title: 7_ko_11-16-17

city: Philadelphia

first: Christina M. Wright

middle: M

last: Wright

state: PA

address: 3615 Civic Center Blvd

department: Department of Pediatrics

institute: Children's Hospital of Philadelphia

description: E14.5 Dlx1/2-/- 4

data_processing:
Aligment using STAR RNA-seq aligner (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/)
Normalized abundance measurements generated using Pipeline of RNA-seq Transformations (PORT); http://bioinf.itmat.upenn.edu/benchmarking/rnaseq/port/index.php
Analyzed using Limma (Voom) in R
Genome_build: mm10 (ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz)
Supplementary_files_format_and_content: high_expressers_gene_sense_P0.txt - high expressors that were filtered with PORT's algorithm, for P0 samples
Supplementary_files_format_and_content: FINAL_master_list_of_gene_counts_MIN.sense.P0AlignedData.txt - sense counts from unique reads that only map to one gene, for P0 samples
Supplementary_files_format_and_content: high_expressers_gene_sense_E14.txt - high expressors that were filtered with PORT's algorithm, for E14.5 samples
Supplementary_files_format_and_content: FINAL_master_list_of_gene_counts_MIN.sense.E14AlignedData.txt - sense counts from unique reads that only map to one gene, for E14.5 samples

source_name: FACS-sorted Dlx1/2;EDNRB-L10A-EGFP+ small intestine

extract_protocol:
Briefly, cells were dissociated using dispase/collagenase, FACS sorted, and RNA was extracted using Qiagen's RNeasy Plus Micro Kit in combination with Qiagen's RNAse-free DNAse Set. RIN was measured on samples using an Agilent Bioanalyzer and used if RIN was greater than 7.0. For more details, see "RNA extraction" under the Methods section of Wright et al., 2020; https://www.ncbi.nlm.nih.gov/pubmed/32017713
cDNA libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian (Takara Biosystems). For more details, see "RNA-seq" under the Methods section of Wright et al., 2020; https://www.ncbi.nlm.nih.gov/pubmed/32017713

tag: age

tag: strain

value: CF1 x C57BL/6J


title: 2-3_ko_11-10-17

status: Public on Feb 17 2020

type: SRA

country: USA

description: E14.5 Dlx1/2-/- 3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: tissue

value: FACS-sorted Dlx1/2;EDNRB-L10A-EGFP+ small intestine


title: R1 ctr input

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description:
genomic DNA
2001_22802_ATCACG

library_source: genomic

data_processing:
FastQ files were aligned against the dm3 genome using Bowtie 0.12.5, allowing for 2 mismatches and reporting only unique hit alignments.
FastQC v011 was used to perform a quality control overview of FastQ files, aligned BAM files, and also for multiple hits and unaligned sequences.
Binary tracks for all reads in TDF format were generated with IGVTools 2.
Immunoprecipitation assessment (Gini coverage inequality) and PCA/MDS plots were genered using htSeqTools (Planet et al. 2012).
Peak Calling with the Drosophila default options was performed for IP vs their respective Input control sample usinc MACS 1.4.2 with options -g dm
Genome_build: dm3
Supplementary_files_format_and_content: BED files in MACS 1.4.2 format for ChIP vs Input peak calling

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: wt S2 cells

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Biowest) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco). dBigH1::FLAG and dBigH1ΔDE::FLAG cells were maintained in Schneider's insect medium (Biowest) supplmented with 0.3 mg/ml Hygromycin B (Sigma) and for performing the experiments cells were grown on the same medium as S2 cells.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αdBigH1 and αH1 antibodies. Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 10 cycles was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

treatment_protocol: Cells were treated with 1mM CuSo4  for 24h.

tag: cell line

value: S2 cells

tag: genotype/variation

value: wt

tag: type

value: Input

tag: replicate

tag: chip antibody


title: 1-4_ko_11-10-17

description: E14.5 Dlx1/2-/- 2


title: R2 ctr IP BigH1

description:
genomic DNA
2001_22802_ACTTGA

value: IP dBigH1

value: polyclonal αdBigH1


title: 1-2_ko_11-27-17

description: E14.5 Dlx1/2-/- 1


title: Fibroblast, MDA micrometastatic lung, biological rep2

type: RNA

city: Heidelberg

first: Maren

last: Pein

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Junior Research Group Metastatic Niches

country: Germany

institute: German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

description: Gene expression of sorted mouse lung fibroblasts from NSG mice 1 week after intravenous injection of MDA-MB-231 breast cancer cells

hyb_protocol: 5 ug of fragmented and labeled SPIA cDNA were hybridized for 17 h at 45 °C on Affymetrix GeneChip® Mouse Genome U430 2.0 Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731).

data_processing: The raw data was normalised with R using function normalize.quantiles from Bioconductor package preprocessCore; normalization method is quantile normalization.

label: biotin

source_name: Fibroblasts sorted from lungs of NSG mice 1 week after i.v. injection of MDA-MB-231 cells (micrometastatic stage)

label_protocol: The Nugene Ovation® Pico WTA System V2 in combination with the Encore Biotin Module was used to generate labeled SPIA cDNA from input amounts of 2.5 ng total RNA. The label used was biotin.

extract_protocol: RNA extraction was performed using the Arcturus PicoPure Extraction Kit (ThermoFisher Scientific) according to the manufacturer’s protocol.

tag: metastatic stage

value: Micrometastasis


title: Sample 4 / CD11C+ B cells

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

country: France

institute: INSERM U905

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit (catalog number 5188-5242). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitril.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1)

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5). Data were normalized by shift to 75 percentile.

organism: Homo sapiens

source_name: B cells from sample 4

label_protocol: Agilent Low input QuickAmp Labeling kit was used according to the manufacturer instructions  for one-color technology (catalog number 5190-2305) with 100ng  of total starting RNA

growth_protocol: PBMC were isolated from healthy donors buffy coat

extract_protocol: Total RNA was extracted using PicoPure (ThermoFisher scientific) following manufacturer's instructions. RNA Integrity Number (RIN) which is a measurement of RNA integrity was assessed by Agilent Bioanalyzer (Agilent Technologies). All RNA samples had a RIN ≥ 9.2.

treatment_protocol: B-cells were isolated using the Dynabeads Untouched Human B-cells kit from PBMC, and then sorted based on CD19 and CD11c expression. CD11C- and paired CD11C+ B cells were sorted using a FACSAria flow cytometer (BD Biosciences). Purification of each sorting experiments were assessed (93-97% purity).

tag: cell type

value: CD11C+ B cells


title: Fibroblast, MDA micrometastatic lung, biological rep1


title: Fibroblast, healthy lung, biological rep3

description: Gene expression of sorted mouse lung fibroblasts from healthy NSG mice

source_name: Fibroblasts sorted from lungs of healthy NSG mice

value: Healthy


title: Sample 3 / CD11C- B cells

source_name: B cells from sample 3

value: CD11C- B cells


title: R1 1mM IP BigH1

description:
genomic DNA
2001_22802_ACAGTG

source_name: wt BigH1 1mM induced S2 cells

value: wt BigH1 1mM induced


title: Fibroblast, healthy lung, biological rep1


title: Fibroblast, healthy lung, biological rep2


title: Sample 5 / CD11C+ B cells

source_name: B cells from sample 5


title: Sample 5 / CD11C- B cells


title: 9_wt_10-26-17

description: E14.5 Dlx1/2+/+ 4


title: Sample 4 / CD11C- B cells


title: 5_wt_2-15-18

description: E14.5 Dlx1/2+/+ 3


title: Sample 2 / CD11C+ B cells

source_name: B cells from sample 2


title: alh-6 day 3 rep 3

city: Los Angeles

first: Sean

last: Curran

state: CA

address: 3715 McClintock Ave

department: Davis School of Gerontology

institute: University of Southern California

description:
s105_D3c
s105_D3vsN2_D3.Differential_analysis_results.xls

data_processing:
Raw reads were first cleaned by removing reads containing adapter, reads contraining ploy-N , and low quality reads. Base quality and phred score relationship with CASAVA v1.8 software from Illumina was used for QC.
Index of reference genome was built using Bowtie v2.2.3 on files available publicly and paired-end clean reads were aligned to reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count reads numbers mapped to each gene. FPKM of each gene was calculated based on length of gene and reads count mapped. FPKM is most commonly used currently (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups was performed using DESeq R package (1.18.0). Resulting p-values were adjusted using Benjamini and Hochberg's approach.
Genome_build: ce11
Supplementary_files_format_and_content: txt file contains fpkm for all samples. Excel sheets contain DESeq results with normalized read counts comparing WT and alh-6 at L4 or day 3 adults.

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were egg prepped and eggs were allowed to hatch overnight. Next day, synchronized L1s were dropped on NGM plates seeded with concentrated OP50. 48 and 120 hrs post drop, L4 animals and day 3 adult animals, respectively, were washed 3 times with M9 and frozen in TRI Reagent at -80°C.

extract_protocol:
Animals are homogenized in Trizol and RNA extraction is performed following protocol in Zymo Direct-zol RNA Isolation Kit. 1ug of RNA was used per sample for library construction using NEBNext® UltraTM RNA Library Prep Kit  for Illumina® (NEB, USA).
Sequencing libraries were generated following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: N2 Bristol

tag: developmental stage

value: Day 3 adult


title: Sample 3 / CD11C+ B cells


title: alh-6 day 3 rep 2

description:
s105_D3b
s105_D3vsN2_D3.Differential_analysis_results.xls


title: 5_wt_1-19-18

description: E14.5 Dlx1/2+/+ 2


title: Sample 2 / CD11C- B cells


title: DNA diploid: DNAseq reads for diploid 6Sa

city: Columbia

first: James

middle: A

last: Birchler

state: MO

address: 310 Tucker hall

institute: University of Missouri

description:
6SA21D_S1
RPKM-normalized_DNA_counts_for_1La_breakpoint.xlsx

data_processing:
Library strategy: DNA-seq
Tuxedo software suite, specifically the Bowtie alignment tool, Tophat (an extension of Bowtie incorporating splice site information), and Cufflinks (specifically Cuffdiff, for recording differential expression at the level of individual genes).
Genome_build: Maize W22 reference genome

organism: Zea mays

source_name: Maize leaf tissue

extract_protocol: Not provided

value: leaf

tag: ploidy

value: diploid


title: Sample 1 / CD11C+ B cells

source_name: B cells from sample 1


title: alh-6 day 3 rep 1

description:
s105_D3a
s105_D3vsN2_D3.Differential_analysis_results.xls


title: 3_wt_11-16-17

description: E14.5 Dlx1/2+/+ 1


title: Set 2, trisomic rep 3

description:
DS2 3_S4
Dosage_series2_counts_RPKM.xlsx

data_processing:
Tuxedo software suite, specifically the Bowtie alignment tool, Tophat (an extension of Bowtie incorporating splice site information), and Cufflinks (specifically Cuffdiff, for recording differential expression at the level of individual genes).
Genome_build: Maize W22 reference genome
Supplementary_files_format_and_content: Excel files include mRNA expression data (RPKM value) for each gene in each sample

extract_protocol:
RNA was extracted using a TRIzol-based protocol.
TruSeq (Illumina) was used for library preparation, involving poly-A enrichment of mRNA using oligo-dT magnetic beads, first-strand cDNA synthesis using reverse transcriptase, second-strand cDNA synthesis using DNA Polymerase I, ligation of adaptors, and PCR amplification.

