title: MCF7ras SOX9OE SOX9 ChIP rep1 (ChIP-seq)

first: Wenjun

last: Guo

state: NY

address: 1301 Morris Park

institute: Albert Einstein College of Medicine

data_processing:
ChIP-seq reads were aligned to the human genome (hg38) using bowtie2 (v2.4.2);
BBTools seal.sh (v38.90, https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/seal-guide/) was used to separate human reads and spike-in mouse reads.
Peaks were called by Genrich (v0.6.1) using MCF7ras ctrl SOX9 ChIP as controls and the option (-q 0.05).
Deeptools (v3.5.0) bamCoverage was used to generate the bigwig file (bin size 10 and normalizing using RPGC).
GRCh38
bigwig files generated by Deeptools (bin size 10 and normalizing using RPGC).
Peak files called by Genrich using input or SOX9 ChIP as controls

source_name: MCF7ras cells

extract_protocol:
Cells were crosslinked with 1% PFA at room temperature for 10 minutes, quenched with 125 mM Glycine, and rinsed twice with 1X PBS. Cells were lysed and sonicated at 4 °C using a Bioruptor Sonicator into 100-600 bp fragments. The samples were incubated overnight at 4 °C with Dynabeads Protein A, which had been pre-coated with 5 µg anti-SOX9 (Millipore, AB5535). The ChIP samples were then washed, eluted, and reverse cross-linked by overnight incubation at 65 °C. Afterward, ChIP-DNA was purified by Phenol:Chloroform:Isoamyl Alcohol and mixed with 5% spike-in mouse gDNA for ChIP-seq.
ChIP-Seq library preparation and sequencing reactions were conducted at GENEWIZ, Inc/Azenta US, Inc. (South Plainfield, NJ, USA). NEB NextUltra DNA Library Preparation kit was used following the manufacturer’s recommendations. Sequencing was performed using a 2x150 Paired End (PE) configuration on Illumina HiSeq 4000.

value: human breast cancer cell line

value: 2 ug/ml doxycycline for three days.

tag: chip antibody

value: SOX9 (Millipore, AB5535)


title: HiMyc_C57BL6_Anterior_2

status: Public on Oct 16 2023

type: SRA

city: Chicago

first: Mindy

middle: Kim

last: Graham

state: IL

address: 303 E. Superior Street Chicago

department: Urology

country: USA

institute: Northwestern University Feinberg School of Medicine

library_source: transcriptomic single cell

data_processing:
Cell Ranger (version 2.2.0) count pipeline was used to align reads to the mm10 mouse transcriptome and create a gene-by-cell count matrix.
To align transgene expression, Kallisto quant (v0.46.0) was used to align the reads against human MYC and mouse Myc reference sequences. Samtools (v0.1.19) was used to extract alignments from BAM files for each sample. An in-house Perl script was used to map the alignments to the original FASTQ reads and create a feature-barcode count matrix. The Cell Ranger matrices were merged with the custom count matrices containing human MYC and mouse Myc.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Tissues were minced with razor blades and digested in 0.25% Trypsin-EDTA (Gibco 25200-072) for 10 min at 37°C, followed by incubation for 2.5 hours at 37°C with gentle agitation in DMEM containing 10% FBS, 1 mg/mL Collagenase Type I (Gibco 17100-017), and 0.1 mg/mL of DNase I (Roche 10104159001). Digested tissues were centrifuged at 400 x g for 5 minutes, washed with HBSS, and further incubated in 0.25% Trypsin-EDTA for 10 min at 37°C. Cells were suspended in DMEM containing 10% FBS and 0.4 mg/mL of DNase I and filtered through a 40 μm cell strainer.
Libraries for scRNA-seq were prepared using the 10x Genomics Chromium Single Cell 3’ Library and Gel bead Kit V2 (CG00052_RevF) according to the manufacturer’s protocol for each dissected mouse prostate lobe and each human prostatectomy tissue punch. The cDNA libraries were sequenced (150 bp paired-end) on the Illumina HiSeqX platform. Each sequenced library was demultiplexed to FASTQ files using Cell Ranger (10x Genomics).

