title: R077, AMD

city: Saint Louis

middle: B

last: Lin

state: MO

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine

data_processing:
We processed the raw FASTQ sequencing files using CellRanger 4.0.0 with alignment to the 10x Genomics human reference genome (refdata-gex-GRCh38-2020-A). We imported the filtered count matrices into Seurat v4, and assigned each cell a unique identifier to prevent overlap of barcodes between different samples. We normalized, log-transformed, and scaled the count matrices to remove unwanted sources of variation such as discrepancies in sequencing depth. We identified the top 2000 highly variable genes for principal component analysis. We integrated across samples to account for any sample- or experiment-specific batch effects using the Harmony package. We utilized these harmony embeddings to run Uniform Manifold Approximation and Projection dimensional reduction to 2 dimensions. We clustered cells according to the Louvain algorithm and identified marker genes for each cluster using Wilcoxon rank sum tests comparing each cluster to all other clusters. We validated that our manual annotation of cell types was consistent with automated annotation assigned using Azimuth using the “pbmcref” reference.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: AMD_PBMC_metadata.csv: Cell-level metadata including sample ID, control/AMD, sex, age, cell type, and UMAP coordinates (containing all samples).
Supplementary files format and content: AMD_PBMC_countmatrix.csv: Raw count matrix (containing all samples).

source_name: peripheral blood mononuclear cells

extract_protocol:
We collected blood from patients by venous blood draw into K2EDTA-coated BD Vacutainer Venous Blood Collection Tubes. To purify PBMCs, we centrifuged the blood, isolated the buffy coat, and lysed red blood cells, leaving nucleated PBMCs behind.
We used the Chromium Single Cell 3’v3.1 Reagent Kit according to the manufacturer's protocol.

value: peripheral blood mononuclear cells

value: AMD


title: siMAPK1_3

status: Public on Oct 06 2023

type: SRA

city: Changchun

first: yue

last: wang

address: 2699 Qianjin Street

country: China

institute: Jilin University

library_source: transcriptomic

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by Bowtie2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The edgeR package version 3.18.1 (R Bioconductor package), which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC>1.5 or <0.67) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: AGS cells

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

tag: cell line

value: AGS cells

tag: cell type

value: MAPK1 knockdown in AGS cell


title: siMAPK1_1


title: C73_A1_VISIUM

city: Toronto

first: Diana

last: Nakib

state: ON

address: 101 College Street

country: Canada

institute: University of Toronto

description: Spatial transcriptomics on OCT-embedded tissue

data_processing:
*library strategy: Spatial transcriptomics
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Assembly: GRCh38-2020-A transcriptome
Supplementary files format and contents:
barcodes.tsv.gz: list of spatial barcodes (raw feature matrix)
features.tsv.gz: list of gene IDs (raw feature matrix)
matrix.mtx.gz: gene expression count data in Matrix Market Exchange format (raw feature matrix)
aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
detected_tissue_image.jpg.gz: image of tissue and spots
scalefactors_json.json.gz: scalefactors in json format
tissue_hires_image.png.gz: hires image of tissue
tissue_lowres_image.png.gz: low-res image of tissue
tissue_positions_list.cv.gz: list of spatial barcodes and the coordinates specifying spots
GEX_Merged.tif: higher resolution tif of tissue slice
metrix_summary.csv: summary of key sample metrics

molecule: cytoplasmic RNA

source_name: Adult Liver

extract_protocol:
Tissue was prepared for Visium Spatial transcriptomics as previously described (https://doi.org/10.1002/hep4.1854)]. Briefly, liver tissue was embedded in OCT media, frozen, and cryosectioned with 16-um thickness at -10ºC (cryostar NX70 HOMP). Sections were placed on a chilled Visium Tissue Optimization Slide (10x Genomics) and processed following the Visium Spatial Gene Expression User Guide. Tissue was permeabilized for 12 minutes, based on an initial optimizations trial. Libraries were prepared according to the Visium Spatial Gene Expression User Guide and samples sequenced on a NovaSeq 6000.
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

tag: tissue

value: Adult Liver

tag: age

tag: Sex

value: M


title: R076, AMD

first: Joseph

country: USA

library_source: transcriptomic single cell

molecule: polyA RNA

tag: disease state


title: CD138+cells from multiple myeloma_Replicate 2

type: RNA

city: Wuhan

first: Han

last: Yan

address: Jiefang  Avenue

institute: Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: lncRNA and mRMA expression data from bone marrow CD138+ cells of multiple myeloma patient 2

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.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

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).

source_name: Bone marrow CD138+ cells,multiple myeloma,replicate 2

label_protocol: 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: Bone marrow CD138+ cells were obtained from multiple myeloma patients and normal individuals by magnetic bead separation. The cells were treated with TRIzol to extract total RNA according to manufactures' instrctions.

value: Multiple Myeloma

value: bone marrow

value: CD138+ cells

tag: gender

value: Male


title: CD138+cells from normal_Replicate 3

description: lncRNA and mRMA expression data from bone marrow CD138+ cells of normal control 3

source_name: Bone marrow CD138+ cells,normal,replicate 3

value: Normal


title: CD138+cells from multiple myeloma_Replicate 3

description: lncRNA and mRMA expression data from bone marrow CD138+ cells of multiple myeloma patient 3

source_name: Bone marrow CD138+ cells,multiple myeloma,replicate 3


title: CD138+cells from normal_Replicate 2

description: lncRNA and mRMA expression data from bone marrow CD138+ cells of normal control 2

source_name: Bone marrow CD138+ cells,normal,replicate 2


title: CD138+cells from normal_Replicate 1

description: lncRNA and mRMA expression data from bone marrow CD138+ cells of normal control 1

source_name: Bone marrow CD138+ cells,normal,replicate 1

value: Female


title: R069, AMD


title: R074, AMD


title: R070, AMD


title: R072, AMD


title: R067, AMD


title: R066, AMD


title: R068, Control

value: Control


title: C73_C1_VISIUM

data_processing:
*library strategy: Spatial transcriptomics
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Assembly: GRCh38-2020-A transcriptome
supplementary files format and content:
barcodes.tsv.gz: list of spatial barcodes (raw feature matrix)
features.tsv.gz: list of gene IDs (raw feature matrix)
matrix.mtx.gz: gene expression count data in Matrix Market Exchange format (raw feature matrix)
aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
detected_tissue_image.jpg.gz: image of tissue and spots
scalefactors_json.json.gz: scalefactors in json format
tissue_hires_image.png.gz: hires image of tissue
tissue_lowres_image.png.gz: low-res image of tissue
tissue_positions_list.cv.gz: list of spatial barcodes and the coordinates specifying spots
GEX_Merged.tif: higher resolution tif of tissue slice
metrix_summary.csv: summary of key sample metrics


title: input-2

library_source: genomic

data_processing:
The libraries were created following the manufacturer's instructions and used with the Illumina NovaSeq 6000 system for 150 nt paired-end sequencing in high-throughput sequencing.
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
ChIP-seq reads were aligned to the GRCh38 genome using Bowtie2. Only uniquely mapping reads with at most four mismatches were retained.
We utilized model-based analysis for ChIP-seq version 1.4 to find the binding locations of MAPK1
The peaks' locations in relation to the transcription start site (TSS) were assigned using DeepTools
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, sonication of cell lysates resulted in DNA fragments of 200-500 bp being centrifuged at   403 12,000g for 10 min.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit. 10 ng of DNA was used as starting material for input and ip samples.

value: input


title: R063, AMD


title: CD138+cells from multiple myeloma_Replicate 1

description: lncRNA and mRMA expression data from bone marrow CD138+ cells of multiple myeloma patient 1

source_name: Bone marrow CD138+ cells,multiple myeloma,replicate 1


title: R056, AMD


title: R057, Control


title: R062, Control


title: R065, Control


title: R055, AMD


title: R064, AMD


title: R053, AMD


title: R054, AMD


title: R061, AMD


title: NC_1

value: AGS cell(control plasmid)


title: R073, AMD


title: R060, Control


title: R050, Control


title: R059, Control


title: R049, Control


title: R048, Control


title: R052, Control


title: R047, AMD


title: R045, AMD


title: R046, AMD


title: R043, AMD


title: R041, AMD


title: R042, Control


title: R040, Control


title: R037, Control


title: R039, AMD


title: R029, Control


title: R035, AMD


title: R031, AMD


title: R032, Control


title: R051, Control


title: R033, Control


title: R028, AMD


title: R026, AMD


title: R023, AMD


title: R025, AMD


title: R022, AMD


title: R024, Control


title: R044, AMD


title: R020, AMD


title: R018, AMD


title: R015, AMD


title: R017, AMD


title: R019, AMD


title: R012, Control


title: R008, AMD


title: R013, AMD


title: R007, AMD


title: R014, AMD


title: R006, AMD


title: R005, AMD


title: R009, Control


title: R003, AMD


title: R001, AMD


title: Sample.6

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
Raw reads were trimmed for adapters, polyA read-through, and low-quality tails (quality <Q20) using BBDuk (version 37.02; sourceforge.net/projects/bbmap/).
Reads were subsequently aligned to the human reference genome (hg38) using STAR (version 2.7.3a; ref Dobin et al., 2013) with default parameters.
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (version 2.0.1; ref Liao et al., 2014) and the Gencode gene annotation for hg38 genome.
Gene counts were normalized to counts per million mapped reads (cpm) using the edgeR package (version 3.28.1; ref Robinson et al., 2010); only genes with a CPM greater than 1 in at least 2 samples were further retained for differential analysis. Differential gene expression analysis was performed using the DESeq function of the DESeq2 package.
Assembly: hg38
Supplementary files format and content: Expression matrix of raw counts for each sample

source_name: MDA-MB 231 cells, sip53

growth_protocol: MDA-MB 231 TNBC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) with DNAse treatment.
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA library construction Kit following manufacturer's protocols.

treatment_protocol: Silencing was performed for 48h.

value: MDA-MB 231

value: TNBC cell line

tag: genotype

value: TP53 knockdown

tag: time


title: Sample.5.S14

source_name: MDA-MB 231 cells, siQ


title: Sample.2.S11


title: R016, Control

value: peripheral blood mononuclear cells


title: TCC_1

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

description:
Test
TCC1

data_processing:
QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. [target gene signal normalized to spike-in ath miR-159a; 2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_ath-miR-159a)]
All the raw data from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).