value: trisomic


title: Set 2, trisomic rep 2

description:
DS2 3_S3
Dosage_series2_counts_RPKM.xlsx


title: WT day 3 rep 3

description:
N2_D3c
s105_D3vsN2_D3.Differential_analysis_results.xls

value: wildtype


title: Sample 1 / CD11C- B cells


title: DNA trisomic: DNAseq reads for trisomic 3DNA

description:
3DNA_S2
RPKM-normalized_DNA_counts_for_1La_breakpoint.xlsx


title: Set 2, trisomic rep 1

description:
DS2 3_S2
Dosage_series2_counts_RPKM.xlsx


title: 3.14.2019-5

description: P0 Dlx1/2-/- 4

source_name: FACS-sorted Dlx1/2;Wnt1-Cre+;R26R-TdTomato+ small intestine

value: CF1 x C57BL/6J x CBA/J


title: WT day 3 rep 2

description:
N2_D3b
s105_D3vsN2_D3.Differential_analysis_results.xls


title: WT day 3 rep 1

description:
N2_D3a
s105_D3vsN2_D3.Differential_analysis_results.xls


title: Set 2, diploid rep 3

description:
DS2 2_S4
Dosage_series2_counts_RPKM.xlsx


title: 2.7.2019-4

description: P0 Dlx1/2-/- 3

value: FACS-sorted Dlx1/2;Wnt1-Cre+;R26R-TdTomato+ small intestine


title: alh-6 L4 rep 3

description:
s105_L4c
s105_L4vsN2_L4.Differential_analysis_results.xls


title: 3.14.2019-9

description: P0 Dlx1/2-/- 5


title: 2.22.2019-3

description: P0 Dlx1/2-/- 2


title: Set 2, diploid rep 1

description:
DS2 2_S1
Dosage_series2_counts_RPKM.xlsx


title: in vitro methylated DNA

type: genomic

city: Pamplona

first: David

last: Guerrero-Setas

state: Navarra

address: C/ Irunlarrea, 3

department: Department of Pathology

institute: Complejo Hospitalario de Navarra

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450  BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: methylated control

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from tissue samples using phenol-chroloform and precipitation with ethanol

tag: disease

value: none, in vitro methylated DNA control


title: genomic DNA from TN tumor (case 7)

description:
tumoral tissue
B45

source_name: triple-negative tumor 7

tag: gender

value: Female

value: tumor


title: genomic DNA from TN tumor (case 6)

description:
tumoral tissue
B44

source_name: triple-negative tumor 6


title: alh-6 L4 rep 1

description:
s105_L4a
s105_L4vsN2_L4.Differential_analysis_results.xls


title: genomic DNA from TN tumor (case 8)

description:
tumoral tissue
B46

source_name: triple-negative tumor 8


title: Set 2, monosomic rep 3

description:
DS2 1_S3
Dosage_series2_counts_RPKM.xlsx

value: monosomic


title: genomic DNA from luminal A tumor (case 9)

description:
tumoral tissue
LA13_42

source_name: luminal A tumor 9


title: genomic DNA from TN tumor (case 4)

description:
tumoral tissue
B42

source_name: triple-negative tumor 4


title: 2.26.2019-4

description: P0 Dlx1/2+/+ 3


title: WT L4 rep 3

description:
N2_L4c
s105_L4vsN2_L4.Differential_analysis_results.xls


title: 3.14.2019-6

description: P0 Dlx1/2+/+ 4


title: Set 2, monosomic rep 2

description:
DS2 1_S2
Dosage_series2_counts_RPKM.xlsx


title: WT L4 rep 2

description:
N2_L4b
s105_L4vsN2_L4.Differential_analysis_results.xls


title: genomic DNA from TN tumor (case 3)

description:
tumoral tissue
B41

source_name: triple-negative tumor 3


title: 2.26.2019-3

description: P0 Dlx1/2+/+ 2


title: WT L4 rep 1

description:
N2_L4a
s105_L4vsN2_L4.Differential_analysis_results.xls


title: Set 2, diploid rep 2

description:
DS2 2_S3
Dosage_series2_counts_RPKM.xlsx


title: alh-6 L4 rep 2

description:
s105_L4b
s105_L4vsN2_L4.Differential_analysis_results.xls


title: genomic DNA from TN tumor (case 5)

description:
tumoral tissue
B43

source_name: triple-negative tumor 5


title: genomic DNA from HER2 tumor (case 6)

description:
tumoral tissue
H36

source_name: HER2 tumor 6


title: Set 2, monosomic rep 4

description:
DS2 1_S4
Dosage_series2_counts_RPKM.xlsx


title: 2.22.2019-1

description: P0 Dlx1/2-/- 1


title: genomic DNA from HER2 tumor (case 7)

description:
tumoral tissue
H37

source_name: HER2 tumor 7


title: genomic DNA from TN tumor (case 2)

description:
tumoral tissue
B40

source_name: triple-negative tumor 2


title: 2.26.2019-1

description: P0 Dlx1/2+/+ 1


title: Peripheral donor 4

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build hg19 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF and the following parameter: --expect-cells=8000.
The ten samples (paired samples from five donors) were collectively aggregated with the cellranger aggr function with the following parameter: --normalized=mapped.
Cells were filtered with the Seurat (v2.3.4) subset function. Cells with nUMIs less than 200 (to remove cells with poor read quality) or greater than 7000 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following commands: mito.genes = grep(pattern = "^MT-", x = rownames(x = seurat_obj@data), value = TRUE); percent.mito = Matrix::colSums(seurat_obj@raw.data[mito.genes,])/Matrix::colSums(seurat_obj@raw.data); seurat_obj = AddMetaData(object = seurat_obj, metadata = percent.mito, col.name = "percent.mito")
Aggregated reads from the ten libraries (paired from five donors) were normalized and clustered in Seurat (v2.3.4) with the following commands: seurat_obj <- NormalizeData(seurat_obj, normalization.method = "LogNormalize", scale.factor = 10000);   seurat_obj <- FindVariableGenes(object = seurat_obj, mean.function = ExpMean;   dispersion.function = LogVMR, x.low.cutoff = 0.0125, x.high.cutoff = 3, y.cutoff = 0.5);  seurat_obj <- ScaleData(object = seurat_obj, vars.to.regress = c("nUMI", "percent.mito"));  seurat_obj <- RunPCA(object = seurat_obj, pc.genes = seurat_obj@var.genes, do.print = TRUE, pcs.print = 1:5, genes.print = 5);  seurat_obj <- FindClusters(object = seurat_obj, reduction.type = "pca", dims.use = 1:last_pca_to_include, resolution = 0.6, print.output = 0, save.SNN = TRUE);  seurat_obj <- RunTSNE(object = seurat_obj, dims.use = 1:14, do.fast = TRUE)
Genome_build: hg19
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format. Log-normalized expression values (from GetAssayData(object = seurat_object) were appended to relevant metadata (barcode, final cluster label, donor number, cell type, region (fovea or periphery), and AIR_status (yes or no) from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values.

source_name: Retina

extract_protocol:
A 2-mm fovea centered and an 8-mm peripheral punch of retina from the inferotemporal region were acquired from two human donors (Donors 4-5). Tissue was dissociated using the Papain Dissociation System (Worthington Biochemical Corporation, Lakewood NJ). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Single-cell RNA libraries were prepared for sequencing using standard 10X genomics protocols. Briefly, cryopreserved samples from donors 4-5 were thawed, and single cells were captured and barcoded using the Chromium System with the v3 single cell-reagent kit (10x Genomics, Pleasanton CA). Sequencing was performed on pooled libraries using the Illumina HiSeq 4000 platform (San Diego, CA), generating 150 base pair paired-end reads.

tag: location

value: Periphery

tag: donor

value: Donor 4


title: genomic DNA from HER2 tumor (case 8)

description:
tumoral tissue
H38

source_name: HER2 tumor 8


title: genomic DNA from TN tumor (case 1)

description:
tumoral tissue
B39

source_name: triple-negative tumor 1


title: genomic DNA from HER2 tumor (case 5)

description:
tumoral tissue
H35

source_name: HER2 tumor 5


title: leaf.wt_R2

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC

description: T-DNA line

data_processing:
for leaf: cutadapt (v2.3) with -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 19 -M 25 --trim-n
for flowers buds: cutadapt (v2.3) with --trim-n --action none -m 19 -M 25
STAR (v2.7.0f) mapping with default parameters
bam2wig.py from RSeQC
wigToBigWig from UCSC
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files, one per strand (plus & minus), also further divided by read length (from 21 to 24), raw digital read count

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Seedlings were surface-sterilized and put directly into soil. Samples grew for 6 weeks in a Percival at 21 degrees C and long-day light conditions.

extract_protocol:
100 mg of leaf tissues with liquid nitrogen was mixed with TRIzol and chloroform to extract total RNA. A milder ethanol-precipitation was performed to get rid of polysaccharides.
1 ug of RNA was used as input in the NEBNext® Multiplex Small RNA Library Prep kit (New England Biolabs) and the small RNA libraries were made following the instructions from the kit

tag: ecotype

value: wt


title: leaf.wt_R3

description: T-DNA line


title: genomic DNA from HER2 tumor (case 2)

description:
tumoral tissue
H32

source_name: HER2 tumor 2


title: CXCL9/10-OE MDA, treated with DMSO, biological rep3

description: Gene expression of DMSO-treated CXCL9/10-OE MDA cells

hyb_protocol: 6.6 ug of fragmented and labeled ds-cDNA were hybridized for 17 h at 45 °C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays, according to user manual Affymetrix 3' IVT Pico Reagent Kit.

data_processing: Raw data was processed using Chipster version 3.14.2 (cdf: Brainarray HGU133Plus2_Hs_ENTREZG_v18); RMA-normalization was used. For subsequent statistical analysis, RMA-normalized data was filtered based on coefficient of variation (cutoff: 0.8) and empirical Bayes test with Benjamini-Hochberg correction for p-values was performed, with pairing based on the sort date.

