat pH5 0.04% CO2


title: S2_R1: aer ret 2-2

source_name: laboratory conditions retentostat S2_2


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-10B


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-10C


title: S1_R5: aer ret 3-1

source_name: laboratory conditions retentostat S3_1


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-10F


title: S1_R8: aer ret 4-1

source_name: laboratory conditions retentostat S4-1


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-10E


title: S2_R8: aer ret 4-2

source_name: laboratory conditions retentostat S4-2


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-3G

source_name: U87MG likely glioblastoma cell line


title: S1_SS: aer ret 1-1

source_name: laboratory conditions retentostat S1_1


title: S2_SS: aer ret 1-2

source_name: laboratory conditions retnetostat S1_2


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-3E


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-3F


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-10D


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-3D


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-3B


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-3C


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-2E


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-2D


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-2G


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-2C


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-2F


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-2B


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-3B

source_name: Adult human post-mortem brain tissue

value: Human NeuN+ nuclei derived from hippocampus


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-3E


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-2E


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-3D


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-1G


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-2F


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-3F


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-3G


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-3C


title: S1_R1: aer ret 2-1

source_name: laboratory conditions retentostat S2_1


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-2C


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-2D


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-1D


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-1G


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-2G


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-1F


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-1E


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-9G


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-9E


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-9F


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-1D


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-1C


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-1E


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-9C


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-9D


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-12E

value: Human NeuN- nuclei derived from hippocampus


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-9B


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-2B


title: Brain_SC_Hipp-NeuNpos_20190321-Plate2-1B


title: HS_15

value: 15 min HS 39ºC


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-12F


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-12D


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-1F


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-8E


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-8F


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-12G


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-12B


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-12C


title: U87MG_SC_2-1-3C_3-1-12C_20190922-Plate2-1C


title: KIN5

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: Single cell RNA-seq

data_processing:
Cell Ranger software used for basecalling.
STAR performs splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the genome. The adopted alignment are as follows: 1) A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise. 2) Reads that align to a single exonic locus but also align to 1 or more non-exonic loci, the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. 3) Reads that are confidently mapped to the transcriptome are used for UMI counting.
In Cell Ranger v2.x and earlier, the following algorithm is used to determine the cutoff for calling a barcode cell-associated: 1) Rank-sort the total UMI counts across all of the detected barcodes that passed the 16bp barcode whitelist filtering criteria. 2)Determine the 99th percentile of the UMI counts among the top N barcodes where N is the provided 'expected recovered cell' parameter passed to the pipeline (--expect-cells=3000 by default). 3) All barcodes with total UMI counts greater than or equal to 10% of the 99th percentile value are classified as cells.
The Seurat R package was applied to identify major cell types. RandomForest was applied to identify subtypes.
The graphs of principal component analysis (PCA) and T-distributed stochastic neighbor embedding (t-SNE) were produced following the scaling process, t
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: cKI5_vs_WT1.all_markers.anno.xls

source_name: Brain

extract_protocol:
Cerebral cortex tissue was digested into single cell suspensions. Then, these suspensions were carried out with 10x Genomics Chromium Single Cell Kit for single cell RNA-seq.
RNA libraries sequencing was performed using standard Illumina protocols.

tag: strain/background

tag: genotype

tag: developmental stage

value: Cerebral cortex


title: WT1

description: Single cell RNA-seq

value: WT


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-11G


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-8D


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-8G


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-11E


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-11C


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-11D


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-8C


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-8B


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-7G


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-11B


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-10G


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-10F


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-7F


title: Cardiomyocytes, Adult MoNuc Rep2

first: Michael

last: Morley

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the mm9 reference genome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm9
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: Heart

extract_protocol:
RNA was isolated by phenol-chloroform extraction followed by precipitation with 75% Ethanol. RNA was then purified using the RNeasy micro Kit
Library prep was conducted by Genewiz using Illumina truSeq stranded mRNA kit and Clontech SMARTer RNA-seq ampliﬁcation kit.