label: TaqMan probe (FAM-MGB)

source_name: serum

label_protocol: The RT reaction and pre-amplification step were set up according to the recommendations. MiRNAs were reverse transcribed with Megaplex Prime Pools (Human Pools A v2:1; Thermo Fisher Sciences). The miRNA expression profiles were determined with a TaqMan miRNA Array Human Card A (Thermo Fisher Sciences).

extract_protocol: The total RNA was extracted from the serum using the miRNeasy Serum/Plasma Advanced Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: The blood serum was separated by centrifugation at 1800 rpm for 10 min.

value: ovarian clear cell carcinoma

value: blood


title: Sample.3.S12


title: Normal_control_3

description:
Control
NC3

value: healthy donor


title: JCC_15

description:
Test
JCC15


title: Normal_control_1

description:
Control
NC1


title: Normal_control_4

description:
Control
NC4


title: Sip53_25_D7

source_name: MDA-MB 231 cells, sip53 25%

growth_protocol: MDA-MB 231 TNBC cells were maintained in medium 100% amino acids: DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics; and in medium 25% amino acids: DMEM w/o amino acids 75% and DMEM 25%, supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Silencing and cell culture condiotions were performed for 72h.

tag: treatment

value: 25% amino acids


title: Sample.1.S10


title: Normal_control_2

description:
Control
NC2


title: R004, Control


title: JCC_14

description:
Test
JCC14


title: JCC_11

description:
Test
JCC11


title: JCC_13

description:
Test
JCC13


title: Sip53_100_C7

source_name: MDA-MB 231 cells, sip53 100%

value: 100% amino acids


title: SiQ_25_B7

source_name: MDA-MB 231 cells, siQ 25%


title: JCC_12

description:
Test
JCC12


title: Sample.4.S13


title: JCC_9

description:
Test
JCC9


title: SiQ_25_B5


title: JCC_8

description:
Test
JCC8


title: JCC_7

description:
Test
JCC7


title: JCC_10

description:
Test
JCC10


title: SiQ_100_A7

source_name: MDA-MB 231 cells, siQ 100%


title: JCC_4

description:
Test
JCC4


title: JCC_5

description:
Test
JCC5


title: MatBlood_61465

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

data_processing:
The read qualities for each fastq file were accessed with FastQC (V 0.11.9), and low-quality bases and adapters were removed with Trimmomatic.
The sequenced reads were mapped to the bovine reference genome (bosTau 9) with the STAR aligner (V 2.7.0b), generating the genome index with the ARS-UCD1.3 assembly.
Read counts were estimated at the gene level, and the counting was done with featureCounts, part of the Subread software (V 2.0.3).
Assembly: bosTau 9
Supplementary files format and content: tab delimited text file containing raw read counts for each sample.

organism: Bos taurus

source_name: maternal blood

extract_protocol:
Blood and tissues samples were shipped on dry ice to Macrogen Europe (Amsterdam, Netherlands), which performed the RNA extraction, quality control, library preparation, and sequencing. One sample from the heart, one from the gonads, and two from the liver were discarded after quality control because of the rRNA ratio and RIN<7.
Libraries were prepared with Truseq-stranded mRNA for all tissue samples and SMARTer Stranded RNA library for the blood samples, followed by PE100 sequencing with the NovaSeq platform, generating ~30 million raw reads per sample in FASQ format.

value: maternal blood

tag: fetal weight

tag: maternal group

tag: gestational age

value: 42 days


title: JCC_6

description:
Test
JCC6


title: MatBlood_91798


title: MatBlood_93063


title: Sip53_25_D5


title: MatBlood_90232


title: JCC_2

description:
Test
JCC2


title: ControlAD_IL10

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Mathildenstraße 1

country: Germany

institute: UNIVERSITAETSKLINIKUM FREIBURG

description:
The gene expression profile of IL10 stimulated control CD4+ T-cells
R27

data_processing:
Illumina adapter clipping with cutadapt v3.4
Quality trimming with trimmomatic v0.39, mode MAXINFO, target read length 75, strictness 0.5
Transcript quantification with salmon v1.5.2, with gcBias correction, with seqBias correction
Generation of a gene count matrix with tximport v1.20.0, countsFromAbundace = lengthScaledTPM
Minimum expression filtering, normalization and batch correction with edgeR v3.34.1, via filterByExpr, calcNormFactors, cpm functions
Assembly: GRCh38, Ensembl release 97
Supplementary files format and content: Tab-delimited text file with isoform identifiers, raw counts and transcripts per million as output by salmon (“quant.sf.txt” file)
Supplementary files format and content: Tab-delimited text file with raw gene counts for each gene per sample
Supplementary files format and content: Tab-delimited text file with normalized gene counts for each gene per sample (counts per million, TMM normalized)

source_name: IL10 stimulated control CD4+ T-cells

growth_protocol: Patient and control PBMCs were stimulated with irradiated allogeneic PBMCs as feeder cells, PHA (2.5 µg/ml, Remel) and IL-2 in IMDM medium, and split every 2–4 d. A second stimulation round was performed 21 days after the first stimulation.

extract_protocol:
The total RNA was extracted from 3 million CD4+ T-cells by using QIAGEN RNA extraction kit according to the manufacturer instructions.
Library preparation and paired-end, unstranded, 150 bp sequencing. NEBNext RNA First Strand Synthesis Module; NEBNext Ultra Directional Second Strand Synthesis Module

treatment_protocol: CD4+ T-cells derived from the long-term T cell cultures described above were isolated by MACS separation and stimulated or not, for one hour, with IL-10 or IL-21  for activating the STAT3 pathway in T-cells

value: Peripheral blood

value: Healthy donor

tag: stimulation

value: female

value: Purified CD4+ T-cells


title: ControlZw_Unst

description:
The gene expression profile of unstimulated control CD4+ T-cells
R35

source_name: Unstimulated control CD4+ T-cells

value: 23 years

value: unstimulated


title: ControlZw_IL21

description:
The gene expression profile of IL21 stimulated control CD4+ T-cells
R36

source_name: IL21 stimulated control CD4+ T-cells


title: MatBlood_40396


title: JCC_1

description:
Test
JCC1


title: JCC_3

description:
Test
JCC3


title: Sip53_100_C5

value: MDA-MB 231


title: p53MUT

description: 10x Genomics

data_processing:
Fastq generation, alignment to the human genome and gene quantification were performed with 10x Cell Ranger v6.1.1.
The UMI count matrix was used for downstream analysis with Seurat v4.0.4 R package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Breast; Mammary gland

extract_protocol:
Mammary glands from 8 week old virgin female mice were enzymatically digested and single cell suspensions were obtained following a standard protocol. Briefly, mammary glands were digested at 37°C for 1–2 hours in Epi-Cult-B medium (StemCell Technologies Inc) with 600 U/ml collagenase (Sigma Aldrich) and 200 U/ml hyaluronidase (Sigma Aldrich). After lysis of the red blood cells with NH4Cl, the remaining cells were washed with HBSS/0.02% w/v EDTA. Cells were then dissociated with 0.25% w/v trypsin, 0.2% w/v EDTA for 2 min by gentle pipetting, then incubated in 5 mg/ml Dispase II (Sigma Aldrich) plus 1 μg/ml DNase I (Sigma Aldrich) for 5 minutes, followed by filtration through a 40 μM cell strainer (BD Falcon).
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Breast; Mammary gland

value: 8 week old


title: MatBlood_20482


title: ControlAD_Unst

description:
The gene expression profile of unstimulated control CD4+ T-cells
R25


title: ControlAD_IL21

description:
The gene expression profile of IL21 stimulated control CD4+ T-cells
R26


title: MatBlood_11444


title: Liver_91798

source_name: fetal liver

value: fetal liver


title: p53WT

description: 10x Genomics


title: SiQ_100_A5

value: TNBC cell line


title: MatBlood_41439


title: H332L_IL21

description:
The gene expression profile of IL21 stimulated STAT3-LoF (H332L) CD4+ T-cells
R23

value: 18 years

value: male


title: Liver_90232


title: H332L_IL10

description:
The gene expression profile of IL10 stimulated STAT3-LoF (H332L)  CD4+ T-cells
R24


title: Liver_61465


title: H332L_Unst

description:
The gene expression profile of unstimulated STAT3-LoF (H332L) CD4+ T-cells
R22

source_name: Unstimulated STAT3-LoF (H332L) CD4+ T-cells


title: LN95X285K_DoxP_R_21

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HiSAT2 aligner (v2.1.0).
gene count measurements were obtained using FeatureCounts using gencode v24 annotation.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file with columns: 1) GeneID, 2) Chr; 3) transcript start position; 4) transcript end position; 5) Strand; 6) Length of transcript; 7) read counts

source_name: LNCap95 with exogenous X285K variant

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN#74104) and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run with 100bp paired-end sequencing protocol.

treatment_protocol: Cells were treated with indicated concentrations of doxycycline (Dox, Sigma, # D9891) for 72 hours. At the 72-hour timepoint, 1 nM synthetic androgen methyltrienolone (R1881, PerkinElmer, #NLP0050) was added (for R1881-untreated samples, an equal volume of ethanol was added) and cells were incubated for an additional 24 hours. At 96-hour timepoint, cells were lysed in TRIzol reagent (Invitrogen#15596018).