source_name: DMSO-treated MDA cells overexpressing CXCL9 and CXCL10

label_protocol: The Affymetrix 3’ IVT Pico Reagent Kit was used to generate labeled single-stranded ds-cDNA from input amounts of 500 pg total RNA . The label used was biotin.

growth_protocol: CXCL9/10-OE MDA-MB-231 breast cancer cells were cultured for 7 days as spheres at a density of 25,000 cells/ml in into ultra-low attachment cell culture flasks with Onco2 medium, consisting of HuMEC-medium (Invitrogen) supplemented 50 U/ml penicillin (Sigma-Aldrich), 50 μg/ml streptomycin (Sigma-Aldrich), 10 ng/ml basic fibroblast growth factor (bFGF, Invitrogen), 20 ng/ml EGF (Sigma-Aldrich), 5 μg/ml human insulin (Sigma-Aldrich) and 2 % vol/vol B27 (Life Technologies). Cells were stimulated with 1 µM AMG-487 or 0.001% DMSO vehicle daily for 7 days.

extract_protocol: RNA extraction was performed using the QIAGEN RNeasy Mini Kit according to the manufacturer’s protocol.

treatment_protocol: Cells were stimulated with 1 µM AMG-487 (CXCR3i)or 0.001% DMSO vehicle daily for 7 days.

tag: treatment

value: DMSO


title: Fovea donor 5

value: Fovea

value: Donor 5


title: Peripheral donor 5


title: CXCL9/10-OE MDA, treated with DMSO, biological rep2


title: genomic DNA from HER2 tumor (case 4)

description:
tumoral tissue
H34

source_name: HER2 tumor 4


title: Fovea donor 4


title: leaf.rrp4-2_R2

description: hypomorphic allele

tag: genotype


title: leaf.rrp4-2_R3

description: hypomorphic allele


title: genomic DNA from luminal-HER2 tumor (case 7)

description:
tumoral tissue
LH29

source_name: luminal-HER2 tumor 7


title: genomic DNA from HER2 tumor (case 3)

description:
tumoral tissue
H33

source_name: HER2 tumor 3


title: leaf.rrp4-2_R1

description: hypomorphic allele


title: leaf.wt_R1

description: T-DNA line


title: AG15821_BRD4_K562_ChIP

city: SEATTLE

first: John

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

data_processing:
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
MAC2 FDR 5% combined replicate peak calls
Genome_build: hg38
Supplementary_files_format_and_content: normalized density bigWig file, combined replicate mac2 peaks bed file

growth_protocol: Grown in IMDM, supplemented with 10%Fetal Bovine Serum (PAA), sodium pyruvate (GIBCO), L-glutamine (GIBCO), penicillin and streptomycin (GIBCO). dBET1 (Tocris) was dissolved in DMSO (Sigma Aldrich) to a concentration of 10mM and cells were treated at a concentration of 1uM for the time indicated.

extract_protocol:
https://elifesciences.org/articles/21856
Low-input single-stranded library construction protocol as per PMIDs 23493070 & 26771485

tag: cell

tag: antibodies

tag: antibody lot number

value: Active Motif 39909

tag: dilution

value: rabbit pAb 1:100


title: AG15822_BRD3_K562_ChIP

value: Active Motif 61489

value: rabbit pAb 6:100


title: flower.wt_R2

description: wild type

source_name: young flower buds

tag: replicate


title: CXCL9/10-OE MDA, treated with CXCR3i, biological rep2

description: Gene expression of CXCR3i-treated CXCL9/10-OE MDA cells

source_name: CXCR3i-treated MDA cells overexpressing CXCL9 and CXCL10


title: CXCL9/10-OE MDA, treated with CXCR3i, biological rep1


title: CXCL9/10-OE MDA, treated with CXCR3i, biological rep3


title: genomic DNA from luminal-HER2 tumor (case 6)

description:
tumoral tissue
LH28

source_name: luminal-HER2 tumor 6


title: flower.wt_R1

description: wild type


title: CXCL9/10-OE MDA, treated with DMSO, biological rep1


title: AG15726_BRD3_K562_ChIP


title: AG15649_BRD2_K562_ChIP

value: Active Motif 61797


title: AG15817_HDAC1_K562_ChIP

value: Active Motif 40967


title: flower.rrp4-2_R2

description: hypomorphic allele


title: flower.rrp4-2_R1

description: hypomorphic allele


title: flower.hen2-5_R2

description: T-DNA line


title: flower.hen2-5_R1

description: T-DNA line


title: SUM-LM1, CXCR3pos, biological rep3

description: Gene expression of sorted CXCR3-positive SUM-159-LM1 cells

hyb_protocol: 11 ug of fragmented and labeled cRNA were hybridized for 17 hours at 45°C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays, according to user manual GeneChip® 3' IVT PLUS Reagent Kit, P/N 703210.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays  (P/N 702731).

data_processing: Raw data was processed using Chipster version 3.8.1; RMA-normalization was used. For subsequent statistical analysis, RMA-normalized data was filtered based on coefficient of variation (cutoff: 0.8) and empirical Bayes test with Benjamini-Hochberg correction for p-values was performed, with pairing based on the sort date.

source_name: sorted CXCR3-positive SUM-159-LM1 cells

label_protocol: The Affymetrix Gene Chip 3´IVT PLUS Reagent Kit was used to generate labeled single-stranded cRNA from input amounts of 100 ng total RNA. The label used was biotin.

growth_protocol: SUM-159-LM1 breast cancer cells were cultured for 7 days as spheres at a density of 25,000 cells/mlin into ultra-low attachment cell culture flasks with Onco2 medium, consisting of HuMEC-medium (Invitrogen) supplemented 50 U/ml penicillin (Sigma-Aldrich), 50 μg/ml streptomycin (Sigma-Aldrich), 10 ng/ml basic fibroblast growth factor (bFGF, Invitrogen), 20 ng/ml EGF (Sigma-Aldrich), 5 μg/ml human insulin (Sigma-Aldrich) and 2 % vol/vol B27 (Life Technologies).

extract_protocol: RNA extraction was performed using the Arcturus PicoPure Extraction Kit (ThermoFisher Scientific) according to the manufacturer’s protocol. cDNA preamplification was conducted using the Ovation Pico WTA System V2 Kit (NuGEN).

treatment_protocol: Cells were stained with 5 μg PE-conjugated anti-human CD183 (CXCR3) antibody (clone G025H7, BioLegend) or PE-conjugated mouse IgG1, κ isotype control (BioLegend) per million cells in 100 μl FACS buffer for 30 min on ice in the dark. CXCR3+ and CXCR3- cells were sorted on a  BD FACSAria1 machine into Arcturus PicoPure Extraction Buffer (ThermoFisher Scientific).

tag: sorted pairs

value: pair 3


title: Set 2, monosomic rep 1

description:
DS2 1_S1
Dosage_series2_counts_RPKM.xlsx

source_name: Maize leaf tissue

tag: tissue

value: leaf


title: AG15823_BRD2_K562_ChIP


title: genomic DNA from luminal-HER2 tumor (case 8)

description:
tumoral tissue
LH30

source_name: luminal-HER2 tumor 8

value: Female


title: SUM-LM1, CXCR3neg, biological rep2

description: Gene expression of sorted CXCR3-negative SUM-159-LM1 cells

source_name: sorted CXCR3-negative SUM-159-LM1 cells

value: pair 2


title: SUM-LM1, CXCR3neg, biological rep3


title: SUM-LM1, CXCR3pos, biological rep2


title: SUM-LM1, CXCR3pos, biological rep1

value: pair 1


title: AG15648_HDAC1_K562_ChIP


title: SUM-LM1, CXCR3neg, biological rep1


title: GLP-1 OFF rep5

city: St. Louis

first: Jian

last: Chen

address: 4523 Clayton Ave.

department: Genetics

institute: Washington University School of Medicine

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.127_q175

data_processing:
Align back to genome with STAR version 2.0.4b.
Gene counts were then quantitated with Subread:featureCount version 1.4.5. The gene counts were then TMM scaled with EdgeR and voomWithQualityWeights transformed with Limma.
A Limma generalized linear model without intercept was then fitted to the data and tested for statistical significance via Limma’s empirical Bayes moderated t-statistics.
Genome_build: Ensembl Release 76 C. elegans genome.
Supplementary_files_format_and_content: excel file include CPM values for each sample.

source_name: dissected germline tumor

growth_protocol: Bleach synchronized L1 animals were grown for 48 hours at 25 °C.

extract_protocol:
Germline were dissected away from the rest of animal body, harvested and then total RNAs extracted with Trizol.
RNA libraries were prepared for sequencing using the Kapa hyper prep kit.

treatment_protocol: No additional treatment prior to dissection of germlines.

tag: strain

value: Bristol

value: germline

tag: age

value: 1 day old adult


title: GLP-1 OFF rep3

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.86_q175


title: Brunello-edited Nalm6 cells, S9_d36_P_CAR19

first: Nathan

last: Singh

data_processing:
sgRNA spacer sequences were aligned to a pre-indexed Brunello library (Addgene) using bowtie
We used MAGeCK to normalize raw counts and to classify enriched and depleted genes (MLE).
Genome_build: hg19
Supplementary_files_format_and_content: The processed files hold the raw sgRNA count for each sample.

source_name: Brunello-edited Nalm6 cells

growth_protocol: Brunello lentivirus was added to Nalm6 cultures at an MOI of 0.2, followed by puromycin selection.

extract_protocol:
At time of DNA extraction, 6 mL of NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8) and 30μL of 20mg/mL Proteinase K were added to the frozen cell sample and incubated at 55°C overnight. The following day, 30μL of 10mg/mL RNase A, diluted in NK Lysis Buffer to 10mg/mL and then stored at 4°C, was added to the lysed sample, which was then inverted 25 times and incubated at 37°C for 30min. Samples were cooled on ice before addition of 2mL of pre-chilled 7.5M ammonium acetate to precipitate proteins. The samples were vortexed at high speed for 20s and then centrifuged at ≥ 4,000×g for 10min. After the spin, a tight pellet was visible in each tube and the supernatant was carefully decanted into a new 15mL tube. 6mL 100% isopropanol was added to the tube, inverted 50 times and centrifuged at ≥ 4,000×g for 10min. Genomic DNA (gDNA) was visible as a small white pellet in each tube. The supernatant was discarded, 6mL of freshly prepared 70% ethanol was added to the tube and inverted 10 times and centrifuged at ≥4,000×g for 1min. The supernatant was discarded by pouring; the tube was briefly spun, and remaining ethanol was removed using a pipette. After air drying for 10-30min, 500μL of 1x TE buffer was added, the tube was incubated at 65°C for 1h and at room temperature overnight to fully resuspend the DNA. The next day, the gDNA samples were vortexed briefly, and gDNA concentration was measured.
Using all collected gDNA (1000x coverage) divided into 100µL PCR reactions with 5µg of DNA per reaction. We used Takara ExTaq DNA Polymerase and the default mix protocol with the following PCR program: (95° 2min, (98° 10sec, 60° 30sec, 72° 30sec) x 24, 72° 5min). PCR products were gel purified using the QiaQuick gel extraction kit (Qiagen). The purified, pooled library was then sequenced on a HiSeq4000 with ~5% PhiX added to the sequencing lane.

