title: NZM_M3_Td2

city: Philadelphia

first: Montserrat

middle: C

last: Anguera

state: PA

address: Rosenthal Building - 3800 Spruce St. Room 304

department: Department of Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.male.d2
NZM3.Td2
NZM.3.Td2

data_processing:
Sample technical replicate files were concatenated. Sample reads were aligned to the mouse reference genome (GRCm38/mm10) using Kallisto (v0.46.0) and annotated (EnsDb.Mmusculus.v79) using ensembldb (v2.16.4).
Transcript counts were generated at the gene level using tximport (v1.20.0).
edgeR (v3.34.1) was used to filter (cpm>1 for n=3 biological replicates) and then normalize the data via the TMM method.
Differentially expressed genes were identified using Limma (v3.48.3).
Assembly: GRCm38/mm10
Supplementary files format and content: "DiffGenes_NZM.female.vs.male.d2" contains the normalized log2cpm for early disease NZM2328 female mice (n=5) and early disease NZM2328 male mice (n=3).
Supplementary files format and content: "DiffGenes_NZM.female.vs.wt.d2" contains the normalized log2cpm for wild-type C57BL6 female mice (n=3) and early disease NZM2328 female mice (n=5)

source_name: spleen

growth_protocol: CD3+ cells were isolated from splenic tissue via negative selection and were cultured in an anti-CD3-coated 96-well round-bottom plate using RPMI supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, 1% non-essential amino acids, 1% sodium pyruvate, 0.1% Beta-mercapto ethanol, and 10 ug/mL anti-CD28, in humidified atmosphere with 5% CO2 at 37C for 48 hours.

extract_protocol:
At Day 2 of culture, cells were aspirated from the corresponding wells, resuspended in TRIzol, and stored at -80C until library preparation.
High quality RNA samples (RIN ≥ 8.6) were selected for library construction according to the Illumina TruSeq Stranded mRNA Library Preparation kit.

treatment_protocol: 96-well round bottom plates were pre-coated with 10 ug/mL of anti-CD3 antibody for 2.5 hours at room temperature prior to cell culture. Immediately prior to plating cells, the wells were washed x3 with D-PBS. Cells were resuspended in anti-CD28-containing media (10 ug/mL) immediately prior to their transfer to the anti-CD3-coated plate.

value: 23 weeks

tag: disease state

value: Early

value: spleen

value: CD3+ T cells

value: anti-CD3 and anti-CD28

value: 48 hrs post-treatment


title: NZM_F4_Td2

status: Public on Sep 20 2022

type: SRA

country: USA

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.wt.d2
DiffGenes_NZM.female.vs.male.d2
NZM14.Td2
NZM.14.Td2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: Sex

value: Female

tag: strain

tag: age

value: 22 weeks

tag: tissue

tag: cell type

tag: treatment

tag: time


title: NZM_M1_Td2

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.male.d2
NZM1.Td2
NZM.1.Td2

value: Male


title: NZM_M2_Td2

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.male.d2
NZM2.Td2
NZM.2.Td2


title: NZM_F5_Td2

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.wt.d2
DiffGenes_NZM.female.vs.male.d2
NZM15.Td2
NZM.15.Td2


title: MeWo, Pict, 24h, Rep3

city: Charlottesville

first: Mohammad

last: Fallahi-Sichani

state: VA

address: 415 Lane Rd

institute: University of Virginia

data_processing:
All processing steps were performed on Galaxy server. Reads were mapped to the human genome (hg38) using HISAT2.
Transcripts were assembled and quantified using StringTie.
Assembly: hg38
Supplementary files format and content: csv files include FPKM/TPM values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: MeWo

extract_protocol:
Samples were washed once with PBS and then lysed with Rneasy Buffer RLT (Qiagen). RNA was extracted using QIAshredder (Qiagen) and Rneasy Mini Kit (Qiagen). RNA was Dnase treated (Qiagen) and then eluted. RNA quality was assessed by Bioanalyzer. All samples had RINs of 9.0 or higher
Prior to poly-A enrichment, 500 ng of each RNA sample was supplemented with 1 μL (1:100 dilution) of ERCC spike-in control. Poly-A RNA enrichment was performed using NEBNext Poly(A) kit. Fragments were end-modified with adaptors using NEBNext Multiplex Oligos for Illumina Set 2, following library amplification (PCR, 11 cycles). Resulting libraries were prepared using NEBNext Ultra II Directional RNA Kit.

tag: cell line

value: MeWo

value: melanoma cells

tag: genotype

value: NF1 loss-of-function

value: Pictilisib (1 µM)

value: 24 hours


title: Patient nCounter 97

type: RNA

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

country: France

institute: University of Bordeaux

description: Total RNA samples runs were performed on the nCounter FLEX Analysis System based on the NanoString PanCancer Immuno-Oncology panel (IO360), made of 770 genes and a custom panel of 30 genes, in which we included genes from Hendrickx et al.’s Immunologic Constant of Rejection (ICR) signature.

hyb_protocol: According to Nanostring protocol

scan_protocol: Sample runs were performed on the nCounter FLEX Analysis System (automated nCounter® Prep station and the nCounter® Digital Analyzer optical scanner, NanoString Technologies, Seattle, WA, USA) according to the manufacturer’s protocol.

data_processing: We refined the 20-housekeeping gene list defined in NanoString IO360 panel using three independent datasets grouping triple negative breast cancer patients retrieved from xenaBrowser [TCGA BRCA primary tumors with 123 patients, Chin et al. 2006 : 41 patients and Hess et al. 2006  : 27 patients]. We computed gene expression variability as the inter-quantile (5%-95%) ratio in each dataset and selected 6 of the 20 genes showing ratios under 1.5 in all datasets: ERCC3, POLR2A, SF3A1, TBC1D10B, TMUB2, UBB.  We normalized the expression values using NanoStringNorm R package v1.2.1.1 with options CodeCount ='geo.mean', Background ='mean.2sd', SampleContent ='housekeeping.geo.mean', round.values = TRUE, take.log = TRUE.

label: biotin

source_name: Residual Triple Negative Breast Cancer

label_protocol: According to Nanostring protocol

extract_protocol: Total tumor RNA was extracted from four to six 10-micron tumor sections after identification of the residual tumor by a pathologist on a corresponding H&E section. RNA was extracted using the High Pure FFPET RNA Isolation Kit (Roche®), following the manufacturer’s instructions. RNA quantity and quality were assessed by Nanodrop 1000 spectrophotometer (ThermoFisher, Waltham, MA, USA) and 2100 Bioanalyser with Agilent RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). 200ng of total RNA was used from each sample for gene expression profiling (acceptation criteria 260/280 ratio: 1.8 -2.3, 230/280 ratio: 1.7-2.3).

tag: lve

tag: tils

tag: metastasis


title: Patient nCounter 96


title: MeWo, Pict, 24h, Rep2


title: NZM_F3_Td2

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.wt.d2
DiffGenes_NZM.female.vs.male.d2
NZM13.Td2
NZM.13.Td2


title: DMSO_3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Gene expression from OCI-AML3_treated with DMSO

hyb_protocol: Labeled fragments were hybridized to Affymetrix Clariom S Human arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: OCI-AML3_treated with DMSO_biological replicate 3

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: OCI-AML3 cells were cultured in RPMI-medium supplemented with 10% Fetal Calf Serum at 37°C and maintained at a desity of 0.1-1.0x10^6 cells/ml.

extract_protocol: After harvesting RNA of OCI-AML3 cells was extracted using miRNAeasy Mini kit and Dnase as described by the manufacturer.

treatment_protocol: OCI-AML3 cells were treated with DMSO, RG7112 (2 µM) or HDM201 (500 nM) for 24 hours.

value: OCI-AML3 cells

tag: agent

value: DMSO

value: wildtype


title: RNA-pol2 HiChIP of Mus musculus: NPC-WT-Rep2

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

country: China

institute: Nankai University

library_source: genomic

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with featureCounts(2.0.3)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of ChIP-seq were mapped to mm10 using bowtie2(version 2.4.4)
Peak calling using MACS2(2.2.7.1)
Clean reads of HiChIP-seq were mapped to mm10 using HiC-Pro(2.11.1)
Loop calling using hichipper(0.7.7)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample;Bigwig file with ChIP signal for every sample; Bedpe file with HiChIP loops for every sample
Library strategy: HiChIP

molecule: genomic DNA

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs (E14) were grown in culture dishes coated with 0.1% gelatin in DMEM supplemented with 15% FBS, 100 nM NEAA, 200 mM L-Glutamate, 1% Penicillin-streptomycin, 50 μM β-mercaptoethanol, 10 ng/mL LIF, 1 μM PD0325901 and 3 μM CHIR99021. The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
For RNA-seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions. For Chip-seq, 10 M cells cells were crosslinked with 1% formaldehyde (methanol free) in DMEM at a volume of 1 mL of formaldehyde for every one million cells. Cells were cross-linked 10 min at room temperature with rotation. Glycine was added into a final concentration of 125 mM to quench the formaldehyde. Samples were incubated 15 min on ice and then spun down at 2500 g for 5 min. The supernatant was discarded, and pelleted nuclei were washed once with 500 μL pre-chilled cell Lysis Buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP-40, 1×protease inhibitors) and then rotated at 4°C for 30 min. Samples were then spun down at 2500 g for 5 min and the supernatant discarded, while pelleted nuclei were washed twice with 500 μL of ice-cold ChIP Lysis Buffer. The volume of pelleted material was brought up to 1mL in Nuclear Lysis Buffer (50mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, 1×protease inhibitors) and incubated 5 min at room temperature. Samples were then divided equally into 3 parts, sheared for 30 cycles (30 s “ON” and 30 s of “OFF”), and then spun down at 16100 g for 15 min. Supernatant were collected into new low-adsorption 1.5mL EP tubes. Then, 60 μL of Protein A beads for every 107 cells were washed in ChIP Dilution Buffer and resuspended in 50 μL Dilution Buffer per tube (100 μL per ChIP). Protein A beads were added to samples, which were rotated 1 h at 4 °C for precleaning. Sample supernatants were then separated using a magnet and transferred into new tubes, and then 7.5 μg antibodies per 107 cells were incubated at 4 °C overnight with rotation. The next day, 60 μL Protein A beads were washed and added to samples and then rotated 2 h at 4 °C. Beads were washed three times each with Low Salt Wash Buffer, High Salt Wash Buffer, and LiCl Wash Buffer. Chip-DNA was de-crosslinking with Proteinase K and purification using AmpureXP beads.For HiChIP:Briefly, 1.5×107 cells were crosslinked with 1% formaldehyde and lysed and then chromatin was digested using 400U MboI (NEB). Then 37.5μL biotin14-d-ATP was added and restriction-cut ends were ligated using 4000U T4 ligase (NEB). Pelleted nuclei were dissolved in nuclear lysis buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% SDS, and protease inhibitors), sonicated and diluted in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 7.5, and 167 mM NaCl). Immunoprecipitation was performed overnight at 4 °C by incubating RNA polⅡ antibodies (Biolegend) precoated on protein A-coated magnetic beads (Thermo Fisher Scientific). Immunocomplexes were washed three times each with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 7.5, and 150 mM NaCl), high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 7.5, and 500 mM NaCl), and LiCl buffer (10 mM Tris-HCl, pH 7.5, 250 mM LiCl, 1% NP−40, 1% Na-Doc, and 1 mM EDTA), and beads were resuspended in DNA elution buffer (50 mM NaHCO3 and 1% SDS). After elution, ChIP samples were incubated with 10 mg/mL proteinase K 4 h at 55 °C, and then DNA was purified using AMPure XP Beads (Beckman).
For RNA-seq: Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Then 3 µl USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.For ChIP-Seq:Chip-seq library preparation was performed using eluted ChIP DNA with NEBNext Ultra DNA Library Prep Kit, according to manufacturer's protocol.For HiChIP:Streptavidin C1 beads were used to capture biotinylated DNA. QIAseq FX DNA Library Kits were used to generate the sequencing library. HiChIP libraries were size-selected to 300–700 bp using AMPure XP beads (Beckman) and subjected to 2 × 150-bp paired-end sequencing on HiSeq XTen (Illumina). Two biological replicates were analyzed for each experimental condition.