value: Prostate cancer cell line

tag: clone #

tag: hoxb13 stable line

tag: dox

value: DOX(+)

tag: r1881 treatment


title: MatBlood_20488

value: maternal blood


title: LN95X285K_DoxP_21

tag: cell line

tag: cell type


title: Liver_41439

tag: tissue

value: 42 days


title: Liver_40396


title: Q288P_1_1_IL10

description:
The gene expression profile of IL10 stimulated STAT3-Q288P CD4+ T-cells
R21

value: Peripheral blood

tag: age

value: 12 years

tag: Sex


title: LN95X285K_DoxN_R_21

value: DOX(-)


title: Liver_20488


title: Gonad_93063

source_name: fetal testicle

value: fetal testicle


title: Liver_11002


title: LN95X285K_DoxP_16


title: Q288P_1_1_IL21

description:
The gene expression profile of IL21 stimulated STAT3-Q288P CD4+ T-cells
R20

value: Purified CD4+ T-cells


title: LN95X285K_DoxN_21


title: MatBlood_11002


title: Gonad_91798


title: Gonad_90232


title: Gonad_61465


title: LN95X285K_DoxP_R_16


title: LN95X285K_DoxN_R_16


title: Q280P_IL10

description:
The gene expression profile of IL10 stimulated STAT3-Q280P CD4+ T-cells
R18

value: 8 years

value: female


title: Gonad_40396


title: Gonad_20488


title: LN95X285K_DoxN_16


title: Q280P_IL21

description:
The gene expression profile of IL21 stimulated STAT3-Q280P CD4+ T-cells
R17


title: Gonad_20482


title: Q280P_Unst

description:
The gene expression profile of unstimulated STAT3-Q280P CD4+ T-cells
R16

source_name: Unstimulated STAT3-Q280P CD4+ T-cells

value: unstimulated


title: Liver_11444


title: Heart_91798

source_name: fetal heart

value: fetal heart


title: LN95X285K_DoxP_12


title: E415L_IL10

description:
The gene expression profile of IL10 stimulated STAT3-E415L CD4+ T-cells
R15

value: 6 years


title: Gonad_11444


title: Heart_90232


title: Heart_41439


title: LN95X285K_DoxN_R_12


title: Heart_61465


title: Heart_40396


title: Heart_20488


title: E415L_IL21

description:
The gene expression profile of IL21 stimulated STAT3-E415L CD4+ T-cells
R14


title: LN95X285K_DoxN_12


title: Heart_20482


title: T716M_IL10

description:
The gene expression profile of IL10 stimulated STAT3-T716M CD4+ T-cells
R12

value: 9 years


title: Heart_11444


title: LN95WT_DoxP_R_39

source_name: LNCap95 with exogenous WT HOXB13


title: Heart_11002


title: T716M_IL21

description:
The gene expression profile of IL21 stimulated STAT3-T716M CD4+ T-cells
R11


title: Adult Brain, Rescue, Rep. 4

city: Laramie

first: Todd

last: Schoborg

state: Wyoming

address: 1000 E. University Ave, Department of Molecular Biology, #3944

department: Molecular Biology

institute: University of Wyoming

data_processing:
Raw sequencing reads were trimmed and filtered using FastQC and Cutadapt with length cutoff of 20 nt
reads were mapped to the Drosophila melanogaster reference genome (dm6) using the RSubread package
Gene expression levels were estimated using FeatureCounts software with default settings
Differential gene expression (DGE) analysis was performed using the EdgeR Bioconductor package, filtering for CPM <1
Genes with a logF.C. ≥ 0.5/≤-0.5 and an adjusted P-value ≤0.05 were assigned as differentially expressed
Assembly: dm6
Supplementary files format and content: tab delimited text file includes raw counts for each sample from FeatureCounts
Supplementary files format and content: tab delimited text file includes logFC, logCPM, F, Pvalue, and FDR for each genotype comparison computed using EdgeR

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: Animals were maintained at 25C on cornmeal-agar; brains were dissected in fresh SF900 cell culture media.

extract_protocol:
Trizol prep, DNAse Treatment (Turbo DNAse)
Per Novogene's polyA enrichment library preparation protocol

value: Brain

tag: developmental stage

value: adult

value: AspMF; AspT25/AspDf


title: Gonad_11002


title: Adult Brain, Rescue, Rep. 3

tag: genotype


title: Adult Brain, Rescue, Rep. 2


title: LN95X285K_DoxP_R_12

value: Prostate cancer cell line

value: DOX(+)


title: LN95WT_DoxP_39


title: T716M_Unst

description:
The gene expression profile of unstimulated STAT3-T716M CD4+ T-cells
R10

source_name: Unstimulated STAT3-T716M CD4+ T-cells


title: LN95WT_DoxN_R_39


title: Adult Brain, Rescue, Rep. 1


title: P715L_IL10

description:
The gene expression profile of IL10 stimulated STAT3-P715L CD4+ T-cells
R09

value: 30 years

value: male


title: Adult Brain, Asp Mutant, Rep. 4


title: E415L_Unst

description:
The gene expression profile of unstimulated STAT3-E415L CD4+ T-cells
R13

source_name: Unstimulated STAT3-E415L CD4+ T-cells

value: Peripheral blood


title: LN95WT_DoxP_R_38


title: P715L_IL21

description:
The gene expression profile of IL21 stimulated STAT3-P715L CD4+ T-cells
R08


title: Adult Brain, WT, Rep. 4


title: Adult Brain, Asp Mutant, Rep. 1


title: Adult Brain, Asp Mutant, Rep. 2


title: P715L_Unst

description:
The gene expression profile of unstimulated STAT3-P715L CD4+ T-cells
R07

source_name: Unstimulated STAT3-P715L CD4+ T-cells


title: LN95WT_DoxP_38


title: Adult Brain, WT, Rep. 3


title: Adult Brain, WT, Rep. 2


title: ControlM_IL10

description:
The gene expression profile of IL10 stimulated control CD4+ T-cells
R06

value: Healthy donor


title: LN95WT_DoxN_R_38

value: DOX(-)


title: ControlM_IL21

description:
The gene expression profile of IL21 stimulated control CD4+ T-cells
R05

value: Purified CD4+ T-cells


title: Adult Brain, WT, Rep. 1


title: Pupal Brain, Rescue, Rep. 4

value: pupal


title: ControlM_Unst

description:
The gene expression profile of unstimulated control CD4+ T-cells
R04

value: female


title: Pupal Brain, Rescue, Rep. 3


title: Adult Brain, Asp Mutant, Rep. 3


title: LN95WT_DoxN_38


title: LN95WT_DoxN_39


title: Pupal Brain, Rescue, Rep. 2


title: Pupal Brain, Rescue, Rep. 1


title: LN95WT_DoxP_R_33


title: ControlS_IL10

description:
The gene expression profile of IL10 stimulated control CD4+ T-cells
R03

value: 45 years


title: Pupal Brain, Asp Mutant, Rep. 4


title: Q288P_1_1_Unst

description:
The gene expression profile of unstimulated STAT3-Q288P CD4+ T-cells
R19

source_name: Unstimulated STAT3-Q288P CD4+ T-cells

value: 12 years

value: unstimulated


title: LN95WT_DoxP_33


title: Pupal Brain, Asp Mutant, Rep. 2


title: NaOH_T4 3

city: REHOVOT

first: NITYANAND

last: BOLSHETTE

address: HRZL STREET

department: Biomolecular sciences

country: Israel

institute: Weizmann Institute of sciences

data_processing:
Reads were trimmed using cutadapt  (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25)
Reads were mapped to mouse genome (mm10) using STAR  v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No)
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count  in union mode.
Further analysis is done for genes having minimum 5 read in at least one sample
Normalization of the counts and differential expression analysis was performed using DESeq2  with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files containing the raw counts for each gene and sample

source_name: Embryonic fibroblasts (NIH3T3)

growth_protocol: NIH3T3 grown in 6cm dish at density of 3x105 cells in DMEM (Biological Industries, 01-055-4A) diluted with 1X with dionized water, supplimented with 10% FBS, 4mM L-Glutamine, 100 units/mL penicillin, and 100 mg/mL streptomycin with 18 mM sodium bicarbonate

extract_protocol:
Standered Trizol (Sigma Industries) reagent protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On the day 4 of the plating, 4 replicates of each either untreated or received low CO2 exposure (1%), 18mM NaOH for 0h, 2h, 4h.


title: ControlS_Unst

description:
The gene expression profile of unstimulated control CD4+ T-cells
R01


title: Pupal Brain, Asp Mutant, Rep. 1


title: Pupal Brain, WT, Rep. 4


title: ControlS_IL21

description:
The gene expression profile of IL21 stimulated control CD4+ T-cells
R02


title: LN95WT_DoxP_26


title: NaOH_T4 1


title: NaOH_T4 2


title: WT_IgECLIL33_ATAC rep1

city: Denver

first: HUA

last: HUANG

state: Colorado

address: 1400 Jackson street, K511

department: Immunology and Genomic Medicine

institute: National Jewish Health

data_processing:
Raw sequencing reads (average 80 million paired-end reads, 2 biological replicates for each treatment) were aligned to the hg38 reference genome using Bowtie2 with very-sensitive and -x 2000 parameters.
The read alignments were filtered using SAMtools to remove mitochondrial genome and PCR duplicates.
Peaks were identified by MACS2 with the q-value cut-off of 0.05
Genome_build: hg38
Supplementary_files_format_and_content: Tdf and bedgraph files for each sample

source_name: HSMCs

growth_protocol: Cells enriched by Percoll density-dependent sedimentation were adjusted to a concentration of 1 × 106 cells/ml in serum-free X-VIVOTM 15 medium (Lonza BioWhittaker) containing 100 ng/ml recombinant human SCF (Peprotech) in 24-well plates. The culture medium was changed weekly and wells were split when cell concentration doubled. The percentages of mast cells were assessed cytochemical by metachromatic staining with toluidine blue. Mature mast cells at ~ 100% purity and viability are obtained by 6-8 wk of culture, and 8- to 16-wk-old mast cells were used in these experiments.

extract_protocol:
Briefly, 50,000 HSMCs that were either untreated or treated with IgE receptor crosslinking were spin down and washed with cold PBS once. Then the cells were resuspended in 50 uL cold ATAC-RSB-lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin) and incubated for 3 minutes. The lysis buffer was immediately washed out with 1 mL ATAC-RSB buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% Tween-20). The cell pellet was resuspended in 50 ul transposition mixture (25 uL 2X TD buffer, 2.5 uL transposase (Illumina, FC-121-1030), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O) and incubated at 37 C for 30 minutes. The reaction was stopped by adding 2.5 uL of 0.5M EDTA pH 8 and transposed DNA was purified using Qiagen MiniElute PCR purification kit (Qiagen).
Purified DNA was amplified using the following condition: 72℃ for 5 min, 98 ℃ for 30 s, and 7 cycles: 98 ℃ for 10 s, 63 ℃ for 30 s, 72 ℃ for 1 min. The amplified libraries were cleaned up, size-selected, and the quality and quantity of libraries were assessed on 4150 TapeStation System (Agilent, CA).

treatment_protocol: IgE receptor cross-linking (IgECL) on HSMCs was accomplished through sensitization with 1 μg/mL chimeric human IgE anti-NP antibody (MCA333S, BIO-RAD, Hercules, CA) for 24 hours. The sensitized hSMCs were challenged with 100 ng/mL NP-HSA (N-5059, LGC, Petaluma, CA) for 2 additional hours.  For single or combined cytokine and IgECL treatments, IL-33 (50 ng/mL, 200-33, PEPROTECH, Cranbury, NJ) was added to hSMCs for a total of 26 hours.