tag: strain

tag: lobe

value: Anterior

tag: genotype

value: Hi-Myc

tag: replicate

tag: age

value: 6 months


title: MCF7ras SOX9OE rep3 (RNA-seq)

city: New York

department: Cell Biology

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned using STAR (version 2.4.0) to the reference human genome (GRCh38.p13) with Ensembl annotation (gencode.v33).
featureCounts (v1.5.0) was used to generate raw counts from aligned reads.
DESeq2 (v1.30.1) R package was applied to analyze the differential expression.
GRCh38.p13
Matrix table with raw gene counts for every gene and every sample generated by featureCounts

molecule: total RNA

organism: Homo sapiens

growth_protocol: MCF7ras tetO-SOX9 cells were generated as described (Guo et al., 2012); MCF7ras ctrl and tetO-SOX9 cells cells were were cultured in Dulbecco’s Modified Eagle Medium with 10% FBS.

extract_protocol:
For RNA-seq, total RNA was isolated from MCF7ras ctrl and SOX9OE cells using Direct-zol RNA Miniprep Plus kit
Total RNA was submitted to Novogene for library preparation (NEBNext Ultra II RNA Library Prep Kit for Illumina, non stranded) and sequencing (Illumina Novaseq 6000 on S4 flowcell, PE150)

treatment_protocol: Cells were treated with 2 μg/ml doxycycline for three days (tetO-SOX9 cells overexpress SOX9 (SOX9OE) with treatment).

tag: cell type

tag: treatment


title: ATAC-Seq - Hippocampus Young Male Replicate 4

city: Los Angeles

first: Kelsey

last: Martin

state: CA

address: 615 Charles E Young Drive South

department: Biological Chemistry

institute: UCLA

library_source: genomic

data_processing:
Adapter content was trimmed using Scythe (https://github.com/vsbuffalo/scythe/) and ATAC-seq reads were mapped to the mouse genome (mm10) using Bowtie 2 (Langmead and Salzberg, 2012). Reads in blacklist regions (Amemiya et al., 2019; Dunham et al., 2012) and reads mapped to mitochondria were removed.
Peaks were called on each individual sample using MACS3 (with parameter settings --nomodel -f BAMPE and FDR cutoff of 0.05) (Zhang et al., 2008). For each sample, read pairs (fragments) were counted for each peak using featureCount (Liao et al., 2014) (with parameter settings -p --countReadPairs -M --fraction).
For quality control, we calculated a transcription start site (TSS) enrichment score using ATACseqQC (Ou et al., 2018) and a FRiP score (fraction of reads/fragments in peaks), and included samples showed a TSS enrichment score > 10 and a FRiP score > 0.2.
For each condition, narrow peak sets were merged, and peaks were included in consensus peak sets for each condition if there was at least a 50% overlap with a peak in at least two replicates . A total consensus peak set (92,233 peaks) was generated by merging the consensus peak sets from each condition.
Fragments were counted for each total consensus peak in each sample using featureCount as described above, and differential analysis was performed using DESeq2, including sequencing batch as a variable (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: Excel table with genomic annotation, normalized counts, fold changes and p-values for all ATAC-seq consensus peaks

molecule: genomic DNA

source_name: hippocampus

growth_protocol: Mice were housed in groups under a 12:12 hr light/dark cycle with food provided ad libitum until they reached the age of 10 weeks (young adult) and 80 weeks (aged).

extract_protocol:
The hippocampus was homogenized with a Dounce tissue grinder (Wheaton 357544) in 2mL HB buffer (1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitor (Sigma-Aldrich 04693159001), 0.3% IGEPAL-630, 0.25 M sucrose, 25 mM MgCl2, 20 mM Tricine-KOH). The homogenate was then filtered through a 40 mm strainer. The filtrate was centrifuged over one volume of cushion buffer (0.5 mM MgCl2, 0.5 mM DTT, protease inhibitor, 0.88 M sucrose) at 2800 g for 10 minutes in a swinging bucket centrifuge at 4°C. The nuclei pellet was resuspended in 20 mL PBS. 1 mL of the nuclei sample was stained with Hoechst 33342 to calculate nuclei concentration, and 50,000 nuclei per sample were used for downstream library preparation.
Libraries were prepared using the Nextera DNA Library Prep kit (Illumina FC-121-1030) and quality was analyzed using the D1000 ScreenTape Assay (Agilent 5067-5582).