treatment_protocol: RNA-seq was performed using neuro induction (12 d) WT and KLF4-KO NPCs, ChIP-Seq was performed using undifferentiated mESCs and KLF4-KO mESCs.

value: embryo, blastocyst embryo, blastocyst

value: WT

value: NPC


title: MeWo, M211, 24h, Rep3


title: MeWo, M211, 24h, Rep2


title: wt24h1

city: Granada

first: Laura

middle: Carmen

last: Terron Camero

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

department: Bioinformática

country: Spain

institute: IPBLN

description: Cd 100uM 24h

hyb_protocol: Hybridization was performed by the Functional Genomics Lab (Univ. Verona, IT) using NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the Functional Genomics Lab (Univ. Verona, IT) using NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Differential expression analysis has been performed with LIMMA (Linear Models Microarray Analysis; G. K. Smyth, 2005) R package and custom functions. Data preprocessing:background correction: normexp, quantile normalization,  internal replicate summarization: median. Statistical analysis:linear models approach for the assessment of differential expression, P values were adjusted for multiplicity with BH method (Benjamini and Hochberg, 1995).

organism: Arabidopsis thaliana

source_name: wt Cd 100uM 24h

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Seedlings were grown for two weeks on solid MS medium, three independent biological replicates, each composed of at least five different seedlings, were used per experimental condition

extract_protocol: Total RNA was isolated from seedlings by the acid guanidine thiocyanate–phenol–chloroform method using the Trizol reagent kit according to the manufacturer's instructions.

treatment_protocol: Seedlings were incubated with 100uM cadmium for 30 minutes or 24 hours. Controls were incubated in a cadmium-free solution.

tag: ecotype

value: leaves

tag: expt condition

value: wt Cd 100uM 24h


title: WT3_F_Td2

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.wt.d2
WT3.Td2
WT3.Td2

value: 17.5 weeks

value: spleen

value: CD3+ T cells

value: anti-CD3 and anti-CD28

value: 48 hrs post-treatment


title: WT4_F_Td2

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.wt.d2
WT4Td2-2
WT4Td2)2

value: Female


title: MeWo, Pict, 24h, Rep1

value: MeWo

value: melanoma cells

value: NF1 loss-of-function


title: NZM_F2_Td2

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.wt.d2
DiffGenes_NZM.female.vs.male.d2
NZM12.Td2
NZM.12.Td2

value: 22 weeks

value: Early


title: Atgox2_30m3

description: Cd 100uM 0.5h

source_name: Atgox2 Cd 100uM 0.5h

value: Atgox2 Cd 100uM 0.5h


title: Patient nCounter 95


title: wt30m1

description: Cd 100uM 0.5h

source_name: wt30m Cd 100uM 0.5h

value: wt30m Cd 100uM 0.5h


title: H3K27ac Chip-Seq of Mus musculus: ESCs-KLF4-KO-input

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with featureCounts(2.0.3)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of ChIP-seq were mapped to mm10 using bowtie2(version 2.4.4)
Peak calling using MACS2(2.2.7.1)
Clean reads of HiChIP-seq were mapped to mm10 using HiC-Pro(2.11.1)
Loop calling using hichipper(0.7.7)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample;Bigwig file with ChIP signal for every sample; Bedpe file with HiChIP loops for every sample

value: embryo, blastocyst embryo, blastocyst

value: ESCs


title: H3K27me3 Chip-Seq of Mus musculus: ESCs-KLF4-KO-input


title: RNA-pol2 HiChIP of Mus musculus: NPC-WT-Rep1

value: WT

value: NPC


title: H3K4me1 Chip-Seq of Mus musculus: ESCs-KLF4-KO-input


title: H3K4me1 Chip-Seq of Mus musculus: ESCs-WT-input


title: Patient nCounter 94


title: H3K27me3 Chip-Seq of Mus musculus: ESCs-KLF4-KO-Rep2


title: H3K27ac Chip-Seq of Mus musculus: ESCs-WT-input


title: atgox2_24h3

description: Cd 100uM 24h

source_name: atgox2 Cd 100uM 24h

value: leaves

value: atgox2 Cd 100uM 24h


title: Patient nCounter 92


title: wt2

description: Control condition

source_name: wt Control condition

value: wt Control condition


title: Patient nCounter 89


title: Patient nCounter 90


title: Patient nCounter 91


title: H3122_LR_1_450K

type: genomic

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

hyb_protocol: Samples were randomly assigned to one of nine Illumina 450K plates and hybridized according to protocol.

scan_protocol: Not provided

data_processing:
Data was analyzed in R (v.3.4.2) using minfi (v.1.30.0). Poorly performing probes (detection p-value < 0.05) and sex chromosome probes were removed from the analysis.
SWAN normalization were performed using the minfi package according author guidelines.
Normalized average beta values included in processed data.

label: Cy3, Cy5

source_name: H3122 lung cancer cell line

label_protocol: Not provided

extract_protocol: DNA was extracted using QIAamp Blood DNA mini kit (QIAGEN). 1 ug of extracted DNA per sample was treated with bisulfite and used in the assay.

value: lung cancer

value: Certinib


title: MeWo, M211, 24h, Rep1

value: 24 hours


title: MeWo, M216, 24h, Rep3

value: MeWo


title: MeWo, M216, 24h, Rep2

value: melanoma cells


title: Patient nCounter 93


title: NZM_F1_Td2

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.wt.d2
DiffGenes_NZM.female.vs.male.d2
NZM11.Td2
NZM.11.Td2

value: Female

value: spleen

value: CD3+ T cells

value: anti-CD3 and anti-CD28

value: 48 hrs post-treatment


title: C57BL/6 Ern2-/- CONV 02

city: Boston

first: Michael

middle: J

last: Grey

state: MA

address: 300 Longwood Avenue, Enders 606

department: Gastroenterology, Hepatology, and Nutrition

institute: Boston Children's Hospital

description: Column 18

data_processing:
Data were processed using the Visualization Pipeline for RNAseq (VIPER) (Cornwell M, Vangala M, Taing L, Herbert Z, Köster J, Li B, et al. VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. BMC Bioinformatics. 2018;19(1):135.).
Sequence reads were aligned using STAR (Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England). 2013;29(1):15-21.)
Raw gene counts were used to calculate differential expression (log2 [Group1/Group2]) between groups with DESeq2 (Love MI, Huber W, and Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology. 2014;15(12):550.)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts per gene for each Sample

source_name: colon

growth_protocol: Colon tissue was harvested, lumenal contents were gently removed, and the tissue was flushed with ice-cold PBS. The tissue was cut open longitudinally, cut into small pieces, washed 3 times with ice cold PBS, and incubated in PBS with 10 mM EDTA for 45 min at 4 °C on a rotary shaker. Epithelial cells were dissociated by vigorous shaking for 5 min, and the cell suspension was decanted into base media (Advanced DMEM/F12 Media, 20% FBS, 10 mM HEPES, 100 ug/mL Penicillin/Streptomycin, 2 mM L-glutamax). The remaining tissue pieces were subjected to a second round of epithelial cell isolation in the same manner. To isolate intact colon crypts, the epithelial cell suspension was passed through a 100 um strainer followed by a 40 um strainer. Intact crypts retained on the 40 um strainer were washed, eluted with base media, and pelleted by centrifugation at 300 xg for 3 min.

extract_protocol:
Total RNA was extract from colon crypt epithelial cells using Qiagen RNeasy Mini Kit with on-column DNase treatment.
Total RNA quality and concentration were measured using Aligent Bioanalyzer and RNA libraries were prepared using KAPA stranded mRNA HyperPrep kits.

value: colon

value: colon crypt epithelial cells

value: Conventionally raised (SPF)


title: H3K27me3 Chip-Seq of Mus musculus: ESCs-WT-input

value: embryo, blastocyst embryo, blastocyst

value: WT

value: ESCs


title: s35Sc1

description: Control condition

source_name: s35Sc Control condition

value: leaves

value: s35Sc Control condition


title: wt24h3

description: Cd 100uM 24h

value: wt Cd 100uM 24h


title: C57BL/6 Ern2-/- CONV 01

description: Column 17


title: MeWo, M216, 24h, Rep1

value: NF1 loss-of-function

value: 24 hours


title: WT1_F_Td2

description:
NZMTd2.rawCounts.xls
DiffGenes_NZM.female.vs.wt.d2
WT1.Td2
WT1.Td2

value: 17.5 weeks


title: MeWo, DMSO, 24h, Rep2

value: MeWo

value: melanoma cells

value: DMSO


title: C57BL/6 WT CONV 02

description: Column 15


title: H3K27me3 Chip-Seq of Mus musculus: ESCs-KLF4-KO-Rep1


title: H3K4me1 Chip-Seq of Mus musculus: ESCs-KLF4-KO-Rep2


title: H3K4me1 Chip-Seq of Mus musculus: ESCs-KLF4-KO-Rep1


title: Patient nCounter 88


title: MeWo, DMSO, 24h, Rep3


title: C57BL/6 Ern2-/- CONV 03

description: Column 19


title: MeWo, DMSO, 24h, Rep1


title: DMSO_4

source_name: OCI-AML3_treated with DMSO_biological replicate 4

value: OCI-AML3 cells

value: wildtype


title: WM3918, Tram, 24h, Rep3

value: Trametinib (0.1 µM)


title: C57BL/6 WT CONV 03

description: Column 16

value: colon

value: colon crypt epithelial cells


title: WM3918, Tram, 24h, Rep2


title: Patient nCounter 85


title: Patient nCounter 87


title: Patient nCounter 86


title: H3K27ac Chip-Seq of Mus musculus: ESCs-KLF4-KO-Rep2

value: embryo, blastocyst embryo, blastocyst


title: H3K4me1 Chip-Seq of Mus musculus: ESCs-WT-Rep2

value: WT


title: H3K27ac Chip-Seq of Mus musculus: ESCs-KLF4-KO-Rep1

value: ESCs


title: Patient nCounter 83


title: H3K4me1 Chip-Seq of Mus musculus: ESCs-WT-Rep1


title: H3K27me3 Chip-Seq of Mus musculus: ESCs-WT-Rep2


title: WM3918, Pict, 24h, Rep3

value: Pictilisib (1 µM)


