title: Vaginal pinch biopsy-LNG-Low-7th(A-)-rep2

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Arrays were washed, stained and scanned as described in the Affymetrix GeneChip® Expression Analysis Technical Manual

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data from .CEL files were analyzed using the 'affy' Bioconductor package and Partek Genomics Suite.

organism: Macaca nemestrina

source_name: Vaginal pinch biopsy-LNG-Low-7th(A-)

label_protocol: Five µg of the amplified cDNA was fragmented, biotinylated, and hybridized to arrays using the NuGEN Ovation Encore Biotin Module, according to kit instructions.

extract_protocol: Total RNA extraction was performed using the RNeasy mini kit (QIAGEN, Hilden, Germany)

value: Vaginal pinch biopsy

tag: animal

tag: treatment

value: LNG

tag: dose

value: Low

tag: condition


title: sig-MeJA-3h-3

status: Public on Jun 07 2020

type: SRA

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

library_source: transcriptomic

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Read counts of genes and their isoformes were calculated by HTseq-count Version 0.11.2
Genome_build: Capsicum annuum v1.6
Supplementary_files_format_and_content: tab-delimited text files include the values of read count for each sample

molecule: total RNA

organism: Capsicum annuum

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

tag: cultivar

value: Bukang

tag: age

value: six weeks

tag: tissue

value: Leaves


title: Vaginal pinch biopsy-LNG-Low-7th-rep1

type: RNA

city: Atlanta

state: GA

country: USA

label: biotin

source_name: Vaginal pinch biopsy-LNG-Low-7th


title: sig-MeJA-3h-2


title: sig-MeJA-3h-1


title: Vaginal pinch biopsy-LNG-Low-5th-rep3

source_name: Vaginal pinch biopsy-LNG-Low-5th


title: Vaginal pinch biopsy-LNG-High-7th(A-)-rep2

source_name: Vaginal pinch biopsy-LNG-High-7th(A-)

value: High


title: sig-MeJA-12h-2


title: sig-MeJA-1h-3


title: Vaginal pinch biopsy-LNG-Low-7th(A-)-rep1


title: Vaginal pinch biopsy-LNG-High-7th(A-)-rep1


title: Vaginal pinch biopsy-LNG-High-5th-rep2

source_name: Vaginal pinch biopsy-LNG-High-5th


title: sig-MeJA-1h-2


title: Vaginal pinch biopsy-LNG-Low-5th-rep2


title: Vaginal pinch biopsy-LNG-Low-5th-rep1


title: Vaginal pinch biopsy-LNG-High-5th-rep1


title: Vaginal pinch biopsy-LNG-High-7th-rep1

source_name: Vaginal pinch biopsy-LNG-High-7th


title: Vaginal pinch biopsy-LNG-High-5th(A-)-rep1

source_name: Vaginal pinch biopsy-LNG-High-5th(A-)


title: Vaginal pinch biopsy-DMPA-2.5-2D2-rep3

source_name: Vaginal pinch biopsy-DMPA-2.5-2D2

value: DMPA


title: sig-MeJA-1h-1


title: Vaginal pinch biopsy-DMPA-0.5-2D2-rep2

source_name: Vaginal pinch biopsy-DMPA-0.5-2D2


title: Vaginal pinch biopsy-DMPA-2.5-2D2-rep2


title: Vaginal pinch biopsy-DMPA-0.5-2D2-rep3


title: Vaginal pinch biopsy-DMPA-1.5-2D2-rep2

source_name: Vaginal pinch biopsy-DMPA-1.5-2D2


title: Vaginal pinch biopsy-DMPA-0.5-2D2-rep1


title: Vaginal pinch biopsy-DMPA-1.5-2D2-rep3


title: sig-SA-24h-3


title: sig-SA-24h-2


title: Vaginal pinch biopsy-DMPA-1.5-2D2-rep1


title: sig-SA-24h-1


title: sig-SA-12h-2


title: sig-SA-6h-3


title: sig-SA-12h-1


title: Vaginal pinch biopsy-DMPA-2.5-2D2-rep1


title: sig-SA-6h-1


title: sig-SA-6h-2


title: sig-SA-3h-3


title: sig-SA-12h-3


title: sig-SA-3h-2


title: sig-SA-3h-1


title: sig-SA-1h-3


title: sig-SA-1h-2


title: sig-SA-1h-1


title: Vaginal pinch biopsy-DMPA-1.5-1D4-rep3

source_name: Vaginal pinch biopsy-DMPA-1.5-1D4


title: sig-ET-24h-3


title: Vaginal pinch biopsy-DMPA-1.5-1D4-rep2


title: Vaginal pinch biopsy-DMPA-0.5-1D4-rep1

source_name: Vaginal pinch biopsy-DMPA-0.5-1D4


title: Vaginal pinch biopsy-DMPA-2.5-1D4-rep2

source_name: Vaginal pinch biopsy-DMPA-2.5-1D4


title: Vaginal pinch biopsy-DMPA-0.5-1D4-rep2


title: sig-ET-24h-2


title: Vaginal pinch biopsy-DMPA-2.5-1D4-rep3


title: sig-ET-24h-1


title: Vaginal pinch biopsy-Baseline-0.0-Le-rep1

source_name: Vaginal pinch biopsy-Baseline-0.0-Le

value: Baseline

value: early luteal


title: Vaginal pinch biopsy-Baseline-0.0-Fl-rep5

source_name: Vaginal pinch biopsy-Baseline-0.0-Fl

value: late follicular


title: Vaginal pinch biopsy-DMPA-1.5-1D4-rep1


title: Vaginal pinch biopsy-DMPA-2.5-1D4-rep1


title: sig-ET-12h-3


title: Vaginal pinch biopsy-Baseline-0.0-Le-rep3


title: Vaginal pinch biopsy-Baseline-0.0-Fl(dup)-rep1

value: late follicular(dup)


title: Vaginal pinch biopsy-Baseline-0.0-Le-rep4


title: Vaginal pinch biopsy-Baseline-0.0-Le-rep2


title: sig-ET-12h-2


title: Vaginal pinch biopsy-Baseline-0.0-Fl-rep3


title: sig-ET-12h-1


title: sig-ET-6h-3


title: Vaginal pinch biopsy-Baseline-0.0-Fl-rep2


title: Vaginal pinch biopsy-Baseline-0.0-Fl-rep4


title: sig-ET-3h-3


title: sig-ET-3h-1


title: sig-ET-6h-1


title: sig-ET-6h-2


title: sig-ET-3h-2


title: sig-ET-1h-3


title: sig-ET-1h-2


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep10

source_name: Vaginal pinch biopsy-Baseline-0.0-Fe

value: early follicular


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep7


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep9


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep8


title: Vaginal pinch biopsy-Baseline-0.0-Fl-rep1


title: sig-ABA-24h-3


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep4


title: sig-ABA-24h-2


title: sig-ABA-24h-1


title: sig-ABA-12h-2


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep5


title: sig-ABA-12h-1


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep6


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep3


title: sig-ET-1h-1


title: Vaginal pinch biopsy-Baseline-0.0-Ll-rep9

source_name: Vaginal pinch biopsy-Baseline-0.0-Ll

value: late luteal


title: Vaginal pinch biopsy-Baseline-0.0-Ll-rep8


title: Vaginal pinch biopsy-Baseline-0.0-Ll-rep6


title: sig-ABA-6h-3

source_name: Leaves


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep2


title: sig-ABA-6h-2


title: Vaginal pinch biopsy-Baseline-0.0-Fe-rep1


title: Vaginal pinch biopsy-Baseline-0.0-Ll-rep5


title: sig-ABA-12h-3


title: sig-ABA-3h-3


title: sig-ABA-3h-1


title: sig-ABA-1h-3


title: Vaginal pinch biopsy-Baseline-0.0-Ll-rep3


title: sig-ABA-6h-1


title: sig-ABA-3h-2


title: Vaginal pinch biopsy-Baseline-0.0-Ll-rep7


title: BJ_GFP48

city: Fort Worth

first: Kejin

last: Hu

state: TX

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

data_processing:
Initial QC was performed with FastQC and low-quality bases were removed with Trim Galore (v. 0.4.5).
Reads were quasi-mapped and quantified with Salmon (v0.12.0, with `--gencode` and `-k 21` flags for index generation and `-l A, `--gcBias` and `--validateMappings` flags for quasi-mapping).
Gene-level summarization was performed with tximport (v1.10.0). Count normalization and differential expression were performed with DESeq2 (v1.16.1).
Genome_build: hg38
Supplementary_files_format_and_content: Comma delimited file which contain the normalized gene-level counts for each biological sample.

organism: Homo sapiens

source_name: Fibroblast, BJ transduced with GFP

growth_protocol: We culture human embryonic stem cells (H1 and H9) in the chemically defined E8 media. Human foreskin BJ fibroblasts (ATCC, CRL-2522) were cultured in fibroblast medium: DMEM, 10% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 100 U ml−1 penicillin, 100 μg ml−1 streptomycin, 0.1 mM MEM NEAA and 4 ng ml−1 human bFGF.

extract_protocol:
Cells were harvested with Trizol reagent and stored at -80 °C until use. Total RNA was extracted using the Direct-zolTM Miniprep kit (R2052).
The standard Agilent SureSelect Strand-Specific RNA sequencing protocol was followed. Briefly, the polyA fraction was purified using two rounds of oligo dT-magnetic bead purification. The resulting polyA fraction was fragmented and first strand cDNA was done with random primers in the presence of Actinomycin D using standard techniques. The resulting first stand cDNA was purified using AMPure Beads and second strand cDNA and end repair was done using standard techniques. The blunt ended double stranded cDNA was incubated with exo- E.coli DNA polymerase to add an adenosine to the ends for T/A cloning of the adaptors. PCR amplification was done in the presence of uracil DNA glycosylase to generate strand specificity. A second round of PCR amplification was done to add unique 6-bp barcodes to each sample and add sequences necessary for flow cell attachment. The resulting mRNA libraries were quantitated using qPCR following the manufacturer's instructions (Kapa Biosystems, Woburn MA).

treatment_protocol: Human BJ fibroblasts were transduced with lentiviral GFP viruses, or OSKM viruses at a MOI of 5 for each virus. The cells were harved at the indicated times (48 hours and 72 hours post viral transduction) for RNA extraction using protocol as described  below.

tag: cell type

value: Fibroblast, BJ

tag: passage number

value: pssage 5

tag: harvest time

value: 48 hours post GFP transduction


title: OSKM72

source_name: Fibroblast, BJ transduced with OSKM

value: passage 5

value: 48 hours post OSKM transduction


title: BJ_GFP48b


title: BJ_GFP72

value: 72 hours post GFP transduction


title: OSKM48

value: 48 hours post OSKM  transduction


title: sig-ABA-1h-2

value: Bukang

value: six weeks


title: sig-ABA-1h-1

value: Leaves


title: H1 [re-analysis]

description:
re-used GSM1632428
hESC_GAGTGG_L005

source_name: Embryonic stem cells

value: Embryonic stem cells

value: passage 40

value: 80% confluence


title: H9 [re-analysis]

description:
re-used GSM1632429
H9_ESC_P43_AGTGGT_L001

value: passage 43


title: sig-mock-24h-3


title: BJ_GFP72b


title: Vaginal pinch biopsy-Baseline-0.0-Ll-rep1

value: Vaginal pinch biopsy

value: Baseline


title: sig-mock-24h-1


title: sig-mock-24h-2


title: BJ_3 [re-analysis]

description:
re-used GSM1632432
BJ72_ATCACG_L004

source_name: Fibroblast, BJ

value: 72 hours post seeding


title: sig-mock-12h-2


title: BJ_1 [re-analysis]

description:
re-used GSM1632430
BJ_48h_CACTTC_L004

value: Fibroblast, BJ

value: passage 8

value: 48 hours post seeding


title: sig-mock-6h-3


title: sig-mock-12h-1


title: BJ_2 [re-analysis]

description:
re-used GSM1632431
BJ48_ATCACG_L001

value: passage 5


title: sig-mock-6h-2


title: sig-mock-3h-3


title: sig-mock-3h-2


title: sig-mock-6h-1


title: sig-mock-1h-3


title: sig-mock-1h-1


title: sig-mock-1h-2


title: sig-mock-3h-1


title: CT26, Pd-l1 KO-4

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

description:
CT26.csv
KO_3

data_processing:
Basecalling performed using bcl2fastq v2.18
RNA-seq data from mouse and human cell lines were respectively aligned to mm10 and hg38 using STAR v2.5.4a (default parameter, except: --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical).
Differential gene expression analysis was performed using the Cuffdiff function in the Cufflinks v2.2.1. Analysis was performed on the gene level.
A significant change is defined by a q value (adjusted p value using the Benjamini-Hochberg Procedure) < 0.05.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each sample with differential gene expression test results

organism: Mus musculus

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium supplemented with 10% FBS, 100 units of penicillin and 100 mg/ml streptomycin. CT26 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 units of penicillin and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was extracted and purified using Qiagen RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PD-L1 (Pd-l1) knockout was performed by lentivirus-mediated CRISPR knockout using

tag: genotype

value: Pd-l1 KO

tag: cell line


title: sig-mock-0h-3


title: CT26, Pd-l1 KO-3

description:
CT26.csv
KO_2


title: sig-mock-0h-2


title: apYki_NelfAi_3

city: Pune

first: Sanket

last: Nagarkar

state: Maharashtra

address: Dr Homi bhabha Road, Pashan

department: Biology

country: India

institute: Indian Institute of Science education and Research

data_processing:
Illumina RTA for basecalling
Illumina package bcl2fastq for generating fastq files
Read alignment and further downstream processing was done using HISAT-StringTie pipeline
Counts per million (CPM) and log fold change were obtained using edgeR package
Genome_build: dm6
Supplementary_files_format_and_content: comma separated files contain log Fold change in gene expression compared to apGFP, logCPM and FDR for corresponding gene.