treatment_protocol: Brunello-edited Nalm6 cells were combined with CART19 cells at an effector:target ratio of 1:4 (200 million Nalm6 cells with 50 million T cells)

tag: cell type

value: Brunello-edited Nalm6 cells

tag: cell line

value: human acute lymphoblastic leukemia cell line

tag: treatment condition

value: 36d CART19 co-culture


title: GLP-1 OFF rep4

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.88_q175


title: genomic DNA from luminal-HER2 tumor (case 2)

description:
tumoral tissue
LH24

source_name: luminal-HER2 tumor 2

tag: gender

tag: disease

value: tumor


title: Chickpea d6

city: Otsu

first: Shigeo

last: Shinohara

state: Shiga

address: 3-31-13 Saigawa

department: Nutraceuticals Division

country: Japan

institute: Otsuka Pharmaceutical Co., Ltd.

description: 3T3-L1 confluent pre-adipocytes were treated for 6 days with differentiation-induction medium containing with 0.5%CP.

hyb_protocol: The purified dye-labeled cDNA were mixed with SSC, SDS, Denhardts solution and salmon sperm DNA to prepare 10μL of hybridization mixture. Eight ul of hybridization mixture were applied to each blockon the microarray slide. The microarray slide was inserted into KURABO hybridization chamber with humidification solution.Then the chamber was kept at 65 ℃ in a water bath for 14 hours. After hybridization, the hybridization mixtures on the slide were flushed away by washing solution and the slide was washed in several kinds of washing solutions. After washing, the slide was dried up by centrifugation.

scan_protocol: The image of the microarray were acquired by Genepix 4200A (Molecular Devices).

data_processing: The adjusted intensity of the genes were quantified by Genepix Pro software (Molecular Devices). The adjusted intensity equals the intensity of each gene minus the background value. The genes with an adjusted intensity less than twofold the background value were regarded as undetectable. The normalized intensity to Gapdh gene were calculated by the following formula. Normalized intensity = (X-Z)/(Y-Z) x 10000, X; the adjusted intensity of target gene, Y; the adjusted intensity of Gapdh gene, Z; median of the adjusted intensities of the negative control genes

label: Alexa Fluor 555

label_protocol: From 10ug of total RNA samples, AlexaFluor 555-labeled cDNA were prepared by reverse transcription with SuperScript III (Invtrogen). The results of dye-labeled cDNA were purified with MinElute PCR Purification Kit (Qiagen).

growth_protocol: 3T3-L1 cells were grown in DMEM supplemented with 10% calf serum and 0.5 µg/ml gentamicin sulfate. For differentiation, 3T3-L1 confluent preadipocytes were treated for 2 days with DMEM supplemented with 10% FBS in the presence of adipogenic inducers 0.5 mM methylisobutylxanthine (MIX), 10 µM dexamethasone, and 5 µg/ml Insulin. After 2 days, the cells were maintained in DMEM supplemented with 10% FBS, 0.5 ug/ml gentamicin sulfate, and 5 µg/ml insulin for 6 days. The medium was changed every 2 days. Cells were grown at 37℃, 5% CO2, and 100% humidity.

extract_protocol: Total RNA was extracted from 3T3-L1 cells samples using TRIzol plus RNA purification kit.

treatment_protocol: 3T3-L1 cells were induced to adipocytes in differentiation-inducing media containing either CP or additive-free media for 8 days

value: adipocyte

value: differentiation-induction medium containing with 0.5% chickpea extract

tag: time

value: 6 d


title: genomic DNA from luminal-HER2 tumor (case 4)

description:
tumoral tissue
LH26

source_name: luminal-HER2 tumor 4


title: Chickpea d8

description: 3T3-L1 confluent pre-adipocytes were treated for 8 days with differentiation-induction medium containing with 0.5%CP.

tag: treatment

value: 8 d


title: genomic DNA from luminal-HER2 tumor (case 5)

description:
tumoral tissue
LH27

source_name: luminal-HER2 tumor 5


title: genomic DNA from luminal-HER2 tumor (case 3)

description:
tumoral tissue
LH25

source_name: luminal-HER2 tumor 3


title: Brunello-edited Nalm6 cells, S8_d36_alone

value: 36d control T cell co-culture


title: genomic DNA from HER2 tumor (case 1)

description:
tumoral tissue
H31

source_name: HER2 tumor 1


title: Chickpea d4

description: 3T3-L1 confluent pre-adipocytes were treated for 4 days with differentiation-induction medium containing with 0.5%CP.

value: 4 d


title: genomic DNA from luminal-HER2 tumor (case 1)

description:
tumoral tissue
LH23

source_name: luminal-HER2 tumor 1


title: Brunello-edited Nalm6 cells, S7_d1_P_NTD_rep2

value: 24h control T cell co-culture


title: GLP-1 OFF rep2

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.57_q175

tag: genotype


title: genomic DNA from luminal B tumor (case 6)

description:
tumoral tissue
LB20

source_name: luminal B tumor 6

value: Female


title: Chickpea d2

description: 3T3-L1 confluent pre-adipocytes were treated for 2 days with differentiation-induction medium containing with 0.5%CP.

value: 2 d


title: Control d6

description: 3T3-L1 confluent pre-adipocytes were treated for 6 days with differentiation-induction medium.

value: differentiation-induction medium


title: Brunello-edited Nalm6 cells, S6_d1_P_NTD_rep1


title: GLP-1 OFF rep1

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.56_q175

value: Bristol


title: genomic DNA from luminal B tumor (case 5)

description:
tumoral tissue
LB19

source_name: luminal B tumor 5


title: Control d8

description: 3T3-L1 confluent pre-adipocytes were treated for 8 days with differentiation-induction medium.


title: Brunello-edited Nalm6 cells, S5_d1_P_CAR19_rep2

value: 24h CART19 co-culture


title: Brunello-edited Nalm6 cells, S4_d1_P_CAR19_rep1


title: Control d4

description: 3T3-L1 confluent pre-adipocytes were treated for 4 days with differentiation-induction medium.


title: GLP-1 ON rep3

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.128_ar202

value: germline

value: 1 day old adult


title: GLP-1 ON rep4

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.129_ar202


title: genomic DNA from luminal B tumor (case 4)

description:
tumoral tissue
LB18

source_name: luminal B tumor 4


title: genomic DNA from luminal A tumor (case 7)

description:
tumoral tissue
LA13

source_name: luminal A tumor 7


title: genomic DNA from luminal B tumor (case 8)

description:
tumoral tissue
LB22

source_name: luminal B tumor 8


title: GLP-1 ON rep2

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.85_ar202 GLP-1 ON rep2


title: Brunello-edited Nalm6 cells, S3_d0_short_term_rep2

value: Brunello-edited Nalm6 cells

value: human acute lymphoblastic leukemia cell line

value: no T cell co-culture


title: Brunello-edited Nalm6 cells, S2_d0_short_term_rep1


title: genomic DNA from luminal B tumor (case 3)

description:
tumoral tissue
LB17

source_name: luminal B tumor 3

value: tumor


title: GLP-1 ON rep1

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.58_ar202


title: Brunello-edited Nalm6 cells, S1_d0_long_term


title: genomic DNA from luminal A tumor (case 6)

description:
tumoral tissue
LA12

source_name: luminal A tumor 6


title: Control d0

description: 3T3-L1 confluent pre-adipocytes

source_name: 3T3-L1 confluent pre-adipocytes

value: pre-adipocyte

value: 0 d


title: LAG-1 48h rep4

description:
Ribosome RNA depleted
all.gene_CPM_HS8.xls

data_processing:
Align back to genome with STAR version 2.0.4b
Gene counts were then quantitated with Subread:featureCount version 1.4.5. The gene counts were then TMM scaled with EdgeR and voomWithQualityWeights transformed with Limma.
A Limma generalized linear model without intercept was then fitted to the data and tested for statistical significance via Limma’s empirical Bayes moderated t-statistics.
Genome_build: Ensembl Release 76 C. elegans genome
Supplementary_files_format_and_content: excel file include CPM values for each sample.

growth_protocol: bleach synchronized L1 animals were grown for 48 hours at 25 °C.

extract_protocol:
Germline were dissected away from the rest of the animal body, harvested and then total RNA recovered with Trizol
RNA libraries were prepared for sequencing using Kapa hyper prep kit

treatment_protocol: auxin (1 mM) treatment (0 hours-control; 2, 4, and 48 hours) were given prior to dissection of germline.

tag: time point

value: LAG-1 48h


title: genomic DNA from luminal B tumor (case 1)

description:
tumoral tissue
LB15

source_name: luminal B tumor 1


title: genomic DNA from luminal A tumor (case 8)

description:
tumoral tissue
LA14

source_name: luminal A tumor 8


title: genomic DNA from luminal B tumor (case 2)

description:
tumoral tissue
LB16

source_name: luminal B tumor 2


title: GC-136

city: Jinan

first: Yingying

last: Qin

state: Shandong

country: China

institute: Shandong University

description: LncRNA expression of granulosa cells from age and BMI matched normal control women

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Then the slides were scanned using the Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs  that at least 10 out of 20 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using R. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: granulosa cells

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen)  according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: granulosa cells

tag: Sex

tag: condition

value: Control


title: LAG-1 48h rep3

source_name: dissected germline tumor


title: GC-138


title: PMN_Runx1KO_Veh_3

city: San Francisco

first: Qin

last: Zhu

address: 600 Minnesota Street

institute: UCSF

data_processing:
RNA-Seq data was mapped using STAR (v2.6.0a)
Gene counts were summrized using featureCounts
Spike-in reads are used for normalization with RUVSeq R package
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: Bone Marrow Neutrophils (PMN)

growth_protocol: Mice were treated according to the University of Pennsylvania’s Animal Resources Center and IACUC protocols.