title: Patient nCounter 84


title: H3K27me3 Chip-Seq of Mus musculus: ESCs-WT-Rep1


title: Patient nCounter 82


title: WM3918, Pict, 24h, Rep2


title: C57BL/6 Ern2-/- GF 02

description: Column 9

value: Germ Free


title: C57BL/6 Ern2-/- GF-Colonized 03

description: Column 13

value: Germ Free, followed by 14 day colonization with WT SPF cecal homogenate


title: C57BL/6 Ern2-/- GF-Colonized 02

description: Column 12


title: C57BL/6 WT CONV 01

description: Column 14

value: Conventionally raised (SPF)


title: C57BL/6 Ern2-/- GF 03

description: Column 10


title: Atgox2_30m1

description: Cd 100uM 0.5h

value: leaves

value: Atgox2 Cd 100uM 0.5h


title: wt30m2

description: Cd 100uM 0.5h

value: wt30m Cd 100uM 0.5h


title: H3122_PR_2_450K

value: lung cancer


title: H3122_PR_1_450K


title: C57BL/6 Ern2-/- GF 01

description: Column 8


title: WM3918, Pict, 24h, Rep1

value: melanoma cells

value: NF1 loss-of-function

value: 24 hours


title: H3K27ac Chip-Seq of Mus musculus: ESCs-WT-Rep2


title: wt3

description: Control condition

value: wt Control condition


title: C57BL/6 WT GF-Colonized 03

description: Column 7

value: colon


title: C57BL/6 Ern2-/- GF-Colonized 01

description: Column 11

value: colon crypt epithelial cells


title: WM3918, Tram, 24h, Rep1

value: Trametinib (0.1 µM)


title: Patient nCounter 80


title: Patient nCounter 81


title: Patient nCounter 79


title: s35Sc2

description: Control condition

value: s35Sc Control condition


title: WM3918, M211, 24h, Rep2


title: C57BL/6 WT GF-Colonized 02

description: Column 6

value: WT


title: RNA-Seq of Mus musculus: NPC-KLF4-KO-Rep2

value: embryo, blastocyst embryo, blastocyst

value: NPC


title: WM3918, M211, 24h, Rep3


title: Patient nCounter 78


title: H3K27ac Chip-Seq of Mus musculus: ESCs-WT-Rep1

value: ESCs


title: C57BL/6 WT GF-Colonized 01

description: Column 5

value: Germ Free, followed by 14 day colonization with WT SPF cecal homogenate


title: WM3918, M211, 24h, Rep1


title: C57BL/6 WT GF 03

description: Column 4

value: Germ Free


title: Patient nCounter 77


title: WM3918, M216, 24h, Rep3


title: RNA-Seq of Mus musculus: NPC-KLF4-KO-Rep1


title: RNA-Seq of Mus musculus: NPC-WT-Rep2


title: C57BL/6 WT GF 02

description: Column 3


title: C57BL/6 WT GF 01

description: Column 2


title: WM3918, M216, 24h, Rep2


title: RNA-Seq of Mus musculus: NPC-WT-Rep1


title: WM3918, M216, 24h, Rep1


title: WM3918, DMSO, 24h, Rep2

value: DMSO


title: Patient nCounter 76


title: SPOTS Spleen Replicate 2 ADT

city: New York

first: Xiang

last: Niu

state: NY

address: 413 E 69th Street

department: Medicine

institute: Weill Cornell Medical College

description:
spleen_rep_2_filtered_feature_bc_matrix.h5
spleen_replicate_2_spatial.tar

data_processing:
spaceranger v1.3.0, 10X Genomics
CITE-seq-Count v1.4.3, https://github.com/Hoohm/CITE-seq-Count
Assembly: GRCm38 (mm10)
Supplementary files format and content: h5, count matrix

source_name: mouse spleen

growth_protocol: All mouse strains involved in this work including wild-type C57BL/6J (Stock No: 000664)  and MMTV-PyMT (Stock No: 022974) were purchased from The Jackson Laboratory (USA). Females of the MMTV-PyMT model developed spontaneous tumors after ~110 days post-birth.

extract_protocol:
Mouse spleen and breast cancer samples were prepared using the Visium Spatial Gene Expression Kit according to the manufacturer’s instructions.
Transcript (GEX) and antibody derived tags (ADT) libraries were constructed according to SPOTS protocol. Spleen data were sequenced on the Illumina Nextseq 500. Breast cancer data were sequenced on the Illumina Nextseq 6000.

treatment_protocol: Mouse spleens and fresh breast tumors were collected, washed three times in PBS-1% BSA, and embedded in OCT for storage at -80C


title: SPOTS Spleen Replicate 2 GEX


title: Patient nCounter 73


title: Patient nCounter 74


title: Mouse, adult tdtomato negative and positive, rep1

city: Stanford

first: Ragni

last: Phansalkar

address: 318 Campus Drive

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
Raw Illumina reads for all datasets were demultiplexed and converted to FASTQ using bcl2fastq (Illu- mina). For mouse, reads were aligned to GRCm38 Ensembl release 81 as well as EGFP and tdTomato sequences and a gene count matrix was obtained using Cell Ranger v3.1.0 (10× Genomics).
GRCm38 Ensembl release 81
The folder e17_filtered_feature_bc_matrix_tdneg contains the CellRanger output for the cells sorted as TdTomato-negative. Within each folder, the matrix.mtx.gz file contains the gene count matrix in the Market Exchange Format, where rows represent genes and columns represent cells. The gene names are located in the features.tsv.gz file within each folder and the cell barcodes (the column names) are located in the barcodes.tsv.gz file within each folder.

source_name: Heart

extract_protocol:
BmxCreER-RosatdTomato/tdTomato males were crossed to CD1 females, which were dosed with tamoxifen at e8.5 and e9.5 (e12 and e17.5) or with 4-OH tamoxifen at e10.5 (adult). Either early in the day on e12, or midday on e17.5, embryos were removed and placed in cold, sterile PBS. Forty-two Cre+ e12 embryos and 9 Cre+ e17.5 embryos were identified by their fluorescent signal and used for single-cell isolation. Five Cre+ adult males were identified by Cre amplification and used for single- cell isolation. Hearts were isolated and dissected to remove the atria and outflow tract, keeping the ventricles, SV, and valves (e12 and e17.5) or to remove the atria, outflow tract, and valves, keeping the ventricles (adult). Hearts were then dissociated in a 600 μl mix consisting of 500 U/ml collagenase IV (Worthington #LS004186), 1.2 U/ml dispase (Worthington #LS02100), 32 U/ml DNase I (Worthington #LS002007), and sterile DPBS with Mg2+ and Ca2+ at 37 degrees for 45 min and resuspended by pipet- ting every 5 min. Once digestion was complete, 5 ml of a cold 5% FBS in PBS mixture was added and the suspension was filtered through a 40 μm strainer. After further rinsing the strainer with 5 ml of 5% FBS/PBS, the cell suspension was centrifuged at 400 g at 4°C for 5 min. The cells were washed and resuspended once more in 1 ml 5% FBS/PBS. The following antibodies were added at the concen- tration of 1:50 and incubated on ice for 45 min: APC/Cy7 Cd45 (Biolegend #103116), APC Pecam1 (Biolegend #102410), APC/Cy7 Ter-119 (Biolegend #116223). DAPI (1.1 μM) was added to the cells immediately before FACS. Once stained, the cells were sorted on a Aria II SORP machine into 1.5 ml tubes. The gates were set up to sort cells with low DAPI, low Cd45 (hematopoietic cells), low Ter119 (erythroid cells), high Pecam1 (endothelial marker), and either high or low PE-Texas Red (tdTomato positive or negative). Compensation controls were set up for each single channel (PE-Texas Red, APC, APC/Cy7) before sorting the final cells.
The samples were then submitted to the Stanford Genome Sequencing Service Center for 10× single-cell v3.1 3’ library preparation. For each stage, libraries from the tdTomato-positive and -negative samples were pooled and sequencing was performed on two lanes of a Illumina NovaSeq 6000 SP flow cell.

value: Heart

value: BmxCreER/+;Rosa-tdTomato


title: Mouse, e17 tdtomato negative, rep1

data_processing:
Raw Illumina reads for all datasets were demultiplexed and converted to FASTQ using bcl2fastq (Illu- mina). For mouse, reads were aligned to GRCm38 Ensembl release 81 as well as EGFP and tdTomato sequences and a gene count matrix was obtained using Cell Ranger v3.1.0 (10× Genomics).
GRCm38 Ensembl release 81
The folder adult_filtered_feature_bc_matrix_tdneg contains the CellRanger output for the cells sorted as TdTomato-negative. Within each folder, the matrix.mtx.gz file contains the gene count matrix in the Market Exchange Format, where rows represent genes and columns represent cells. The gene names are located in the features.tsv.gz file within each folder and the cell barcodes (the column names) are located in the barcodes.tsv.gz file within each folder.
The folder e17_filtered_feature_bc_matrix_tdpos contains the CellRanger output for the cells sorted as TdTomato-positive. Within each folder, the matrix.mtx.gz file contains the gene count matrix in the Market Exchange Format, where rows represent genes and columns represent cells. The gene names are located in the features.tsv.gz file within each folder and the cell barcodes (the column names) are located in the barcodes.tsv.gz file within each folder.


title: Patient nCounter 72


title: Patient nCounter 71


title: SPOTS Spleen Replicate 1 ADT

description:
spleen_rep_1_filtered_feature_bc_matrix.h5
spleen_replicate_1_spatial.tar


title: SPOTS Spleen Replicate 1 GEX


title: Mouse, e12 tdtomato negative and positive, rep1

data_processing:
Raw Illumina reads for all datasets were demultiplexed and converted to FASTQ using bcl2fastq (Illu- mina). For mouse, reads were aligned to GRCm38 Ensembl release 81 as well as EGFP and tdTomato sequences and a gene count matrix was obtained using Cell Ranger v3.1.0 (10× Genomics).
GRCm38 Ensembl release 81
The folder e12_filtered_feature_bc_matrix_tdneg contains the CellRanger output for the cells sorted as TdTomato-negative. Within each folder, the matrix.mtx.gz file contains the gene count matrix in the Market Exchange Format, where rows represent genes and columns represent cells. The gene names are located in the features.tsv.gz file within each folder and the cell barcodes (the column names) are located in the barcodes.tsv.gz file within each folder.
The folder e12_filtered_feature_bc_matrix_tdpos contains the CellRanger output for the cells sorted as TdTomato-positive. Within each folder, the matrix.mtx.gz file contains the gene count matrix in the Market Exchange Format, where rows represent genes and columns represent cells. The gene names are located in the features.tsv.gz file within each folder and the cell barcodes (the column names) are located in the barcodes.tsv.gz file within each folder.