organism: Drosophila melanogaster

source_name: Wing imaginal disc tissue

extract_protocol:
L3 larvae of all respective genotypes were dissected in RNase free PBS and wing imaginal discs were removed after cleaning undesired tissue from it. These wing discs were pooled in TRIzol reagent in numbers suitable to obtain >1ug of RNA from each genotype..
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 3rd Larval instar

tag: growth phenotype

value: Neoplastic overgrowth

value: ap>UAS GFP, UAS NelfA RNAi; UAS Yki, Gal80ts


title: sig-mock-0h-1

value: Bukang

value: six weeks


title: apYki_NelfAi_2


title: H1_2 [re-analysis]

description:
re-used GSM4101207
H1_ESC_P41_ATGCCT_L007

value: Embryonic stem cells

value: passage 41


title: BJ_4 [re-analysis]

description:
re-used GSM4101206
BJ_72h_CCAGTT_L007

value: passge 5


title: apYki_3

value: Mild overgrowth/hyperplasia

value: ap>UAS GFP; UAS Yki, Gal80ts


title: sig-mock-12h-3

value: Leaves


title: apYki_2


title: CT26, Pd-l1 KO-2

description:
CT26.csv
KO_1


title: CT26-Pd-l1 KO/Pd-l1 K262Q-2

description: alias in processed data file: KO_KQ

data_processing:
RNA-seq data were aligned to mm10 using STAR v2.5.4a (default parameter, except: --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical).
Differential gene expression analysis was performed using the Cuffdiff function in the Cufflinks v2.2.1. Analysis was performed on the gene level.
A significant change is defined by a q value (adjusted p value using the Benjamini-Hochberg Procedure) < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each sample with differential gene expression test results

source_name: CT26-Pd-l1 KO/Pd-l1 K262Q

growth_protocol: CT26 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 units of penicillin and 100 mg/ml streptomycin.

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

treatment_protocol: To make stable subclones, Pd-l1 knockout cells were infected with retrovirus and then selected by puromycin.

value: Colorectal carcinoma cell line

tag: genotype/variation

value: rescued by K262Q Pd-l1


title: CT26-Pd-l1 KO/Pd-l1 K262Q-3

description: alias in processed data file: KO_KQ


title: CT26-Pd-l1 KO/Pd-l1 K262Q-1

description: alias in processed data file: KO_KQ


title: apYki_1


title: CT26-Pd-l1 KO/Pd-l1 WT-3

description: alias in processed data file: KO_WT

source_name: CT26-Pd-l1 KO/Pd-l1 WT

value: rescued by wild type Pd-l1


title: CT26-Pd-l1 KO/Pd-l1 WT-2

description: alias in processed data file: KO_WT


title: CT26-Pd-l1 KO/Pd-l1 WT-1

description: alias in processed data file: KO_WT


title: apYki_NelfAi_1


title: Vaginal pinch biopsy-Baseline-0.0-Ll-rep4

value: Vaginal pinch biopsy

value: Baseline

value: late luteal


title: apNelfAi_2

value: 3rd Larval instar

value: Wild type tissue

value: ap>UAS GFP, UAS NelfA RNAi; Gal80ts


title: Vaginal pinch biopsy-Baseline-0.0-Ll-rep2


title: CT26, Pd-l1 KO-1

description:
CT26.csv
KO_0

value: Pd-l1 KO


title: CT26, Pd-l1 WT-4

description:
CT26.csv
WT_3

value: wild type


title: apNelfAi_1


title: CT26-Pd-l1 KO-3

description: alias in processed data file: KO

source_name: CT26-Pd-l1 KO


title: CT26, Pd-l1 WT-3

description:
CT26.csv
WT_2


title: CT26, Pd-l1 WT-2

description:
CT26.csv
WT_1


title: apGFP_3

value: ap>UAS GFP; Gal80ts


title: CT26-Pd-l1 KO-2

description: alias in processed data file: KO


title: ATCCNCB

city: Madison

first: Bryan

last: Zabel

state: wi

address: 3329 Agriculture Dr

department: GEM

institute: International Flavors & Fragrances Inc

description:
A600= 0.5-0.9
ATCCNCB

data_processing:
Paired-end reads were imported and mapped to the B. longum subsp. infantis Bi-26 genome (SAMN10380491) using the “Geneious for RNA” Mapper with default settings in Geneious v. 11.0.4
Transcript levels in the resulting assemblies were calculated using the “Calculate Expression Levels” function, which enabled the comparison of replicates and experiments using the “Compare Expression Levels” with the DESeq2 method and parametric fit type.
The assemblies were exported as BAM files and imported into ArrayStar v. 1.2 (DNAStar, Madison, WI), processed using QSeq, and normalized by reads per kilobase of transcript per million mapped reads (RPKM).
Regression analyses of the RNA data were made in ArrayStar software using the Student’s t-test with FDR correction. Statistical analyses between sets of samples were analyzed using DESeq2 method as above. Differences in expression were considered significant if the Absolute Confidence (-Log10 adjusted p-value) was +1.00, and the Log2 ratio was at + 1.00, representing p < 0.05 and a > 2x fold change, respectively, after normalization.
Genome_build: RJJM00000000
Genome_build: NC_011593
Supplementary_files_format_and_content: gene count tables and alignment using Geneious Prime  v. 2020.0.5

molecule: polyA RNA

organism: Bifidobacterium longum subsp. infantis

source_name: Bacterial culture

growth_protocol: For all experiments, we modified the basal media from Asakuma et al. 8 to create modified basal media (mBasal) containing: 10 g/L BD peptone, 2 g/L yeast extract, 5 g/L NaCl, 2 g/L diammonium citrate, 0.2 g/L magnesium sulfate, 2 g/L dipotassium hydrogen phosphate. The pH was adjusted to 6.4. After autoclaving, we added filter-sterilized (0.2uM, PES membrane) 0.05% (w/v) L-cysteine HCl and 1% (w/v) of the indicated carbon source.

extract_protocol:
After each sample reached its desired A600 range, cells were centrifuged for 10 min. at 4,063 x g. The supernatant was removed and 1 mL of TRIzol (p/n: 15596026, Thermo) was added. The pellet was re-suspended by vortexing and the tubes were immediately frozen at -80°C. The cell pellets were later thawed, transferred to a Lysing Matrix B 2mL tube (p/n: 116911050, MPBio, Santa Ana, CA), and disrupted using a Mini-Beadbeater. The lysate was subjected to a chloroform organic extraction and followed by purification using RNeasy Mini Kit (p/n: 74104, Qiagen, Hilden, Germany).
Quality checks and quantifications of the isolated RNA were carried out on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Ribosomal RNA was removed prior to library construction using Ribo-Zero rRNA Removal Kit Gram-Positive Bacteria (p/n: MRZGP126, Illumina). Stranded cDNA libraries were prepared using TruSeq Stranded mRNA Kit (p/n: 20020594, Illumina), quantitated by Agilent TapeStation, pooled quimolarly, and sequenced on one flowcell lane for 75 cycles using paired-end 75 basepair sequencing on Illumina 2500 HiSeq Rapid Cluster Kit v. 2 (p/n: PE-402-4002, Illumina) and HiSeq Rapid SBS Kit v. 2 (p/n: FC-402-4021, Illumina).

treatment_protocol: Carbon source

tag: strain

tag: carbon source

value: No carb added

tag: growth phase

value: Mid-log


title: PD-L1 Rep2 Input

library_source: genomic

data_processing:
ChIP-seq reads were aligned to hg38 using Bowtie 2 v2.2.9.
Peak calling was performed using MACS2 v2.1.1 with corresponding input controls (default parameter, except: --broad, and --broad-cutoff 0.05).
Genome_build: hg38
Supplementary_files_format_and_content: Peak file in '.broadPeak' format

molecule: genomic DNA

growth_protocol: MDA-MB-231 subclone cells were cultured in DMEM medium supplemented with 10% FBS, 100 units of penicillin and 100 mg/ml streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with HA antibody.
Approximately 2-5 ng of ChIPed DNA from each condition was used to generate the ChIP-seq library using the Ovation Ultralow DR Multiplex System 1-8 Kit (NuGEN Technologies), according to the manufacturer’s protocol.

treatment_protocol: No treatment

tag: tumor type

value: Triple-negative breast cancer

tag: chip antibody


title: apGFP_1


title: ATCClacB

description:
A600= 0.5-0.9
ATCClacB

value: Lactose


title: ATCCgluB

description:
A600= 0.5-0.9
ATCCgluB

value: glucose


title: CT26-Pd-l1 KO-1

description: alias in processed data file: KO

value: Colorectal carcinoma cell line


title: ATCClacA

description:
A600= 0.5-0.9
ATCClacA


title: ATCCNCA

description:
A600= 0.5-0.9
ATCCNCA


title: ATCCgluA

description:
A600= 0.5-0.9
ATCCgluA


title: CT26, Pd-l1 WT-1

description:
CT26.csv
WT_0


title: PD-L1 Rep2

value: HA antibody (Abcam, ab9110)


title: ATCCfucb

description:
A600= 0.5-0.9
ATCCfucb

value: fucose


title: MDA-MB-231, PD-L1 KO-3

description:
MDA-MB-231.csv
KO_2

value: PD-L1 KO


title: MDA-MB-231, PD-L1 KO-2

description:
MDA-MB-231.csv
KO_1


title: ATCC3FLB

description:
A600= 0.5-0.9
ATCC3FLB


title: ATCCDiFLA

description:
A600= 0.5-0.9
ATCCDiFLA

value: difucosyllactose


title: ATCCfucA

description:
A600= 0.5-0.9
ATCCfucA


title: ATCCdiFLB

description:
A600= 0.5-0.9
ATCCdiFLB


title: MDA-MB-231, PD-L1 KO-1

description:
MDA-MB-231.csv
KO_0


title: ATCC3FLA

description:
A600= 0.5-0.9
ATCC3FLA


title: ATCC2FLA

description:
A600= 0.5-0.9
ATCC2FLA


title: bi26NCmid_B

description:
A600= 0.5-0.9
Nocarb2b


title: MDA-MB-231, PD-L1 KO-4

description:
MDA-MB-231.csv
KO_3


title: MDA-MB-231, PD-L1 WT-4

description:
MDA-MB-231.csv
WT_3


title: MDA-MB-231, PD-L1 WT-2

description:
MDA-MB-231.csv
WT_1


title: MDA-MB-231, PD-L1 WT-3

description:
MDA-MB-231.csv
WT_2


title: bi26DiFLlate_A

description:
A600= 1.0+
DiFL3

value: Late-log


title: bi26NCmid_A

description:
A600= 0.5-0.9
Nocarb2


title: bi26DiFLlate_B

description:
A600= 1.0+
DiFL3b


title: bi26NCearly_A

description:
A600= 0.5-0.9
Nocarb1

value: Early


title: MDA-MB-231, PD-L1 WT-1

description:
MDA-MB-231.csv
WT_0

treatment_protocol: PD-L1 (Pd-l1) knockout was performed by lentivirus-mediated CRISPR knockout.