treatment_protocol: For sample collection, mice were deeply anesthetized with isoflurane and euthanized by cervical dislocation. The brain was quickly removed and cooled for one minute in ice-cold PBS before the hippocampus from each hemisphere was dissected on ice and processed immediately.

tag: tissue

value: hippocampus

value: Young Adult

tag: Sex

value: Male


title: CD25+_Bcl11b_neg_sgStat5a+sgStat5b_rep2

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

data_processing:
Basecalls performed using RTA 1.13.48.0 and converted to Fastq files using bcl2fastq 1.8.4.
RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (v2.4.0).
Gene expression from RNA-seq was calculated with RSEM(v1.2.25) by following the ENCODE RNA-seq pipelines.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Count table and FPKM table

source_name: BM progenitor-derived T  progenitor cells (DNs)

growth_protocol: Multipotent bone marrow progenitor cells were cultured with OP9-Dll1 cells in  OP9 medium (20% FBS, 2mM glutamine, 100 IU/ml penicillin, 100 mg/ml streptomycin, and 50 µM β-ME in α-MEM).   Cells were supplemented with  IL-7, Flt3-ligand  (10 ng/ml each) for 6 days under 37 °C, 7% CO2 environment.

extract_protocol:
For total RNA extraction, the RNeasy Micro Kit (QIAGEN) was used.
Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: For sgRNA delivery, bone marrow progenitor cells were incubated with IL-7, Flt3l, and SCF for overnight and sgRNA was deliverered by retroviral transduction.  After infection, cells were removed from the viral particles and cultured with OP9-Dll1 for 6 days with IL-7 and FLt3l (10 ng/ml each).

tag: growth conditions

value: Cultured on OP9-DLL1

value: B6. CRISPR-Cas9/Bcl2

tag: sample type

value: Pre-commitment perturbation


title: CD25+_Bcl11b_neg_sgStat5a+sgStat5b_rep1


title: MCF7ras SOX9OE rep2 (RNA-seq)


title: HiMyc_C57BL6_Anterior_1


title: CD25+_Bcl11b_pos_sgStat5a+sgStat5b_rep2

value: Post-commitment perturbation


title: MCF7ras SOX9OE SOX9 ChIP rep2 (ChIP-seq)


title: Normal SAP development D29-30, hashtag3 , scRNAseq

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

description: 10x Genomics

data_processing:
The sequenced libraries were quantified with Cell Ranger software (version 6.0.0) (Zheng et al., 2017) with default parameters.
The standard reference provided with Cell Ranger (version 2020-A) was used. This version was build on a GRCh38 human genome (bundle 3.0.0) and a filtered version of Gencode v32.
In addition, HTO surface antibodies were quantified with the Cell Ranger count feature reference option. The feature reference file is provided on GitHub (https://github.ugent.be/DePreterLab/Sympatho-adrenergic-differentiation-track)
Assembly: GRCh38 human genome
Supplementary files format and content: Tab-separated barcodes, features and matrix files