extract_protocol:
Hind limbs were harvested from mice and crushed using a mortar and pestle in PBS + 2% FBS to harvest bone marrow. 1 million bone marrow neutrophils (CD11b+, Siglec F-, F4/80-, Ly6G+) were sorted into Hanks + 25 mM HEPES +10% FBS and treated for 2 hours with vehicle or 100 ng/mL LPS. Following treatment, cells were washed 2 times PBS and resuspended in Trizol. RNA was purified using the RNeasy Micro Kit (Qiagen) with the DNAse step performed on column. Spike-in RNA (ERCC RNA Spike-In Mix, Life Technologies) was added following the manufacturer’s instructions.
RNA libraries were prepared for sequencing by Genewiz using their Ultra-Low Input for RNA-Seq protocol for Illumina.

treatment_protocol:
Treated with Vehicle in Hanks + 25 mM HEPES +10% FBS for 2 hrs
See individual samples for treatment protocol

value: Runx1 KO

tag: facs

value: CD11b+, Siglec F-, F4/80-, Ly6G+


title: PMN_Runx1KO_Veh_2


title: GLP-1 ON rep5

description:
Ribosome RNA depleted
all.gene_CPM_HS7.xls
sample.130_ar202


title: AG15820_BRD4_K562_ChIP

tag: cell

tag: antibodies

tag: antibody lot number

value: Active Motif 39909

tag: dilution

value: rabbit pAb 6:100


title: LAG-1 48h rep2

tag: strain

value: Bristol

tag: tissue

tag: age


title: genomic DNA from luminal A tumor (case 5)

description:
tumoral tissue
LA11

source_name: luminal A tumor 5

value: Female


title: PMN_Runx1KO_Veh_1


title: LAG-1 48h rep1

value: germline


title: GC-133

tag: cell type


title: PMN_Runx1KO_LPS_3

treatment_protocol:
Treated with 100 ng/mL LPS in Hanks + 25 mM HEPES +10% FBS for 2 hrs
See individual samples for treatment protocol


title: GC-131


title: PMN_Runx1KO_LPS_1


title: PMN_Control_Veh_3


title: genomic DNA from luminal A tumor (case 3)

description:
tumoral tissue
LA9

source_name: luminal A tumor 3

tag: gender


title: genomic DNA from luminal A tumor (case 4)

description:
tumoral tissue
LA10

source_name: luminal A tumor 4

tag: disease


title: LKS-_Runx1 KO

description: 10X sc-RNA-seq with cells from dissociated mouse embryos

data_processing:
Data was processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to mm10 reference genome.
Filtering was performed on the raw gene-barcode matrix output by the Cell Ranger cellranger count function, removing barcodes that have fewer than 1000 transcripts and 1000 expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: gene_by_cell_count_matrix.txt contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, cell type, etc.) for each cell. gene_annotation.csv contains a data frame with gene id and gene short name.

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Hind limbs were harvested from mice and crushed using a mortar and pestle in PBS + 2% FBS to harvest bone marrow. Bone marrow hematopoietic progenitors (Lineage-, c-Kit+, Sca1-) were sorted into Hanks + 25 mM HEPES +10% FBS. Using the Chromium controller (10x Genomics) and reagents from the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics), cells were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) where each cell's trascriptome was indexed with a specific 10x BarCode. cDNA were amplified and purified for library preparation.
cDNA were used for library preparation using the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics) according to manufacturer’s protocol (CG000183, Rev A).

value: Lineage-, c-Kit+, Sca1-


title: LAG-1 4h rep3

description:
Ribosome RNA depleted
all.gene_CPM_HS9.xls

value: 1 day old adult

value: LAG-1 4h


title: LKS-_Control


title: LAG-1 4h rep2


title: GC-95


title: LAG-1 4h rep4


title: GC-117


title: GC-121


title: GC-109


title: PMN_Control_Veh_2


title: genomic DNA from luminal A tumor (case 1)

description:
tumoral tissue
LA7

source_name: luminal A tumor 1


title: genomic DNA from luminal A tumor (case 2)

description:
tumoral tissue
LA8

source_name: luminal A tumor 2


title: genomic DNA from luminal B tumor (case 7)

description:
tumoral tissue
LB21

source_name: luminal B tumor 7


title: Set 1, disomic haploid rep 2

description:
DS1 H14
Dosage_series1_counts_RPKM.xlsx

source_name: Maize leaf tissue

value: leaf

tag: ploidy

value: disomic haploid


title: PMN_Control_Veh_1


title: LAG-1 4h rep1


title: GC-94


title: LAG-1 2h rep4

value: LAG-1 2h


title: genomic DNA from normal breast tissue 5

description:
non-tumoral mammary tissue
N5

source_name: non-tumoral mammary tissue 5

value: normal


title: genomic DNA from normal breast tissue 6

description:
non-tumoral mammary tissue
N6

source_name: non-tumoral mammary tissue 6


title: Set 1, disomic haploid rep 1

description:
DS1 H11
Dosage_series1_counts_RPKM.xlsx


title: PMN_Control_LPS_3


title: LAG-1 2h rep3


title: PMN_Control_LPS_2


title: Set 1, haploid rep 2

description:
DS1 H6
Dosage_series1_counts_RPKM.xlsx

value: haploid


title: GC-92

value: granulosa cells


title: Control d2

description: 3T3-L1 confluent pre-adipocytes were treated for 2 days with differentiation-induction medium.

value: adipocyte

tag: cell line

tag: treatment

value: differentiation-induction medium

tag: time

value: 2 d


title: GI-142

tag: Sex

value: bPOI


title: LAG-1 2h rep1

tag: time point

tag: genotype


title: LAG-1 ctr rep4

value: LAG-1 ctr


title: GI-135

tag: condition


title: GI-121


title: Set 1, haploid rep 3

description:
DS1 H7
Dosage_series1_counts_RPKM.xlsx


title: LAG-1 2h rep2

value: Bristol


title: GI-113

value: Female


title: PMN_Control_LPS_1

value: Control

tag: facs

value: CD11b+, Siglec F-, F4/80-, Ly6G+


title: LAG-1 ctr rep3

value: germline

value: 1 day old adult


title: genomic DNA from normal breast tissue 3

description:
non-tumoral mammary tissue
N3

source_name: non-tumoral mammary tissue 3


title: Set 1, tetrasomic rep 2

description:
DS1 76
Dosage_series1_counts_RPKM.xlsx

value: leaf

value: tetrasomic


title: LAG-1 ctr rep2


title: Set 1, haploid rep 1

description:
DS1 H1
Dosage_series1_counts_RPKM.xlsx


title: genomic DNA from normal breast tissue 1

description:
non-tumoral mammary tissue
N1

source_name: non-tumoral mammary tissue 1


title: LAG-1 ctr rep1


title: genomic DNA from normal breast tissue 2

description:
non-tumoral mammary tissue
N2

source_name: non-tumoral mammary tissue 2


title: Set 1, tetrasomic rep 3

description:
DS1 82
Dosage_series1_counts_RPKM.xlsx


title: genomic DNA from normal breast tissue 4

description:
non-tumoral mammary tissue
N4

source_name: non-tumoral mammary tissue 4


title: Q2-30h

city: Shanghai

first: Kuipu

last: Zhang

address: 130  Meilong Rd.

department: State  Key  Laboratory  of  Bioreactor  Engineering

institute: East  China  University  of  Science and Technology

data_processing:
Basecalling online_YX BasecallVersion0.5.6.153
Sequenced reads were filtered by removing adaptor sequences and low-quality reads
Sequenced reads were mapped to reference sequence S.erythraea NRRL2338 (Genbank accession number: NC_009142) using Geneious Prime version 2019.1.3.
Genome_build: Streptomyces albus (high GC Gram+) Strain: DSM 41398 genome (version: GCA_000827005.1)（NCBI Taxonomy ID 1888）
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Streptomyces albus

source_name: engineered strain,  at 30h

extract_protocol:
Total RNA was extracted with an RNAeasy Plus Mini kit (Qiagen, Germany) using glass beads to mechanically disrupting cells with a FastPrep (30 s ×4; M.P. Biomedical, USA). DNase treatment by RNase-Free DNase Set (Qiagen, Germany) aided to digest DNA in samples.
rRNA was removed with Illumina Ribo-zero rRNA removal kit(bacteria) after total RNA was collected. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dATPs,dGTPs,dCTPs,dUTPs, RNase H and DNA polymerase I respectively after removing dNTPs. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adapters. Then, the UNG enzyme was used to degrade the second-strand cDNA, and the product was purified by MiniElute PCR Purification Kit before PCR amplification.

value: at 30h


title: Set 1, tetrasomic rep 1

description:
DS1 29
Dosage_series1_counts_RPKM.xlsx


title: Q3-30h


title: Set 1, trisomic rep 4

description:
DS1 37
Dosage_series1_counts_RPKM.xlsx

value: trisomic


title: Set 1, trisomic rep 5

description:
DS1 68
Dosage_series1_counts_RPKM.xlsx


title: input DNA whole animal

data_processing:
Peak were called with MACS2.0 with following command line.
Command line: callpeak -t FLAG_IP.markdup.bam -c Input_DNA.markdup.bam -n FLAG_IP_minus_Input_DNA -g ce --call-summits --down-sample
Genome_build: ce10
Supplementary_files_format_and_content: excel files show the peak identified

source_name: whole animal

growth_protocol: bleach synchronzied animalsvwere grown to the  L4 stage on plates seeded with NA22 bacteria.

extract_protocol:
Animal lysates were prepared following the protocol of Berkseth et al., 2013.
Libraries were prepared with the kapa hyper prep kit.

value: whole animal

tag: passages

value: ND

tag: chip antibody


title: A3-30h

source_name: parental strain, at 30h

tag: strain

value: wildtype


title: GI-103

source_name: granulosa cells

value: granulosa cells


title: A1-30h


title: GI-100


title: GI-94


title: GI-95


title: TB-SP-PMN-MDSCs

city: Nanjing

first: Xinyu

last: Tian

email: jipinxinyu@163.com, sjwjs@ujs.edu.cn

state: Please select a state below

address: 321 Zhongshan Road, Nanjing Drum Tower Hospital

institute: The Affiliated Hospital of Nanjing University Medical School

description: LncRNA and associated mRNA expression in PMN-MDSCs from spleens of tumor-bearing mice

hyb_protocol: Step 5 Hybridization  Kit and Instruments:  Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):  10X Blocking Agent  25X Fragmentation Buffer  2x GEx Hybridization Buffer HI-RPM  Hybridization Chamber, stainless (Agilent p/n G2534A)  Hybridization Chamber gasket slides (Agilent p/n G2534-60003)  Hybridization oven (Agilent p/n G2545A)  Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029)    Procedure:  1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  For 1*244K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.5ug  10X Blocking Agent 50ul  Nuclease-free water ×ul  25X Fragmentation Buffer 10ul  Total volume 250ul    For 2*105K array Amount  cyanine 3-labeled, linearly amplified cRNA 1. 5ug  10X Blocking Agent 25ul  Nuclease-free water ×ul  25X Fragmentation Buffer 5ul  Total volume 125ul    For 4*44K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.65ug  10X Blocking Agent 11ul  Nuclease-free water ×ul  25X Fragmentation Buffer 2.2ul  Total volume 55ul    For 8*15K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul    For 8*60K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul      4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60k  cRNA from Fragmentation Mix 250ul 125ul 55ul 25ul 25ul  2* GEx Hybridization Buffer HI-RPM 250ul 125ul 55ul 25ul 25ul    7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60K  Volume Prepared 500ul 250ul 110ul 50ul 50ul  Hybridization Sample Volume 490ul 245ul 100ul 40ul 40ul    12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.