title: Mouse, e17 tdtomato positive, rep1

data_processing:
Raw Illumina reads for all datasets were demultiplexed and converted to FASTQ using bcl2fastq (Illu- mina). For mouse, reads were aligned to GRCm38 Ensembl release 81 as well as EGFP and tdTomato sequences and a gene count matrix was obtained using Cell Ranger v3.1.0 (10× Genomics).
GRCm38 Ensembl release 81
The folder adult_filtered_feature_bc_matrix_tdpos contains the CellRanger output for the cells sorted as TdTomato-positive. Within each folder, the matrix.mtx.gz file contains the gene count matrix in the Market Exchange Format, where rows represent genes and columns represent cells. The gene names are located in the features.tsv.gz file within each folder and the cell barcodes (the column names) are located in the barcodes.tsv.gz file within each folder.


title: WM3918, DMSO, 24h, Rep3

value: melanoma cells


title: Patient nCounter 75


title: Hmgcs2 KO mouse heart, P3, biol rep 2

city: Nanjing

first: Danyang

last: Chong

state: Jiangsu

address: 101 Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing Medical University

data_processing:
Raw data were filtered and processed by Q30 and aligned to the mouse reference genome GRCm38/mm10 with Hisat2 software.
Quantification of the transcripts was accomplished with featureCounts software guided by the Ensembl gtf gene annotation file (http://www.ensembl.rog/).
Reads Per Kilobase Per Million Reads (RPKM) were used for the measurements of the relative abundances of the transcripts.
Assembly: mm10
Supplementary files format and content: Comma separated-values (CSV) include log 2 (RPKM) values for each sample

extract_protocol:
Total RNA was extracted with TrizolTM X-100 (Thermo Fisher Scientific, USA) treatment and a total amount of 2 µg RNA per sample was used for the construction of sequencing libraries.
Sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep Kit (Illumina, USA).

value: Hmgcs2 KO

value: Postnatal 3rd day

value: Male

value: No treatment


title: Hmgcs2 KO mouse heart, P3, biol rep 3


title: Hmgcs2 KO mouse heart, P3, biol rep 1


title: SMCs, RNA, WT2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC
Trimmomatic version 0.36 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.6.0c with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts tool from the Subread package 1.6.0. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: counts.matrix.norm_anno_rna.tx - library size normalized counts

source_name: control replicate 2

extract_protocol:
RNA was isolated from sorted smooth muscle cells using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA
50ng of total RNA was used as input for ribosomal depletion with RiboGone-Mammalian (Clontech) followed by library preparation using SMARTer Stranded Total RNA Sample Prep Kit (Clontech).

value: Lung

value: smooth muscle cells (SMCs)


title: SMCs, RNA, WT1

source_name: control replicate 1


title: SMCs, RNA, Mut2

source_name: Tet inactivation 2

value: Mut


title: Patient nCounter 68

source_name: Residual Triple Negative Breast Cancer


title: Patient nCounter 70


title: WM3918, DMSO, 24h, Rep1

value: NF1 loss-of-function

value: 24 hours


title: WT mouse heart, P3, biol rep 2

value: WT


title: SMCs, RNA, Mut1

source_name: Tet inactivation 1


title: WT mouse heart, P3, biol rep 1


title: Patient nCounter 67


title: SMCs, ChIP, WT_Input_2

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.36 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides.  Only reads between 30 and 150 nucleotides were cleared for further analyses.
Reads were further deduplicated using Picard 2.17.10 to eleminate PCR artefacts.
The Macs2 peak caller version 2.1.0 was employed to accommodate for the range of peak widths typically expected.
To be able to compare peaks in different samples to assess reproducibility, the resulting lists of significant peaks were overlapped and unified to represent identical regions and recounted.. A background-correction was performed to correct read counts on various regions (unified peaks, promoters, genes).
Treatment and Input samples were normalized for sequencing depth, before subtracting reads of the Input sample from reads of the respective Treatment sample in windows of 50nt length. All windows with negative values (Input > Treatment) were set to zero. Background-corrected counts for regions were calculated using bigWigAverageOverBed and normalized with DESeq2.
Peaks were annotated with the promoter (TSS +- 5000 nt) of the gene most closely located to the centre of the peak based on reference data from GENCODE v25.
Finally, DESeq2 was used to identify significantly differentially modified peaks based on background-corrected read counts from recounted unified peak regions.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP_peak_counts.txt - library size normalized counts

source_name: input DNA

extract_protocol:
3 million FACS-purified SMCs were treated by DRB (100 µmol) at 4oC for 1 hour. 50 µg sheared genomic DNA was subjected to immunoprecipitation with 4 µg RNA Pol II Ser5 antibody according to the established protocol.
0.5-10ng of DNA was used as input for TruSeq ChIP Library Preparation Kit (Illumina) with size selection by SPRI-bead based approach after final PCR with 18 cycles.

tag: chip antibody


title: Patient nCounter 65


title: Patient nCounter 69


title: WT organoid at day 90 (H6)

first: Christopher

middle: A

last: Walsh

address: 3 Blackfan Circle

department: Genetics and Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 and v5.0.0
Cellranger-output filtered feature matrics were loaded into R using Seurat, which was used for subsequent feature filtering, normalization, variance-stabilization, sample integration, PCA, and cell type annotation
Assembly: GRCh38-1.2.0
Supplementary files format and content: Processed gene x single-cell matrix in CSV file
Supplementary files format and content: Metadata for processed gene x single-cell matrix in CSV file

source_name: Human brain organoid

extract_protocol:
Live organoids were dissociated into single cells using papain.
Libraries of single cells from dissociated organoids (loaded at a concentration of approximately 1000cells/µL) were prepared using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 protocol from 10x Genomics.

value: Human brain organoid

value: Day 90


title: WT organoid at day 90 (H8)


title: WT organoid at day 90 (H7)


title: 081619_BW7324_s4080

first: Sean

last: Lawler

address: 75 Francis St

institute: Brigham and Women's Hospital

data_processing:
Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance.
The final pool was sequenced on an Illumina NovaSeq 6000 targeting 40 million 150bp read pairs per library at the Dana-Farber Cancer Institute Molecular Biology Core Facilities
Sequenced reads were aligned to the UCSC mm10 reference genome assembly and gene counts were quantified using STAR (v2.7.3a)
Assembly: mm10
Supplementary files format and content: STAR_Gene_Counts.csv: raw read counts in csv format
Supplementary files format and content: Cuff_Gene_Counts.csv: FPKM normalized gene counts generated using cufflinks in csv format

source_name: LysM-Cre:Ribotag +BDL

extract_protocol:
Rnaeasy Kit (Qiagen)
rRNA depletion was performed using Qiagen FastSelect reagents according to manufacturers protocols. Libraries were prepared using Roche Kapa RNA HyperPrep strand specific sample preparation kits from 100ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7

value: Liver

value: Myeloid cells

value: bile duct ligation 17d


title: Patient nCounter 64

data_processing: We refined the 20-housekeeping gene list defined in NanoString IO360 panel using three independent datasets grouping triple negative breast cancer patients retrieved from xenaBrowser [TCGA BRCA primary tumors with 123 patients, Chin et al. 2006 : 41 patients and Hess et al. 2006  : 27 patients]. We computed gene expression variability as the inter-quantile (5%-95%) ratio in each dataset and selected 6 of the 20 genes showing ratios under 1.5 in all datasets: ERCC3, POLR2A, SF3A1, TBC1D10B, TMUB2, UBB.  We normalized the expression values using NanoStringNorm R package v1.2.1.1 with options CodeCount ='geo.mean', Background ='mean.2sd', SampleContent ='housekeeping.geo.mean', round.values = TRUE, take.log = TRUE.


title: 081619_BW7324_s4066


title: WT organoid at day 60 (A8)

value: Day 60


title: SMCs, ChIP, WT_IP_2

source_name: Pol II pSer5 ChIPSeq

value: RNA Pol II ser5 (Abcam ab5408)


title: SMCs, ChIP, WT_IP_1


title: Patient nCounter 62


title: 081619_BW7324_s4236

source_name: LysM-Cre:Hmoxflfl:Ribotag +BDL


title: WT organoid at day 60 (A7)


title: Patient nCounter 63


title: WT organoid at day 60 (A6)


title: SMCs, ChIP, Mut_Input_2


title: SMCs, ChIP, WT_Input_1


title: WT mouse heart, P3, biol rep 3

value: Heart


title: 081619_BW7324_s4234


title: SMCs, ChIP, Mut_Input_1


title: Patient nCounter 66


title: 081619_BW7324_s4624

value: control


title: WT organoid at day 60 (A5)


title: Patient nCounter 61


title: KIF26A KO organoid at day 90 (G12)

value: KIF26A KO


title: WT organoid at day 90 (G9)


title: 081619_BW7324_s5810


title: 081619_BW7324_s4598


title: SMCs, ChIP, Mut_IP_2


title: SMCs, ChIP, Mut_IP_1


title: 081619_BW7324_ s4597


title: Patient nCounter 60


title: Patient nCounter 57


title: ileum, LCM, H246, NEC

city: Pittsburgh

first: David

last: Peters

address: 204 Craft Avenue

institute: Magee-Womens Research Institute

data_processing:
DNA sequence reads were quality trimmed and adaptor sequences were removed using Trim-Galore.
The reads were aligned to the human refrence sequence using Bismark Bisulfite Read Mapper in paired-end, bowtie2 mode. Any unmapped reads were aligned in single-end, bowtie2 mode.
Read duplicates were removed using Bismark.
Methylation was called on paired-end and single-end files and then merged to determine the methylation status for each CpG site.
DNA methylation signatures were determined using the beta-binomial test implemented in the R packages methylSig and DSS.
Assembly: GRCh38
Supplementary files format and content: Bismark Coverage output merged from PE and SE methylation extractor outputs. <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: ileum

extract_protocol:
Snap-frozen specimens were mounted on appropriate embedding molds with clear OCT compound and sectioned on a cryostat instrument. These sections were mounted on membrane slides, stained with toluidine blue and air-dried. Laser dissection and capture of the chosen tissue region of interest (ROI) were cut by the laser capture microdissection (LCM) Instrument. The ROI laser capture tissue samples were subsequently collected into appropriate PCR tube for further DNA extraction and subsequent studies. DNA was extracted from LCM tissue using the Nucleospin Tissue XS Kit (Macherey–Nagel) with the modifcations suggested for LCM.
DNA was sheared with Covaris to a size of ~175bp. Libraries were prepared using the KAPA HyperPrep Kit. Libraries were bisulfite converted post-ligation using the EZ DNA Methylation-Direct Kit and amplified 12 cycles. Libraries were sequenced on an Illumina HiSeqX using 150-bp paired-end reads.

treatment_protocol: Intestinal tissue samples were procured if resected for NEC or other noninflammatory indications, such as reanastomosis, spontaneous intestinal perforation or anorectal malformation. Resections of intestinal tissue were snap frozen and stored at -80 degrees Celsius until further analysis. Non-NEC tissue samples were healed NEC tissue obtained during surgical reanastomosis.