title: bi26DiFLearly_B

description:
A600= 0.2
DiFL1b


title: bi26DiFLmid_A

description:
A600= 0.5-0.9
DiFL2


title: bi26DiFLmid_B

description:
A600= 0.5-0.9
DiFL2b


title: Sample218_Arg1ko

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

data_processing:
filter mapping with bwa mem v0.7.14-r1136 to rRNA/tRNA FASTA
quality trimming with fqtrim v0.9.5
alignment to GRCm38.85 reference using STAR v2.5.2b
feature counting with subread v1.5.3 featureCounts
differential expression analysis using DESeq2 v1.16.1
Genome_build: GRCm38.85
Supplementary_files_format_and_content: tab-separated text containing rlog normalized counts

source_name: colon tissue

growth_protocol: Conditional Arg1-deficient mice and respective Arg1-expressing littermate controls on the B6 background were age and sex matched and used at 7 to 12 weeks of age. All mice were raised in a specific pathogen-free environment according to the Institutional Animal Care and Use Committee guidelines.

extract_protocol:
Intestines of mice were removed, cleaned from feces and Peyer's patches and cut into small pieces. The intestinal pieces were transferred into a conical flask containing pre-warmed 1mM EDTA PBS. Intestinal epithelial cells were separated from the underlying tissue by incubation in 30 mM EDTA in Ca2+- and Mg2+-free PBS for 10 min at 37°C followed by vigorous shaking. Cells were harvested by centrifugation, washed, and multicellular epithelial aggregates were purified by repeated differential sedimentation at 1g in ice-cold PBS from contaminating cells and residual tissue. Total RNA was then extracted using the TRIfast reagent (Peqlab) according to the manufacturer's instructions.
Profiling of whole-genome transcriptomic patterns was performed with 1000ng high quality total RNA per sample. Libraries of the samples were generated using the Illumina stranded mRNA library kit according to the manufacturer's instructions.

treatment_protocol: Colitis was induced by the administration of 2.5% DSS in drinking water for one week followed by normal drinking water until day 10 in cell-specific Arg1-deficient and Arg1-expressing littermates which were separated 2-3 weeks before the onset of the experiments.

value: colon

value: Arg1 ko

tag: induction

value: DSS


title: S04 - B2

city: Shijiazhuang

first: Xuemin

last: Niu

address: 139 Ziqiang Road

country: China

institute: The Third Hospital of Hebei Medical University

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

source_name: serum

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA), and then treated with RNase-free DNase I (TianGen, Beijing, China) to remove genomic DNA contamination. The quality of RNA was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: diagnosis

value: HCV-induced fibrosis


title: S03 - B1


title: S08 - B6


title: S07 - B5


title: S06 - B4


title: S05 - B3


title: S02 - A2


title: bi26DiFLearly_A

description:
A600= 0.2
DiFL1


title: Sample217_Arg1ko


title: ATCC2FLB

description:
A600= 0.5-0.9
ATCC2FLB


title: bi263FLlate_B

description:
A600= 1.0+
3FL3b


title: bi263FLlate_A

description:
A600= 1.0+
3FL3


title: Sample216_Arg1ko


title: S01 - A1


title: bi263FLmid_A

description:
A600= 0.5-0.9
3FL2


title: bi263FLmid_B

description:
A600= 0.5-0.9
3FL2b


title: Sample215_Arg1ko


title: bi263FLearly_B

description:
A600= 0.2
3FL1b


title: bi262FLlate_B

description:
A600= 1.0+
2FL3b


title: Sample203_wt

value: Arg1 wt


title: bi263FLearly_A

description:
A600= 0.2
3FL1


title: bi262FLlate_A

description:
A600= 1.0+
2FL3


title: bi262FLmid_A

description:
A600= 0.5-0.9
2FL2


title: bi262FLmid_B

description:
A600= 0.5-0.9
2FL2b


title: bi262FLearly_B

description:
A600= 0.2
2FL1b


title: Sample200_wt


title: bi262FLearly_A

description:
A600= 0.2
2FL1


title: Sample201_wt


title: bi26lacmid_B

description:
A600= 0.5-0.9
Lac2b


title: PD-L1 Rep1 Input

value: wild type


title: FT237-p181a-knockdown-2

city: Ann Arbor

first: Analisa

last: DiFeo

state: MI

address: 1600 Huron Parkway

department: Pathology

institute: The University of Michigan

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Data was check for quality before being assessed on the Affymetrix Clariom S Human MicroArray. Changes in mRNA expression were then identified using the Clariom S Human MicroArray. On this array expression for each gene was assessed by approximately 11 probes, which were tiled throughout the transcript. The array provides basic gene level coverage of known genes.  Labeled samples were hybridized to the arrays overnight in a rotating Hybridization Oven.  Arrays were stained and washed in Affymetrix FS45U Fluidics Stations according to Affymetrix automated procedures. Data is collected using the GC3000 scanner with autoloader. The Clariom S Assays for the microarray data were downloaded. The data was pre-processed with RMA (Robust multichip average algorithm) using the R/Bioconductor package Oligo (42) where background subtraction, quantile normalization, and summarization (via median-polish) was accomplished.

source_name: human fallopian tube cells

label_protocol: Affymetrix

growth_protocol: FTSECs were cultured in a 1:1 ratio of DMEM and Ham’s F12 media (Corning) supplemented with L-glutamine, 15mM HEPES, 10% FBS (v/v) (Denville Scientific), and 0.6% Penicillin/Streptomycin (v/v) (Corning).

extract_protocol: mRNA was isolated using a total RNA isolation kit (Norgen). Total RNA was extracted from cell lysates of FT237-001, p181a, and p181a inhibitor in triplicate and submitted for Microarray using Affymetrix Human Clariom S array and the WT Plus chemistry. In brief, for the WT Plus assay, 150ng of total RNA was labeled using a reverse transcription priming method to prime the entire length of each RNA transcript, including both polyA and non-polyA mRNA to provide complete and unbiased transcriptome coverage. This protocol efficiently generated amplified and biotinylated sense-stranded DNA targets, avoiding loss of specificity due to antisense strand interference.

tag: group

value: p181a inhibitor


title: bi26lacmid_A

description:
A600= 0.5-0.9
Lac2

value: Mid-log


title: PD-L1 Rep1

value: Triple-negative breast cancer


title: bi26lacearly_B

description:
A600= 0.2
Lac1b

value: Lactose


title: bi26lacearly_A

description:
A600= 0.2
Lac1


title: STROMA24T

status: Public on Jun 06 2020

city: Beijing

first: Min

last: Zhang

state: Beijing

address: No. 8 East Road, Fengtai District

department: The Fifth Medical Center of Chinese PLA General Hospital

institute: Academy of Military Medical Sciences

data_processing:
10X Genomics CellRanger version 2.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 2.1.0) with default mapping arguments.  Reads with adapter contaminants or low-quality bases (N > 20%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to hg19 human transcriptome (UCSC) using Hisat2 (version 2.10). Uniquely mapped reads were counted by HTSeq package83 and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: human intrahepatic cholangiocarcinoma

extract_protocol:
We used a negative selection strategy removing EpCAM+CD31+CD45+ cells to enrich fibroblast population in two tumor samples (ICC32S and STROMA24T)
Fluorescence-activated cell sorting (FACS)-sorted viable cells (7-AAD-negative) and negative enriched fibroblasts (7-AAD/CD45/CD31/EpCAM-negative), respectively, were loaded into a well of a microfluidic chip to generate a cDNA library using a commercial 10x Genomics platform. Single-cell transcriptomic amplification and library preparation was performed by Capitalbio Technology Corporation (Beijing, China) using single-cell 3′ v2 or v3 chemistry (10x Genomics) according to manufacturer’s instructions. The libraries were then pooled and sequenced across six lanes on an Illumina Xten or NovaSeq 6000 system.

tag: tissue

value: tumor


title: FT237-p181a-knockdown-1


title: FT237-p181a-knockdown-3


title: Multiplex LB Stationary Phase C11

city: Paris

first: Alaksh

last: Choudhury

address: 16 Rue Henri Huchard

department: IAME

country: France

institute: INSERM

data_processing:
Library strategy: DNA-seq
Reads were assembled using PandaSeq tool
The merged reads were aligned to a database of known sequences using usearch to map reads to a sequence
Genome_build: N/A
Supplementary_files_format_and_content: tab delimited text table containing query from nextseq, target, %identity, aln_len, number mismatches, number indels, qrow, trow and alignment qrowdots

organism: Escherichia coli

source_name: Escherichia coli genome

growth_protocol: The cells were grown at 30 deegrees C on LB+Agar plates overnight.

extract_protocol:
Fifty µL of the scraped cell suspension was subjected to centrifugation in a 1.5 mL tube. The cells were washed twice with PBS and as much of the supernatant was removed as possible. Finally, the cells were suspended in 50 µL TE buffer (pH 8.0). The resuspended cells were boiled at 100 OC for 10 minutes.
The genomic region to be sequenced was amplified using primers with Illumina Nextera adapters

treatment_protocol: Cells for genome sequencing were scraped from LB agar plates with 1X PBS after overnight growth of the recovery mixture. Care was taken to collect at least 250-500 colonies for adequate representation of the population.

tag: grna seqeunce

value: Mixture of gRNA 2,5,6

tag: galk location

value: 0.82 MB from ter

tag: cas9 promoter

value: araC

tag: repair donor type

value: Circular


title: FT237-181a1


title: FT237-p0013


title: Multiplex LB Exponential C10


title: Multiplex LB Exponential C9


title: FT237-181a2


title: bi26laclate_B

description:
A600= 1.0+
Lac3b

value: Late-log


title: bi26laclate_A

description:
A600= 1.0+
Lac3


title: Multiplex LB Stationary Phase C12


title: FT237-p0011


title: Cassette 4 ProC Cas9 gRNA only pSIM5 induced C8

value: ACAAATCGCGCTTAACGGTC

value: proC


title: Cassette 4 ProC Cas9 gRNA only pSIM5 uninduced C6


title: Sample199_wt

value: colon

tag: genotype


title: FT237-p0012


title: FT237-181a3


title: Cassette 4 ProC Cas9 gRNA only pSIM5 uninduced C5


title: Cassette 5 ProC Cas9 gRNA only pSIM5 induced C4

value: GGCTAACTACGTTCGTGGCG


title: ProD Cassette 4 2 (G47)


title: Cassette 5 ProC Cas9 gRNA only pSIM5 induced C3


title: Cassette 5 ProC Cas9 gRNA only pSIM5 uninduced C1


title: Cassette 5 ProC Cas9 gRNA only pSIM5 uninduced C2


title: Pro1 Cassette 4 2 (G47)


title: ProC Cassette 4 1 (G47)


title: Pro1 Cassette 4 1 (G47)


title: ProC Cassette 4 2 (G47)


title: Cassette 4 ProC Cas9 gRNA only pSIM5 induced C7


title: SP SS9 Cassette 5 1 (G57)

value: 2.28 MB from ter


title: SP SS9 Cassette 7 2 (G56)

value: AGGCGCCTGAATGGTGTGAG


title: SP SS9 Cassette 5 2 (G57)


title: SP SS9 Cassette 7 1 (G56)


title: SP SS3 Cassette 6 1 (R10)

value: TGAAGCGGAAGAACTTAACC

value: 0.30 MB from ter


title: SP SS9 Cassette 3 1 (G52)

value: TGCGACAATGGGCGCATCGA


title: ProD Cassette 4 1 (G47)

value: proD


title: SP SS9 Cassette 3 2 (G52)


title: SP SS3 Cassette 5 2 (G57)


title: SP SS3 Cassette 3 2 (G52)


title: SP SS3 Cassette 7 2 (G56)


title: SP SS3 Cassette 6 2 (R10)


title: SP WT Cassette 6 1 (R10)


title: SP WT Cassette 6 2 (R10)


title: SP SS3 Cassette 3 1 (G52)


title: SP WT Cassette 7 2 (G56)


title: SP WT Cassette 5 1 (G57)


title: SP SS9 Cassette 6 2 (R10)


title: SP WT Cassette 7 1 (G56)


title: PRO1 PSIM Cassette 1 2 (GALK_OFF)

value: ATGATAAAGCTGCTGCAATA

value: Linear


title: PRO1 PSIM Cassette 6 2 (R10)


title: PRO1 PSIM Cassette 1 1 (GALK_OFF)


title: SP WT Cassette 3 1 (G52)


title: PRO1 PSIM Cassette 6 1 (R10)


title: SP WT Cassette 3 2 (G52)


title: SP SS9 Cassette 6 1 (R10)


title: PRO1 PSIM Cassette 5 2 (G57)


title: SP SS3 Cassette 5 1 (G57)


title: SP SS3 Cassette 7 1 (G56)


title: PRO1 PSIM Cassette 7 2 (G56)


title: PRO1 PSIM Cassette 5 1 (G57)