scan_protocol: Step 7 Scanning  Instrument:  Agilent Microarray Scanner (Agilent p/n G2565BA)    Procedure:  1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Step 8 Extract data using Agilent Feature Extraction Software  Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

label_protocol: Step 3 Prepare labeling reaction  Kit:  Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)    Procedure:  1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.   Volume(ul) per reaction  5×First Strand Buffer 4  0.1M DTT 2  10mM dNTP mix 1  MMLV-RT 1  RNaseOut 0.5  Total volume 8.5  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.   Volume(ul) per reaction  Nuclease-free water 15.3  4X Transcription Buffer 20  0.1 M DTT 6  NTP mix 8  50% PEG 6.4  RNaseOUT 0.5  Inorganic pyrophosphatase 0.6  T7 RNA Polymerase 0.8  Cyanine-3-CTP 2.4  Total volume 60  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.     Step 4 Purify the labeled/amplified RNA and labeled cRNA QC  Kit and instrument:  RNeasy Mini Kit (Qiagen p/n 74104)  NanoDrop ND-1000    Procedure:  1. Add 20 μL of nuclease-free water to your cRNA sample, for a total volume of 100 μL.  2. Add 350 μL of Buffer RLT and mix well by pipetting.  3. Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge.  4. Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube.  5. Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube.  6. Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube.  7. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm.  8. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.  9.  Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report ”Labeling Efficiency-QC”).   From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50.   Blank the instrument with 1.5 μL of 1x labeling solution.   Use 1.5 μL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3).   The specific activity (pmol dyes per μg genomic DNA) of the labeled genomic DNA can be obtained by the following calculation:  (Concentration of Cy3)  Specific Activity =——————————————— = pmol Cy3 per μg cRNA  (Concentration of cRNA) * 1000  * If the yield is <1.65 μg and the specific activity is <9.0 pmol Cy3 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

extract_protocol: Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C. At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C. Then total RNA clean-up was performed. RNA-QC was confirmed using a NanoDrop-1000 spectrophotometer.

treatment_protocol: PMN-MDSCs used for microarray analysis were first isolated from the spleens of wild-type mice and tumor tissue of tumor-bearing mice using a mouse MDSC isolation kit (Miltenyi Biotec, Auburn, CA) following the manufacturer’s protocol. Then, the enriched cells were stained with anti-mouse CD11b-PE/Cy5.5 (0.25 μg for 1×106 cells) (clone: M1/70) (eBioscience, San Diego, CA) and anti-mouse Ly6G-PE (0.25 μg for 1×106 cells) (clone: RB6-8C5) (eBioscience, San Diego, CA) for 30 minutes at 4°C. Stained cells were collected and further sorted with FACS (FACSAriaII, BD Biosciences) to eliminate interference from other cells. Lyse cells in TRIzol Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10×10^6 of PMN-MDSCs.

value: 6-8 weeks

value: Male

tag: tissue

value: Spleen

value: PMN-MDSCs


title: WT-SP-PMN-MDSCs

description: LncRNA and associated mRNA expression in PMN-MDSCs from spleens of wild-type mice

tag: age


title: Set 1, trisomic rep 3

description:
DS1 34
Dosage_series1_counts_RPKM.xlsx

data_processing:
Tuxedo software suite, specifically the Bowtie alignment tool, Tophat (an extension of Bowtie incorporating splice site information), and Cufflinks (specifically Cuffdiff, for recording differential expression at the level of individual genes).
Genome_build: Maize W22 reference genome
Supplementary_files_format_and_content: Excel files include mRNA expression data (RPKM value) for each gene in each sample

extract_protocol:
RNA was extracted using a TRIzol-based protocol.
TruSeq (Illumina) was used for library preparation, involving poly-A enrichment of mRNA using oligo-dT magnetic beads, first-strand cDNA synthesis using reverse transcriptase, second-strand cDNA synthesis using DNA Polymerase I, ligation of adaptors, and PCR amplification.


title: GFP3_ChIPSeq

tag: cell type

value: Bristol

value: GFP


title: GFP2_ChIPSeq


title: Set 1, trisomic rep 2

description:
DS1 21
Dosage_series1_counts_RPKM.xlsx


title: FLAG_ChIPSeq

value: FLAG


title: 300mM NaCl treated sample of Suaeda salsa leaves replication 3

first: Luoyan

address: wenhuadong 88

institute: shandong normal university

data_processing:
The basic reads were converted into sequence data by base calling.
Clean reads were obtained by removing adapter-containing reads, ploy-N-containing reads and low-quality reads from raw data.
Q20, Q30, GC content and sequence duplication level of the clean data were calculated
The remaining high-quality reads were used for transcriptome assembly using the Trinity software pipeline with default parameters.

organism: Suaeda salsa

source_name: leaves

extract_protocol:
Total RNA was extracted from tissues by using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaves

tag: stress

value: 300mM NaCl


title: TB-Tumor-PMN-MDSCs

description: LncRNA and associated mRNA expression in PMN-MDSCs from tumor tissues of tumor-bearing mice

tag: gender

value: Tumor tissue


title: GI-91

value: Female

value: bPOI


title: Set 1, trisomic rep 1

description:
DS1 2
Dosage_series1_counts_RPKM.xlsx

value: leaf

tag: ploidy

value: trisomic


title: 300mM NaCl treated sample of Suaeda salsa leaves replication 1


title: Set 1, diploid rep 4

description:
DS1 66
Dosage_series1_counts_RPKM.xlsx

value: diploid


title: 300mM NaCl treated sample of Suaeda salsa leaves replication 2


title: GI-78


title: germline_LAG-1_ChIPseq rep3

data_processing:
Peak were called with MACS2.0 with following command line.
Command line: callpeak -t Biotag-boss-1.markdup.bam -c Input.markdup.bam -n Biotag-boss-1_minus_Input -g ce --down-sample --call-summits
Genome_build: ce10
Supplementary_files_format_and_content: excel files show the peak identified

source_name: germline

growth_protocol: Bleach synchronzied animals were grown to the L4 stage on plates seeded with NA22 bacteria.

extract_protocol:
Animal lysates were prepared following the protocol of Berkseth et al., 201.3
Libraries were prepared with the kapa hyper prep kit.

value: germline

value: ND


title: input DNA


title: MDA-LM2, micrometastatic lung, biological rep3

description: Gene expression of highly lung metastatic MDA-MB-231-LM2 breast cancer cells sorted from NSG mouse lungs 1 week after tail vein injection

hyb_protocol: 11 ug of fragmented and labeled cRNA were hybridized for 17 hours at 45°C on Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA 2.0), according to user manual GeneChip® 3' IVT PLUS Reagent Kit, P/N 703210.

data_processing: Raw data was processed using Chipster version 3.8.1; RMA-normalization was used with chiptype annotation (human-hta20) for gene annotation. For subsequent statistical analysis, empirical Bayes test with Benjamini-Hochberg correction for p-values was performed.

source_name: MDA-MB-231-LM1 breast cancer cells sorted from mouse lungs 1 week after i.v. injection

extract_protocol: RNA extraction was performed using the Arcturus PicoPure Extraction Kit (ThermoFisher Scientific) according to the manufacturer’s protocol. cDNA preamplification was conducted using the GeneChip WT Pico Reagent Kit (Affymetrix) according to the manufacturer’s protocol.

tag: metastatic stage

value: Micrometastasis

tag: source

value: in vivo (NSG mouse lung)


title: germline_LAG-1_ChIPseq rep2


title: Control sample of Suaeda salsa leaves replication 3

value: No


title: MDA-LM2, micrometastatic lung, biological rep1


title: Set 1, diploid rep 2

description:
DS1 27
Dosage_series1_counts_RPKM.xlsx


title: Set 1, diploid rep 3

description:
DS1 53
Dosage_series1_counts_RPKM.xlsx


title: Set 1, diploid rep 1

description:
DS1 1
Dosage_series1_counts_RPKM.xlsx


title: Control sample of Suaeda salsa leaves replication 1


title: wild type (sample 3)

status: Public on Feb 16 2020

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: wild type (sample 3)

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using tophat2 with '--very-sensitive' option.
For counting reads which mapped to each CDS, featureCounts in Subread package was used.
Finally, normalization of retrieved counts and fold change calculation between groups were performed by DESeq2 package.
Genome_build: C. neoformans var. grubii H99 (GCA_000149245.3)
Supplementary_files_format_and_content: Normalized counts, fold change values and related p-values were listed as a xlsx format for each sample.

organism: Cryptococcus neoformans H99

growth_protocol: C. neoformans cells were cultured in YNB + BPS with or without 100 μM of FeCl3 at 30˚C for 6 hours.

extract_protocol:
Total RNA was extracted using RiboPure-Yeast Kit (Ambion, #AM1926) following manufacturer's instructions.
Library was constructed using Illumina TruSeq RNA Library Prep Kit V2 following manufacturer's instructions.