value: ileum

value: laser capture microdissection

value: epithelial

tag: disease state

value: NEC


title: Patient nCounter 59


title: ileum, LCM, G211, non-NEC

value: non-NEC


title: Patient nCounter 58


title: KIF26A KO organoid at day 90 (G11)


title: Patient nCounter 55


title: KIF26A KO organoid at day 60 (A11)


title: MeDIP_FA4-IP

city: beijing

first: shan

last: wang

address: 2yabao road

institute: Capital Institute of Pediatrics

data_processing:
Raw reads (Raw Data) were generated after sequencing on the Illumina NovaSeq6000 sequencer, image analysis, base calling and quality control.
Using Q30 for quality control. Then, using cutadapt software (v1.9.1) to remove connectors, remove low-quality reads, and obtain high-quality reads (clean reads)
The clean reads were aligned to the genome using bowtie2 software (v2.2.4).
Using MACS software (v2.1.1) for methylation enrichment peak identification (Peak Calling) and diffReps software (v1.55.4) to identify differentially methylated regions.Then, using UCSC RefSeq database for annotation, link methyl Peak and gene information.
Assembly: mm10
Supplementary files format and content: excel format for demethylated sites

source_name: sv 129 cells,FA4-IP

growth_protocol: Sv 129 cells were maintained in Dulbecco’s modifed Eagle’s medium  (DMEM, Gibco) supplemented with 15% fetal bovine serum (FBS) and antibiotics. Sv129 cells were placed at 37°C, 5% CO2 in a humidified incubator and passaged every 2–3 days. The culture medium was changed daily.

extract_protocol:
Genomic DNA was extracted and fragmented to 100-300 bp using DNeasy kit (QIAGEN Inc., Germany).
Adapter sequences (Illumina, Inc., USA) were added to the fragmented DNA. Heat-denatured to single-stranded DNA sequences were immunoprecipitated with 5mC antibody (Diagenode, USA), and the pellet was purified. Library amplification and purification reactions were performed on IP DNA that had been immunoprecipitated and input DNA that had not been immunoprecipitated.

treatment_protocol: The cells was respectively cultured by control medium (final concentration: 4mg/L) and folate-deficiency medium (final concentration:0mg/L).

value: mouse embryonic stem cells

tag: ip antibody

value: 5mC antibody (Diagenode, USA)

value: folate-treated


title: ileum, LCM, H114, NEC


title: MeDIP_FA0-IP

source_name: sv 129 cells,FA0-IP

value: folate-deficiency-treated


title: KIF26A KO organoid at day 60 (A10)

value: Human brain organoid


title: colon, LCM, G49, non-NEC

source_name: colon

value: colon


title: Patient nCounter 56


title: MeDIP_FA0-Input

source_name: sv 129 cells,FA0-input

value: none (input)


title: ileum, LCM, G230, NEC


title: KIF26A KO organoid at day 60 (A9)

value: Day 60


title: Patient nCounter 53


title: Human, 22wk gestation, rep1

data_processing:
Raw Illumina reads for all datasets were demultiplexed and converted to FASTQ using bcl2fastq (Illu- mina). For human, sequencing adapter and PCR primer sequences were trimmed from reads using cutadapt 2.7 (Martin, 2011). For human, reads were aligned with STAR v2.7.1a (Dobin et al., 2013) to GRCh38 Ensembl release 98, and a gene count matrix was obtained using the featureCounts function of Subread v1.6.0 (Liao et al., 2014).
GRCh38 Ensembl release 98
22wk_counts.txt is a gene expression matrix where each row represents a gene and each column represents either a gene characteristic or a cell. The column names for this matrix are in the 22wk_counts.txt file. The row names for this matrix are located in the file 22wk_gene_rownames.txt

extract_protocol:
The experiment was performed using the same procedure as the mouse samples unless noted here. The heart was kept in cold, sterile PBS. It was dissected to remove the atria, outflow tract, and valves, keeping only the ventricles. Dissociation was performed as described for the mouse samples except that multiple tubes of the 600 μl mix were used for each heart. The antibodies used for staining were: Pacific Blue CD235a (Biolegend #349107), FITC CD36 (Biolegend #336204), APC/Cy7 PECAM1 (Biolegend #303119), Pacific Blue CD45 (Biolegend #304021). The gates were set up to sort cells with low DAPI, low CD45 (hematopoietic cells), low CD235A (erythroid cells), high PECAM1 (endo- thelial marker), and low FITC. After staining each cell was sorted into a separate well of a 96-well plate containing 4 μl lysis buffer. Cells were spun down after sorting and stored at −80°C until cDNA synthesis. A total of 1920 PECAM1+ CD36 and PECAM1+ cells were sorted and processed for cDNA synthesis. Cells were analyzed on the AATI 96-capillary fragment analyzer, and a total of 1382 cells that had sufficient cDNA concentration were barcoded and pooled for sequencing.
Synthesis of cDNA and library preparation for the fetal human heart cells was performed using the Smart-seq2 method as previously described (Picelli et al., 2014; Su et al., 2018). Libraries from the fetal human heart cells were part of a pool of samples that was sequenced on four lanes of a Illumina NovaSeq 6000 S4 flow cell.

value: Wt


title: Patient nCounter 52


title: Human, 14wk gestation, rep1

data_processing:
Raw Illumina reads for all datasets were demultiplexed and converted to FASTQ using bcl2fastq (Illu- mina). For human, sequencing adapter and PCR primer sequences were trimmed from reads using cutadapt 2.7 (Martin, 2011). For human, reads were aligned with STAR v2.7.1a (Dobin et al., 2013) to GRCh38 Ensembl release 98, and a gene count matrix was obtained using the featureCounts function of Subread v1.6.0 (Liao et al., 2014).
GRCh38 Ensembl release 98
14wk_counts.txt is a gene expression matrix where each row represents a gene and each column represents either a gene characteristic or a cell. The column names for this matrix are in the 14wk_counts.txt file. The row names for this matrix are located in the file 14wk_gene_rownames.txt

extract_protocol:
The experiment was performed using the same procedure as the 22-week heart unless noted here. The antibodies used for staining were PerCP/Cy5.5 CD235a (Biolegend #349110), PerCP/Cy5.5 CD45 (Biolegend #304028), FITC CD36 (Biolegend #336204), APC/Cy7 PECAM1 (Biolegend #303119). The gates were set up to sort cells with low DAPI, low CD45 (hematopoietic cells), low CD235A (erythroid cells), high PECAM1 (endothelial marker), and either low or high FITC. A total of 1824 PECAM1+ CD36-, PECAM1+ CD36+ and PECAM1+ cells from the 11-week heart and 1920 PECAM1+ CD36-, PECAM1+ CD36+ and PECAM1+ cells from the 14-week heart were sorted and processed for cDNA synthesis. A total of 1530 11-week and 1272 14-week cells that had sufficient cDNA concentration were barcoded and pooled for sequencing.
Synthesis of cDNA and library preparation for the fetal human heart cells was performed using the Smart-seq2 method as previously described (Picelli et al., 2014; Su et al., 2018). Libraries from the fetal human heart cells were part of a pool of samples that was sequenced on four lanes of a Illumina NovaSeq 6000 S4 flow cell.

value: Heart


title: RNA-seq_FA4

data_processing:
PCR enrichment and purification of PCR contributed to eatablish final library assessing using Agilent 2100 BioAnalyzer.
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters.
The processed reads from each sample were aligned using HISAT2 against the reference genome.
The gene expression analyses were performed with StringTie(v1.3.3b).
DESeq(v1.28.0) was used to analyze the DEGs between samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: sv129 cells, with folate-treated

extract_protocol:
Sv 129 cells was used to manufactured as total RNA which selected TRIzol reagent (Invitrogen).
The NEB Next Ultra RNA Library Prep Kit for llumina (NEB) was used to construct the libraries for sequencing following manufacturer's protocols.


title: ileum, LCM, G161, non-NEC


title: RNA-seq_FA0

source_name: sv129 cells, with folate-deficiency-treated


title: hMeDIP_FA4-IP

data_processing:
Raw reads (Raw Data) were generated after sequencing on the Illumina NovaSeq6000 sequencer, image analysis, base calling and quality control.
Using Q30 for quality control. Then, using cutadapt software (v1.9.1) to remove connectors, remove low-quality reads, and obtain high-quality reads (clean reads)
The clean reads were aligned to the mouse genome (MM10) using bowtie2 software (v2.2.4).
Using MACS software (v2.1.1) for hydroxymethylation enrichment peak identification (Peak Calling) and diffReps software (v1.55.4) to identify differentially hydroxymethylated regions.Then, using UCSC RefSeq database for annotation, link hydroxymethyl Peak and gene information.
Assembly: mm10
Supplementary files format and content: excel format for demethylated sites
Library strategy: hMeDIP-seq

extract_protocol:
Genomic DNA was extracted and fragmented to 100-300 bp using DNeasy kit (QIAGEN Inc., Germany).
Adapter sequences (Illumina, Inc., USA) were added to the fragmented DNA. After adding the adapter, a part of the DNA marked as "Input" (about 10%) was retained, and the rest was subjected to immunoprecipitation with the GenSeq® hMeDIP Kit (GenSeq Inc., China). Library amplification and purification reactions were performed on immunoprecipitated DNA and unimmunoprecipitated input DNA, respectively.

tag: medip antibody

value: hMeDIP Kit (GenSeq Inc., China)


title: KIF26A KO organoid at day 60 (A12)

value: KIF26A KO


title: Patient nCounter 51

extract_protocol: Total tumor RNA was extracted from four to six 10-micron tumor sections after identification of the residual tumor by a pathologist on a corresponding H&E section. RNA was extracted using the High Pure FFPET RNA Isolation Kit (Roche®), following the manufacturer’s instructions. RNA quantity and quality were assessed by Nanodrop 1000 spectrophotometer (ThermoFisher, Waltham, MA, USA) and 2100 Bioanalyser with Agilent RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). 200ng of total RNA was used from each sample for gene expression profiling (acceptation criteria 260/280 ratio: 1.8 -2.3, 230/280 ratio: 1.7-2.3).

tag: age


title: Human, 11wk gestation, rep1

data_processing:
Raw Illumina reads for all datasets were demultiplexed and converted to FASTQ using bcl2fastq (Illu- mina). For human, sequencing adapter and PCR primer sequences were trimmed from reads using cutadapt 2.7 (Martin, 2011). For human, reads were aligned with STAR v2.7.1a (Dobin et al., 2013) to GRCh38 Ensembl release 98, and a gene count matrix was obtained using the featureCounts function of Subread v1.6.0 (Liao et al., 2014).
GRCh38 Ensembl release 98
11wk_counts.txt is a gene expression matrix where each row represents a gene and each column represents either a gene characteristic or a cell. The column names for this matrix are in the 11wk_counts.txt file. The row names for this matrix are located in the file 11wk_gene_rownames.txt

source_name: Heart

tag: tissue


title: ileum, LCM, G155, non-NEC

value: ileum

tag: cell type


title: hMeDIP_FA0-IP

tag: treatment


title: hMeDIP_FA0-Input


title: sv 129 cells, with folate-treated, input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Total DNA was extracted by Simple ChIP Enzymatic chromatin IP kit (9005, CST) based on the manufacturer’s protocol.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 200-500 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.