title: SP WT Cassette 5 2 (G57)


title: PRO1 PSIM Cassette 7 1 (G56)


title: PRO1 PSIM Cassette 3 1 (G52)


title: EQ LIN SS9 Cassette 6 2 (R10)


title: PRO1 PSIM Cassette 2 2 (G22)

value: CGAACTTTACGGTCATCGCG


title: EQ LIN SS9 Cassette 5 1 (G57)


title: PRO1 PSIM Cassette 2 1 (G22)

value: 0.82 MB from ter


title: PRO1 PSIM Cassette 3 2 (G52)

value: araC


title: EQ LIN SS9 Cassette 3 2 (G52)


title: EQ LIN SS9 Cassette 2 2 (G22)


title: EQ LIN SS9 Cassette 3 1 (G52)


title: EQ LIN SS9 Cassette 5 2 (G57)


title: EQ LIN SS3 Cassette 6 2 (R10)


title: EQ LIN SS9 Cassette 2 1 (G22)


title: EQ LIN SS9 Cassette 6 1 (R10)


title: EQ LIN SS3 Cassette 6 1 (R10)


title: EQ LIN SS9 Cassette 7 1 (G56)


title: EQ LIN SS3 Cassette 5 2 (G57)


title: EQ LIN SS3 Cassette 7 2 (G56)


title: EQ LIN SS3 Cassette 5 1 (G57)


title: EQ LIN SS3 Cassette 7 1 (G56)


title: EQ LIN SS3 Cassette 3 2 (G52)


title: EQ LIN SS3 Cassette 2 2 (G22)


title: EQ LIN SS3 Cassette 3 1 (G52)


title: EQ LIN SS3 Cassette 2 1 (G22)


title: EQ LIN WT Cassette 6 2 (R10)


title: EQ LIN SS9 Cassette 7 2 (G56)


title: EQ LIN WT Cassette 6 1 (R10)


title: EQ LIN WT Cassette 5 2 (G57)


title: EQ LIN WT Cassette 7 2 (G56)


title: EQ LIN WT Cassette 7 1 (G56)


title: EQ LIN WT Cassette 5 1 (G57)


title: EQ LIN WT Cassette 3 1 (G52)


title: EQ LIN WT Cassette 2 2 (G22)


title: EQ LIN WT Cassette 3 2 (G52)


title: EQ LIN WT Cassette 2 1 (G22)


title: 10 LIN SS9 Cassette 6 2 (R10)


title: 10 LIN SS9 Cassette 3 1 (G52)


title: 10 LIN SS9 Cassette 5 1 (G57)


title: 10 LIN SS9 Cassette 7 2 (G56)


title: 10 LIN SS9 Cassette 7 1 (G56)


title: 10 LIN SS9 Cassette 3 2 (G52)


title: 10 LIN SS9 Cassette 6 1 (R10)


title: 10 LIN SS9 Cassette 2 1 (G22)


title: 10 LIN SS9 Cassette 2 2 (G22)


title: 10 LIN SS3 Cassette 6 2 (R10)


title: 10 LIN SS3 Cassette 5 2 (G57)


title: 10 LIN SS3 Cassette 6 1 (R10)


title: 10 LIN SS3 Cassette 5 1 (G57)


title: 10 LIN SS3 Cassette 7 2 (G56)


title: 10 LIN SS3 Cassette 3 2 (G52)


title: 10 LIN SS3 Cassette 3 1 (G52)


title: 10 LIN SS3 Cassette 2 2 (G22)


title: 10 LIN WT Cassette 6 2 (R10)


title: 10 LIN SS3 Cassette 2 1 (G22)


title: 10 LIN WT Cassette 5 2 (G57)


title: 10 LIN WT Cassette 5 1(G57)


title: 10 LIN WT Cassette 7 2 (G56)


title: 10 LIN SS9 Cassette 5 2 (G57)


title: 10 LIN WT Cassette 6 1 (R10)


title: 10 LIN WT Cassette 3 1 (G52)


title: 10 LIN WT Cassette 2 2 (G22)


title: 10 LIN WT Cassette 7 1 (G56)


title: 100 LIN SS9 Cassette 6 2 (R10)


title: 100 LIN SS9 Cassette 5 1 (G57)


title: 100 LIN SS9 Cassette 5 2 (G57)


title: 10 LIN SS3 Cassette 7 1 (G56)


title: 100 LIN SS9 Cassette 3 2 (G52)


title: 100 LIN SS9 Cassette 7 1 (G56)


title: 100 LIN SS9 Cassette 7 2 (G56)


title: 10 LIN WT Cassette 2 1 (G22)


title: 100 LIN SS9 Cassette 2 1 (G22)


title: 100 LIN SS9 Cassette 6 1 (R10)


title: 100 LIN SS3 Cassette 5 2 (G57)


title: 100 LIN SS9 Cassette 2 2 (G22)


title: 100 LIN SS3 Cassette 6 2 (R10)


title: 100 LIN SS3 Cassette 5 1 (G57)


title: 100 LIN SS3 Cassette 7 1 (G56)


title: 10 LIN WT Cassette 3 2 (G52)


title: 100 LIN SS3 Cassette 7 2 (G56)


title: 100 LIN SS3 Cassette 3 2 (G52)


title: 100 LIN SS3 Cassette 3 1 (G52)


title: 100 LIN SS3 Cassette 2 2 (G22)


title: 100 LIN WT Cassette 6 2 (R10)


title: 100 LIN WT Cassette 7 2 (G56)


title: 100 LIN WT Cassette 5 2 (G57)


title: 100 LIN WT Cassette 7 1 (G56)


title: 100 LIN WT Cassette 3 2 (G52)


title: 100 LIN WT Cassette 5 1 (G57)


title: 100 LIN WT Cassette 6 1 (R10)


title: 100 LIN WT Cassette 2 2 (G22)


title: 100 LIN WT Cassette 3 1 (G52)


title: 100 LIN SS9 Cassette 3 1 (G52)


title: M9 Cassette 5 SS9 1 (G57)

value: Circular


title: M9 Cassette 7 SS9 2 (G56)


title: 100 LIN SS3 Cassette 6 1 (R10)


title: 100 LIN WT Cassette 2 1 (G22)


title: M9 Cassette 2 SS9 2 (G22)


title: M9 Cassette 2 SS9 1 (G22)


title: M9 Cassette 5 SS9 2 (G57)


title: M9 Cassette 7 SS3 2 (G56)


title: M9 Cassette 5 WT 2 (G57)


title: M9 Cassette 2 SS3 1 (G22)


title: 100 LIN SS3 Cassette 2 1 (G22)


title: M9 Cassette 7 WT 2 (G56)


title: M9 Cassette 7 WT 1 (G56)


title: M9 Cassette 5 WT 1 (G57)


title: M9 Cassette 2 WT 2 (G22)


title: M9 Cassette 2 WT 1 (G22)


title: Cassette 4 SS3 2 (G47)


title: M9 Cassette 7 SS9 1 (G56)


title: Cassette 4 SS9 1 (G47)


title: Cassette 4 SS3 1 (G47)


title: M9 Cassette 5 SS3 2 (G57)


title: Cassette 4 SS9 2 (G47)


title: Cassette 4 WT 1 (G47)


title: proC Cassette 2 N8 2 (G22 N8)

value: cgaactttacggGcatcgcg


title: M9 Cassette 5 SS3 1 (G57)


title: proC Cassette 3 N4 2 (G52 N4)

value: TGCGACAATGGGCGCcTCGAG


title: proC Cassette 2 N4 2 (G22 N4)

value: cgaactttacggtcatTgcg

value: proC


title: proC Cassette 3 N12 1 (G52 N12)

value: TGCGACAAgGGGCGCATCGA


title: Cassette 4 WT 2 (G47)

value: ACAAATCGCGCTTAACGGTC


title: M9 Cassette 2 SS3 2 (G22)


title: proC Cassette 2 N12 2 (G22 N12)

value: cgaactttGcggtcatcgcg


title: proC Cassette 2 N8 1 (G22 N8)


title: M9 Cassette 7 SS3 1 (G56)

value: AGGCGCCTGAATGGTGTGAG


title: proC Cassette 3 N12 2 (G52 N12)


title: proC Cassette 3 N8 2 (G52 N8)

value: TGCGACAATGGGaGCATCGA


title: proC Cassette 2 N4 1 (G22 N4)


title: proC Cassette 3 N4 1 (G22 N4)


title: proC Cassette 2 N12 1 (G22 N12)


title: proC Cassette 3 N8 1 (G52 N8)


title: araC Cassette 3 N12 2 (G52 N12)


title: araC Cassette 2 N12 2 (G22 N12)


title: araC Cassette 3 N8 2 (G52 N8)


title: araC Cassette 3 N4 2 (G52 N4)


title: araC Cassette 2 N8 2 (G22 N8)


title: araC Cassette 2 N4 2 (G22 N4)


title: araC Cassette 3 N12 1 (G52 N12)


title: araC Cassette 3 N8 1 (G52 N8)


title: araC Cassette 2 N4 1 (G22 N4)


title: araC Cassette 2 N12 1 (G22 N12)


title: proD Cassette 5 2 (G57)

value: GGCTAACTACGTTCGTGGCG


title: araC Cassette 2 N8 1 (G22 N8)


title: proD Cassette 8 1 (G58)

value: TTCCGCTTCACTGGAAGTCG

value: proD


title: proD Cassette 5 1 (G57)


title: proD Cassette 3 1 (G52)

value: TGCGACAATGGGCGCATCGA


title: proD Cassette 6 1 (R10)

value: TGAAGCGGAAGAACTTAACC


title: proD Cassette 3 2 (G52)

value: 0.82 MB from ter


title: proD Cassette 2 2 (G22)

value: CGAACTTTACGGTCATCGCG


title: proD Cassette 6 2 (R10)

value: Circular


title: proD Cassette 2 1 (G22)


title: proD Cassette 7 1 (G56)


title: proD Cassette 1 2 (GALK_OFF)

value: ATGATAAAGCTGCTGCAATA


title: proD Cassette 1 1 (GALK_OFF)


title: proC Cassette 8 2 (G58)


title: proC Cassette 5 2 (G57)


title: proC Cassette 8 1(G58)


title: proC Cassette 6 2 (R10)


title: proC Cassette 7 1 (G56)


title: proC Cassette 6 1 (R10)


title: proC Cassette 3 2 (G52)


title: proC Cassette 5 1 (G57)


title: proC Cassette 3 1 (G52)


title: proC Cassette 7 2 (G56)


title: araC Cassette 3 N4 1 (G52 N4)

value: TGCGACAATGGGCGCcTCGAG

value: araC


title: proD Cassette 8 2 (G58)


title: proD Cassette 7 2 (G56)


title: proC Cassette 2 2 (G22)

value: proC


title: proC Cassette 1 2 (GALK_OFF)


title: pro1 Cassette 8 1 (G58)


title: pro1 Cassette 5 1 (G57)


title: proC Cassette 2 1 (G22)


title: proC Cassette 1 1 (GALK_OFF)


title: pro1 Cassette 7 2 (G56)


title: pro1 Cassette 6 2 (R10)


title: pro1 Cassette 3 2 (G52)


title: pro1 Cassette 5 2 (G57)


title: pro1 Cassette 3 1 (G52)


title: pro1 Cassette 2 2 (G22)


title: pro1 Cassette 6 1 (R10)


title: pro1 Cassette 7 1 (G56)


title: pro1 Cassette 1 1 (GALK_OFF)


title: pro1 Cassette 1 2 (GALK_OFF)


title: pro1 Cassette 2 1 (G22)


title: No Targeted Recombination  SS9 Cassette 5 2 (G57)

value: 2.28 MB from ter


title: No Targeted Recombination  SS9 Cassette 8 2 (G58)


title: No Targeted Recombination  SS9 Cassette 5 1 (G57)


title: No Targeted Recombination  SS9 Cassette 8 1 (G58)


title: No Targeted Recombination  SS9 Cassette 7 2 (G56)


title: No Targeted Recombination  SS9 Cassette 6 1 (R10)


title: No Targeted Recombination  SS9 Cassette 6 2 (R10)


title: No Targeted Recombination  SS9 Cassette 7 1 (G56)


title: No Targeted Recombination  SS9 Cassette 2 2 (G22)


title: No Targeted Recombination  SS9 Cassette 3 2 (G52)


title: pro1 Cassette 8 2 (G58)


title: No Targeted Recombination  SS9 Cassette 2 1 (G22)


title: No Targeted Recombination  SS9 Cassette 1 2 (GALK_OFF)


title: No Targeted Recombination  SS9 Cassette 3 1 (G52)