value: wild type

tag: culture condition

value: YNB low iron medium


title: PMN_Runx1KO_LPS_2

source_name: Bone Marrow Neutrophils (PMN)

value: Runx1 KO

value: CD11b+, Siglec F-, F4/80-, Ly6G+


title: wild type that treated iron (sample 2)

description: wild type that treated iron (sample 2)

value: YNB low iron medium + 100 μM of FeCl3


title: Control sample of Suaeda salsa leaves replication 2

value: leaves


title: MDA, micrometastatic lung, biological rep2

first: Maren

description: Gene expression of parental MDA-MB-231 breast cancer cells sorted from NSG mouse lungs 1 week after tail vein injection

source_name: MDA-MB-231 breast cancer cells sorted from mouse lungs 1 week after i.v. injection


title: wild type (sample 1)

description: wild type (sample 1)


title: MDA, micrometastatic lung, biological rep3


title: germline_LAG-1_ChIPseq rep1

value: Bristol


title: wild type (sample 2)

description: wild type (sample 2)


title: MDA-LM2, micrometastatic lung, biological rep2


title: hapX mutant that treated iron (sample 2)

value: hapX mutant


title: hapX mutant (sample 3)

description: hapX mutant (sample 3)


title: hapX mutant (sample 2)

description: hapX mutant (sample 2)


title: hapX mutant that treated iron (sample 3)


title: hapX mutant (sample 1)

description: hapX mutant (sample 1)


title: hapX mutant that treated iron (sample 1)


title: cir1 mutant (sample 3)

description: cir1 mutant (sample 3)

value: cir1 mutant


title: cir1 mutant (sample 1)

description: cir1 mutant (sample 1)


title: MDA, micrometastatic lung, biological rep1


title: cir1 mutant that treated iron (sample 2)


title: CS11_yolk_sac_10x

city: Beijing

first: Tao

last: Huang

state: Beijing

address: Dong Da Jie No.8

institute: The Fifth Medical Center of Chinese PLA General Hospital

data_processing:
FASTQ were demultiplexed using 10X Genomics CellRanger version 2.1 and aligned to the Grch38 human reference genome. Cell barcodes and unique molecular identifiers (UMIs) were extracted and ‘‘Raw’’ UMI matrix generated for each sample, providing with the number of UMIs for each gene that are associated with individual cell barcode.
Genome_build: hg19
Supplementary_files_format_and_content: mtx files and tsv files  providing the number of UMIs for each gene that are associated with individual cell barcode.

source_name: human embryonic cells

extract_protocol:
The human yolk sacs were carefully dissected under the microscope. After washing in PBS 3 times to remove any residual blood contamination, the yolk sacs were transferred to pre-warmed digestion medium containing 0.1 g/mL Collagenase I (Sigma, C2674, preheated to 37 °C) in RPMI 1640 medium. The samples were enzymatically digested at 37 °C in a humidified incubator for 20-30 minutes, with the samples being shaken periodically every five minutes until digested to single cell suspension. The cells were then filtered through a 70 mm cell strainer after neutralizing enzymes. The following antibodies were used for staining of the embryonic cells:7-amino-actinomycin D (7-AAD) (PerCP-Cy5.5, 00699350 eBioscience).Cells were sorted with the Aria 2 Flow Cytometer (BD Bioscience). Data were analyzed with BD FACSDIVA V8.0.1.
10x Genomics Chromium Single Cell 3' Reagent Kit (v2 chemistry)

value: Yolk sac

tag: developmental stage

tag: facs type


title: CS15_yolk_sac_10x


title: cir1 mutant that treated iron (sample 1)

tag: genotype


title: wild type that treated iron (sample 3)

description: wild type that treated iron (sample 3)


title: wild type that treated iron (sample 1)

description: wild type that treated iron (sample 1)


title: Il25 KO rep3

city: Seattle

first: Jakob

middle: Helmuth

last: von Moltke

state: Washington

address: 750 Republican Street

department: Immunology

institute: University of Washington

data_processing:
Analytic pipeline was managed on the Galaxy platform. Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
Sequence alignment was performed using STAR aligner (v2.4.2a) with the GRCm38 reference genome and gene annotations from Ensembl release 91.
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), and HTSeq-count
Genome_build: GRCm38
Supplementary_files_format_and_content: The file "P233-7_RawGeneCounts.csv" is a comma-separated matrix. The first four columns ("geneId", "geneName", "description", and "geneBiotype") describe one gene per row, with the "geneId" column containing Ensembl gene IDs. The remaining columns are named as "sampleId - libraryId" and contain raw read counts assigned to each library. Counts have not been filtered or normalized.

source_name: small intestine

extract_protocol:
Before tissue collection, mice were anesthetized with ketamine/xylazine. Next, the small intestine was nicked at the stomach and transected at the cecum and flushed with 20 mL 37˚C HBSS (no Ca+2/Mg+2) + 10 mM HEPES. The mice were then perfused through the heart with 40 mL of 30 mM EDTA + 10 MM HEPES in HBSS (no Ca+2/Mg+2). Five minutes after initiating perfusion, the first 5 cm of the proximal SI were harvested, fileted open, transferred to 35 mL ice cold HBSS (no Ca+2/Mg+2) + 10 MM HEPES and shaken vigorously for 30 seconds to release epithelial cells. Intestinal pieces were stored in HBSS + 5% FCS on ice and then transferred into pre-warmed digest buffer composed of 5ml HBSS (with Ca+2/Mg+2) supplemented with 3% FCS, 10mM HEPES, 30 μg/ml DNase I (Sigma Aldrich), and 0.1 Wunsch/ml Liberase TM (Sigma Aldrich), shaking at 37° C for 30 minutes. Tissues were vortexed and cells were passed through a 70 μm filter and washed. The resulting pellet was resuspended in 40% Percoll (Sigma Aldrich), centrifuged for 5 minutes at 1500 rpm, and supernatant discarded. Pelleted cells were then washed and stained for flow cytometry and sorting.
Following Nextera XT library preparation protocol

treatment_protocol: SPF mice without treatment

value: Duodenum ILC2

value: 6-10 weeks old


title: Alox5 KO rep3

value: Alox5 (-/-); Il13 smart13/smart13


title: Il25 KO rep2


title: WT rep3

value: Wild type B6; Il13 smart13/smart13


title: Alox5 KO rep4


title: WT rep2


title: Alox5 KO rep2


title: Il25 KO rep1


title: St2 KO rep3


title: St2 KO rep4


title: Alox5 KO rep1


title: St2 KO rep2


title: WT rep1


title: cir1 mutant (sample 2)

description: cir1 mutant (sample 2)


title: cir1 mutant that treated iron (sample 3)


title: MKL-1 Combo-2

city: ALLSTON

first: Donglim

last: Park

state: MA

address: 4 Price Rd, Apt11

department: Medical oncology

institute: Dana-Farber Cancer Institute

data_processing:
For analysis, the adapters were removed using NGmerge and the reads were mapped to hg38 reference using Bowtie2 and sorted by SAMtools.
peaks were called using using the default parameters of MACS2 relative to the input samples.
ATAC-seq peaks were merged, annotated, and visualized using the BEDtools and the ChIPseeker, ChIPpeakAnno, and DiffBind R packages and Integrative genome viewer (IGV; Broad Institute)
Genome_build: hg38

source_name: MKL-1 MCC Cells

growth_protocol: MCC cell lines were grown in RPMI supplemented with 10% FBS and antibiotics.

extract_protocol:
Cells were washed with PBS twice to achieve >85% viable cells in pellets. ATAC-seq protocol was modified from Corces et al.
The transpose reaction was performed using TDE1 Tn5 transposase (15027865; Illumina) and TD buffer (15027866; Illumina). The reactions were cleaned up using MinElute PCR Purification Kit (28004; Qiagen) and amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541S; New England Biolabs Inc.) with a total of 7 cycles. The libraries were cleaned up using MinElute PCR Purification Kit and additionally with AMPure XP beads (Beckman Coulter) to remove primer dimers and large fragments.

treatment_protocol: Two independent replicates of 70,000 MKL-1 MCC cells were harvested for ATAC-seq after treatment with GSK-LSD1 0.1µM, dBRD9 0.1µM, or both for three days.

value: MCC tumor derived cell line

tag: cell line


title: MKL-1 LSD1i-2


title: MKL-1 dBRD9-2


title: MKL-1 dBRD9-1


title: Il25 KO rep4


title: MKL-1 Control-2


title: MKL-1 LSD1i-1


title: ATOH1_2

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using the BWA aligner
peaks were called using using the default parameters of MACS2 relative to the input samples.
Genome_build: hg19
Supplementary_files_format_and_content: .narrwPeak.bed and .xls peak files were generated using MACS2.

extract_protocol:
The ChIP method was modified from protocols described in Schmidt et al.(Schmidt et al., 2009). MKL-1 cells were cross-linked using dual cross-linking with disuccinimidyl glutarate (DSG) and formaldehyde. After cross-linking, cells were lysed using SimpleChIP buffer A and B (Cell signaling) and DNA was processed with the Micrococcal nuclease (New England Biolabs Inc.) for 30 minutes at 37°C followed by sonicating for 20s pulses 5 times at 4°C.
30 ng of DNA from ChIP experiments or input DNA were prepared for sequencing with NEBNext ChIP-seq Library Prep Reagent Set for Illumina (New England BioLabs). Amplified libraries were cleaned up using AMPure XP beads (Beckman Coulter) and checked on a Bioanalyzer (Agilent) to confirm a narrow distribution with a peak size around 275 bp. Diluted libraries were used for 50 cycles single-end sequencing on NextSeq 550 systems  (Illumina) at the Molecular Biology Core Facilities (MBCF) at Dana-Farber Cancer Institute following the manufacturer’s protocol.


title: both3

data_processing:
The Illumina NextSeq500 was used to generate reads.
STAR was used to map reads to the hg19 genome and reads were  aligned using samtools.
The count (TPM) files were generated using the htset-count function.
Genome_build: hg19

extract_protocol: RNA libraries were prepared for sequencing using TruSeq Stranded mRNA library prep kit

treatment_protocol: Cells were treated with either GSK-LSD1 and or dBRD for 6 days and harvested for RNA using Qiagen Rneasy plus kit

tag: tumor type

value: Merkel cell carcinoma

value: tumor derived cancer cell line

tag: treatment compound

value: GSK-LSD1 0.1uM + dBRD9 1uM

tag: treatment time

value: 6 days


title: both1


title: WT rep4

tag: strain


title: MKL-1 Control-1


title: St2 KO rep1


title: MKL-1 Combo-1


title: UISO_D2

source_name: UISO

treatment_protocol: Cells were treated with either GSK-LSD1 or CPI-670242 for 1 or 3 days and harvested for RNA using Qiagen Rneasy plus kit

value: UISO

value: Control

value: 1 day


title: UISO_D3


title: DMSO3


title: dBRD9_1

value: dBRD9 1uM


title: dBRD9_3


title: UISO_D1


title: UISO_L3


title: LSD1i_1

value: GSK-LSD1 0.1uM


title: DMSO1


title: UISO_L2


title: broli_L3

source_name: BroLi

value: BroLi


title: UISO_L1


title: LSD1i_3


title: broli_L2


title: broli_D1


title: PETA_L2

source_name: PeTa

value: PeTa


title: PETA_L3


title: broli_D2


title: PETA_D2


title: PETA_D1


title: waga_L2

source_name: WaGa

value: WaGa


title: waga_L3


title: waga_L1


title: broli_L1


title: waga_D2


title: waga_D3


title: waga_D1


title: broli_D3


title: MS1_L2

value: 3 days


title: PETA_L1


title: PETA_D3


title: Elute_Expt.2_2

city: Redwood City

first: Yuping

address: 309 Oak Ave

institute: Stanford University

data_processing:
Step 1: Aligned with Bowtie2 to Candida albicans genome and output unalignable reads for alignment to Saccharomyces cerevisiae genome
Step 2: Aligned the output reads from Step 1
Step 3: rRNA reads were removed with custom perl scripts
Step 4: RPKM values were measured using SeqMonk
Step 5: Linear regression and slopes of RPKM vs time or size were calculated with custom R script
Genome_build: saccharomyces_cerevisae_R64-1-1_20110208 (obtained from the SGD (S288C R64-1-1), corresponding to R64-1-1 on Ensembl, GCA_000146045.2)
Supplementary_files_format_and_content: .xlsx; slopes