title: ABE, SB505124, R2

city: Shanghai

first: Mingliang

last: zhang

address: No.280 Chongqing South Road

institute: Shanghai Jiao Tong University school of medicine

data_processing:
After quantified by TBS380 (Picogreen), paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 platform sequencer (2 ×150bp read length). The raw paired end reads were trimmed and quality controlled by Cutadapt (v1.15) software to get high quality sequence (Clean Data) for further analysis.
Then clean reads were mapping to the reference genome using HISAT2 v2.0.5 software. The mapped reads of each sample was used HTseq (0.9.1) statistics to compare the Read Count values, and the DEGs (differential expression genes) via different groups were used by FPKM to standardize the expression. Then DEGs were analyzed by DESeq (1.30.0).
Assembly: hg38
Supplementary files format and content: Microsoft EXCEL xlsx. Files include reads count, log2FC and Class.

extract_protocol:
Total RNA was extracted from HEK293 using TRIzol Reagent (Invitrogen) and genomic DNA was removed using DNase I (Takara). Quality of samples were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies) and qualified using the ND-2000(Nanodrop Technologies).
An amount of 3μg total RNA was used for RNA-seq transcriptome library preparation following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA).After quantified by TBS380 (Picogreen), paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 platform sequencer (2 ×150bp read length). The raw paired end reads were trimmed and quality controlled by Cutadapt (v1.15) software to get high quality sequence (Clean Data) for further analysis .

value: A cell line exhibiting epithelial morphology that was isolated from human embryo kidney tissue

tag: transfection

value: a plasmid expressing ABE7.10 and gRNA targeting site 18


title: colon, LCM, G208, non-NEC

value: laser capture microdissection

value: epithelial


title: ileum, LCM, G152, non-NEC

value: non-NEC


title: Patient nCounter 50


title: ABE, SB505124, R1

tag: cell line


title: Patient nCounter 48


title: colon, LCM, G80, NEC

value: NEC


title: Patient nCounter 49


title: colon, LCM, G62, non-NEC


title: ABE, ITD1, R2


title: ABE, ITD1, R1


title: sv 129 cells, with folate-treated, IP

value: folate-treated


title: sv 129 cells, with folate-deficiency-treated, input

value: folate-deficiency-treated


title: colon, LCM, G54, non-NEC


title: Patient nCounter 46


title: ABE, DMSO, R2

value: DMSO


title: ileum, LCM, G20, non-NEC


title: ABE, DMSO, R1


title: sv 129 cells, with folate-deficiency-treated, IP


title: ileum, LCM, G8, non-NEC


title: 20m_M_R3 [EH_12]

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

data_processing:
Reads were aligned to GRCm39/GENCODE M26 using STAR v.2.7.6.a with --sjdbOverhang 149
Trancripts were assmbled with the aid of Gencode M26 annotations using StringTie v.2.1.1 with -e
The stringtie PrepDE.py script was used to assembl the stringtie.gtf files into a read count matrix
Assembly: GRCm39
Supplementary files format and content: Gene count matrix in flat text file

extract_protocol:
RNA was extracted usingZymo Direct-zol RNA kit following manufacturer's instruction.
PolyA+ mRNA was selected using oligo-T beads and libraries were constructed using NEBNext Ultra II RNA Library Prep (unstranded)

tag: strain

tag: genotype

value: WT

value: 20 months

tag: Sex

value: male


title: colon, LCM, G7, NEC

value: colon


title: 20m_M_R2 [EH_11]

value: Heart


title: Patient nCounter 47

tag: lve

tag: tils

tag: metastasis


title: ileum, LCM, G250, non-NEC


title: 20m_F_R3 [EH_09]

value: female


title: 20m_F_R2 [EH_08]


title: 20m_F_R1 [EH_07]


title: 20m_M_R1 [EH_10]


title: Patient nCounter 45


title: 4m_M_R3 [EH_06]

value: 4 months


title: Pancreatic cancer 3D in vitro vascular network

city: Davis

first: Matthew

last: Curtis

address: One Shields Dr.

institute: University of California, Davis

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0
Assembly: GRCh38-3.0.0
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: ECFC-Ecs and pancreatic cancer-associated fibroblasts

extract_protocol:
Cells were digested out of 3D in vitro fibrin hydrogels with 1 hour treatment of 50 unit/mL nattokinase and 10 min. of 0.05% Trypsin-EDTA.  Cells were washed and filtered through 40 um filter before sequencing.
Library was performed according to the manufacturerÆs instructions (single cell 3Æ v3 protocol, 10x Genomics).

tag: growth protocol

value: vascular network


title: Pancreas 3D in vitro vascular network

description: 10x Genomics

source_name: ECFC-Ecs and normal hepatic stellate cells


title: Heart 3D in vitro vascular network

description: 10x Genomics

source_name: ECFC-Ecs and cardiac fibroblasts

value: ECFC-Ecs and cardiac fibroblasts


title: Lung 3D in vitro vascular network

description: 10x Genomics

source_name: ECFC-Ecs and normal human lung fibroblasts


title: 2D in vitro ECFC-EC monolayer

description: 10x Genomics

source_name: ECFC-Ecs

value: ECFC-Ecs

value: monolayer


title: Skin 3D in vitro vascular network

description: 10x Genomics

source_name: ECFC-Ecs and normal human dermal fibroblasts


title: Bone marrow 3D in vitro vascular network

description: 10x Genomics

source_name: ECFC-Ecs and bone marrow stromal cells

value: ECFC-Ecs and bone marrow stromal cells


title: ileum, LCM, G223, NEC

value: ileum

value: laser capture microdissection

value: epithelial


title: ileum, LCM, G33, non-NEC

value: non-NEC


title: ileum, LCM, G63, non-NEC


title: ileum, LCM, G154, NEC

value: NEC


title: 4m_M_R2 [EH_05]

value: WT


title: ileum, LCM, G34, non-NEC


title: 4m_M_R1 [EH_04]


title: TJ46-1

city: Beijing

first: Chao

last: Chen

address: Datun

department: CAS Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Sequencing reads were qualified using FASTQC (v0.11.9) followed by connector removal and reserving the reads with length at least 5 bases using Trim Galore (v0.6.7).
The processed reads were aligned to GRCh19 (hg19) reference genome using BWA (V0.7.9a) followed by sorted using samtools (v0.1.19).
The  Duplication Reads (PCR repeated Reads) were compared by Picard (v1.115) , and realigned the sequences around InDel to reduce false positives in SNP detection by GenomeAnalysisTK-3.8.
Assembly: GRCh19
Library strategy: Whole Genome Sequencing

source_name: a GBM primary tissue

growth_protocol: TJ46 cells (2 × 106) in a 10-cm dish were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% dialyzed fetal bovine serum (HyClone) and 1% penicillin-streptomycin.

extract_protocol:
DNA extraction assay was performed by using the Dneasy Blood and Tissue Kits (Qiagen, #51304).
Sequencing libraries were prepared using the NEBNext DNA Library Prep Master Mix Set (Illumina) according to the manufacturer’s instructions.

treatment_protocol: TJ46 cells were cultured for 24 hours

value: GBM cell lines


title: 4m_F_R2 [EH_02]


title: 4m_F_R3 [EH_03]


title: TJ46-2


title: colon, LCM, G26, NEC


title: colon, LCM, G205, NEC


title: colon, LCM, G11, non-NEC


title: ileum, LCM, G6, NEC


title: colon, LCM, G75, NEC


title: ileum, LCM, G13, NEC


title: GBM Glc(+) IgG rep

description: Glcplus_IgG_repvsGlc(+)_Input_rep.rmdup.subtract.bw

data_processing:
Sequencing reads were qualified using FASTQC (v0.11.9) followed by connector removal and reserving the reads with length at least 36 bases using Trim Galore (v0.6.7).
The processed reads were aligned to GRCh38 (hg38) reference genome using BWA (v0.7.17) followed by duplicate reads removal using sambamba (v0.8.0).
The peaks were called from alignment results using call peak function of MACS2 (v2.2.7.1) with default parameters and annotated by the annotatePeaks.pl function of HOMER (v4.8.3)
Assembly: GRCh38
Supplementary files format and content: bw

source_name: GBM cell line

growth_protocol: U87 cells (2 × 107) in a 15-cm dish were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% dialyzed fetal bovine serum (HyClone) and 1% penicillin-streptomycin.

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay was performed by using the SimpleChIP Enzymatic Chromatin IP kit (#9003, Cell Signaling Technology) according to the manufacturer’s instructions.
Sequencing libraries were prepared using the NEBNext DNA Library Prep Master Mix Set (Illumina) according to the manufacturer’s instructions.

treatment_protocol: U87 cells were deprived of glucose or 25mM for 18 hours

tag: chip antibody

value: IgG

value: glucose 25mM


title: GBM Glc(+) TF rep

description: Glc(+)_TF_repvsGlc(+)_Input_rep.rmdup.subtract

value: ATF4(Cell Signaling Technology,#11815)


title: GBM Glc(+) Input rep


title: GBM Glc(+) TF


title: Patient nCounter 32

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

institute: University of Bordeaux

source_name: Residual Triple Negative Breast Cancer


title: Patient nCounter 54


title: Patient nCounter 42


title: Patient nCounter 33


title: Patient nCounter 34


title: Patient nCounter 44


title: Patient nCounter 35


title: Patient nCounter 38


title: Patient nCounter 43


title: Patient nCounter 37


title: 4m_F_R1 [EH_01]

value: Heart

value: female


title: GBM Glc(+) Input


title: GBM Glc(+) IgG


title: colon, LCM, G251, non-NEC

value: colon

tag: disease state


title: colon, LCM, G176, non-NEC


title: colon, LCM, G174, non-NEC


title: nanoCT H3K27me3

city: Stockholm

first: Marek

last: Bartosovic

address: Solnavagen 9

country: Sweden

institute: Karolinska Institute

data_processing:
Fastq files were demultiplexed based on antibody barcode
R1 and R3 are biological paired end reads.
R2 is modality index + linker regions used for demultiplexing (ATAC/H3K27ac/H3K27me3). I1 is sample index.
Demultiplexed files were processed using cellranger-atac v1.2.0
Cells that pass the QC were called using custom scripts by the number of reads per cell and fraction fo reads in peak region parameters
Peak calling was performed using MACS2 callpeak
Reduction of dimensionality was performed using LSI and UMAP implemented in packages Seurat and Signac
Marker peak regions were called using seurat/signac
bigwig tracks per cluster were generated by filtering possorted_bam.bam file (cellranger) by cell barcodes and generating bigwig using deeptools tool coverageBam
Assembly: mm10
Supplementary files format and content: bigwig tracks per cluster, csv files with marker regions per cluster, seurat object that can be directly loaded into R,bed file contatining fragment files with single-cell barcodes, h5seurat object that can be loaded into R/python

source_name: Brain

growth_protocol: Brain was dissociated using Miltenyi neural tissue dissociation kit P (130-092-628), cleared with Debris removal solution (130-109-398), filtered through 50 um strainer and cell suspension was used for nuclei extraction.