tag: cells

value: Human skin mast cells

value: Skin biopsy

value: IL33, IgE anti-NP and NP-HSA


title: LN95WT_DoxP_R_26


title: Pupal Brain, WT, Rep. 3

value: Brain


title: NaOH_T4 4

tag: treatment


title: NaOH_T2 1


title: Pupal Brain, WT, Rep. 2


title: Pupal Brain, WT, Rep. 1


title: LN95WT_DoxN_R_26

value: Prostate cancer cell line


title: WT_IgECL_ATAC rep1

value: IgE anti-NP and NP-HSA


title: WT_IL33_ATAC rep2


title: NaOH_T2 2


title: LN95WT_DoxN_R_33


title: Larval Brain, Rescue, Rep. 4

value: larval

value: AspMF; AspT25/AspDf


title: LN95WT_DoxN_33


title: LN95WT_DoxN_26


title: NaOH_T2 3


title: WT_IgECLIL33_ATAC rep2


title: LN95WT_DoxP_19

value: DOX(+)


title: Larval Brain, Rescue, Rep. 3


title: WT_IL33_ATAC rep1


title: NaOH_T2 4


title: LN95WT_DoxP_R_19


title: 1% CO2_T4 2

description: 1% CO2_T4


title: Larval Brain, Rescue, Rep. 1


title: LN95WT_DoxN_R_19


title: WT_IgECLIL33TSLPIL25_RNA rep1

description: HSMCs_4IgE_VS_2IgEIL33IL25TSLP_gene_exp.diff

data_processing:
The raw reads were analyzed and quality checked by FastQC.
The reads were aligned to the hg38 reference genome using the Spliced Transcripts Alignment to a Reference (STAR, version 2.4.0.1) software
The aligned reads were assembled into reference transcripts using Cufflinks (version 2.2.1). The differential gene expression between the resting and stimulated samples was analyzed using Cuffdiff (Trapnell et al., 2012).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample .

extract_protocol:
Total RNA was extracted from HSMCs that were untreated, treated with various stimuli using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacture’s protocol. The quality of input RNA was analyzed by running the RNA sample on 4150 TapeStation System (Agilent, CA)
PolyA mRNA was isolated using the NEBNext® Poly(A) mRNA magnetic isolation module (E7490, New England Biolabs, Ipswich, MA). RNA-seq libraries were obtained using the NEB-Next® UltraTM II RNA library prep kit for Illumina® (E7770S, New England Biolabs, Ipswich, MA). The isolated mRNA was fragmented, reverse transcribed into cDNA, end-repaired, and adapter-ligated. The ligated samples were digested by USER enzyme, amplified by PCR and purified using AMPure-XP beads (Beckman Coulter Life Sciences, A63881, Indianapolis, IN). The quantity and quality of RNA libraries were assessed on an Agilent Technologies 2100 Bioanalyzer.

treatment_protocol: IgE receptor cross-linking (IgECL) on HSMCs was accomplished through sensitization with 1 μg/mL cells chimeric human IgE anti-NP antibody (MCA333S, BIO-RAD, Hercules, CA) for 24 hours. The sensitized hSMCs were challenged with 100 ng/mL NP-HSA (N-5059, LGC, Petaluma, CA) for 2 additional hours.  For single or combined cytokine and IgECL treatments, IL-33 (50 ng/mL, 200-33, PEPROTECH, Cranbury, NJ), TSLP (50 ng/mL, 300-62, PEPROTECH, Cranbury, NJ) or IL-25 (50 ng/mL, 200-24, PEPROTECH, Cranbury, NJ) were added to hSMCs for a total of 26 hours.

value: IL33, IL25,TSLP, IgE anti-NP and NP-HSA


title: Larval Brain, Rescue, Rep. 2


title: WT_IgECLIL33TSLPIL25_RNA rep2


title: WT_IgECL_ATAC rep2


title: LN95WT_DoxN_19

value: DOX(-)


title: 1% CO2_T4 1

description: 1% CO2_T4


title: LN95NT_DoxP_5

source_name: LNCap95 with endogenous WT HOXB13


title: WT_IL33TSLPIL25_RNA rep2

description: HSMCs_4UN_VS_2IL33IL25TSLP_gene_exp.diff

value: IL33, IL25 and TSLP


title: 1% CO2_T4 4

description: 1% CO2_T4


title: Larval Brain, Asp Mutant, Rep. 3


title: LN95NT_DoxP_R_5


title: WT_IL33TSLPIL25_RNA rep1


title: 1% CO2_T4 3

description: 1% CO2_T4


title: WT_IgECLIL25_RNA rep2

value: IL25, IgE anti-NP and NP-HSA


title: LN95NT_DoxN_R_5


title: Larval Brain, Asp Mutant, Rep. 2


title: 1% CO2_T2 4

description: 1% CO2_T2


title: WT_IgECLIL25_RNA rep1


title: 1% CO2_T2 1

description: 1% CO2_T2


title: LN95NT_DoxN_5


title: Larval Brain, Asp Mutant, Rep. 1


title: WT_IgECLTSLP_RNA rep2

value: TSLP, IgE anti-NP and NP-HSA


title: Larval Brain, WT, Rep. 4


title: LN95NT_DoxP_4


title: 1% CO2_T2 3

description: 1% CO2_T2


title: 1% CO2_T2 2

description: 1% CO2_T2


title: Larval Brain, Asp Mutant, Rep. 4


title: WT_IgECLIL33_RNA rep2


title: 5% CO2_T0 3

description: 5% CO2_T0

value: no


title: Larval Brain, WT, Rep. 3


title: LN95NT_DoxN_R_4


title: LN95NT_DoxN_4


title: Larval Brain, WT, Rep. 2


title: 5% CO2_T0 1

description: 5% CO2_T0


title: WT_IL25_RNA rep2


title: LN95NT_DoxP_15


title: 5% CO2_T0 4

description: 5% CO2_T0


title: WT_IL25_RNA rep1


title: 5% CO2_T0 2

description: 5% CO2_T0


title: LN95NT_DoxP_R_4


title: LN95NT_DoxN_R_15


title: LN95NT_DoxP_R_15


title: WT_TSLP_RNA rep2

value: TSLP


title: hopx_dam3

city: Wooloongabba

first: Seth

last: Cheetham

state: QLD

address: Level 4, 37 Kent St

country: Australia

institute: Mater Research Institute-University of Queensland

data_processing:
Reads were aligned to hg38 using bowtie2
Reads were binned into GATC fragments
Reads were binned into GATC fragments using the damidseq_pipeline
The ratio of WT to HOPX KD reads was calculated using the damidseq_pipeline normalized to reads per million.
The ratios were averaged and peaks were called using the DamID peak caller with the specification –frac=500000, FDR<0.01, fold-change>2 (https://github.com/owenjm/find_peaks)
Assembly: hg38
Supplementary files format and content: wild type and hopx knockdown enriched peaks in BED format
Supplementary files format and content: wild type and hopx knockdown enriched regions in BEDgraph format
Library strategy: DamID-seq

source_name: cardiomyocytes

extract_protocol:
DamID seq (Marshall et al., Nat. Protoc., 2016)
NEB UltraII for Illumina

value: cardiomyocytes

value: HOPX-knockdown


title: WT_IgECLIL33_RNA rep1

value: Human skin mast cells

value: Skin biopsy


title: hopx_dam1


title: hopx_dam2


title: WT_TSLP_RNA rep1


title: wt_dam3

value: mock


title: WT_IgECLTSLP_RNA rep1


title: Ctrl_TILs

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

data_processing:
processed with 10X standardard cellranger (3.0.2) pipeline reference (cellranger-mm10-3.0.0) using STAR aligner (version 2.6)
Assembly: cellranger-mm10-3.0.0
Supplementary files format and content: standard output of cellranger with gzipped barcode, features (gene), and Unique Molecular Identifier (UMI)

source_name: Endogenous TILs from Ctrl group

extract_protocol:
IRF4-GFP or GFP-control-transduced Pmel-1 cells were used to treat B16-F10 melanoma three days after tumor implantation. Fourteen days after tumor implantation, tumor-infiltrating IRF4-GFP and GFP-control-transduced Pmel-1 cells, as well as endogenous CD45+ TILs from both the IRF4 and control groups, were sorted using a cell sorter.
The Single Cell Gene Expression Library was prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3 (10x Genomics)
A single nucleus suspension, reverse transcription reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded onto a Chromium controller (10x Genomics) to generate single cell GEMs (Gel Beads-In-Emulsions), where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMs were broken, and cDNA from each single cell was pooled. After cleanup using Dynabeads MyOne Silane Beads, the cDNA was amplified by PCR. The amplified product was fragmented to an optimal size before undergoing end-repair, A-tailing, and adaptor ligation. The final library was generated through amplification, and its quantity was determined using the KAPA Library Quantification kit (Roche)

tag: strain

value: B16F10 Tumor

value: CD45+ cells


title: Larval Brain, WT, Rep. 1

value: Brain

value: larval


title: wt_dam2


title: Ctrl_Pmel

source_name: Control GFP Pmel-1

value: CD8+ T cells


title: WT_IL33_RNA rep2


title: M238_ERKi+IFNg_expt_2

city: Los Angeles

first: Ameya

last: Champhekar

state: California

address: 700 Tiverton Ave, 11-272 Factor Bldg

department: Medicine, HemOnc Division

institute: University of California, Los Angeles

data_processing:
Sequencing was performed on Illumina HiSeq 3000 for Single-End 1 x 50 bp run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
Raw FASTQ files were aligned to the GRCh38 genome using HISAT2 version 2.1.0 using default parameters.
Gene expression was quantified by HTseq-counts version 0.6.1p1 and Stringtie version v1.3.3b, outputting counts and FPKM (Fragments Per Kilobase per Million) respectively.
Assembly: GRCh38
Supplementary files format and content: Tab delimited file containing raw counts for all samples
Supplementary files format and content: Tab delimited file containing FPKM values for all samples

growth_protocol: M230 and M238 cells were cultured in RPMI supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES, and antibiotic and antimycotic agents. Cultured cells were grown in a 37C incubator with 5% CO2.

extract_protocol:
Cell pellets were solubilized in TRIzol and the RNA containing aqueous phase obtained after chloroform addition was applied to RNeasy (Qiagen) columns. Total RNA was eluted in 50 µl UltraPure water (Invitrogen) after following standard RNeasy kit protocol.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit with RiboErase Kit following the recommended kit protocol.