organism: Saccharomyces cerevisiae

growth_protocol: YEP supplemented with 1% Ethanol

extract_protocol:
Hot acid phenol total RNA extraction
Ovation Universal RNA-Seq System (NuGEN)

treatment_protocol: Supplemented with known amount of Candida albicans strain BWP17 grown over-night in YEPD supplemented with 80 microgram/ml uridine before RNA extraction

tag: genotype/variation

tag: size (fl)

tag: treatment

value: Elutriation followed by addition of 1NM-PP1


title: Elute_Expt.3_1


title: Elute_Expt.1_5


title: MS1_L1

tag: cell type


title: Elute_Expt.3_3


title: Elute_Expt.2_3


title: Elute_Expt.1_3


title: E17 Prdm16cKO B

city: New York

first: Qiangqiang

state: NY

address: 430 East 67th St

institute: Memorial Sloan-Kettering Cancer Center

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E17mutB__E17cKO

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Chui_et_al_Processed_Data_Files.xls: Excel file containing normalized counts.

source_name: ventricular zone embryonic cortical tissue

extract_protocol:
Ventricular tissue were isolated from three pairs of wild-type (WT) and Prdm16 cKO (conditional knockout) mutant E11.5, E13.5, E15.5, and E17.5 embryos. RNA was isolated using Qiagen RNeasy Micro Kit (QIAGEN).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 125-150ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102). Samples were barcoded and ran on the HiSeq 4000 platform, using the HiSeq 3000/4000 SBS Kit (Illumina).

value: Prdm16 conditional knockout

value: Embryonic day 17.5

tag: tissue

value: Ventricular zone embryonic cortical tissue


title: Elute_Expt.1_2


title: 1NM-PP1_Control_6

value: WT

tag: time-point (hr)

value: Time-course post addtion of 1NM-PP1


title: MKL2_L3

value: Merkel cell carcinoma

value: tumor derived cancer cell line


title: MS1_D1


title: Elute_Expt.1_1


title: Elute_Expt.2_1


title: E17 wildtype C

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E17C2cont__E17wildtype

value: Wildtype


title: E17 Prdm16cKO C

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E17mutC__E17cKO


title: E17 Prdm16cKO A

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E17mutA__E17cKO


title: MS1_L3


title: 1NM-PP1_Control_5


title: MS1_D2

value: Control


title: Elute_Expt.3_2


title: MS1_D3


title: E17 wildtype B

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E17B2cont__E17wildtype


title: 1NM-PP1_Control_4


title: MKL2_L2

value: 1 day


title: 1NM-PP1_Control_3


title: 1NM-PP1_Control_2


title: MKL2_L1


title: 1NM-PP1_Expt_5


title: 1NM-PP1_Control_1


title: MKL2_D3


title: 1NM-PP1_Expt_7


title: MKL2_D1


title: 1NM-PP1_Expt_6


title: E15 Prdm16cKO C

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E15mutC__E15cKO

value: Embryonic day 15.5


title: E15 Prdm16cKO A

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E15mutA__E15cKO


title: MKL2_D2


title: E15 Prdm16cKO B

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E15mutB__E15cKO


title: MKL1_L3

value: GSK-LSD1 0.1uM


title: Elute_Control_6


title: 1NM-PP1_Expt_2


title: 1NM-PP1_Expt_1


title: E15 wildtype B

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E15contB__E15wildtype


title: MKL1_L2


title: E17 wildtype A

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E17A2cont__E17wildtype


title: Elute_Control_5


title: 1NM-PP1_Expt_4


title: MKL1_L1


title: Elute_Control_3


title: 1NM-PP1_Expt_8


title: Elute_Control_2


title: E15 wildtype A

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E15contA__E15wildtype


title: MKL1_D3


title: E15 wildtype C

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E15contC__E15wildtype


title: Elute_Control_4


title: 1NM-PP1_Expt_3


title: MKL1_D2


title: E13 Prdm16cKO C

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E13mutC__E13cKO

value: Embryonic day 13.5


title: Pten KO EBs-3

city: Hong Kong

first: Wuming

last: Wang

address: Sha Tin

institute: The Chinese University of Hong Kong

data_processing:
The raw reads were cleaned using internal software SOAPnuke (Version v1.5.2, Website: https://github.com/BGI-flexlab/SOAPnuke) by removing adapter sequences, reads in which unknown bases are more than 10%, and low quality reads.
The clean reads were stored in FASTAQ format.
We used HISAT (Version v2.0.4, Website: http://www.ccb.jhu.edu/software/hisat) to do the mapping step, and calculated gene expression with a software package called RSEM (Version v1.2.12, Website: http://deweylab.biostat.wisc.edu/ RSEM).
FPKM method was used in calculated expression level, and the calculated gene expression can be directly used for comparing the difference of gene expression among sample.
Genome_build: HG19
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: embryoid bodies

growth_protocol: Mouse ESCs were cultured in DMEM/F12 containing GlutaMAX and sodium pyruvate (Life Technologies, 10565) with 15% fetal bovine serum (Hyclone, SH30071), nonessential amino acid solution (Life Technologies, 11140), -mercaptoethanol (Life Technologies, 31350) with 1 × 103 units/ml LIF (Millipore, ESG1106), 1 uM PD0325901 (Sigma, PZ0162), and 2.5 uM CHIR99021 (Sigma, SML1046). The mouse ESCs were grown on gelatin-coated plates and the medium was replaced every other day. The ESC cultures were passaged every 2 days.

extract_protocol:
ESCs and embryoid bodies were collected, and RNA was harvested using Trizol reagent. The quality of the isolated RNA was determined with Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). The RNA was converted into a template molecules library for sequencing on the BGISEQ-500.
Briefly, total RNA samples were ribo-depleted and then fragmented. The fragmented samples were reversed transcribed to cDNA, end-repaired and 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified, and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. Denature the PCR products by heat, and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: The Pten-/- ESCs and Pten-A3 mutant ESCs were generated by the CRISPR-Cas9 system. ESCs were cultured in 6-well plates and transfected with donor plasmid and constructs containing Cas9 and target sequences using lipofectamine 3000, and these were then subjected to cell sorting of GFP-positive cells after transfection for 48 h. The enriched gene-modified cell populations were cultured in 60-mm dishes for 4-5 days, and each cell clone was passaged into 24-well plates. Finally, the Pten−/− and Pten-A3 mutant cell lines were identified by sequencing, and the cells were stored in liquid nitrogen.

value: embryoid bodies

value: Pten-/-


title: Elute_Control_1


title: MKL1_D1

value: 3 days


title: Pten KO EBs-2


title: Input_2

value: MCC tumor derived cell line

tag: chip antibody


title: Pten KO EBs-1


title: E13 Prdm16cKO B

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E13mutB__E13cKO

value: Prdm16 conditional knockout


title: E13 Prdm16cKO A

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E13mutA__E13cKO


title: Input_1


title: WT EBs-1

value: wild type


title: Pten-A3 mutant ESC-2

source_name: embryonic stem cells

value: embryonic stem cells

value: Pten-A3 mutant


title: E13 wildtype A

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E13A2cont__E13wildtype

value: Ventricular zone embryonic cortical tissue


title: Pten-A3 mutant ESC-1


title: RCOR2_2

value: Merkel cell carcinoma

value: RCOR2 (Proteintech; rabbit; 23969-1-AP)


title: WT ESC-4


title: WT ESC-5


title: E11 Prdm16cKO C

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E11mutC__E11cKO

value: Embryonic day 11.5


title: Pten KO ESC-2


title: Pten KO ESC-3


title: RCOR2_1


title: WT EBs-3


title: WT EBs-2


title: WT ESC-2


title: E13 wildtype C

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E13C2cont__E13wildtype

value: Wildtype


title: Pten KO ESC-1


title: E11 wildtype C

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E11contC__E11wildtype


title: E11 Prdm16cKO A

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E11mutA__E11cKO


title: E13 wildtype B

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E13B2cont__E13wildtype


title: MKN_74_ONECUT2

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

description:
MKN74_OC2_over
processed data file: cpm_normalized_log2.xlsx

data_processing:
ChIP-seq: Base calling performed using CASAVA version 1.7
ChIP-seq: mapped to hg19 whole genome using bowtie2 v.2.1.0
ChIP-seq: Enrichment levels were called using homer v.4.9.1. ONECUT2 ChIP-seq was prossed with homer transcription factor option.
RNA-seq: Illumina Casava1.7 software used for basecalling.
RNA-seq: mapped to hg19 whole genome using STAR v2.5.1.
RNA-seq: Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using a edgeR v.3.12.1. The CPM values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using homer.
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

extract_protocol:
The RNA sequencing library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA). and For ChIP-seq, Cells were fixed using 1% formaldehyde, lysed and sonicated using a Bioruptor (Diagenode Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols. For ChIP-seq, immunoprecipitation was performed with anti-ONECUT2(proteintech, catalog no. 21916-1-AP). 250-400 bp genomic libraries were generated from the input and immunoprecipitated DNA and sequenced using Illumina NextSeq_500 to generate 75 bp single-end reads.

value: gastric cancer cell line


title: E11 wildtype B

description:
processed data file: Chui_et_al_Processed_Data_Files.xls
s_E11contB__E11wildtype


title: WT ESC-1


title: ML-2-FST344

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
The raw sequencing reads were filtered for adapter and low quality sequences using cutadapt (Martin, 2011) and custom scripts. Low quality reads were defined as sequencing reads with more than 5% unknown bases (‘N’) and reads with more than 50% of the bases.
Alignment, expression estimation and tests for differential expression were processed by RSEM 1.2.31 (Li and Dewey, 2011) and EBSeq Version 1.10.0 (Leng et al, 2013). Resulting values were indicated by Transcript Per Million (TPM).
Genome_build: Human genome (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Acute myeloid leukemia cells

extract_protocol:
Total RNA from different samples were extracted (Rnaeasy mini kit, Qiagen), and used for construction of sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FST344 ovexpression