treatment_protocol: Cardiomyocytes were isolated from Mlc2vcre:R26REYFP mice and mononucleated and binucleated cardiomyocytes were sorted by FACS directly into Trizol-LS.

value: Adult

value: Heart

value: cardiomyocytes

tag: # of nuclei


title: Cardiomyocytes, Adult BiNuc Rep2


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-10D


title: Cardiomyocytes, Adult BiNuc Rep1


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-12E


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-10B


title: Cardiomyocytes, Adult MoNuc Rep1


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-10E


title: Cardiomyocytes, Adult MoNuc Rep3


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-7D


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-6F

value: Human NeuN+ nuclei derived from cortex


title: Cardiomyocytes, Adult BiNuc Rep3


title: Cardiomyocytes, P7 BiNuc Rep3


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-6D


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-7C


title: Cardiomyocytes, P7 MoNuc Rep3


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-6E


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-6C


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-10C


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-6B


title: Brain_SC_Hipp-NeuNneg_20190321-Plate2-11F


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-7B


title: Cardiomyocytes, P7 BiNuc Rep2


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-5G


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-5D


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-5F


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-6G


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-12G


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-5C


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-12F


title: Cardiomyocytes, P7 MoNuc Rep2


title: Cardiomyocytes, P7 BiNuc Rep1


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-12E


title: Cardiomyocytes, P7 MoNuc Rep1


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-12D


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-5B


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-4F


title: Cardiomyocytes, E18.5 BiNuc Rep3


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-12C


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-4D


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-4C


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-4E


title: Cardiomyocytes, E18.5 BiNuc Rep2


title: U87MG_SC_2-1-3C_3-1-6B_20190922-Plate2-11E


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-11G


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-11F


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-12B


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-3C


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-3G


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-3D


title: Cardiomyocytes, E18.5 BiNuc Rep1


title: Cardiomyocytes, E18.5 MoNuc Rep3


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-2G


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-11D


title: Cardiomyocytes, E18.5 MoNuc Rep1


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-2E


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-3E


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-3F


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-4B


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-11E


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-2B


title: Cardiomyocytes, E18.5 MoNuc Rep2


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-2D


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-3B


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-10G


title: S10_p3c0: p3c0-3

value: Glucose

value: Chemostat pH3 0.04% CO2


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-1G


title: KO_Light_1

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Mouse brown adipocytes  RNA-seq by Illumina HiSeq 2500

data_processing:
Paired-end sequencing reads from HiSeq 2500 were subjected to adaptor-trimming using cutadapt Version 1.1 , and quality-trimmed using Trimmomatic Version 0.32.
TopHat (version 2.0.14) was used with the default parameters to map the reads to the reference genome (GRCm38, mm10).
Counts were calculated using Cufflinks (version2.2.1) with a transcriptome reference (Ensembl Mouse Transcript).
Genome_build: GRCm38, mm10
Supplementary_files_format_and_content: CSV file contains read counts.

source_name: Brown adipocytes

extract_protocol:
Total RNA was extracted from cells using the spin column kit (Zymo Research).
The Illumina TruSeq Stranded mRNA protocol was used for the preparation of RNA sequencing (RNA-Seq) libraries.