treatment_protocol: Cells were plated a day ahead of treatment with DMSO (control), recombinant Human IFNg (Peprotech, 100 U/ml) and/or Ulixertinib (SelleckChem, 6 µM). Cells were harvested 24 hours later and total RNA was prepared for RNAseq.

value: Melanoma cell line

value: ERKi+IFNg


title: IRF4_TILs

source_name: Endogenous TILs from IRF4 group


title: WT_IL33_RNA rep1


title: wt_dam1


title: M238_ERKi_expt_2

value: ERKi


title: IRF4_Pmel

source_name: IRF4 transdeuced Pmel-1


title: M238_DMSO+IFNg_expt_2

value: DMSO+IFNg


title: NUP93-shD

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark St

institute: Northwestern University

data_processing:
Reads were aligned using HISAT2. Alignments were quality filtered using samtools. Counting mapped reads was done using HTSeq count. DESeq2 was used to determine differential expression.
Assembly: hg19
Supplementary files format and content: RNA-seq data analysis is presented in a table format with normalized counts data for each gene and DESeq2 output information.

source_name: Foreskin

growth_protocol: Prior to treatment, keratinocytes were cultured in keratinocyte SFM and Cascade Biologics Medium 154 supplemented with Human keratinocyte Growth supplement, antibiotic antibiotic-antimycotic, and antibiotic penicillin streptomycin. Cells were grown at 37 C, 5% CO2 and maintained under 60% confluency at all times.

extract_protocol:
RNA was extracted and DNase treated using the Quick-RNA Miniprep Kit by Zymo Research.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina was used to prepare RNA-seq libraries.

treatment_protocol: For shRNA-mediated knockdown, keratinocytes were seeded to 20% confluency prior to spin infection. shRNA lentivirus was diluted and added to keratinocytes along with 20 ug/mL of polybrene. Spin infection was performed at 32 C,  1250 rpm for 1 hour. The infected keratinocytes were then washed gently with PBS twice and keratinocyte media was added. One day post infection, cells were split to maintain confluency below 60%. Two days post infection, 2 ug/mL of puromycin was added to infected cells. Puromycin selection was done for 48 hours. Two days post puromycin selection, the cells were collected.

value: human keratinoctyes

value: primary human neonatal keratinocytes

value: Foreskin

value: NUP93 shRNA


title: Tcf7WT-Tcrgd

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

data_processing:
Raw 10x Chromium scRNA-seq data were quantified using the cellCounts function in Bioconductor package Rsubread (ver 2.3.6). Sequencing reads were mapped to the GRCm38/mm10 reference genome. Mapped reads were deduplicated and counted to the NCBI mouse RefSeq genes (build 38.1) to produce unique molecular identifier (UMI) counts for each gene in each cell. Genes that failed to express in at least three cells in at least one sample were excluded from analysis. An expressed gene in a cell has at least one UMI count. Mitochondrial genes, ribosomal genes and genes with no known symbols were all excluded from analysis. Cells were excluded from analysis if they expressed < 200 genes or > 2500 genes, or had > 20% of mitochondrial gene content, or had > 40% of ribosomal gene content. Seurat (version 3.0.0) was used to perform t-distributed stochastic neighbour embedding (t-SNE) dimension reduction and unsupervised cell clustering.
The unsupervised cell clustering was performed by using shared nearest neighbour (SNN) modularity optimisation with a resolution parameter of 0.5 and nearest neighbour number of 20.
Assembly: mm10
Supplementary files format and content: zipped sparse matrix files (in the Matrix Market format) of UMI counts

source_name: intraepitehlial lymphocytes (IELs)

extract_protocol:
IELs were extracted from mice colons and sorted leukocytes were then loaded onto to the 10X ChromiumTM Single Cell 3’ Chip to be encapsulated forming Gel Beads in Emulsion (GEM) and cDNA was generated as per 10X genomics protocol.
Single cell RNA sequencing libraries were prepared according to 10X Genomics protocol and using the ChromiumTM Single Cell 3’ Library and Gel Bead Kit (v2)

value: Colon

value: Live CD3+ TCRgamma+ CD8alpha+


title: WT_IgECL_RNA rep3

value: Human skin mast cells

value: Skin biopsy

value: IgE anti-NP and NP-HSA


title: Tcf7KO-Tcrgd


title: NUP93-shC


title: M238_DMSO_expt_2

value: DMSO


title: M238_ERKi+IFNg_expt_1


title: NUP93-shB


title: Tcf7WT-Tcrb

value: Live CD3+ TCRbeta+ CD8alpha+


title: WT_IgECL_RNA rep1


title: LN95NT_DoxN_15

value: Prostate cancer cell line

value: DOX(-)


title: WT_IgECL_RNA rep2


title: NUP93-shA


title: WT_UN_RNA rep4


title: CTRL-shRNA2

value: Ctrl shRNA


title: M238_DMSO+IFNg_expt_1

value: Melanoma cell line


title: WT_UN_RNA rep3


title: WT_IgECL_RNA rep4


title: M238_DMSO_expt_1


title: Stomach-IEL

data_processing:
Raw 10x Chromium scRNA-seq data were quantified using the cellCounts function in Bioconductor package Rsubread (ver 2.3.6). Sequencing reads were mapped to the GRCm38/mm10 reference genome. Mapped reads were deduplicated and counted to the NCBI mouse RefSeq genes (build 38.1) to produce unique molecular identifier (UMI) counts for each gene in each cell. Genes that failed to express in at least three cells in at least one sample were excluded from analysis. An expressed gene in a cell has at least one UMI count. Mitochondrial genes, ribosomal genes and genes with no known symbols were all excluded from analysis. Cells were excluded from analysis if they expressed < 200 genes or > 2500 genes, or had > 20% of mitochondrial gene content, or had > 40% of ribosomal gene content. Seurat (version 3.0.0) was used to perform t-distributed stochastic neighbour embedding (t-SNE) dimension reduction and unsupervised cell clustering.
The unsupervised cell clustering was performed by using shared nearest neighbour (SNN) modularity optimisation with a resolution parameter of 0.5 and nearest neighbour number of 20.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

extract_protocol:
IELs were extracted from mice colons and sorted CD45.2+ leukocytes were then loaded onto to the 10X ChromiumTM Single Cell 3’ Chip to be encapsulated forming Gel Beads in Emulsion (GEM) and cDNA was generated as per 10X genomics protocol.
Single cell RNA sequencing libraries were prepared according to 10X Genomics protocol and using the ChromiumTM Single Cell 3’ Library and Gel Bead Kit (v2)

value: Stomach

value: Live CD45+ cells

tag: infection


title: WT_UN_RNA rep2


title: Small_Intestine-IEL

value: Small intestine


title: M230_ERKi+IFNg_expt_2

value: ERKi+IFNg


title: Colon-IEL


title: WT_UN_RNA rep1


title: Differentiated si-Eya3#2-3

city: Chapel Hill

first: Jimena

last: Giudice

state: NC

address: 6340B MBRB, Campus Box 7545

department: Cell Biology and Physiology

institute: UNC - Chapel Hill

data_processing:
Sequenced reads were aligned to the mm10 genome with STARv2.7.6a
Gene counts were generated using Salmonv1.4.0
Differential gene expression was determined using DESeq2
Assembly: mm10

source_name: C2C12 myoblasts

extract_protocol:
RNA was extracted following 96hr of differentiation
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: myoblasts/myotubes

value: myotubes

tag: biological replicate


title: M230_ERKi_expt_2

value: ERKi


title: M238_ERKi_expt_1


title: Tcf7KO-Tcrb

value: Colon


title: Differentiated si-Eya3#1-3


title: Cecum-IEL

value: Cecum


title: Tcrd.KO.BigTumor, S14

data_processing:
Sequencing reads were mapped to GRCm38/mm10 reference genome using the Subread aligner in the Rsubread package. Only uniquely mapped reads were retained. Gene-wise read counts were obtained using the featureCounts program included in the Rsubread package. Only genes that achieved a CPM (counts per million) value greater than 0.5 in at least two samples and had known symbols were included in the downstream analysis. Predicted genes (gene names starting with “Gm”), ribosomal genes and genes on chromosomes X and Y were removed from analysis.
Counts were converted to log2-CPM, quantile-normalized, and precision-weighted with the voom function in the limma package. Log2-CPM values were then converted to log2-FPKM (Fragments Per Kilobases per Million) values. A linear model was fitted to each gene to estimate expression levels of genes, which were then used to compute log2 fold changes of gene expression. GSEA was used to discover enriched Hallmark pathways included in the MSigDB database.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts_bulkRNA.txt, includes raw read counts for genes in each sample (sample 4 and its tech replicate were merged).

source_name: epithelial cells

growth_protocol: Tumors were induced by AOM-DSS

extract_protocol:
Live Epcam+ epithelial cells were extracted from mouse tumors and RNA was isolated from epithelial cells for Nextseq sequencing using 150cyc High output kit (400M).
Libraries were generated following the manufacturer's protocol.

treatment_protocol: Tumors were collected after 8-12 weeks following AOM-DSS treatment.

value: Tcrdko

value: colon tumors

value: Live Epcam+ cells


title: siMETTL3_3_input

city: Shanghai

first: Xiao

last: Han

state: Select state...

address: 399 Wanyuan Rd, Minhang, Shanghai, China

institute: Children’s Hospital of Fudan University

data_processing:
library strategy: meRIP-seq
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.Meanwhile, Use the SortMeRNA software for ribosomal RNA reads removal.After discarded the rRNA reads, the remainly clean reads were mapped to the reference genome GRCh38.p12 using HISAT2 with default parameters. Unique reads with high mapping quality were retained
The m6A-enriched peaks in each m6A immunoprecipitation sample were identified by MeTDiff peak calling software with the corresponding input sample serving as control. MeTDiff was run with options (‘FRAGMENT_LENGTH=200,PEAK_CUTOFF_PVALUE = 0.05, PEAK_CUTOFF_FDR = 0.05’) for peak detection. Called peaks were annotated by intersection with gene architecture using ChIPseeker
Differential analysis for m6A-Seq identifies differences in RNA methylome in a case-control study, The differential peak were detected by MeTDiff with parameter  (‘FRAGMENT_LENGTH = 200, PEAK_CUTOFF_PVALUE = 0.01,DIFF_PEAK_CUTOFF_FDR = 0.05, PEAK_CUTOFF_FDR = 0.05’), after which,differential peak were annotated by ChIPseeker
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: peak text files of every group
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every input sample

source_name: human macrophages

growth_protocol: Human THP1 cell lines (purchased from the American Type Culture Collection (ATCC), USA) were maintained in RPMI-1640 medium, 10% heat-inactivated FBS. To generate macrophage-like cells, THP-1 cell were seeded along with 200 nM PMA for 48 h. Cells were incubated at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
We utilized input and post m6A-IP positive fraction for library construction utilizing the Illumina TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: THP1-derived macrophages were transfected with METTL3 siRNA pools or control siRNA for 48 h. Then, macrophages were stimulated with  IL-4 (20 ng/ml)  for 24 h.