source_name: SAP developmental cells

extract_protocol:
Prior to scRNAseq the cells of selected time-points were hashed and pooled together for scRNAseq analysis. The time-points D25-26, D27-28, D29-30 and D31-32 were hashed for the WT cells. For the ALK mutant cells time-points D25-27-29-32 were hashed. After dissociating the cells with Accutase for 25 minutes we prepared a 50μl single cell suspension at a concentration between 1x105 cells/mL and 2x107 cells/mL for each hasing group in Cell Staining Buffer (BioLegend, Cat nr. 420201) for cell labelling. 5μl Of cell solution was used to record total cell count and cell viability using Trypan Blue. To the remaining 45μl, 0.1X volume (5 μL) of Human TruStain FcX (BioLegend, Cat nr. 422301) was added. This was allowed to incubate for 10 minutes at 4°C. During this incubation time a solution of 1μg /50μl was prepared for each hashing antibody (B0251 – B0256, see key resource table). The hashing antibody solution was centrifuged at 14,000g at 4°C for 10 minutes. The antibody solution was thereafter carefully withdrawn, whilst avoiding touching the bottom of the tube, and transferred on the corresponding cell solution. This was allowed to incubate for 30 minutes at 4°C, simultaneously the cell staining buffer was cooled down to 4°C. After incubation the cell solution was diluted 10 times by adding 0.9 mL cell staining buffer and transferred to a 12 x 75mm Falcon Round-Bottom Polystyrene Tube. Subsequently we added 2.5ml of cell staining buffer for a final dilution of 35 times. The cell solutions where thereafter  centrifuged at 400g at 4°C for 5 minutes. Next the supernatant was aspirated leaving 50-100μl, this was repeated two more times for a total of 3 washes. It is very important to perform these washes carefully, leaving as little supernatant as possible. After the last wash the different cell solutions (each with their own hashtag) were combined into one tube, centrifuged and resupsended in DMEM-F12, as this medium was compatible with the 10XGenomics pipeline, for a final concentration of 1000 cells/μl.
The single-cell RNA-Seq was performed on Chromium instrument (10X genomics) following the user guide manual (Reagent Kit 3’ v3.1). Each sample, containing approximately 10,000 cells at a final dilution of ~1,000 cells/µl was loaded onto the cartridge following the manual. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). The individual transcriptomes of encapsulated cells were barcoded during RT step and resulting cDNA purified with DynaBeads followed by amplification per manual guidelines. Next, PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to the sequencing adapters and indexed by PCR. The indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina NovaSeq S4 platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher).

value: iPSCs (J2)

value: SAP developmental cells

tag: library type

value: cell hashing


title: CD25+_Bcl11b_pos_sgStat5a+sgStat5b_rep1


title: CD25+_Bcl11b_pos_sgControl_rep2


title: MCF7ras SOX9OE input rep1 (ChIP-seq)


title: CD25+_Bcl11b_pos_sgControl_rep1


title: MCF7ras SOX9OE input rep2 (ChIP-seq)


title: C57BL6_Anterior_3

value: WT


title: MCF7ras ctrl SOX9 ChIP rep2 (ChIP-seq)

value: human breast cancer cell line


title: FVB_Anterior_2

source_name: FVB/NJ

value: FVB/NJ


title: MCF7ras ctrl SOX9 ChIP rep1 (ChIP-seq)

value: 2 ug/ml doxycycline for three days.

value: SOX9 (Millipore, AB5535)


title: Normal SAP development Start, Bio_Rep3 , Bulk- RNAseq

data_processing:
Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina Cat nr. TG-410-1002).
FASTQ files were mapped using STAR (v2.7.3a).
The counts per gene were normalized using DESeq2 (Love et al., 2014)
The counts for each gene in each sample is divided by the geometric mean of the gene across all samples.
The median of the ratios for the genes in a sample is the estimated size “scaling” size factor used to adjust the total mapped reads count from each sample.
Assembly: GRCh38.96
Supplementary files format and content: Tab-delimited text files include STAR counts per sample

source_name: J2 (MRC5-IPSC)

growth_protocol: Stem cells were maintained in E8 medium with E8 supplement in humidified atmosphere with 5% CO2 at 37C. The cells were passaged biweekly by treatment with accutase for 15min. Accutase was neutralised with E8 medium in a ratio of 3:1. The cell suspension was counted and centrifuged at 120 x g for 3 min. Eventually, 20-30,000 cells/well were seeded on previously prepared Matrigel-coated six well plates.

extract_protocol:
Cell pellets were snapfrozen for analysis at selected time-points over the differentiation process. To extract RNA from the cells, phase separation in cells lysed in TRIzol Reagent was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 125-500ng of total RNA with an RNA integrity number varying from 7.8-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina, with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit.