value: KO

tag: light condition

value: Light


title: KO_Light_2


title: KO_Dark_3

value: Dark


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-10F

value: U87MG likely glioblastoma cell line


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-1F


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-10E


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-1D


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-1C


title: KO_Dark_2


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-1B


title: KO_Dark_1


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-6G

value: Human NeuN- nuclei derived from cortex


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-10D


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-6F


title: WT_Light_3


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-6E


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-10C


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-6D


title: WT_Light_2


title: WT_Light_1


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-10B


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-5G


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-9G


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-6C


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-2F


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-9F


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-5B


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-5E


title: WT_Dark_3


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-5F


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-5C


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-9D


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-9E


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-5D


title: WT_Dark_1


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-2C


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-4F


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-4E


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-9C


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-4D


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-4C


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-6B


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-4G


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-9B


title: WT_Dark_2


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-9G


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-8G


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-9E


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-9D


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-8F


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-8E


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-9C


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-9B


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-8G


title: Brain_SC_Cortex2-NeuNneg_20190321-Plate2-4B


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-8F


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-8D


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-11B


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-8D


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-8E


title: U87MG_SC_2-1-3C_3-1-10G_20190922-Plate2-7E


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-8C


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-5E


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-8C


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-7G


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-1E


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-8B


title: Brain_SC_Cortex2-NeuNpos_20190321-Plate1-4G


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-9F


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-7F


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-7F


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-7E


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-7E


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-7C


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-7D


title: Brain_SC_Cortex1-NeuNpos_20190321-Plate1-7B


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-12G


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-7D


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-12F


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-12E


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-7C


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-7G


title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-7B


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-12D


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-12B


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-11G


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-12C


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-11F


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-6G


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-11E


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-6F


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-11D


title: Xenograft 5-Fu 2-circRNA seq

city: Guangzhou

first: li

middle: ping

last: gong

address: No.600 Tianhe Road

institute: The Third Affiliated Hospital, Sun Yat-sen University

description: pooling12-Xenograft 5-Fu-2_HL757CCXY_L3

data_processing:
sequencing reads that aligned contiguously and full length to the genomes by TopHat2 were removed.
the unmapped reads were processed to 20-nt anchors from both ends and aligned in the reverse orientation (head-to-tail) representing a back-spliced junction.
The total number of reads that spanned back-spliced junctions was used as an absolute measure of circRNA abundance.
The genomic regions that mapped to inferred circRNAs were annotated according to RefSeq,
the corresponding gene of this transcript fragment was defined as the host gene for each circRNA.
Genome_build: the reference human genome (GRCh38/hg38) was obtained from the UCSC genome browser (http://genome.ucsc.edu/), and the reference EBV genome (Accession No. NC_007605.1) was obtained from NCBI GenBank (http://www.ncbi.nlm.nih.gov/).
Supplementary_files_format_and_content: tab-delimited text files include circRNA count and annotation for each Sample

source_name: Xenograft 5-Fu

growth_protocol: Parental SNU719 cells were passaged in 4-week-old female NOD/SCID mice (Model Animal Research Center of Nanjing University, Nanjing, China) by injecting 2×10^6 cells into left subscapular subcutaneous. 5-Fu (20mg/kg, Selleck, Houston, Texas, USA) was injected into the tail vein weekly. When the diameter of xenografts reached 1.5 cm, the mice were euthanized and single-cell suspensions were obtained by collagenase digestion.And the purified single-cell  were passaged in 5-Fu-treated NOD/SCID mice as above. After four successive generations, we obtained a highly malignant EBVaGC cell line SNU-4th which from the  fourth passage xenografts treated with 5-Fu

extract_protocol:
Total RNA was extracted from  three pairs of the fourth passage tumor xenografts treated with 5-Fu or PBS using TRIzol reagent (Invitrogen, Carlsbad, CA, USA)
The total RNA samples of three pairs of tumor xenografts were subjected to the RiboMinus Eukaryote Kit (Qiagen) to remove ribosomal RNA, followed by linear RNA depletion using RNase R before constructing the RNA sequencing libraries. Strand-specific RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Beverly, MA) following the manufacturer’s instructions.

treatment_protocol: 5-Fu (20mg/kg, Selleck, Houston, Texas, USA) was injected into the tail vein of NOD/SCID mice  weekly

tag: cell line background

value: snu-4th highly malignant

value: EBV-positive gastric cancer stem cell lines

value: the fourth passage Xenograft

tag: molecule subtype

value: circular RNA


title: Xenograft 5-Fu 3-circRNA seq

description: pooling6-Xenograft 5-Fu-3_HHY73CCXY_L6

tag: tissue


title: Xenograft 5-Fu 1-circRNA seq

description: pooling12-Xenograft 5-Fu-1_HL757CCXY_L3

tag: cell type


title: Lung M2-T2: Lung control vs treatment replicate 2

first: Shuang

address: Haidian District

institute: Peking University Cancer Hospital

description: Biological replicate 2 of 3. Control MDSC, untreated vs treated, harvested from lung.