value: THP1 monocyte cell line -derived macrophages

value: transfected with METTL3 siRNA pools for 48 h.

tag: rip antibody


title: M230_DMSO+IFNg_expt_2

value: DMSO+IFNg


title: siMETTL3_3

value: Anti-m6A (Synaptic Systems, Cat. No 202 003)


title: M230_DMSO_expt_2

value: DMSO


title: siMETTL3_2_input


title: Differentiated si-Ctrl-3 (EYA3 control)

value: si-Ctrl


title: Differentiated si-Eya3#2-2


title: M230_ERKi+IFNg_expt_1

value: Melanoma cell line


title: Tcrd.KO.SmallTumor, S12


title: Differentiated si-Eya3#1-2


title: CTRL-shRNA1

value: human keratinoctyes

value: primary human neonatal keratinocytes

value: Foreskin

value: Ctrl shRNA


title: siMETTL3_2


title: Tcrd.KO.SmallTumor, S11


title: Differentiated si-Ctrl-2 (EYA3 control)

value: myotubes


title: M230_ERKi_expt_1

value: ERKi


title: CA.WT.Tumor, S10

value: WT


title: M230_DMSO+IFNg_expt_1


title: Differentiated si-Eya3#2-1


title: Differentiated si-Eya3#1-1


title: CA.WT.Tumor, S9


title: CA.WT.Tumor, S8


title: siMETTL3_1


title: siNC_2

value: transfected with  control siRNA for 48 h.


title: M230_DMSO_expt_1


title: Differentiated si-Ctrl-1 (EYA3 control)

source_name: C2C12 myotubes


title: 311E cell line 9nM ABBV075 96hr H3K27ac rep 2 Experiment 2

city: Boston

first: Chris

last: French

state: MA

address: 77 avenue louis Pasteur, NRB 652

department: Pathology

institute: Brigham and Women's Hospital

description:
23122FL-07-02-06
311E_abbv_k27ac_subtract_igg_2.tdf

data_processing:
library strategy: CUT&RUN
Reads were trimmed for adaptor sequences using trimmomatic v0.36 and then aligned to concatenated mm39/Genome Reference Consortium mouse Reference 39 (GRCm39) assembly of the human genome, using bowtie2 v2.3.1 with options --local --very-sensitive-local --no-unal --nomixed --no-discordant --phred33. Only reads with a MAPQ ≥ 30 were retained using samtools v1.3.1. PCR duplicates were removed with picard MarkDuplicates v2.9.2. Coverage-based tracks were generated with deepTools bamCoverage with options --binSize 1 -normalizingUsing RPGC --effectiveGenomeSize 2800000000 -extendReads --samFlagInclude 64. CUT&RUN profiles were then calibrated by spike-in normalization using the E. Coli DNA as the internal reference using a similar method as that done for ChIP-seq[25]. Specifically, the Occupancy Ratio (OR) was calculated as the product of IgG spike-in reads and immunocleaved (IC) human reads, divided by the product of IgG human reads and IC spike-in reads. Spike-in normalized tracks were generated with deepTools bamCoverage with options --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2800000000 --extendReads --samFlagInclude 64 --scaleFactor OR.epic2 v0.0.52 was used for domain calling on the canonical human chromosomes with options --bin-size 200 --gaps-allowed 5 with the corresponding IgG library set as the control. Called domains were filtered by signal strength and by domain size using the ROSE algorithm (Rank Ordering of Super-Enhancers)[26]. Domains that exceeded both the signal cutoff and the size threshold were retained. We frequently observed closely spaced filtered domains that corresponded to larger domains based on CUT&RUN signal tracks. To span and capture these regions filtered domains within 25 kb of one another were combined. A high confidence list of “megadomains” was created by merging filtered domains identified in both logical replicates.
Assembly: GRCm39/mm39

source_name: 311E cell line

growth_protocol: DMEM, 10% fetal bovine serum, 1x glutamax, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 0.1% formaldehyde for 1 minute. Tissue was fixed with 0.2% formaldehyde for 2 minutes. Cells were bound to Con-A beads and incubated overnight with target antibodies. Bead bound cells were washed and incubated with pAG-MNase for 60 minutes at 4degC before being washed and incubated with CaCl2 to activate MNase. Reaction was stopped with EGTA,EDTA containing buffer and incubated for 10minutes at 37degC to release DNA. SDS and proteinase K were added to each sample before overnight incubation at 55degC to reverse cross link. DNA was purified using oligo clean and concentrator. Yields were determined using Qubit 2.0 Fluorometer with 1x dsDNA HS assay kit
Immunoprecipitated DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA) and quality was assessed by Tapestation genomic DNA Assay (Agilent Technologies, California, USA). Library preparation was performed using KAPA Hyper Prep kit with PCR (Roche, Basel, Switzerland) per manufacturer’s recommendations. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio ® 5 System (Applied systems, California, USA). Illumina® 8-nt unique dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus 10B (Illumina, California, USA) with a read length configuration of 150 PE for 8M PE reads (4M in each direction).

value: 311E cell line

value: Genetically engineered mouse model of NUT Carcinoma

tag: cut&run antibody


title: Tcrd.KO.BigTumor, S13

value: Tcrdko

value: colon tumors

value: Live Epcam+ cells


title: m238_br_2_ifng

data_processing:
Sequencing was performed on Illumina NextSeq 500. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
MAGeCK software package v0.5.9.4 was used to analyze CRISPR screen data. sgRNA counts were obtained with the "mageck count" command using the FASTQ files with sgRNA sequences from the appropriate library.
Assembly: Not applicable
Supplementary files format and content: Tab delimited files containing sgRNA counts for control and IFNg-treated samples
Supplementary files format and content: A separate file is provided for each sgRNA library used for screening
Library strategy: CRISPR screen

growth_protocol: M238 cells were cultured in RPMI supplemented with 10% FBA, 10 mM HEPES, and antibiotic and antimycotic agents. Cultured cells were grown in a 37C incubator with 5% CO2

extract_protocol:
Genomic DNA was extracted using the PureLink Genomic DNA mini kit (Invitrogen) following the kit protocol.
Library preparation was performed as described in Joung et al, Nature protocols, 2017; https://doi.org/10.1038/nprot.2017.016.

treatment_protocol: Cells were treated with or without recombinant Human IFNg (Peprotech, 800 U/ml) and harvested after 10-14 days for genomic DNA extraction.


title: siNC_2_input

value: THP1 monocyte cell line -derived macrophages


title: Pupal Brain, Asp Mutant, Rep. 3

source_name: Brain

value: Brain

value: pupal


title: m238_br_2_control

value: Melanoma cell line


title: siNC_1

value: Anti-m6A (Synaptic Systems, Cat. No 202 003)


title: 311E cell line 9nM ABBV075 96hr H3K37me3  rep 1 Experiment 2


title: 311E cell line 9nM ABBV075 96hr H3K27ac  rep 1 Experiment 2

description:
23122FL-07-02-05
311E_abbv_k27ac_subtract_igg_2.tdf


title: CA.WT.Tumor, S7


title: siMETTL3_1_input

value: transfected with METTL3 siRNA pools for 48 h.


title: siMETTL3-6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Differentially expressed genes were identified using Cuffdiff. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR). The fold-changes were also estimated according to the FPKM in each sample.
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide

value: peripheral blood

value: THP1-derived macrophages were transfected with METTL3 siRNA pools for 48 h.


title: siNC_1_input


title: 311E cell line 9nM ABBV075 96hr H3K27me3  rep 2 Experiment 2


title: m238_br_1_control


title: siMETTL3-5


title: m238_br_1_ifng


title: siMETTL3-4


title: m238_gecko_ifng


title: 311E cell line 9nM ABBV075 96hr IgG  rep 1 Experiment 2

value: IgG (EpiCypher, 13-0042K)


title: siNC-3

value: THP1-derived macrophages were transfected with  control siRNA for 48 h.


title: 311E cell line DMSO 96hr H3K27ac  rep 1 Experiment 2

description:
23122FL-07-01-05
311E_dmso_k27ac_subtract_igg_2.tdf

value: DMSO, 96hr


title: siNC-2


title: m238_gecko_control


title: siNC-1


title: 311E cell line H3K27me3 96hr IgG  rep 1 Experiment 2


title: CD138+cells from multiple myeloma_Replicate 2 [miRNA-Seq]

city: Wuhan

first: Han

last: Yan

address: Jiefang  Avenue

institute: Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
FastQC 0.11.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Cutadapt 1.14), and filtered for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie software.
Counts per million reads (CPM) were calculated using miRDeep2 0.0.8 software.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: Bone marrow CD138+ cells

extract_protocol:
Bone marrow CD138+ cells were obtained from multiple myeloma patients and normal individuals by magnetic bead separation. The cells were treated with TRIzol to extract total RNA according to manufactures' instrctions.
miRNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Multiple Myeloma

value: CD138+ cells

tag: gender

value: Male


title: 311E cell line 9nM ABBV075 96hr IgG  rep 2 Experiment 2

value: 311E cell line

tag: cell line

value: Genetically engineered mouse model of NUT Carcinoma


title: CD138+cells from multiple myeloma_Replicate 3 [miRNA-Seq]

tag: cell type


title: P6_bone_marrow [scATAC-seq]