extract_protocol:
Nuclei were extracted using NP-40 / Digitonin buffer. Nano-Cut&Tag was performed with 1:100 diluted primary antibody and 1:100 diluted in house produced nanobody-Tn5 fusion. Tagmentation was perfmed for 1h at 37C in transposition buffer containing 10 mM MgCl2. Tagmented nuclei were processed using the 10x scATAC-seq kit according to manufactureres instructions skipping Step 1 "Transposition" and continuing from Step 2.0 "Generation and barcoding".
The barcoded DNA was recovered from droplet emulsion according to Chromium NextGEM SingleCell ATAC ReagentKits v1.1(Step 3). Recovered DNA was tagmented using MeB (P7) loaded Tn5, purified using Zymo DNA clean and concentrator kit and library amplified by PCR

value: Brain

value: H3K27me3 (Cell Signaling, 9733T)


title: nanoCT ATAC H3K27ac H3K27me3 rep 1

value: H3K27me3 (Abcam, Ab6002)

tag: barcodes


title: SPOTS Breast cancer ADT

description:
mmtv_pymt_ADT.csv
mmtv_pymt_spatial.tar

data_processing:
spaceranger v1.3.0, 10X Genomics
CITE-seq-Count v1.4.3, https://github.com/Hoohm/CITE-seq-Count
Assembly: GRCm38 (mm10)
Supplementary files format and content: h5, count matrix

source_name: mouse breast tumor

extract_protocol:
Mouse spleen and breast cancer samples were prepared using the Visium Spatial Gene Expression Kit according to the manufacturer’s instructions.
Transcript (GEX) and antibody derived tags (ADT) libraries were constructed according to SPOTS protocol. Spleen data were sequenced on the Illumina Nextseq 500. Breast cancer data were sequenced on the Illumina Nextseq 6000.

value: MMTV-PyMT


title: nanoCT H3K27ac H3K27me3 rep 1

value: H3K27ac:ATAGAGGC, H3K27me3:CCTATCCT


title: colon, LCM, G130, non-NEC

source_name: colon

value: laser capture microdissection


title: Patient nCounter 40

city: Bordeaux


title: Patient nCounter 39


title: Patient nCounter 41


title: colon, LCM, G173, NEC

value: epithelial


title: SPOTS Breast cancer GEX

description:
mmtv_pymt_GEX_filtered_feature_bc_matrix.h5
mmtv_pymt_spatial.tar


title: Patient nCounter 31


title: 4WK_CT_2

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

data_processing:
Sequenced were mapped to GRCh38 whole genome using STAR 2.7.0d with parameters --readFilesCommand zcat --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
feature counted with htseq-count version 0.11.2
Assembly: GRCh38 release 96
Supplementary files format and content: raw table of counts for each sample

source_name: Endothelial Progenitor Cells

extract_protocol:
Total RNA was isolated from cells using a Maxwell RSC instrument (Promega) following manufacturer’s instructions
Libraries were prepared using a TruSeq stranded mRNA-seq library from total RNA

tag: condition

value: Diabetic Control

value: Endothelial Progenitor Cells

value: 5mM D-glucose


title: 4WK_DG_3

value: Diabetic

value: 25mM D-glucose


title: 4WK_CT_3


title: 4WK_DG_2


title: colon, LCM, G196, non-NEC

value: non-NEC


title: KIF26A KO organoid at day 90 (G10)

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 and v5.0.0
Cellranger-output filtered feature matrics were loaded into R using Seurat, which was used for subsequent feature filtering, normalization, variance-stabilization, sample integration, PCA, and cell type annotation
Assembly: GRCh38-1.2.0
Supplementary files format and content: Processed gene x single-cell matrix in CSV file
Supplementary files format and content: Metadata for processed gene x single-cell matrix in CSV file

source_name: Human brain organoid

extract_protocol:
Live organoids were dissociated into single cells using papain.
Libraries of single cells from dissociated organoids (loaded at a concentration of approximately 1000cells/µL) were prepared using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 protocol from 10x Genomics.

value: Human brain organoid

value: KIF26A KO

tag: time

value: Day 90


title: colon, LCM, G195, non-NEC

data_processing:
DNA sequence reads were quality trimmed and adaptor sequences were removed using Trim-Galore.
The reads were aligned to the human refrence sequence using Bismark Bisulfite Read Mapper in paired-end, bowtie2 mode. Any unmapped reads were aligned in single-end, bowtie2 mode.
Read duplicates were removed using Bismark.
Methylation was called on paired-end and single-end files and then merged to determine the methylation status for each CpG site.
DNA methylation signatures were determined using the beta-binomial test implemented in the R packages methylSig and DSS.
Assembly: GRCh38
Supplementary files format and content: Bismark Coverage output merged from PE and SE methylation extractor outputs. <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

extract_protocol:
Snap-frozen specimens were mounted on appropriate embedding molds with clear OCT compound and sectioned on a cryostat instrument. These sections were mounted on membrane slides, stained with toluidine blue and air-dried. Laser dissection and capture of the chosen tissue region of interest (ROI) were cut by the laser capture microdissection (LCM) Instrument. The ROI laser capture tissue samples were subsequently collected into appropriate PCR tube for further DNA extraction and subsequent studies. DNA was extracted from LCM tissue using the Nucleospin Tissue XS Kit (Macherey–Nagel) with the modifcations suggested for LCM.
DNA was sheared with Covaris to a size of ~175bp. Libraries were prepared using the KAPA HyperPrep Kit. Libraries were bisulfite converted post-ligation using the EZ DNA Methylation-Direct Kit and amplified 12 cycles. Libraries were sequenced on an Illumina HiSeqX using 150-bp paired-end reads.

tag: tissue

value: colon


title: Patient nCounter 36

data_processing: We refined the 20-housekeeping gene list defined in NanoString IO360 panel using three independent datasets grouping triple negative breast cancer patients retrieved from xenaBrowser [TCGA BRCA primary tumors with 123 patients, Chin et al. 2006 : 41 patients and Hess et al. 2006  : 27 patients]. We computed gene expression variability as the inter-quantile (5%-95%) ratio in each dataset and selected 6 of the 20 genes showing ratios under 1.5 in all datasets: ERCC3, POLR2A, SF3A1, TBC1D10B, TMUB2, UBB.  We normalized the expression values using NanoStringNorm R package v1.2.1.1 with options CodeCount ='geo.mean', Background ='mean.2sd', SampleContent ='housekeeping.geo.mean', round.values = TRUE, take.log = TRUE.

tag: age


title: 4WK_CT_1

tag: cell type

tag: treatment


title: D2

first: Yan

last: Hu

address: 99th Shangda Rd

institute: Shanghai University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: tibia plateau

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: Subchondral bone pellets of about 1-2 cm were carefully acquired with a bone rongeur from the opposite side of cartilage, and then treated with collagenase

tag: disease

value: osteoarthritis

value: 74 years old

value: TKA

tag: subchondral bone subset

value: medial plateau


title: C2

value: lateral plateau


title: 4WK_DG_1


title: Patient nCounter 25


title: Patient nCounter 27


title: Patient nCounter 23


title: Patient nCounter 26


title: Patient nCounter 24


title: colon, LCM, G102, NEC

value: laser capture microdissection

value: NEC


title: colon, LCM, G149, non-NEC

value: epithelial


title: D1

value: 72 years old


title: nanoCT ATAC H3K27ac H3K27me3 rep 2

value: Brain

tag: strain

value: H3K27me3 (Abcam, Ab6002)


title: nanoCT H3K27ac H3K27me3 rep 2

value: H3K27ac:ATAGAGGC, H3K27me3:CCTATCCT


title: IM3: Immortalized Fibroblast MG132

city: Madison

last: Morrow

state: Wisconsin

address: 1111 Highlange Ave.

institute: University of Wisconsin - Madison

data_processing:
Firstly, Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 [2] to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/. The mapped reads of each sample were assembled using StringTie [3]. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie [3] and edgeR [4] was used to estimate the expression levels of all transcripts.
StringTie [3] was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR [4].
Genome_build: Mus musculus (Version: v88)
Supplementary_files_format_and_content: Table S1 - RNA Sequencing TPM Normalized to ERCC

source_name: tail

growth_protocol: Fibroblasts were cultured with 37°C/5% CO2 in RPMI with Glutamine (Invitrogen 11875-093), 10% FBS (Invitrogen 16000044), 55 µM β-Mercaptoethanol (Invitrogen 21985-023), 100 µM asparagine and 100 µg/ml Penicillin-Streptomycin (Invitrogen 15140122), 25 µg/mL Amphoterecin B (Sigma-Aldrich A9528)

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen 74104) according to the manufacturer’s instructions.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: All samples were treated to generate distinct cell states as indicated in each sample and additionally treated with either DMSO or MG132

value: Fibroblast

tag: cell state

value: Immortalized


title: TF-Glc_rep

data_processing:
Sequencing reads were qualified using FASTQC (v0.11.9) followed by connector removal and reserving the reads with length at least 36 bases using Trim Galore (v0.6.7).
The processed reads were aligned to GRCh38 (hg38) reference genome using BWA (v0.7.17) followed by duplicate reads removal using sambamba (v0.8.0).
The peaks were called from alignment results using call peak function of MACS2 (v2.2.7.1) with default parameters and annotated by the annotatePeaks.pl function of HOMER (v4.8.3)
Genome_build: GRCh38
Supplementary_files_format_and_content: bw

treatment_protocol: U87 cells were deprived of glucose for 18 hours

value: GBM cell lines

value: ATF4(Cell Signaling Technology,#11815)

value: glucose deprivation


title: IM2: Immortalized Fibroblast MG132


title: control IgG rep2

city: Kyoto

first: Yuji

last: Fukushima

address: 53 Shogoin Kawahara-cho

country: Japan

institute: Kyoto University

data_processing:
RTA3 software was used for base-calling.
Adaptor sequences and low quality bases were trimed using Trimmomatic-0.38.
Trimmed reads were mapped to reference genome with HISAT2-2.1.0.
Transcript assembly and quantification was performed with StringTie-2.1.3b.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: xlsx file including TPM with adjusted p-values.

source_name: Enriched CD153+ PD-1+ CD44hi CD4+ T cells

extract_protocol:
RNA was extracted form the in vitro stimulated cells using Trizol reagent.
RNA-seq analysis was performed at Macrogen Japan (Kyoto, Japan). Libraries were generated using SMART-seq v4 Ultra Low Input RNA Kit (Takara Bio) and then sequenced on Illumina NovaSeq 6000.

value: spleen

value: anti-CD3/CD28 Abs + control IgG


title: control IgG rep3


title: RM153 rep1

value: anti-CD3/CD28 Abs + RM153


title: RM153 rep2


title: RM153 rep3


title: control IgG rep1


title: colon, LCM, G14, NEC

value: colon


title: colon, LCM, G25, NEC


title: colon, LCM, G52, NEC


title: colon, LCM, G19, non-NEC

value: non-NEC


title: 20R319: CU-REWIRE3.0-r3

first: zefeng

address: 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology

data_processing:
For deep sequencing analysis of targeted sites, indexs were generated using the targeted site sequence(upstream and downstream 200-nt) of each transcript.
Reads were aligned and quantified using BWA(0.7.17-r1188). Alignment BAMs were then sorted by Samtools(1.9), and RNA editing sites were analyzed using REDitools(1.2) with the following parameters: -t 20 -p -u -m20 -T6-6 -W -v 1 -n 0.0 -e -d -l.
AWK scripts were used to filtered out all the A-to-I or C-to-U conversions within the REWIRE targeting region, which were considered significant if the Fisher’s exact test yielded a p-value less than 0.05.
The mutations that appeared in control and experimental groups simultaneously were considered to be due to single nucleotide polymorphism.
Supplementary_files_format_and_content: Matrix table with the editing rate (from RNA-seq and Sanger-seq) of the on-target site of each sample

source_name: HEK293T cell

growth_protocol: 293T human embryonic kidney cell line was cultured in DMEM (high glucose) medium containing 10% fetal bovine serum (FBS, Hyclone)

extract_protocol:
The RNAs were isolated with TRIzol reagent following the manufacturer’s instructions.
Libraries were generated  using the NEBNext RNA Library  Kit (NEB, cat#E6310X, E7760L, E6609L).