hyb_protocol: 65°C/10RPM 17hr

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing:
Microarray data were analyzed with R package limma as described in the manual.
Normalization within arrays and between arrays was performed utilizing the ‘losses’ and ‘Aquantile’ methods.

source_name: Myeloid-derived suppressor cells

growth_protocol: primary cells

extract_protocol: After total cellular RNA was extracted using the TRIzol method (Life Technologies), RNA concentration was determined using the NanoDrop machine and software (Thermo Fisher Scientific). Around 400ng of total RNA was used to generate cDNA with the QuantiTect Reverse Transcription Kit (Quanta Biosciences).

treatment_protocol: MDSCs were isolated from BM or lungs by FACS. RNA preparations were obtained from lung or bone marrow M-MDSCs pooled from 3–6 mice (Aza plus entinosta treatment group) or from 1-2 mice (vehicle treatment group).

value: Myeloid-derived suppressor cells

value: mock

tag: age

value: 6-8 weeks

value: Lung

value: epigenetic treatment


title: Lung M3-T3: Lung control vs treatment replicate 3

description: Biological replicate 3 of 3. Control MDSC, untreated vs treated, harvested from lung.

tag: treatment


title: Lung M1-T1: Lung control vs treatment replicate 1

description: Biological replicate 1 of 3. Control MDSC, untreated vs treated, harvested from lung.


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-11C


title: BM M3-T3: BM control vs treatment replicate 3

description: Biological replicate 3 of 3. Control MDSC, untreated vs treated, harvested from bone marrow.

value: Bone marrow


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-11B


title: BM M2-T2: BM control vs treatment replicate 2

description: Biological replicate 2 of 3. Control MDSC, untreated vs treated, harvested from bone marrow.


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-6D


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-10F


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-10G


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-10D


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-6C


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-10E


title: Xenograft PBS 2-circRNA seq

description: pooling12-Xenograft PBS-2_HL757CCXY_L3

source_name: Xenograft PBS

value: snu719 parental

value: EBV-positive gastric cell lines

value: PBS


title: Xenograft PBS 1-circRNA seq

description: pooling12-Xenograft PBS-1_HL757CCXY_L3


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-6B


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-10B


title: p53_MUT8-COMB

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
S4
p53 R158G mutant cell line treated with Belinostat.

data_processing:
bcl2fastq 2.17.1.14 were used for basecalling.
Sequenced reads were mapped to hg19 using bowtie v2.1.053 with parameters -N 23 1 –sensitive -p 2 –no-unal
Peaks were called using MACS2 v2.0.936.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-seq signal in bigwig for each sample.

source_name: Cell Line

growth_protocol: Cell lines were obtained directly from the American Type Culture Collection (ATCC), and were maintained in a humidified 37°C incubator, in culture medium (RPMI for Calu-1) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 μg/mL streptomycin and 100 U/mL penicillin.

extract_protocol:
In brief, cells were crosslinked with 1% formaldehyde, glycine quenched, lysed with cell lysis buffer (Sigma, #2978) supplemented with 1 mM PMSF, and subjected to pulse sonication (20s with 30s internal, 5 cycles). The supernatant was then immunoprecipitated with the p53 and rabbit IgG antibodies (Cell Signaling, #9282 and #2729) at 4°C overnight and incubated with Magna ChIP Protein G magnetic beads (Millipore, #16-662).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

treatment_protocol: Cell lines were cultured in petri dishes and treated with either 0.01% DMSO or 0.1uM belinostat with 10uM cisplatin for 48 hours.