treatment_protocol:
Stem cells were transitioned to truncal neural crest cells (truncal NCC) in a 16-day long process. First cells were seeded on geltrex coated 24 well plates at a concentration of 100k/cm² in medium consisting of E6 supplemented with 10µM Rock inhibitor. After allowing the cells to attach for 24hrs the medium was changed to E6 with 100ng/mL FGF2, 10µM SB431542, 3µM CHIR, 1ng/µL BMP4 for the following 2 days. Hereafter the medium was adjusted to E6 medium with 10µM SB431542 and 1,5µM CHIR which was used until D16 where we enriched for NCC using FACS sorting. After sorting the cells were centrifuged and resuspended in neurobasal medium with 1/50 B27 supplement, 1/100 N2 supplement, 2mM L-glutamine, 1/100 non assential amino acids, (together making up Basal NB medium), 10ng/mL FGF2 and 3µM CHIR. The cells were subsequently plated out on ultra-low attachment plates (Corning, Cat Nr. 3471) to generate spheres and allow for larger increase of cell numbers. The spheres were allowed to grow for 4 days after which they were plated on previously prepared PO/FN/LM coated 24 well plates.
24Hrs after plating out the spheres the medium was changed to NB basal medium with 50ng/mL BMP4 and 50ng/mL SHH for a total of 4 days, renewed every 2 days. Subsequently the medium is changed to NB basal medium with 200µM Ascorbic Acid. This was renewed every 4 days until the end of the differentiation.

tag: cell line

value: J2 (MRC5-IPSC)

value: iPSC

value: SAP differentiation

tag: time

value: Day 0


title: MCF7ras ctrl rep2 (RNA-seq)


title: CD25+_Bcl11b_neg_sgControl_rep2


title: MCF7ras ctrl input rep2 (ChIP-seq)


title: C57BL6_Anterior_2

value: Anterior

value: 6 months


title: CD25+_Bcl11b_neg_sgControl_rep1

value: Cultured on OP9-DLL1

value: B6. CRISPR-Cas9/Bcl2


title: MCF7ras ctrl rep1 (RNA-seq)


title: C57BL6_Anterior_1


title: MCF7ras ctrl input rep1 (ChIP-seq)


title: VGluT2+ sorted sample 4

status: Public on Oct 15 2023

city: Modena, Italy

first: Giordano

last: Lippi

address: 10550 North Torrey Pines, DNC-202

institute: The Scripps Research Institute

data_processing:
Data processing and analysis were carried out using the Galaxy suite of bioinfomatic tools (Goecks et al., 2010) and publicly available in-house tools. All statistical analyses were carried out in R using Bioconductor packages (Gentleman et al., 2004).
Assembly: mm10
Supplementary files format and content: logFC,logCPM,LR,PValue,FDR

source_name: dorsal hippocampus

extract_protocol:
Dorsal hippocampi were microdissected at P8 in Hibernate A buffer without Ca2+. Tissue chunks were dissociated in papain (2 mg/mL in Hibernate A) at 37 C for 60 minutes and inverted 4-5 times every 5 minutes. DNAseI (1 mg/mL) was added, and tissue was triturated through pipettes of decreasing diameter and supernatants kept on ice. Supernatants were filtered through 70 um filter, centrifuged at 500 rcf for 10 min at 4 C. The pellet was resuspended in PBS with 3% FBS and DAPI for FACS. Fluorescent cells were collected using a 100 um nozzle. Collected cells were centrifuged at 4 C, 500 rcf for 10 minutes, resuspended in TRIzol LS, and frozen on dry ice.
Libraries were prepared using the Illumina Truseq protocol.

value: dorsal hippocampus

value: VGluT2+ neurons

value: VGluT2-IRES-Cre; Ai14

value: FACS


title: MCF7ras SOX9OE rep1 (RNA-seq)


title: VGluT2+ sorted sample 2


title: VGluT2+ sorted sample 1


title: VGAT+ sorted sample 3

description: vgat.csv

value: GABAergic neurons

value: VGAT-IRES-Cre; Ai14


title: VGAT+ sorted sample 1

description: vgat.csv


title: FVB_Anterior_1

value: FVB/NJ

value: WT


title: MCF7ras ctrl rep3 (RNA-seq)

value: human breast cancer cell line

value: 2 ug/ml doxycycline for three days.


title: miR-218-2+/+ wt sample 3

extract_protocol:
Dorsal hippocampi were microdissected at P15 and homogenized in Qiazol using a 23-gauge needle and syringe and snap-frozen on dry ice.
Libraries were prepared using the Illumina Truseq protocol.