title: No Targeted Recombination  SS3 Cassette 8 1 (G58)

value: 0.30 MB from ter


title: No Targeted Recombination  SS3 Cassette 8 2 (G58)


title: No Targeted Recombination  SS9 Cassette 1 1 (GALK_OFF)


title: No Targeted Recombination  SS3 Cassette 5 1 (G57)


title: No Targeted Recombination  SS3 Cassette 6 1 (R10)


title: No Targeted Recombination  SS3 Cassette 6 2 (R10)


title: No Targeted Recombination  SS3 Cassette 7 2 (G56)


title: No Targeted Recombination  SS3 Cassette 5 2 (G57)


title: No Targeted Recombination  SS3 Cassette 3 2 (G52)


title: No Targeted Recombination  SS3 Cassette 3 1 (G52)


title: No Targeted Recombination  SS3 Cassette 2 2 (G22)


title: No Targeted Recombination  SS3 Cassette 1 1 (GALK_OFF)


title: No Targeted Recombination  SS3 Cassette 1 2 (GALK_OFF)


title: No Targeted Recombination  SS3 Cassette 7 1 (G56)


title: No Targeted Recombination  SS3 Cassette 2 1 (G22)


title: SS9 Cassette 5 1 (G57)


title: SS9 Cassette 8 2 (G58)


title: SS9 Cassette 3 2 (G52)


title: SS9 Cassette 7 1 (G56)


title: SS9 Cassette 6 1 (R10)


title: SS9 Cassette 7 2 (G56)


title: SS9 Cassette 2 1 (G22)


title: SS9 Cassette 2 2 (G22)


title: SS3 Cassette 8 2 (G58)


title: SS9 Cassette 6 2 (R10)


title: SS9 Cassette 1 1 (GALK_OFF)


title: SS3 Cassette 8 1 (G58)


title: SS9 Cassette 1 2 (GALK_OFF)


title: SS3 Cassette 6 2 (R10)


title: SS3 Cassette 5 1 (G57)


title: SS3 Cassette 6 1 (R10)


title: SS3 Cassette 5 2 (G57)


title: SS9 Cassette 8 1 (G58)


title: SS3 Cassette 3 1 (G52)


title: SS3 Cassette 7 1 (G56)


title: SS3 Cassette 1 2 (GALK OFF)


title: SS3 Cassette 1 1 (GALK OFF)


title: WT Cassette 5 2 (G57)


title: WT Cassette 8 1 (G58)


title: WT Cassette 8 2 (G58)


title: WT Cassette 5 1 (G57)


title: WT Cassette 6 2 (R10)


title: SS3 Cassette 3 2 (G52)


title: WT Cassette 7 2 (G56)


title: WT Cassette 7 1 (G56)


title: WT Cassette 3 2 (G52)


title: SS3 Cassette 2 2 (G22)


title: WT Cassette 3 1 (G52)


title: SS3 Cassette 7 2 (G56)


title: SS9 Cassette 5 2 (G57)


title: WT Cassette 1 2 (GALK_OFF)


title: WT Cassette 1 1 (GALK_OFF)


title: Parkinson's Disease Patient PD1-2 neurons [small RNA-seq]

first: Ioannis

middle: S

last: Vlachos

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

description:
DP2
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt

data_processing:
Raw RNA-Seq reads were quality checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Contaminants were detected and removed utilizing a combination of an in-house-developed algorithm and already available tools such as Minion and Cutadapt.
Pre-processing was performed using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
microRNA expression was quantified using miRDeep2 (Mackowiak 2011) with miRBase v20 annotation (Kozomara and Griffiths-Jones 2014).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: *.genecounts.txt: Tab-delimited text files include read counts.
Supplementary_files_format_and_content: miRNAs_expressed_all_samples_1390083537.txt: Tab-delimited text file; Sample value 1: Read counts. Total number of counts equals the number of reads mapped on miRNAs. In cases of reads mapping to more than one miRNA, equal read fractions were assigned (1/number of matches); Sample value 2: Normalized read counts. Read counts have been normalized for library size differences. This normalization is for visualization purposes and user convenience only.

source_name: iPSC-derived neurons

growth_protocol: NPCs were dissociated with accutase and plated onto poly-L-ornithine (PLO; 20 µg/ml; Sigma-Aldrich)/ laminin (5 µg/ml; Sigma-Aldrich)-coated coverslips (Passage 1; P1) in Neurobasal/ B27/N2-medium supplemented with 200 ng/ml human recombinant sonic hedgehog (SHH, R&D Systems) and 100 ng/ml murine recombinant fibroblast growth factor 8b (FGF-8b, R&D Systems) for 8 DIV, followed by a cocktail consisting of 20 ng/ml brain-derived neurotrophic factor (BDNF, R&D Systems), 10 ng/ml glial cell-derived neurotrophic factor (GDNF, R&D Systems), 200 µM ascorbic acid (AA, Sigma-Aldrich) and 0.5 mM cyclic AMP (cAMP, Sigma-Aldrich) for at least 3 weeks. Half of the medium was replaced every other day. After 30-35 DIV of neuronal differentiation, corresponding to a total of 43-48 DIV, cells were harvested for RNA extraction.

extract_protocol:
Total RNA was extracted from cell pellets using the TRIzol® Reagent (Life Technologies).
Small RNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina.

tag: cell type

value: neuron

value: Parkinson's Disease Patient

tag: clone


title: WT Cassette 2 1 (G22)


title: WT Cassette 2 2 (G22)


title: Parkinson's Disease Patient PD1-1 neurons [small RNA-seq]

description:
DP1
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt


title: Healthy Control C1-2 neurons [small RNA-seq]

description:
DH2
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt

value: Healthy Control


title: Parkinson's Disease Patient PD1-2 NPCs [small RNA-seq]

description:
NP2
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt

source_name: iPSC-derived NPCs

growth_protocol: iPSC colonies were dissociated with accutase (Life Technologies) for 10 min and re-suspended in EB medium supplemented with 10 µM ROCK inhibitor Y-27632 (Tocris Bioscience). After 5 days DIV, neural induction was achieved by dual suppression of the SMAD signaling pathway19 using a combination of Noggin (250 ng/ml; R&D Systems) and SB431542 (10 µM; Tocris Bioscience) in DMEM: F12/N2-medium (Neural induction medium) for 8 DIV to generate neural precursor cells (NPCs).

value: Neural progenitor cell


title: SS9 Cassette 3 1 (G52)


title: Parkinson's Disease Patient PD1-1 NPCs [small RNA-seq]

description:
NP1
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt


title: Reference HUES-neurons [small RNA-seq]

description:
EDN
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt

source_name: HUES-derived neurons

growth_protocol: NPCs were dissociated with accutase and plated onto poly-L-ornithine (PLO; 20 µg/ml; Sigma-Aldrich)/ laminin (5 µg/ml; Sigma-Aldrich)-coated coverslips. Dopaminergic patterning and neuronal differentiation was initiated for 8 days in Neurobasal medium supplemented with ascorbic acid (AA, Sigma-Aldrich; 200μM), human recombinant sonic hedgehog (SHH, R&D Systems; 200ng/ml), recombinant basic fibroblast growth factor 2 (bFGF-2, R&D Systems; 10ng/ml), recombinant fibroblast growth factor 8b (FGF-8b, R&D Systems; 100ng/ml), containing also 1% N2 supplement, 2% B-27 supplement and 1% Glutamax, followed by a cocktail consisting of brain-derived neurotrophic factor (BDNF, R&D Systems; 20ng/ml), ascorbic acid (200μM), glial cell-derived neurotrophic factor (GDNF, R&D Systems; 10ng/ml), and cyclic-AMP (cAMP, Sigma-Aldrich; 0.5mM) for further 21-26 days to allow neuronal maturation. Half of the medium was replaced every other day. At the end of the protocol, corresponding to a total of 43-48 DIV, cells were harvested for RNA extraction.

tag: cell line

value: Reference


title: Reference HUES-NPCs [small RNA-seq]

description:
NES
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt

source_name: HUES-derived NPCs

growth_protocol: HUES cell colonies were dissociated with accutase (Life Technologies) for 10 min and re-suspended in EB medium supplemented with 10 µM ROCK inhibitor Y-27632 (Tocris Bioscience). After 5 days DIV, neural induction was achieved by dual suppression of the SMAD signaling pathway19 using a combination of Noggin (250 ng/ml; R&D Systems) and SB431542 (10 µM; Tocris Bioscience) in DMEM: F12/N2-medium (Neural induction medium) for 8 DIV to generate neural precursor cells (NPCs).


title: Healthy Control C1-1 NPCs [small RNA-seq]

description:
NH1
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt


title: Parkinson's Disease Patient PD1-2 iPSCs [small RNA-seq]

description:
IP2
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt

source_name: iPSCs

growth_protocol: iPSCs were generated by transduction of human fibroblasts with retroviral vectors expressing the human cDNAs of OCT4, SOX2, KLF4 and C-MYC. iPSCs were cultured on irradiated mouse embryonic fibroblasts (MEFs, Globalstem) in iPSC medium consisting of KnockOut DMEM (KO-DMEM, Life Technologies), 20% Knockout Serum Replacement (KSR, Life Technologies), 2 mM GlutaMax, MEM Non-Essential Amino Acids (100x MEM NEAA, Life Technologies), 100 mM β-mercaptoethanol (Life Technologies) and 10 ng/ml human basic FGF (bFGF, Miltenyi).

value: Induced pluripotent stem cell


title: Healthy Control C1-2 NPCs [small RNA-seq]

description:
NH2
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt


title: Healthy Control C1-2 iPSCs [small RNA-seq]

description:
IH2
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt


title: Reference HUES [small RNA-seq]

description:
HES
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt

source_name: HUES6 cells

growth_protocol: HUES cells were cultured on irradiated mouse embryonic fibroblasts (MEFs, Globalstem) in HUES/iPSC medium consisting of KnockOut DMEM (KO-DMEM, Life Technologies), 20% Knockout Serum Replacement (KSR, Life Technologies), 2 mM GlutaMax, MEM Non-Essential Amino Acids (100x MEM NEAA, Life Technologies), 100 mM β-mercaptoethanol (Life Technologies) and 10 ng/ml human basic FGF (bFGF, Miltenyi).

value: Embryonic stem cell


title: Parkinson's Disease Patient PD1-1 iPSCs [small RNA-seq]

description:
IP1
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt


title: Parkinson's Disease Patient PD1-2 neurons [RNA-seq]

extract_protocol:
Total RNA was extracted from cell pellets using the TRIzol® Reagent (Life Technologies).
Total cellular RNA was sequenced on an Illumina HiSeq sequencer. RNA libraries were prepared with the TruSeq RNA Sample Preparation Kit V2 (Illumina).


title: Parkinson's Disease Patient Fibroblasts [small RNA-seq]

description:
HFP
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt

source_name: Skin

growth_protocol: Fibroblasts were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, Life Technologies), 2mM GlutaMax (Life Technologies) and 1% penicillin/streptomycin (Life Technologies).

value: Adult - Primary skin


title: Reference Fibroblasts [small RNA-seq]

description:
HFF
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt

source_name: Human fetus

value: Fetal fibroblast


title: Healthy Control C1-1 neurons [RNA-seq]


title: Parkinson's Disease Patient PD1-1 neurons [RNA-seq]


title: Parkinson's Disease Patient PD1-1 NPCs [RNA-seq]


title: Reference HUES-neurons [RNA-seq]


title: Reference HUES-NPCs [RNA-seq]


title: Parkinson's Disease Patient PD1-2 NPCs [RNA-seq]


title: Parkinson's Disease Patient PD1-1 iPSCs [RNA-seq]


title: Healthy Control C1-2 NPCs [RNA-seq]


title: Healthy Control C1-2 iPSCs [RNA-seq]


title: Healthy Control C1-1 iPSCs [RNA-seq]


title: Healthy Control C1-1 neurons [small RNA-seq]

description:
DH1
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt


title: Healthy Control C1-1 iPSCs [small RNA-seq]

description:
IH1
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt


title: Healthy Control Fibroblasts [RNA-seq]


title: Healthy Control Fibroblasts [small RNA-seq]

description:
HFH
Small RNA-Seq
miRNAs_expressed_all_samples_1390083537.txt


title: Reference Fibroblasts [RNA-seq]


title: Parkinson's Disease Patient Fibroblasts [RNA-seq]


title: Healthy Control C1-2 neurons [RNA-seq]


title: Healthy Control C1-1 NPCs [RNA-seq]


title: Parkinson's Disease Patient PD1-2 iPSCs [RNA-seq]


title: Sample 15: Cre

city: Saint Louis

first: Yosuef

last: Abu-amer

state: MO

address: 660 South Euclid Ave

department: Orthopedic Surgery

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

source_name: Primary Sternal Chondrocytes

growth_protocol: Chondrocytes were cultured in DMEM with 10% FBS in tissue culture plates under normoxic conditions. No passaging was performed

extract_protocol:
Trizol was added directly to samples in 24 well plates. Chloroform was added 20% by volume and samples were centrifuged at 12000 g for 15 mins. Aqueous layer was utilized in Purelink RNA mini kit for isolation of RNA
KAPA Ribo-Erase

treatment_protocol: WT chondrocytes were treated with IL-1b and/or FX11 for 24 hours. LDHA flox, NAMPT flox and NFKBIZ flox chondrocytes were infected with adeno-GFP or adeno-cre for 24 hours. Cells were then treated with or without IL-1b for 24 hours.