treatment_protocol: To transient transfect plasmids into cells, 2μg of plasmids were transfected into cells in 6 well plate, using lipofectamine 3000 (Invitrogen) according to the manufacturer’s instruction. After 48 h, cells were collected for further analysis of RNA and protein levels.

value: embryonic kidney

tag: cell line


title: Input_rep


title: IM1: Immortalized Fibroblast MG132


title: Patient nCounter 28

tag: lve

tag: tils


title: C1

value: osteoarthritis

value: TKA

value: lateral plateau


title: ID3: Immortalized Fibroblast DMSO

value: DMSO


title: IgG_rep

value: IgG


title: Patient nCounter 22

tag: metastasis


title: GBM TF-Glc

data_processing:
Sequencing reads were qualified using FASTQC (v0.11.9) followed by connector removal and reserving the reads with length at least 36 bases using Trim Galore (v0.6.7).
The processed reads were aligned to GRCh38 (hg38) reference genome using BWA (v0.7.17) followed by duplicate reads removal using sambamba (v0.8.0).
The peaks were called from alignment results using call peak function of MACS2 (v2.2.7.1) with default parameters and annotated by the annotatePeaks.pl function of HOMER (v4.8.3)
Genome_build: GRCh38

tag: chip antibody


title: GBM Input


title: K177Q-METTL3 reconstituting MDA-MB-231 polysome rep2

city: Taiyuan

first: Xiaoniu

last: He

address: No.99 Longcheng Street

institute: Shanxi Bethune Hospital

data_processing:
The expression of gene transcripts was quantified using stringtie (v2.1.5).
differential gene expression analysis was conducted using STAR 2.7.
Differentially expressed genes were identified as those with FC ≥ 1.5 and with a FDR ≤ 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: txt files include gene FPKM values

source_name: Breast cancer cell

growth_protocol: MDA-MB-231 cells infected by the indicated lentiviruses were maintained in DMEM (Gibco) supplemented with 10% FBS. Cells were maintained at 37°C in a saturated humidity atmosphere containing 95% air and 5% CO2.

extract_protocol:
Collected fractions were pulled into sub-polysome fraction and polysome fraction. Total RNA was isolated from samples with TRIzol reagents following the manufacturer’s instructions.
Poly(A)-selected mRNAs were purified and used for library construction using NEBNext® Ultra™ Directional RNA Library ep Kit for Illumina®. Sub-polysome and polysome samples were subjected to RNA-seq.

treatment_protocol: Cells were treated with 100 µg/mL cycloheximide for 5 min at 37°C. Cells were then lysed with RNasin and layered onto 10–50% sucrose gradient tube and centrifuged at 35,000 rpm using SW41Ti rotor in Beckman Coulter (Optima L-80 ultra centrifuge) for 2 h at 4°C. Gradients were fractionated and monitored at absorbance 260 nm (Biocomp).

tag: genotype

tag: rna type

value: RNA associated with polysome


title: Patient nCounter 30

extract_protocol: Total tumor RNA was extracted from four to six 10-micron tumor sections after identification of the residual tumor by a pathologist on a corresponding H&E section. RNA was extracted using the High Pure FFPET RNA Isolation Kit (Roche®), following the manufacturer’s instructions. RNA quantity and quality were assessed by Nanodrop 1000 spectrophotometer (ThermoFisher, Waltham, MA, USA) and 2100 Bioanalyser with Agilent RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). 200ng of total RNA was used from each sample for gene expression profiling (acceptation criteria 260/280 ratio: 1.8 -2.3, 230/280 ratio: 1.7-2.3).


title: GBM IgG


title: QM3: Quiescent Fibroblast MG132

value: Fibroblast

value: Quiescent


title: ID1: Immortalized Fibroblast DMSO

value: Immortalized


title: QM2: Quiescent Fibroblast MG132


title: 20R317: CU-REWIRE3.0-r1


title: 19R851: CU-REWIRE2.0-r2


title: 19R850: CU-REWIRE2.0-r1


title: 20R318: CU-REWIRE3.0-r2


title: K177Q-METTL3 reconstituting MDA-MB-231 sub-polysome rep2

value: RNA associated with sub-polysome


title: 19R852: CU-REWIRE2.0-r3


title: 19R849: CU-REWIRE1.0-r3


title: ID2: Immortalized Fibroblast DMSO


title: QM1: Quiescent Fibroblast MG132


title: WT-METTL3 reconstituting MDA-MB-231 polysome rep2


title: 19R848: CU-REWIRE1.0-r2


title: WT-METTL3 reconstituting MDA-MB-231 sub-polysome rep2


title: 19R847: CU-REWIRE1.0-r1


title: METTL3-deficient MDA-MB-231 input rep2

data_processing:
Library strategy: MeRIP-seq
MeRIP and input sequencing data were sent to Cutadapt (v2.5) to remove low quality reads and adaptor sequence contaminants under default parameters.
Remaining reads were then aligned to human Ensemble genome GRCh38 using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”.
m6A peaks were identified using exomePeak R package (v2.13.2)　with PEAK_CUTOFF_PVALUE=0.05, PEAK_CUTOFF_FDR=NA, FRAGMENT_LENGTH=200 parameters.
Differential m6A peaks were identified using exomePeak R package (v2.13.2) with FDR<0.05.
The expression of gene transcripts was quantified using featurecount (v1.6.3), and differential gene expression analysis was conducted using DESeq2 R package (1.18.1).
Genome_build: hg38
Supplementary_files_format_and_content: bw files include m6A peaks and genes expression

extract_protocol:
Total RNA was isolated from samples with TRIzol reagents following the manufacturer’s instructions.
Poly(A)+ RNAs were purified using Dynabeads mRNA purification kit, followed by fragmentation and immunoprecipitation with anti-m6A antibody in IP buffer (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.1% NP-40) for 2 h at 4°C. The m6A-IP mixture was then incubated with Dynabeads protein A for an additional 2 h at 4°C. The bound RNA was eluted by competition with N6-methyladenosine and purified using an RNA cleanup kit.

value: untreated


title: 20R355: AI-REWIRE4.1-r2


title: CTRL MDA-MB-231 input rep2


title: K177Q-METTL3 reconstituting MDA-MB-231 input rep2


title: Patient nCounter 29


title: 20R354: AI-REWIRE4.1-r1


title: 20R356: AI-REWIRE4.1-r3


title: WT-METTL3 reconstituting MDA-MB-231 input rep2


title: QD2: Quiescent Fibroblast DMSO


title: SM3: Senescent Fibroblast MG132

value: Senescent


title: SM2: Senescent Fibroblast MG132


title: QD3: Quiescent Fibroblast DMSO


title: QD1: Quiescent Fibroblast DMSO


title: Patient nCounter 14


title: Patient nCounter 15


title: Patient nCounter 16


title: Patient nCounter 17


title: SM1: Senescent Fibroblast MG132


title: 19R409: AI-REWIRE3.1-r3


title: 19R165: AI-REWIRE3.1-r2


title: METTL3-deficient MDA-MB-231 RIP rep2

tag: merip antibody

value: anti-m6A (202003, Synaptic Systems)


title: SD3: Senescent Fibroblast DMSO


title: Patient nCounter 10


title: SD2: Senescent Fibroblast DMSO


title: 19R408: AI-REWIRE3.0-r3


title: K177Q-METTL3 reconstituting MDA-MB-231 RIP rep2


title: Patient nCounter 18


title: Patient nCounter 20


title: Patient nCounter 21


title: PM3: Proliferating Fibroblast MG132

value: Proliferating


title: WT-METTL3 reconstituting MDA-MB-231 RIP rep2


title: SD1: Senescent Fibroblast DMSO


title: 19R403: AI-REWIRE3.1-r1


title: PM2: Proliferating Fibroblast MG132


title: Patient nCounter 19


title: 19R402: AI-REWIRE3.0-r1


title: Patient nCounter 8


title: Patient nCounter 7


title: Patient nCounter 12


title: Patient nCounter 4


title: Patient nCounter 13


title: Psoriatic skin from donor 9709PC [PP-9709PC]

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced using a NovaSeq6000 SP 100-cycle flow cell (Illumina).
Fastq files were generated using Cellranger mkfastq (version 4.0.0). The raw reads were mapped to the  human genome (hg38) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with raw gene counts for every gene and every cell

source_name: Psoriatic skin

extract_protocol:
6-mm punch biopsies were taken from healthy skin from healthy donors, lesional and non-lesional skin from psoriasis patients.
Samples were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), and strained through a 70μM mesh. Dermis was minced, digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in plain medium for 1.5 hours at 37°C, and strained through a 70μM mesh. Epidermal and dermal cells were combined in 1:1 ratio and libraries were constructed by the University of Michigan Advanced Genomics Core on the 10X Chromium system.

tag: subject id

value: donor 9709PC

tag: subject status

value: psoriasis patient

tag: tissue type

value: Psoriatic skin

value: Epidermal and dermal cells


title: Patient nCounter 3

tag: age


title: Patient nCounter 5


title: Patient nCounter 9


title: Patient nCounter 6


title: CTRL MDA-MB-231 RIP rep2

tag: treatment


title: Patient nCounter 1


title: Psoriatic skin from donor 929 [PP-929]

value: donor 929

tag: cell type


title: 19R715: PUF-10R-Ctrl-r3

tag: tissue

value: embryonic kidney


title: PM1: Proliferating Fibroblast MG132

tag: strain


title: 19R164: AI-REWIRE3.0-r2


title: PD2: Proliferating Fibroblast DMSO

tag: cell state

value: DMSO


title: 19R713: PUF-10R-Ctrl-r1

tag: cell line


title: 19R554: Mut.CU-REWIRE1.0-r3


title: 19R714: PUF-10R-Ctrl-r2


title: Psoriatic skin from donor 8940 [PP-8940]

value: donor 8940


title: Psoriatic skin from donor 7802ED [PP-7802ED]

value: donor 7802ED


title: 19R553: Mut.CU-REWIRE1.0-r2


title: PD3: Proliferating Fibroblast DMSO

value: Fibroblast


title: Psoriatic skin from donor 6215B [PP-6215B]

value: donor 6215B


title: Psoriatic skin from donor 5851 [PP-5851]

value: donor 5851


title: Psoriatic skin from donor 369PC [PP-369PC]

value: donor 369PC