tag: genotype/variation

value: p53 R158G mutant

value: Belinostat

tag: chip antibody

value: p53 (#9282, Cell Signaling)


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-6E

value: U87MG likely glioblastoma cell line


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-5G


title: BM M1-T1: BM control vs treatment replicate 1

description: Biological replicate 1 of 3. Control MDSC, untreated vs treated, harvested from bone marrow.


title: p53_MUT8-DMSO

description:
S3
p53 R158G mutant cell line treated with DMSO.

tag: cell line

value: DMSO


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-9F

value: Human NeuN+ nuclei derived from cerebellum


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-9E


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-9C


title: p53_WT-COMB

description:
S2
p53 wild type cell line treated with Belinostat.

value: p53 wild type


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-9D


title: Xenograft PBS 3-circRNA seq

description: Pooling14-Xenograft PBS-3_HL7LTCCXY_L5

value: the fourth passage Xenograft

value: circular RNA


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-5E


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-8G


title: p53_WT-DMSO

description:
S1
p53 wild type cell line treated with DMSO.


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-5F


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-9B


title: Brain_SC_Cortex1-NeuNneg_20190321-Plate1-10C

value: Human NeuN- nuclei derived from cortex


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-5D


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-8F


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-8E


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-5C


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-9G


title: U87MG_SC_2-1-1D_3-1-10E_20190922-Plate1-11C


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-8D


title: FCRL6_pos_FL_S13

city: Birmingham

first: Randall

middle: S

last: Davis

state: AL

address: 1825 University Blvd SHEL402

institute: UAB

data_processing:
Initial QC was performed with FastQC and low-quality bases were removed with Trim Galore (v. 0.4.5). Reads were aligned with STAR (v2.5.2a, during `runMode genomeGenerate`, the option `sjdbOverhang` was set to 74). BAM files were indexed with SAMtools (v.1.6) and gene-level counts were generated using the function `featureCounts` from the R package, Rsubread (v1.26.1; r-base v3.4.1) with the `Mus_musculus.GRCm38.90.gtf` file from Ensembl.
The parameters used in `featureCounts` included: isGTFAnnotationFile=TRUE, useMetaFeatures=TRUE, allowMultiOverlap=FALSE, isPairedEnd=TRUE, requireBothEndsMapped=TRUE, strandSpecific=2, and autosort=TRUE. Additional parameters were kept as default. Count normalization and differential expression were performed with DESeq2 (v1.16.1).
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated values files which contain the normalized gene-level counts for each biological sample.

source_name: pro B cell fetal liver of embryonic day 18

extract_protocol:
mRNA was isolated using RNeasy Plus kits (Qiagen) and sequencing was performed on an Illumina NextSeq 500 (paired-end sequencing 2x75bp) instrument. Briefly, the quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer (all samples had RIN values of >9.9) followed by two rounds of poly(A) selection and conversion to cDNA.
TruSeq library generation kits were constructed by random fragmentation of the polyA mRNA, followed by cDNA production using random primers (Agilent Technologies). The ends of the cDNA were repaired, A-tailed, and adaptors were ligated for flow cell attachment, sequencing, and indexing as per the manufacturer’s instructions (Agilent Technologies). cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems) prior to sequencing.