value: Primary Sternal Chondrocytes

tag: strain

value: LDHA flox

tag: treatment

value: Cre


title: Sample 12: Cre + IL-1b

value: NFKBIZ flox

value: Cre + IL-1b


title: Sample 19: Cre

value: NAMPT flox


title: Sample 14: GFP + IL-1b

value: GFP + IL-1b


title: Sample 20: Cre + IL-1b


title: Sample 16: Cre + IL-1b


title: Sample 13: GFP

value: GFP


title: Reference HUES [RNA-seq]


title: Sample 17: GFP


title: Sample 11: Cre


title: Sample 9: GFP


title: Sample 10: GFP + IL-1b


title: Sample 6: GFP + IL-1b


title: Sample 8: Cre + IL-1b


title: Sample 7: Cre


title: Sample 4: WT- IL-1b + FX11

value: wild type

value: IL-1b + FX11


title: Sample 18: GFP + IL-1b


title: Sample 5: GFP


title: Mouse_POMC_SKO_1

city: CAMBRIDGE

first: Jeong

last: Rih

address: 650 East Kendall Street

institute: IPSEN Bioscience

description: Gene expression data from mouse pituitary tissue with heterozygous knock-out of POMC gene

hyb_protocol: The hybridization protocl was according to the manufacture (Affymetrix)

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip 3000 7G Scanner.

data_processing: The array data were processed using Expression Console (Affymetrix) then normalized using the Robust Multichip Average (RMA) algorithm built in the GeneSpring GX.

label_protocol: The label protocol was according to the manufacture protocol (Affymetrix) on samples with RIN >7

growth_protocol: mouse model

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

treatment_protocol: no treatment performed

value: pituitary gland


title: Mouse_POMC_DKO_2

description: Gene expression data from mouse pituitary tissue with homozygous knock-out of POMC gene


title: Mouse_POMC_SKO_4

source_name: mouse pituitary tissue with heterozygous knock-out of POMC gene


title: Mouse_POMC_SKO_3


title: Mouse_POMC_SKO_8


title: Mouse_POMC_SKO_5


title: Mouse_Normal_2

description: Gene expression data from mouse normal pituitary tissue

source_name: mouse normal pituitary tissue


title: Mouse_Normal_1


title: Mouse_POMC_SKO_2


title: 12: Cre + IL-1b


title: 8: Cre + IL-1b


title: Mouse_POMC_SKO_7


title: Mouse_POMC_DKO_1

source_name: mouse pituitary tissue with homozygous knock-out of POMC gene


title: 10: GFP + IL-1b


title: Mouse_POMC_SKO_6


title: 9: GFP


title: 3: WT- IL-1b


title: Sample 2: WT- FX11


title: 2: WT- FX11


title: 11: Cre


title: 6: GFP + IL-1b


title: Sample 3: WT- IL-1b


title: 5: GFP


title: 1: WT- Untreated

value: Untreated


title: 4: WT- IL-1b + FX11


title: MNT IP in  mRPMaxKO pCW MAX Set3

city: Seattle

first: Arnaud

middle: A

last: Augert

state: Washington

address: 100 Fairview Avenue N. Thomas Building Room D4

institute: Fred Hutchinson Cancer Research Center

data_processing:
Library strategy: CUT&RUN
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Alignment to mm10 with Bowtie 2,  reads >700bp filtered out, samples spike-in normalized
BigWigs were created using bedtools (genomecov) and WigToBigWig scripts
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Small cell lung cancer cell line

growth_protocol: Polyclonal population of mRPMaxKO cells transduced with a doxycycline inducible lentiviral vector, puromycin selected and expanded.

extract_protocol: CUT&RUN libraries were prepared for sequencing using custom protocols

treatment_protocol: Doxycycline treatment was performed for 4 days on both mRPMaxKO pCW Empty and pCW MAX lines. CUT&RUN protocol followed.

value: small cell lung cancer

tag: antibody

value: MNT Bethyl Labs A303-627A; RRID:AB_11205638


title: RNApolII p-Ser5 IP in  mRPMaxKO pCW MAX Set3 Rep1

value: RNA pol II phospho Ser5 Cell Signaling 13523; RRID:AB_2799721


title: RNApolII p-Ser5 IP in  mRPMaxKO pCW MAX Set3 Rep2


title: Sample 1: WT- Untreated


title: 7: Cre


title: MGA IP in  mRPMaxKO pCW MAX Set3 Rep2

value: MGA Suske Lab Stielow et al., 2018


title: MGA IP in  mRPMaxKO pCW MAX  Set3 Rep1


title: MAX IP in  mRPMaxKO pCW MAX Set3

value: MAX Proteintech 10426-1-AP; RRID:AB_2141660


title: Rabbit IgG mRPMaxKO pCW MAX Set3

value: GFP Cell Signalling 2956S; RRID:AB_1196615


title: MAX IP in mRPMaxKO pCW MAX Set2


title: MNT IP in mRPMaxKO pCW Empty Set3


title: Rabbit IgG in mRPMaxKO pCW Empty  Set3


title: MAX IP in mRPMaxKO pCW MAX Set1


title: MAX IP in mRPMaxKO pCW Empty  Set2


title: MGA IP in mRPMaxKO pCW Empty  Set3 Rep 2


title: Rabbit IgG mRPMaxKO pCW MAX Set2


title: MNT IP in mRPMaxKO pCW MAX Set1


title: Rabbit IgG in mRPMaxKO pCW Empty Set2


title: MGA IP in mRPMaxKO pCW Empty Set3 Rep 1


title: MNT IP in mRPMaxKO pCW Empty Set1


title: MAX IP in mRPMaxKO pCW Empty Set1


title: RNApolII p-Ser5 IP in mRPMaxKO pCW Empty Set3 Rep1


title: MAX IP in mRPMaxKO pCW Empty  Set3


title: RNApolII IP in sgMax preSC Rep1

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Alignment to mm10 with Bowtie 2,  reads >700bp filtered out, samples spike-in normalized
BigWigs were created using bedtools (genomecov) and WigToBigWig scripts
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: preSC

growth_protocol: Polyclonal population of preSCs transduced with sgRNA control or sgRNA Max, puromycin selected and expanded. preSCs were grown in RPMI supplemented with 10% FBS. Both groups of cells were cultured on 15cm dishes

extract_protocol:
Cells were crosslinked in formaldehyde and ChIP was performed
Libraries were constructed using the NEB Ultra II kit for Illumina

treatment_protocol: No treatment was performed

tag: transduction

value: sgRNA against Max

value: RNApol II Active Motif 39097; RRID:AB_2732926


title: RNApolII IP in sgMax preSC Rep2


title: MYC IP in sgMax preSC Rep2

value: MYC Cell Signaling 13987; RRID:AB_2631168


title: MYC IP in sgMax preSC Rep1


title: MAX IP in sgMax preSC Rep2


title: MAX IP in sgMax preSC Rep1


title: MNT IP in sgMax preSC Rep2


title: Input control in sgMax preSC Rep2


title: Input control in sgMax preSC Rep1


title: RNApolII IP in sgCtrl preSC Rep2

value: sgRNA control


title: RNApolII IP in sgCtrl preSC Rep1


title: MYC IP in sgCtrl preSC Rep2


title: MNT IP in sgCtrl preSC Rep2


title: RNApolII p-Ser5 IP in mRPMaxKO pCW Empty Set3 Rep2


title: MYC IP in sgCtrl preSC Rep1


title: MAX IP in sgCtrl preSC Rep2


title: MNT IP in sgMax preSC Rep1


title: MNT IP in sgCtrl preSC Rep1


title: Control-2

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to mm9 using STAR 2.5.2a in 2-pass mode.  Counts were generated from STAR alignments at the gene-level using featureCounts from the Subread package v1.6.0.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by featureCounts

source_name: mRPMaxKO

extract_protocol:
RNA was extracted using TRIZOL according to the manufacturer’s recommendations (15596018, ThermoFisherScientific).
For RNA-seq analyses, the Ultra RNA Library Prep Kit for Illumina (E7530L, New England BioLabs) was used to generate libraries from total RNA (500ng)

treatment_protocol: Doxycycline treatment was performed for 4 days

value: cell line derived from RPMax-/- lung tumor

tag: passages

value: <20 passages

value: control


title: Control-3


title: MAX IP in sgCtrl preSC Rep1


title: Input control in sgCtrl preSC Rep2


title: RPMaxWT T6

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to mm9 using TopHat v2.0.12  Counts were generated from Tophat alignments at the gene-level employing the "intersection-strict" overlap mode in HTSeq v0.6.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include counts genreated at the gene-level by HTSeq-count.

source_name: lung tumors

growth_protocol: Mouse lung tumors isolated from RPMax-wt and RPMax-null mice

treatment_protocol: Gene deletion was achieved following an intratracheal instillation of Ad.CMV.Cre viruses

value: lung tumors

value: wild type


title: MAX-1

value: MAX restored


title: Input control in sgCtrl preSC Rep1


title: Control-1


title: RPMaxWT T5


title: RPMaxWT T2


title: MAX-2


title: MAX-3


title: RPMaxWT T4


title: RPMaxWT T7


title: RPMaxWT T1


title: RPMax-/-  T9

value: Max -/-


title: RPMax-/-  T7


title: RPMaxWT T3


title: RPMax-/-  T4


title: RPMax-/-  T6


title: RPMax-/-  T8


title: RPMax-/-  T5


title: RPMax-/-  T3


title: RPMax-/-  T2


title: Ctrl#4

growth_protocol: Polyclonal population of preSCs transduced with sgRNA control or sgRNA Max, puromycin selected and expanded.

value: preSC


title: Ctrl#3


title: RPMax-/-  T1


title: Ctrl#2


title: Ctrl#1


title: MaxKO#3

value: Max KO


title: MaxKO#2


title: MaxKO#1


title: Liver, med23 ko_1

city: Shanghai

first: Zhichao

last: Wang

address: 320 YueYang Road

institute: SIBCB

data_processing:
After quality assessment of the corresponding FASTQ files with FastQC, adapter sequences were trimmed from the reads.
Raw reads were mapped to mm10 using Tophat  with default parameters.
Differential gene expression was analyzed with Cuffdiff using the University of California Santa Cruz (UCSC) mm10 assembly as the reference sequence. In addition, genes with an expression fold change of >|2| were selected for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample. The columns are gene symbols, fold_change and FPKM.

source_name: liver tissue

growth_protocol: Eight-week-old male mice were intraperitoneally injected with 0.6 μl/g body weight CCl4 (1:4 vol/vol in sunflower oil from Sigma) ,all animals were euthanized 24 hours after CCl4 injection

extract_protocol:
Total RNAs was extracted using Trizol reagent (Invitrogen), and 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: med23 ko

tag: gender

value: male

tag: age

value: 8-weeks old

value: ccl4 24h


title: Liver, wt_3

value: wt


title: Liver, med23 ko_3


title: Liver, wt_1


title: Liver, wt_2


title: M199-TNFalfa_rep_4

city: London

first: Francesca

last: Patella

address: Gower St

department: LMCB

country: United Kingdom

institute: University College London

data_processing:
Sequencing was performed using a NextSeq 500 System (Illumina) with High-Output run and 75 bp paired end. Sequencing quality control was done using MultiQC (http://multiqc.info/).
Sequence Fastq files were aligned to the reference genome HG19 using STAR aligner implemented in BaseSpace (RNA-Seq Alignment pipeline v 1.1.0, Illumina).
BAM file outputs from STAR were annotated using Partek Genomic Suite (v6.6) and the RefSeq data base (RefSeq 21)
Differential analysis (control vs treated samples) was performed using Partek Genomic Suite (v6.6) running ANOVA (n=4 independent replicates). Only hits with a threshold criteria for significance of p-value <0.05 and fold change of >2 were considered.
Genome_build: UCSC hg19

source_name: human umbelical vein endothelial cells (HUVECs)

growth_protocol: HIVECs pooled from multiple donors were purchased from PromoCell and expanded for 3 passages in M199 additioned with 20% FBS, 30 μg/ml endothelial cell growth supplement from bovine neural tissue and 10 U/ml heparin.