value: all cells

value: wt


title: VGAT+ sorted sample 2

description: vgat.csv


title: miR-218-2+/+ wt sample 1


title: miR-218-2+/- KO sample 4


title: miR-218-2+/+ wt sample 2


title: miR-218-2+/- KO sample 2


title: miR-218-2+/- KO sample 5


title: miR-218-2+/- KO sample 1


title: a.Ctrl LNA Sample 3

extract_protocol:
Dorsal hippocampi were microdissected at P8 and homogenized in Qiazol using a 23-gauge needle and syringe. Samples were snap-frozen on dry ice. RNA was extracted using TRIzol and treated with DNase I
Libraries were prepared using the Illumina Truseq protocol.

treatment_protocol: Animals were injected with LNA AntagomiR at P2.


title: miR-218-2+/- KO sample 3


title: M3_Unstable1

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

description: 10x Genomics 3' standard v1 Visium Spatial Gene Expression; spaceranger-1.2.2

data_processing:
spaceranger-1.2.2 for samples M1 to M11
spaceranger-1.3.0 for samples M13 to M16
Pathological annotations by V Cockenpot, breast pathologist at Centre Léon Bérard, Lyon (FR)
Assembly: GRCh38
Supplementary files format and content: per-sample matrix of counts per spot in hierarchical data format
Supplementary files format and content: pathological annotations, as annotated and exported via Loupe Browser
Library strategy: Spatial transcriptomics: single-spot UMI-based RNA-seq

source_name: Breast

extract_protocol:
After optimisation, RNA permeabilisation on the Visium slide was set to 12 minutes and processed according to the manufacturer's protocol (10X Genomics)
Visium 3' V1 protocol (10X Genomics)

value: Breast

value: Cancer

tag: cell subtype

value: Unstable


title: a.Ctrl LNA Sample 2


title: a.Ctrl LNA Sample 1


title: a.218 LNA Sample 3


title: a.218 LNA Sample 2


title: a.218 LNA Sample 1


title: VGluT2+ sorted sample 3


title: Genomic DNA from breast tissue 31651 tumor

type: genomic

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

description:
Genomic DNA from breast tissue
tumor breast tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC 850K Beadchip using standard Illumina protocol

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

data_processing:
R v.4.2.2
Functionally normalized average beta

label: Cy3 and Cy5

source_name: frozen tumor breast tissue

label_protocol: Standard Illumina protocol

extract_protocol: genomic DNA was extracted and purified from breast tissue samples using the Qiagen DNeasy Blood and Tissue Kit according to standard instructions

tag: methylation id (basenames)