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Pl

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Sequencing data were processed by Cell Ranger ATAC version 1.2.0.
This pipeline performed de-multiplexing,  alignment (hg38), and barcode processing to generate peak-cell matrices used for downstream  analysis.
Genome_build: hg38
Supplementary_files_format_and_content: cell ranger count matrix for peaks vs single cells in each sample

source_name: patient 6

extract_protocol:
Flow-sorted CD34/CD45-positive cells were captured with the Chromium Controller (10x Genomics).
libraries were prepared with the Chromium Single Cell ATAC Kit v1.1 (10x Genomics)

value: bone marrow CD34/CD45+


title: CD138+cells from multiple myeloma_Replicate 1 [miRNA-Seq]


title: P1_bone_marrow [scATAC-seq]

source_name: patient 1


title: CD138+cells from normal_Replicate 3 [miRNA-Seq]

value: Normal


title: 311E cell line H3K27me3 96hr IgG  rep 2 Experiment 2

tag: tissue


title: 311E cell line DMSO 96hr H3K27ac rep 2 Experiment 2

description:
23122FL-07-01-06
311E_dmso_k27ac_subtract_igg_2.tdf


title: P6_bone_marrow [scRNA-seq]

data_processing:
Sequencing data were run on Cell Ranger version 3.1.0 to generate feature barcode matrices.
This pipeline performed de-multiplexing,  alignment (hg38), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: hg38
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

extract_protocol:
Flow-sorted CD34/CD45-positive cells were captured with the Chromium Controller (10x Genomics).
libraries were prepared with Chromium Single Cell Gene Expression 3′ v3 Kits (10x Genomics).


title: CD138+cells from normal_Replicate 2 [miRNA-Seq]

tag: age


title: Crlf3-mutant hippocampi

city: Saint Louis

first: David

last: Gutmann

address: 660 S. Euclid Ave

institute: Washington University in St. Louis School of Medicine

description: 10x Genomics

data_processing:
chemistry: Single Cell 5' PE
The demultiplexing, barcode processing, gene couning and aggregation were made using the cellranger pipline v6.1.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
genome build: mm10-2020-A
single cell data were processed using Partek® Flow® (Version 10.0) https://www.partek.com/partek-flow/
All the single cell RNA sequencing data were analyzed in Partek® Flow® software (version 10.0.23). Cell quality was evaluated by number of reads, detected gene count, and percentage of mitochondrial read, followed by CPM (counts per million) normalization and PCA analysis. To account for library chemistry, and other possible unknown differences between experiments, cells were integrated using the Seurat3 integration method to produce batch-corrected data. The subsequent graph-based clustering using Louvain algorithm, and t-SNE plot generation employing Euclidean distance, were conducted on the first 20 principal components of the integrated expression data. Differential analyses were performed using Hurdle model (MAST)
Assembly: mm10-2020-A
Supplementary files format and content: sequences corresponding to every barcode in the matrix table
Supplementary files format and content: sequences corresponding to every feature in the matrix table
Supplementary files format and content: matrix table with the number of unique molecular identifiers for every feature by row and every barcode by column

source_name: brain

growth_protocol: fresh brain

extract_protocol:
Crlf3-mutant and wild type hippocampi, midbrains, and cortices were collected from four 4-week-old mice (4 hippocampi, 4 cortices, and 2 midbrains mice per genotype) and pooled to prepare single-cell isolations for each region, as previously reported . After collection, the brain tissues were dissociated using the neural dissociation kit (Miltenyi Biotec, 130-095-942) as per manufacturer’s instructions followed by debris (Miltenyi Biotech, 130-107-677) and myelin (Miltenyi Biotec, 130-096-733) removal. The cells were then stained with 7-AAD and sorted using the MO-FLO. The live cells were collected and sent for sequencing. For all samples in the experiment, raw sequencing data was processed using the 10X Genomics Cell Ranger pipeline (version 6.1.1) to generate gene count matrices, and then aligned to the mouse reference genome (mm10-2020-A).
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 5’ Reagent Kit (v2 Chemistry Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: brain

value: 4 weeks old


title: P1_bone_marrow [scRNA-seq]


title: 311E cell line DMSO 96hr IgG  rep 2 Experiment 2


title: CD138+cells from normal_Replicate 1 [miRNA-Seq]

value: Female


title: 311E cell line DMSO 96hr IgG  rep 1 Experiment 2


title: CD8+ T cell scr No stim Rep1

status: Public on Oct 05 2023

city: Portland

first: Robert

last: Eil

state: Oregon

address: 3266 SW Research Drive

institute: Oregon Health and Science University

data_processing:
From Azenta US, Inc.:
cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. Following validation and quantification, the sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded on the Illumina instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.
Image analysis and base calling were conducted by the control software.
Raw sequence data (.bcl files) generated from the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using the DESeq2 R package, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.
Assembly: GRCm39
Supplementary files format and content: .txt files suffixed ".counts" provide the total number of transcripts mapped to each murine ENSEMBL gene.

source_name: splenocytes

growth_protocol: CD8+ T cells from BL/6 mice were electroporated with cas9 complexed to atp1a1i or scrambled sgRNAs and subsequently stimulated in vitro with plate-bound anti-CD3 and anti-CD28. They were expanded in RPMI 1640 containing 10% FBS and 100 IU/mL of IL-2 for four days.

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy Plus Universal Mini Kit per manufacturer's instructions (Qiagen, Hilden, Germany).
RNA was checked for quantity and integrity, then libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina as per manufacturer's instructions (New England Biolabs, Ipswich, MA, USA). Briefly, Oligod(T)-enriched mRNA was fragmented for 15 mins at 94°C and first and second strand cDNA subsequently synthesized.

treatment_protocol: Bulk cells were harvested on the fourth day of culture, washed four times with ice cold PBS, and frozen as cell pellets.

value: splenocytes

value: CD8+ T cell

value: wild type

value: no stim


title: CD8+ T cell scr No stim Rep3


title: Wild type hippocampi

description: 10x Genomics


title: mGB2-BKO-Tet3KD-rep3

type: genomic

first: Pavle

last: Boskovic

address: 4515 McKinley Ave

institute: Washington University in Saint Louis

description: mouse glioblastoma stem-cell line (spheroids)

hyb_protocol: standard Illumina protocol for the Illumina Infinium MouseMethylation array

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

data_processing: Analysis in R (libaries: knitr, limma, minfi, missMethyl and others)

label: Cy5 and Cy3

source_name: Cultured glioblastoma stem cells

extract_protocol: Total genomic DNA was extracted using the QIAGEN DNA extration kit

tag: replicate


title: mGB2-BKO-Tet3KD-rep2

label_protocol: standard Illumina protocol for the Illumina Infinium MouseMethylation array


title: CD8+ T cell scr No stim Rep2


title: CD8+ T cell ATP1a1 KO No stim Rep3

value: ATP1a1 KO


title: mGB2-BKO-Tet1KD-rep3


title: mGB2-BKO-Tet1KD-rep2


title: mGB2-BKO-Tet3KD-rep1


title: CD8+ T cell ATP1a1 KO No stim Rep2


title: CD8+ T cell ATP1a1 KO No stim Rep1


title: WD KO1

city: Barcelona

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

country: Spain

institute: IDIBAPS/ICREA

data_processing:
RNA-seq reads mapped using STAR software v2.5.3a with ENCODE parameters.
Annotated genes quantified by RSEM v1.3.0
Annotation version gencode M25
Assembly: GRCm38
Supplementary files format and content: Matrix with samples as columns and raw gene counts as rows

source_name: Macrophage

extract_protocol:
Whole aortas were harvested and separated from perivascular adipose tissue, then digested for 40 minutes at 37ºC in RPMI containing 450 U/ml Collagenase I, 125 U/ml Collagenase XI and 60 U/ml Hyaluronidase. Viable CD45+ and F4/80+ cells were sorted in a FACS Aria II and recovered in lysis buffer.
cDNA was harvested using SMART-Seq v4 Ultra Low Input RNA Kit  following manufacturer's protocols.

value: Macrophage

value: KO

value: Western Diet


title: mGB2-BKO-rep3

state: MO

value: BKO


title: WD KO3


title: mGB2-BKO-Tet1KD-rep1


title: WD WT1

value: WT


title: WD WT2


title: E13.5-pool 4

city: Sutton Bonington

first: Ramiro

last: Alberio

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

description: 10X Genomics

data_processing:
Raw fastq files were processed with Cell Ranger 6.1.2 with default mapping arguments for all samples apart from samples X, X, X and X where the 'forcecells' argument was used and the inputs were given as X, X, x and X respectively.
Reads were mapped to the Sus_scrofa_ V11.1 genome
The cell ranger output for each sample is in a separate folder containing a barcode, feature and matrix files
The combined counts for all the processed samples are available as csv file with a separate metadata file
Assembly: Sus_scrofa_v11.1
Supplementary files format and content: barcodes.tsv: List of cell barcodes
Supplementary files format and content: matrix.mtx: Gene count matrix
Supplementary files format and content: features.tsv: List of features (genes)
Supplementary files format and content: All_samples_processed.csv: Matrix containing the raw count of all samples after processing
Supplementary files format and content: All_sample_metadata.csv: Metadata information for all cells, this includes celltypes, subtypes and UMAP coordiantes

organism: Sus scrofa

source_name: Embryo

extract_protocol: Single cell suspensions were processed according to the 10x Chromium protocol. Cell suspensions were added to individual 10X Chip channels . Captured cells were lysed and RNA was barcoded through reverse transcription in individual GEMs. RNA libraries were prepared for sequencing using the standard 10x Single Cell 3' Library & Gel Bead Kit v3 protocol.

value: Embryo

tag: time point


title: E13-pool 4

description: 10X Genomics


title: E13.5-pool 3

description: 10X Genomics


title: WD KO2

tag: genotype


title: mGB2-BKO-rep2


title: E13-pool 2

description: 10X Genomics


title: E15-pool 2

description: 10X Genomics


title: E13-pool 5

description: 10X Genomics


title: E15-pool 3

description: 10X Genomics


title: E15-pool 1

description: 10X Genomics


title: E12.5-pool 2

description: 10X Genomics


title: E13-pool 3

description: 10X Genomics


title: E14-pool 2

description: 10X Genomics


title: E13.5-pool 2

description: 10X Genomics


title: E13.5-pool 1

description: 10X Genomics


title: E14.5-pool 4

description: 10X Genomics


title: mGB2-BKO-rep1


title: E11.5-pool 2

description: 10X Genomics


title: mGB2-control-rep3

value: control


title: E14-pool 1

description: 10X Genomics


title: E12-pool 1

description: 10X Genomics


title: E14.5-pool 2

description: 10X Genomics


title: E12-pool 2

description: 10X Genomics


title: mGB2-control-rep2


title: E13-pool 1

description: 10X Genomics


title: E12.5-pool 1

description: 10X Genomics


title: DAMI-HMGA1 ChIP-seq

city: BALTIMORE

first: Linda

last: Resar

state: Maryland

address: 720 Rutland Avenue

department: Department of Medicine / Division of Hematology

institute: Johns Hopkins University

data_processing:
Bowtie2.2.1 was used for mapping the paired end reads to the hg19 human reference genome. Default parameters were used.
Samtools0.1.19 was used to convert, sort and index SAM files.
MACS2.1.1 was used to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files were obtained from MACS2 in bed format

source_name: DAMI cell

growth_protocol: DAMI cells (ATCC, CRL-9792) were cultured in RPMI 1640 medium (Corning) supplemented with 10% fetal bovine serum (Sigma).