value: BALB/cJ

value: embryonic day 18

value: fetal liver

value: pro B cells

tag: sorted cell type


title: RD1_S9


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-5B


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-8B


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-7G


title: RD2_S10


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-8C


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-4G


title: FCRL6_neg_FL_S14


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-7D


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-7E


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-7C


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-4E


title: FCRL6_pos_BM_S11

source_name: pro B cell bone marrow of adult 8-12 week mice

value: adult 8-12 week

value: bone marrow


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-4F


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-7B


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-4D


title: FCRL6_neg_BM_S12


title: Brain_10cell_Hipp-NeuNpos_20190321-Plate2-3A

value: Human NeuN+ nuclei derived from hippocampus


title: BM_M6_pos_S5


title: Brain_10cell_Cortex2-NeuNpos_20190321-Plate1-6A

value: Human NeuN+ nuclei derived from cortex


title: Brain_10cell_Hipp-NeuNneg_20190321-Plate2-12A

value: Human NueN- nuclei derived from hippocampus


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-4C


title: Brain_10cell_Cortex2-NeuNpos_20190321-Plate1-3A


title: BM_M6_neg_S4


title: U87MG_SC_2-1-10F_3-1-11F_20190922-Plate1-4B


title: Brain_10cell_Cortex1-NeuNneg_20190321-Plate1-12A


title: Brain_10cell_Cortex1-NeuNpos_20190321-Plate1-9A


title: YBEY KO #3

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
KO_rep3_sort
mtDNA
processed data file: counts_stranded.txt

data_processing:
Reads libraries were converted from bam format to fastq format with the bamtofastq version v2.26.0 from the bedtools package. Adapters were trimmed with cutadapt version 1.15. Reads were then mapped to the Mitochondrion genome Genbank accession J01415.2 using Segemehl version 0.1.7 with -q and -p options for paired reads. The generated sam files were converted to bam files using samtools version 1.4 with qview and -bS options.
Feature quantification was done using featureCounts version v1.4.6 from the Subread package with the following options -T (10) -p -t (exon) -0 -g (gene_id) -s 1 with a manually curated mitochondrion genome annotation provided in appendix.
Differential analysis was done with the DeSeq2 package version 1.16.1 in R version 3.4.4. All conditions were compared.
Genome_build: Homo sapiens mitochondrion, complete genome GenBank version: J01415.2.
Supplementary_files_format_and_content: counts_stranded.txt: Tab-delimited text file.

source_name: HEK293T-REx cells

extract_protocol:
RNA was extracted from isolated mitochondria with Trizol.
Standard stranded RNA-seq protocol without any enrichment.
Paired-end RNA-seq; HiSeqV4 PE50.

value: YBEY KO


title: Brain_SC_Cereb-NeuNpos_20190321-Plate2-7F


title: p53-R158G cell treated with belinostat (0.1uM) + 10uM Cisplatin

description:
Calu-1 lung cancer cell line with p53-R158G mutant treated with Belinostat and Cisplatin
IonXpress_014

data_processing:
For AmpliSeq, fastq files was analyzed with the ampliSeqRNA plugin available for Ion Torrent sequencing platforms that used the Torrent Mapping Alignment Program (TMAP). TMAP first identify a list of Candidate Mapping Locations (CMLs) and aligned with Smith Waterman algorithm for specific and sensitive mapping.
Genome_build: hg19
Supplementary_files_format_and_content: RPM normalization values for each samples

growth_protocol: Cell lines were obtained directly from the American Type Culture Collection (ATCC), and were maintained in a humidified 37°C incubator, in culture medium (RPMI for Calu-1 and H2170; EMEM for MRC-5) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 μg/mL streptomycin and 100 U/mL penicillin.

extract_protocol:
Cells were treated with the indicated treatment for 48hours, and RNA was extracted using Qiagen RNAeasy kit.
For Ion AmpliSeq Transcriptome Human Gene Expression (Thermo Fisher), 10 ng RNA was used for barcoded cDNA library preparation using PCR-based targeted-amplicon amplification according to manufacturer’s protocol. Pooled libraries were amplified emulsion PCR on Ion Torrent OneTouch2 instruments (OT2) and sequenced on Ion Torrent Proton sequencing system.

treatment_protocol: Cell lines were cultured in petri dishes and treated with either 0.01% DMSO or 0.1uM belinostat with 10uM cisplatin for 48 hours

value: p53 R158G mutant

value: belinostat (0.1µM) + 10µM Cisplatin


title: p53-R158G cell treated with DMSO

description:
Calu-1 lung cancer cell line with p53-R158G mutant treated with DMSO
IonXpress_013

value: DMSO