extract_protocol:
Cells in 12well plates were processed for RNA (Qiagen RNeasy kit). RNA was quantified using a Nanodrop (Thermofisher Scientific) and quality analysis was performed  using a Bioanalysar (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, 100 ng of total RNA was used as a template for NEB Ultra directional RNA library prep kit with mRNA selection (New England Biolabs). Library quantification (QuBit, Thermofisher Scientific) and quality assessment (Tape Station,  D1000 tape, Agilent) were performed. Sequencing was performed using a NextSeq 500 System (Illumina) with High-Output run and  75 bp paired end.

treatment_protocol: As specified in the Samples section

value: primary endothelial cells

value: treated with 50ng/ml TNFa for 3h, grown in M199_


title: EBM2_rep_3

value: untreated, grown in EBM2_


title: EBM2_rep_1


title: M199-TNFalfa_rep_3


title: M199-TNFalfa_rep_2


title: M199-TNFalfa_rep_1


title: nitrogen_starvation_rep2

city: Chapel Hill

first: Henrik

last: Dohlman

state: NC

address: 120 Mason Farm Rd, 4th Floor

department: Pharmacology

institute: University of North Carolina at Chapel Hill

description: column n2 in normalized_counts_DESeq2

data_processing:
STAR (2.7.3a) genome indices was generated by using Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa as --genomeFastaFiles and Saccharomyces_cerevisiae.R64-1-1.99.gtf as --sjdbGTFfile. All fa and gtf files are downloaded from Ensembl.org
STAR (2.7.3a) and the previously generated genome indices were used for alignment with parameter --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
generate transcriptome FA file by using gffread in SALMON (1.2.1) with -g Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa Saccharomyces_cerevisiae.R64-1-1.99.gtf
quantification was performed with SALMON (1.2.1) quant mode, with parameters -l SF
Genome_build: R64-1-1 (Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database), INSDC Assembly GCA_000146045.2, Sep 2011
Supplementary_files_format_and_content: sf files are TSV format file listing the name (Name) of each transcript, its length (Length), effective length (EffectiveLength) (more details on this in the documentation), and its abundance in terms of Transcripts Per Million (TPM) and estimated number of reads (NumReads) originating from this transcript
Supplementary_files_format_and_content: csv files are comma delminated matrix with genes on the rows and samples on the columns. the numbers are DESeq2 normalized counts with batch effect taken into control (design = ~batch+treatment).

organism: Saccharomyces cerevisiae

source_name: log phase yeast

growth_protocol: yeast cells were grown to OD600 about 1.000 in Synthetic Complete medium

extract_protocol:
cells were spin down and flash frozen in liquid nitrogen. Total RNA was extracted with RNeasy Mini kit (Qiagen 74104) with on-column removal of DNA using the RNase-Free DNase Set (Qiagen 79254)
library was prepared with the KAPA mRNA HyperPrep Kit (Roche 08098115702, KAPA Code KK8580), barcoded with NEBNext Multiplex Oligos (Illumina E7710S)

treatment_protocol: one set of cells is kept growing for 1 h without any treatment (control); one set of cells is starved for nitrogen for 1h (nitrogen starvation); one set of cells is starved for potassium for 1h (potassium starvation).

value: nitrogen starvation 1h

tag: batch


title: potassium_starvation_rep2

description: column k2 in normalized_counts_DESeq2

value: potassium starvation 1h


title: potassium_starvation_rep1

description: column k1 in normalized_counts_DESeq2


title: Omentum Sample 2

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Raw sequencing reads were processed using CellRanger v2.2.0 using default parameters
Genome_build: mm10 (mouse) and GRCh38 (human)
Supplementary_files_format_and_content: UMI count matrix: Cellranger count output from filtered_gene_bc directory. Contains UMI counts for each cell. Gene identifiers: Cellranger count output from filtered_gene_bc directory. Contains gene identifiers for the count matrix. Cell barcode list: Cellranger count output from filtered_gene_bc directory. Contains cell barcodes for the count matrix.

source_name: Omentum

extract_protocol:
Single-cell suspensions from omental adipose tissue from mouse or human were prepared as follows: for mouse, CD45+ cells were sorted using BD FACSAria III (n=3 mice/group pooled); human CD45+ cells (from n=3 bariatric surgery subjects, as above) were isolated using the Miltenyi Human CD45 MicroBead MS selection kit (Miltenyi, 130-045-801) according the manufacturer’s instructions.  Cells were processed using the 10X Genomics Chromium v2 Single Cell 3’ RNA-seq (10X Genomics, Pleasanton, CA) and Illumina next generation sequencing technologies (Illumina NextSeq 500 Sequencer) and carried out by the uOttawa StemCore Laboratories (mouse) or the UNGC Sequencing Core at UCLA (human). Input cells were quantified and checked for viability using the Countess II (Thermo Fisher). Suspended cells were loaded on a Chromium controller Single-Cell instrument to generate barcoded single-cell Gel Bead-In-Emulsions (GEMs). GEMs were broken and the barcoded cDNA were amplified using the C1000 Touch Thermal cycler with 96- Well Reaction Module. The amplified barcoded cDNA was then fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3′ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32854) and the fragment size distribution of the libraries were determined using the AATI Fragment analyzer High Sensitivity NGS kit (DNF-486-0500). Pooled libraries were then sequenced using Illumina Nextseq. All samples were sequenced to an average of >50,000 reads per cell, as per 10x Genomics recommendation.
cDNA synthesis and library construction was performed using the 10x Genomics Single Cell 3' Reagent Kit (v2)

tag: tissue

value: Omentum

value: CD45+ cells


title: Omentum Sample 1


title: OE33-control RNA-Seq

city: Los Angeles

first: Qian

last: Yang

state: CA

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

data_processing:
Single-end 49bp or pair-end 150bp reads were aligned to the hg19 reference genome using Bowtie. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using STAR.
Adaptors were removed using Trim galore software. Each replicate, the raw reads were aligned to masked version of the reference human genome hg19.
PCR duplicate reads were removed using Picard MarkDuplicates in Chip-seq
Blacklist regions were removed using ENCODE blacklist file in Chip-seq
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

source_name: Esophageal Adenocarcinoma cell line

growth_protocol: Eso26 cells are cultured in RPMI-1640 medium, OE33 cells are cultured in DMEM medium, media are supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL), and the Anti-PPARG for ChIP-Seq is Cell Signaling Technology, 2443.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Total RNA was extracted by RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions.
Standard Illumina library preparation protocol

treatment_protocol: ESO26 and OE33 cells were transfected with non-silencing siRNA or siPPARG siRNA by Lipofectamine RNAiMAX (Thermo Fisher, USA, 13778150)

value: Esophageal adenocarcinoma cell line


title: control_rep2

description: column ck2 in normalized_counts_DESeq2


title: MaxKO#4


title: M199-Untreated_rep_3

value: untreated, grown in M199_


title: M199-Untreated_rep_2


title: Liver, med23 ko_2


title: Eso26-control RNA-Seq


title: control_rep1

description: column ck1 in normalized_counts_DESeq2


title: EBM2_rep_2


title: EBM2_rep_4


title: OE33-siPPARG RNA-Seq


title: Eso26-siPPARG RNA-Seq


title: ZR-75-1 Cells, Knock Down, Triptolide treated, biological rep3

city: Santiago

first: Ricardo

last: Armisen

state: Macul

address: Obispo Arturo Espinoza Campos 2526

country: Chile

institute: Pfizer Chile

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.4.2a (--runThreadN 6, SortedByCoordinate, outSAMstrandField intronMotif  --outSAMmapqUnique 60  --outFilterType BySJout  --outFilterMultimapNmax 20  --outFilterMismatchNmax 999  --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  --twopassMode Basic)
Read counting was performed using htseq-count (v0.6.1) using the following options -f bam -r pos -s no -q, using gencode v25lift37 gtf file
Differential expression analysis was performed using DEseq2 v1.4.5 (R v3.1)
Genome_build: Human Gencode realease 19 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

growth_protocol: ZR-75-1 SHC and ZR-75-1 ADAR KD cells were cultured in RPMI supplemented with 10% FBS and 1X Penicillin/streptomycin and seeded for treatment 24 h before treatment in 6 well chambers (70% confluence)

extract_protocol:
Treatments were removed and cells were washed two times in PBS, to further extract total RNA using Qiagen Rneasy columns. Illumina TruSeq Stranded Total RNA LT Kit was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ZR-75-1 SHC and ZR-75-1 ADAR KD cells were cultured in RPMI supplemented with 1% FBS and 1X Penicillin/streptomycin in prescence of Triptolide (100 nM), DMSO (100 nM) or not treated during 16 h before RNA extraction

value: ADAR knock down

value: Triptolide treated


title: Eso26_PPARG ChIP-Seq

value: Esophageal Adenocarcinoma cell line


title: si-VWF_rep_4

value: nucleofected with si-VWF


title: OE33_PPARG ChIP-Seq


title: ZR-75-1 Cells, Knock Down, DMSO treated, biological rep3

source_name: ZR-75-1 Cells, Knock Down, DMSO treated

value: DMSO treated


title: nitrogen_starvation_rep1

description: column n1 in normalized_counts_DESeq2


title: si-VWF_rep_3


title: M199-Untreated_rep_4


title: si-VWF_rep_1


title: si-VWF_rep_2


title: ZR-75-1 Cells, Control, DMSO treated, biological rep3

source_name: ZR-75-1 Cells, Control, DMSO treated

value: control


title: ZR-75-1 Cells, Control, Triptolide treated, biological rep3


title: Mock_rep_4

value: mock nucleofected


title: Mock_rep_3


title: M199-Untreated_rep_1


title: ZR-75-1 Cells, Control, not treated, biological rep3

source_name: ZR-75-1 Cells, Control, not treated

value: Not treated


title: Mock_rep_2

value: primary endothelial cells


title: ZR-75-1 Cells, Knock Down, Triptolide treated, biological rep2


title: ZR-75-1 Cells, Knock Down, DMSO treated, biological rep2


title: ZR-75-1 Cells, Knock Down, not treated, biological rep3

source_name: ZR-75-1 Cells, Knock Down, not treated


title: ZR-75-1 Cells, Knock Down, not treated, biological rep2


title: SATP98

city: Calgary

first: Matthew

last: Workentine

state: Alberta

address: 3280 Hospital Drive NW

institute: University of Calgary

description: counts.txt

data_processing:
Transcripts were quantified with kallisto 0.43.1 using Homo sapiens GRCh38 (Ensembl release 90) cDNA, with sequence bias correction turned on and 100 bootstraps
The tximport R package, was used to import the kallisto results and aggregate transcript abundances to the gene level
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized counts output from DESeq2, tab-delimited text file, rows are Ensembl gene IDs and columns are sample names

source_name: Dermal progenitor cells

growth_protocol: Skin tissue was washed and epithelium removed by incubating with dispase (5 mg/ml) for 3-4 hr at 37 °C. Then remaining dermis was minced finely with scalpels and dissociated in collagenase type XI to single cells. Cells were then cultured as speherical colonies in media composed of 3:1 DMEM/F12 supplemented with 1% PenStrep, 1 ug/mL Fungizone, 2% B27, 40 ng/mL FGF2 and 25ng/ml PDGF-BB and collected after 2 consecutive passages.

extract_protocol:
Cell suspensions were centrifuged at 600g, media was removed, and cell pellets were collected for RNA isolation. RNA from each sample was isolated using the Qiagen RNeasy® kit following the manufacturers procedures. RNA quality and quantity of each sample were analysed with the 2200 Tapestation (Agilent). Samples with high RNA integrity number (RIN) of 9-10 and at least 5µg of total RNA collected were used further analysis
For each sample, a total of 5ug of RNA was prepared into sequencing libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and each library was sequenced to the depth of 4-7 × 107 reads/sample with the Illumina NextSeq500 75bp sequencing at the Centre for Health Genomics and Informatics at the University of Calgary.