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

value: DAMI cell

value: leukemic cells

value: MPN/AML

tag: chip antibody


title: E14.5-pool 3

description: 10X Genomics


title: E14.5-pool 1

description: 10X Genomics


title: DAMI HMGA1 KD rep 3

data_processing:
Bowtie2.2.1 was used for mapping the paired end reads to the hg19 human reference genome. Default parameters were used.
Samtools0.1.19 was used to convert, sort and index SAM files.
Genrich was used to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files are formatted with default setting

extract_protocol: The cells were extracted and processed as per ATAC-seq protocol (Buenrostro et al. Nature Methods 2013). Cells (50,000) were subjected to tagmentation reactions with 2 ul Tn5 Transposase (Illumina) for 45 minutes at 37° C.

treatment_protocol: Lentivirus is concentrated using Amicon Ultra-15 Centrifugal Filter Unit (sigma) at 4,000 × g for 0.5 hours, 4 °C. The virus pellet was resuspended in a fresh medium, and stored at −80°C until use. For lentivirus transduction, we used magnetic nanoparticles.

tag: treatment

value: shHMGA1 lentivirus infected


title: DAMI TRC rep 3

value: Control lentivirus infected


title: E11.5-pool 1

description: 10X Genomics


title: mGB2-control-rep1

tag: strain


title: DAMI HMGA1 KD rep 1


title: Input DNA


title: DAMI TRC rep 2


title: DAMI TRC rep 1


title: DAMI-H3 ChIP-seq


title: DAMI HMGA1 KD rep 2


title: Periferal blood father [PL947_Father]

city: Maastricht

first: Rick

last: Essers

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

institute: Maastricht University Medical Centre (MUMC+)

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing:
The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into haplarithmisis (Zamani Esteki et al. 2019, Nature medicine).
Image data was analyzed using Genomestudio with genotyping module (Illumina). Subsequently, genotype calls (AA,AB,BB,or NC (no call), SNP B-allele frequency values, LogR.

label: Cy3, Cy5

source_name: Periferal blood

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: The tissues were chopped with scissors to small fragments, and long-term cultures were set up in 25 cm2 flasks with 5 mL of DMEM/F12 (1:1) medium (Gibco) supplemented with 20% fetal bovine serum (HyClone), 1% MEM NEAA solution (Gibco), 1% Pen-Strep (Gibco). Tissues were incubated at 37°C with once-weekly medium renewal.

extract_protocol: Genomic DNA was extracted using a standard phenol-chloroform extraction method that allows for the isolation of up to 900 ng DNA from the tissues. Likewise, genomic DNA was extracted from peripheral blood of parents using the standard phenol-chloroform method.

treatment_protocol: The two tissues were mechanically separated and the yield of chorionic cytotrophoblast cells was increased by maceration of chorionic villi under an Axiovert 200 inverted microscope (Carl Zeiss, Germany) and treatment with 70% acetic acid for 3-5 min followed by three washes of the obtained cell suspension with PBS according to a modified protocol (Simoni, G. et al. Efficient direct chromosome analyses and enzyme determinations from chorionic villi samples in the first trimester of pregnancy. Human Genetics 63, 349-357 (1983)).

value: Male

tag: family member

value: Father

value: Periferal blood


title: Chorionic villi fetal biopsy [PL947_CV1844]

source_name: Chorionic villi

value: Female

value: Product of conception

value: Chorionic villi


title: Periferal blood mother [PL934_Mother]

value: Mother


title: Chorionic villi fetal biopsy [PL934_CV1801]


title: Extraembryonic mesoderm fetal biopsy [PL920_EM1854]

source_name: Extraembryonic mesoderm

value: Extraembryonic mesoderm


title: Periferal blood mother [PL920_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL934_EM1801]


title: Periferal blood mother [PL915_Mother]


title: Periferal blood father [PL920_Father]


title: Periferal blood father [PL915_Father]


title: Extraembryonic mesoderm fetal biopsy [PL915_EM1728]


title: Chorionic villi fetal biopsy [PL915_CV1728]


title: Extraembryonic mesoderm fetal biopsy [PL947_EM1844]


title: Periferal blood father [PL934_Father]


title: Periferal blood mother [PL822_Mother]


title: Chorionic villi fetal biopsy [PL920_CV1854]


title: Extraembryonic mesoderm fetal biopsy [PL822_EM1819]

value: ND


title: Periferal blood mother [PL947_Mother]


title: Chorionic villi fetal biopsy [PL822_CV1819]


title: Periferal blood father [PL822_Father]


title: hMSC_24h_Rosi-2

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

institute: ErasmusMC

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 24 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 2
SAMPLE 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was background subtracted, vst transformation and a quantile normalization was applied using bioconductor package lumi. Probes that were detected at least once in the experiments (illumina detection p-value <0.01), were considered to be expressed and further analyzed for differential expression using Limma.

label: biotin

source_name: MSC treated with rosiglitazone for 24 h

label_protocol: cDNA and Biotinylated cRNA were prepared with the Illumina Totalprep RNA Amplification kit (Ambion)

growth_protocol: alphaMEM, 20mM HEPES, strep/pen, 1.8 mM CaCl2, 10% FCS, 10 mM beta-glycerophosphate, 100 nM dexamethasone

extract_protocol: Total RNA extracted using Trizol (invitrogen)

treatment_protocol: 10 microM rosiglitazone, final dilution of etoh (vehicle) in culture medium: 1/200 (0.5 %).

value: Bone Marrow


title: hMSC_1h_EtOH-2

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with vehicle (etoh) for 1 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 2
SAMPLE 2

source_name: MSC treated with vehicle (etoh) for 1 h


title: hMSC_1h_Rosi-2

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 1 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 2
SAMPLE 4

source_name: MSC treated with rosiglitazone for 1 h


title: hMSC_24h_Rosi-1

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 24 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 1
SAMPLE 9


title: hMSC_3h_Rosi-2

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 3 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 2
SAMPLE 6

source_name: MSC treated with rosiglitazone for 3 h


title: hMSC_1h_Rosi-1

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 1 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 1
SAMPLE 3


title: hMSC_6h_Rosi-1

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 6 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 1
SAMPLE 7

source_name: MSC treated with rosiglitazone for 6 h


title: Extraembryonic mesoderm fetal biopsy [PL714_EM1699]


title: Periferal blood father [PL714_Father]


title: Extraembryonic mesoderm fetal biopsy [PL777_EM1802]


title: Periferal blood mother [PL714_Mother]


title: Chorionic villi fetal biopsy [PL777_CV1802]


title: Periferal blood father [PL777_Father]


title: hMSC_48h_Rosi-2

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 48 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 2
SAMPLE 12

source_name: MSC treated with rosiglitazone for 48 h


title: hMSC_3h_Rosi-1

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 3 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 1
SAMPLE 5


title: hMSC_48h_Rosi-1

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 48 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 1
SAMPLE 11


title: Chorionic villi fetal biopsy [PL714_CV1699]


title: hMSC_6h_Rosi-2

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with 10 microM rosiglitazone for 6 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 2
SAMPLE 8


title: Periferal blood mother [PL668_Mother]


title: hMSC_1h_EtOH-1

description:
Bone marrow derived Mesenchymal Stem cells differentiating towards osteoblasts and treated with vehicle (etoh) for 1 h backwards from time-point of harvest (i.e. 48 h after induction of osteogenic differentiation), replicate 1
SAMPLE 1


title: Periferal blood father [PL668_Father]


title: Periferal blood mother [PL777_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL668_EM1642]


title: Periferal blood father [PL649_Father]


title: Chorionic villi fetal biopsy [PL668_CV1642]


title: Extraembryonic mesoderm fetal biopsy [PL649_EM1641]


title: Periferal blood mother [PL649_Mother]


title: Chorionic villi fetal biopsy [PL649_CV1641]


title: Periferal blood father [PL588_Father]


title: Extraembryonic mesoderm fetal biopsy [PL524_EM1796]


title: Periferal blood father [PL524_Father]


title: Extraembryonic mesoderm fetal biopsy [PL524_EM1555]


title: Chorionic villi fetal biopsy [PL524_CV1555]


title: Periferal blood mother [PL558_Mother]


title: Chorionic villi fetal biopsy [PL455_CV1441]


title: Extraembryonic mesoderm fetal biopsy [PL444_EM1448]


title: Periferal blood father [PL445_Father]


title: Extraembryonic mesoderm fetal biopsy [PL455_EM1441]


title: Periferal blood mother [PL401_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL401_EM1359]


title: Periferal blood mother [PL384_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL384_EM1332]


title: Chorionic villi fetal biopsy [PL558_CV1551]


title: Extraembryonic mesoderm fetal biopsy [PL558_EM1551]


title: Periferal blood mother [PL524_Mother]


title: Periferal blood mother [PL455_Mother]


title: Periferal blood father [PL455_Father]


title: Chorionic villi fetal biopsy [PL383_CV1316]


title: Periferal blood mother [PL379_Mother]


title: Periferal blood mother [PL445_Mother]


title: Periferal blood father [PL401_Father]


title: Periferal blood father [PL379_Father]


title: Periferal blood mother [PL444_Mother]


title: Chorionic villi fetal biopsy [PL524_CV1796]


title: Periferal blood father [PL444_Father]


title: Chorionic villi fetal biopsy [PL444_CV1448]


title: Chorionic villi fetal biopsy [PL290_CV1136]


title: Extraembryonic mesoderm fetal biopsy [PL281_EM1216]


title: Periferal blood mother [PL281_Mother]


title: Periferal blood father [PL384_Father]


title: Chorionic villi fetal biopsy [PL445_CV1431]


title: Periferal blood mother [PL383_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL278_EM952]


title: Chorionic villi fetal biopsy [PL401_CV1359]


title: Extraembryonic mesoderm fetal biopsy [PL379_EM1311]


title: Periferal blood father [PL278_Father]


title: Chorionic villi fetal biopsy [PL278_CV952]