tag: Sex

value: F


title: ZR-75-1 Cells, Control, Triptolide treated, biological rep2


title: SATP95

description: counts.txt


title: ZR-75-1 Cells, Control, DMSO treated, biological rep2


title: ZR-75-1 Cells, Control, not treated, biological rep2


title: Liver_5%PSC 5

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

hyb_protocol: After checking the quality and quantity of the labeled cRNA, cRNA was fractionated and hybridized with the Affymetrix GeneChips. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station FS450. The GeneChips were then scanned with an Affymetrix GeneChip scanner 3000 7G. All procedures were performed according to Affymetrix protocols (GeneChip expression analysis, Technical manual from Affymetrix). The quality of hybridization was assessed in all samples following the manufacturer´s recommendations.

scan_protocol: After scanning the arrays, cell intensity files containing a single intensity value for each probe cell were computed from the image data with the Affymetrix GeneChip Command Console Software.

data_processing: Probe cell intensity data were further analyzed in the Affymetrix Expression Console software using the Robust Multichip Analysis (RMA) algorithm.

label: Biotin

organism: Rattus norvegicus

source_name: Liver 5%PSC

label_protocol: The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

growth_protocol: The four-week feeding trial was approved by the local Animal Care and Use Committee (Regierungspräsidium Giessen; permission no: JLU 648_M). All experimental procedures described followed established guidelines for the care and handling of laboratory animals. This study used 24 male, 5-6-week-old, homozygous (fa/fa) obese Zucker rats (Crl:ZUC-Leprfa). The rats were randomly assigned to two groups of 12 rats each [obese control (OC), obese 5% PSC (OPSC)], with similar initial body weights (BW) (OC: 277 ± 23 g; OPSC: 279 ± 23 g; mean ± SD; n = 12/group). The rats were kept in groups of two per cage under controlled conditions (22 ± 1°C room temperature, 50-60 % relative humidity, light from 07.00 a.m. to 07.00 p.m.).

extract_protocol: Total RNA from aliquots of liver (≈ 20 mg) was isolated using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s protocol. Transcript profiling in liver was carried out for 6 randomly selected rats per group. Following an RNA quality check using an Agilent 2100 Bioanalyzer (Agilent technologies, Böblingen, Germany), the total RNA samples were processed at the Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany) using an  Affymetrix Rat Gene 2.0 ST array, which represents 19,212 porcine genes, according to the manufacturer´s instructions. A260:A280 ratios and RNA integrity number values (mean ± SD) for all samples (n = 12) were 1.90 ± 0.01 and 8.01 ± 0.38, respectively.

treatment_protocol: Two different diets - one with 5% PSC supplementation and the other with no supplementation (control) but with comparable levels of gross energy and crude nutrients were fed. Nutrient concentrations in the diets were sufficient to meet requirements of the rats for maintenance according to National Research Council (NRC). PSC was produced biotechnologically using a side stream from the agricultural industry as the sole carbon source. The diets were offered ad libitum and feed consumption was recorded weekly. BWs were recorded once per week. Water was constantly available ad libitum from a nipple drinker system. At day 29, the rats were killed by decapitation under CO2 anesthesia. Aliquots of the liver were excised, washed in ice-cold NaCl solution (0.9 %) and snap-frozen in liquid nitrogen.

tag: condition

value: 5% PSC

value: male

value: liver

value: obese Zucker rats


title: Liver_5%PSC 3


title: Mock_rep_1


title: Liver_5%PSC 6


title: SATP92

description: counts.txt


title: BTx623, chitin treatment, replicate #3

city: Columbia

first: Gary

last: Stacey

state: Missouri

address: 1201 Rollins st.

department: Divisions of Plant Science and Biochemistry

institute: University of Missouri

data_processing:
Reads for each sample are aligned to the reference genome with TopHat
The alignment files are provided to Cufflinks to assemble transcripts for each sample.
Samples from the same condition are then merged together using Cuffmerge.
The merged assembly are fed to Chuffdiff, which calculates expression levels and tests the statistical significance of observed changes between two conditions.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sorghum bicolor

source_name: BTx623, chitin treatment,

growth_protocol: Sorghum seeds of BTx623 and SC155-14E were surface sterilized (70% ethanol for 1 min and then 10% bleach for 10 min, rinsed with autoclaved water) and planted in autoclaved Sunshine potting mix and germinated in growth chambers (16hr/8hr light/dark, 28/26 oC, 60-70% humidity). Fifteen-day old plants were used for experiments.

extract_protocol:
The RNA extraction was performed using the Direct-zol RNA Miniprep Plus kit from Zymoresearch (catalog #R2071) according to the manufacturer’s instructions.
Non-strand-specific RNA-seq libraries.

treatment_protocol: Leaf discs of the second youngest leaves of fifteen-day old Sorghum bicolor lines were treated with 10 ml of water (mock), 1 µM of flg22 or 100  µg/ml chitin (Sigma-Aldrich, catalog# C3641) for 1 hr. The samples were collected and stored at -80 oC for RNA extraction.

tag: line


title: Liver_5%PSC 4


title: ZR-75-1 Cells, Knock Down, Triptolide treated, biological rep1


title: Liver_Control 5

source_name: Liver Control


title: BTx623, chitin treatment, replicate #2


title: Liver_5%PSC 1


title: Liver_Control 3


title: BTx623, chitin treatment, replicate #1


title: SATP82

description: counts.txt


title: SATP91

description: counts.txt


title: BTx623, flg22 treatment, replicate #2

source_name: BTx623, flg22 treatment,


title: Liver_Control 4


title: ZR-75-1 Cells, Knock Down, DMSO treated, biological rep1


title: BTx623, flg22 treatment, replicate #3


title: Liver_Control 2


title: SATP75

description: counts.txt

value: M


title: ZR-75-1 Cells, Knock Down, not treated, biological rep1


title: BTx623, mock (treated with water), replicate #3

source_name: BTx623, mock (treated with water)


title: SATP68

description: counts.txt


title: BTx623, flg22 treatment, replicate #1


title: SATP154

description: counts.txt


title: ZR-75-1 Cells, Control, Triptolide treated, biological rep1


title: SC155-14E, chitin treatment, replicate #3

source_name: SC155-14E, chitin treatment,


title: BTx623, mock (treated with water), replicate #1


title: BTx623, mock (treated with water), replicate #2


title: Liver_5%PSC 2


title: ZR-75-1 Cells, Control, DMSO treated, biological rep1


title: SC155-14E, chitin treatment, replicate #1


title: SATP140

description: counts.txt


title: SC155-14E, flg22 treatment, replicate #3

source_name: SC155-14E, flg22 treatment,


title: ZR-75-1 Cells, Control, not treated, biological rep1


title: Liver_Control 1


title: SC155-14E, flg22 treatment, replicate #2


title: MDA-MB-231-ADAR-N3, ADAR1 transduced, biological rep3

description:
Gene-count-table.txt
MDA-A3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.5.2a (--runThreadN 6, SortedByCoordinate, outSAMstrandField intronMotif   --outSAMmapqUnique 60   --outFilterType BySJout   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --twopassMode Basic)
Read counting was performed using featureCounts (v1.5.1) using the following options -p -T 6 -F GTF -a $GTF_FILE -t exon -g gene_id -s $STRAND -B -C $FEATURECOUNTS_OVERLAP, using gencode v25lift37 gtf file
Differential expression analysis was performed using DEseq2 v1.4.5 (R v3.1)
Genome_build: Human Gencode realease 19 (hg19)
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for each sample

source_name: MDA-MB-231-ADAR-N3, ADAR1 transduced

growth_protocol: MDA-MB-231 cells were cultured in DMEM-F12 supplemented with 10% FBS and 1X Penicillin/streptomycin and seeded for treatment 24 h before treatment

extract_protocol:
media were removed and cells were washed two times in PBS, to further extract total RNA using Qiagen Rneasy columns. Illumina TruSeq Stranded Total RNA Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 cells were cultured in DMEM-F12 supplemented with 10% FBS and 1X Penicillin/streptomycin  were transduced with adenoviral particles (MOI:200) in 6 well chambers. 16h after transduction, media was changed and total RNA was extracted 48h after treatment.

value: Breast cancer tumor cell line

value: MDA transduced with ADARp110 cds


title: SC155-14E, flg22 treatment, replicate #1


title: SATP125

description: counts.txt


title: SATP137

description: counts.txt


title: MDA-MB-231-ADAR-N2, ADAR1 transduced, biological rep2

description:
Gene-count-table.txt
MDA-A2

source_name: MDA-MB-231-ADAR-N2, ADAR1 transduced


title: SATP120

description: counts.txt


title: SC155-14E, mock (treated with water), replicate #3

source_name: SC155-14E, mock (treated with water)


title: SC155-14E, chitin treatment, replicate #2


title: MDA-MB-231-ADAR-N1, ADAR1 transduced, biological rep1

description:
Gene-count-table.txt
MDA-A1

source_name: MDA-MB-231-ADAR-N1, ADAR1 transduced


title: SATP119

description: counts.txt


title: MDA-MB-231-GFP-N3, GFP transduced, biological rep3

description:
Gene-count-table.txt
MDA-G3

source_name: MDA-MB-231-GFP-N3, GFP transduced

value: MDA transduced with GFP particles


title: SC155-14E, mock (treated with water), replicate #2


title: SATP116

description: counts.txt


title: SC155-14E, mock (treated with water), replicate #1


title: adr-1- L1 neural cells

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

institute: Indiana University, Bloomington

description:
poly-A selected RNA
adr1.L1.sailoroutput.csv

data_processing:
Reads were aligned to C. elegans reference genome using STAR (v2.5.2b)
Differential gene expression analysis was performed using Feature counts and DeSeq2
A-to-I editing sites were de novo identified using SAILOR program
Variant calling was performed to quantify editing levels throughout C. elegans neural development.
Genome_build: C. elegans WS269
Supplementary_files_format_and_content: tab-delimited text files include the counts for each gene in L1 and adult neural RNA in WT and adr-2(-) backgrounds
Supplementary_files_format_and_content: .bed files from the de novo identification of SAILOR output include all the predicted sites and the confidence score for each predicted site

organism: Caenorhabditis elegans

source_name: Neural cells

growth_protocol: After hatching L1 was plated to grow upto 50 hr to obtain adults.

extract_protocol:
Worms were digested into single cell suspension and GFP positive neural cells were isolated using FACS.
Poly-A selected mRNA library preparation was done using KAPPA stranded library preparation kit

treatment_protocol: Worms were grown under optimum conditions.

tag: sample type

value: Rab-3 driven GFP expressed neural cells

value: 6 hr after hatching


title: SATP105

description: counts.txt


title: MDA-MB-231-GFP-N1, GFP transduced, biological rep1

description:
Gene-count-table.txt
MDA-G1

source_name: MDA-MB-231-GFP-N1, GFP transduced


title: adr-2- L1 neural cells rep3

description:
poly-A selected RNA
adr-2.adultvsL1.txt


title: SATP100

description: counts.txt


title: infantile hemangioama normal tissue microRNA 2

city: Jinan

first: Cong

last: Fu

state: Shandong

address: No. 324, jingwu Road, Huaiyin Dist

institute: Shandong provincial hospital

description: microRNAexpression data from Homo sapiens skin

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 48C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: skin normol tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: IH and matched non-tumor skin tissues

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

treatment_protocol: Tissues from IH surgury were immersed overnight in RNAlater at 4 ℃ and preserved at -80 ℃.

value: 4 months

value: female


title: infantile hemangioama normal tissue microRNA 1


title: infantile hemangioama tumor tissue microRNA 3

description: microRNA expression data from infantile hemangioma (IH) tumor tissue

source_name: infantile hemangioma (IH) tumor tissue

value: 6 months


title: Healthy donor 4

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

data_processing:
The raw data was processed with cellanger from 10XGenomics company.
Paired-end reads were mapped to the hg19 genome with STAR for read counts of genes annotated in ENSEMBL.
Genome_build: hg19

source_name: human bone marrow

extract_protocol: Libraries were generted using Genomics Chromium Single Cell ‘3 Solution Kit V2 from 10XGenomics.

tag: markers

tag: subject

value: healthy donor


title: adr-2- L1 neural cells rep2

description:
poly-A selected RNA
adr-2.adultvsL1.txt


title: 63_75Y_P2

description: counts.txt

source_name: Dermal progenitor cells


title: MDA-MB-231-GFP-N2, GFP transduced, biological rep2

description:
Gene-count-table.txt
MDA-G2

source_name: MDA-MB-231-GFP-N2, GFP transduced

tag: cell type


title: Healthy donor 3


title: adr-2- L1 neural cells rep1

description:
poly-A selected RNA
adr-2.adultvsL1.txt


title: 57_50Y_P2

description: counts.txt


title: infantile hemangioama normal tissue microRNA 3

value: 5 months


title: N2- L1 neural cells rep3

description:
poly-A selected RNA
WT.adultvsL1.counts.txt