tag: rnaseqid

value: tumor

tag: race

value: European American

value: F

tag: ndi continuous

tag: dichtomized ndi status

tag: ndi quartiles

tag: er status

value: POS

tag: ajcc stage

value: II

tag: molecular subtype

value: HR+


title: Genomic DNA from breast tissue 32007 tumor


title: Genomic DNA from breast tissue 30503 tumor

value: African American

value: I


title: Genomic DNA from breast tissue 30823 tumor


title: Genomic DNA from breast tissue 29901 tumor

value: NEG

value: TNBC


title: Genomic DNA from breast tissue 29367 tumor


title: Genomic DNA from breast tissue 29581 tumor


title: Genomic DNA from breast tissue 30264 tumor


title: Genomic DNA from breast tissue 28571 tumor

value: III


title: Genomic DNA from breast tissue 28525 tumor


title: Genomic DNA from breast tissue 29528 tumor


title: Genomic DNA from breast tissue 28355 tumor


title: Genomic DNA from breast tissue 27618 tumor


title: Genomic DNA from breast tissue 29483 tumor


title: Genomic DNA from breast tissue 27334 tumor


title: Genomic DNA from breast tissue 29493 tumor


title: Genomic DNA from breast tissue 29108 tumor

value: M


title: Genomic DNA from breast tissue 29334 tumor


title: Genomic DNA from breast tissue 28999 tumor


title: Genomic DNA from breast tissue 27115 tumor


title: Genomic DNA from breast tissue 28909 tumor


title: Genomic DNA from breast tissue 27130 tumor


title: Genomic DNA from breast tissue 27106 tumor


title: Genomic DNA from breast tissue 27107 tumor


title: Genomic DNA from breast tissue 27103 tumor


title: Genomic DNA from breast tissue 26599 tumor


title: Genomic DNA from breast tissue 27122 tumor


title: Genomic DNA from breast tissue 30393 tumor


title: Genomic DNA from breast tissue 27101 tumor


title: Genomic DNA from breast tissue 26432 tumor


title: Genomic DNA from breast tissue 27113 tumor


title: Genomic DNA from breast tissue 27108 tumor


title: Genomic DNA from breast tissue 29202 tumor


title: Genomic DNA from breast tissue 25801 tumor


title: Genomic DNA from breast tissue 25649 tumor


title: Genomic DNA from breast tissue 25692 tumor


title: Genomic DNA from breast tissue 26130 tumor


title: Genomic DNA from breast tissue 25330 tumor

value: Asian


title: Genomic DNA from breast tissue 25412 tumor


title: Genomic DNA from breast tissue 25300 tumor


title: Genomic DNA from breast tissue 24980 tumor


title: Genomic DNA from breast tissue 24834 tumor


title: Genomic DNA from breast tissue 25139 tumor


title: Genomic DNA from breast tissue 24716 tumor


title: Genomic DNA from breast tissue 24508 tumor


title: Genomic DNA from breast tissue 24471 tumor


title: Genomic DNA from breast tissue 24231 tumor


title: Genomic DNA from breast tissue 24242 tumor


title: Genomic DNA from breast tissue 24243 tumor


title: C57BL6_Lateral_2

tag: strain

tag: lobe

value: Lateral

tag: genotype

value: WT

tag: replicate

tag: age

value: 6 months


title: Genomic DNA from breast tissue 23969 tumor

tag: sample type

tag: Sex


title: Genomic DNA from breast tissue 23964 tumor


title: Genomic DNA from breast tissue 25388 tumor


title: Genomic DNA from breast tissue 20805 tumor

tag: diabetes

value: Yes


title: Genomic DNA from breast tissue 19842 tumor

tag: methylation id (basenames)

value: tumor

tag: grade

value: Low grade


title: Genomic DNA from breast tissue 25373 tumor

tag: rnaseqid

tag: race

value: European American

value: F


title: Genomic DNA from breast tissue 19566 tumor

value: POS


title: Genomic DNA from breast tissue 19075 tumor

value: HR+


title: Genomic DNA from breast tissue 20874 tumor

value: African American


title: Genomic DNA from breast tissue 19576 tumor

value: II


title: Genomic DNA from breast tissue 19826 tumor

value: NEG


title: Genomic DNA from breast tissue 19526 tumor


title: Genomic DNA from breast tissue 18395 tumor

value: I


title: Genomic DNA from breast tissue 18973 tumor

value: TNBC


title: Genomic DNA from breast tissue 17351 tumor


title: Genomic DNA from breast tissue 17952 tumor


title: Genomic DNA from breast tissue 17014 tumor


title: Genomic DNA from breast tissue 18084 tumor


title: Genomic DNA from breast tissue 17373 tumor

value: M

tag: ndi continuous

tag: dichtomized ndi status

value: No


title: Genomic DNA from breast tissue 16666 tumor

tag: er status


title: Genomic DNA from breast tissue 24576 tumor

tag: ndi quartiles

tag: ajcc stage


title: Genomic DNA from breast tissue 19943 tumor

tag: molecular subtype


title: Genomic DNA from breast tissue 16404 tumor


title: Genomic DNA from breast tissue 16387 tumor


title: Genomic DNA from breast tissue 16163 tumor

value: III


title: Genomic DNA from breast tissue 16086 tumor


title: Genomic DNA from breast tissue 15881 tumor


title: Genomic DNA from breast tissue 15878 tumor


title: Genomic DNA from breast tissue 15842 tumor


title: Genomic DNA from breast tissue 16047 tumor


title: Genomic DNA from breast tissue 15868 tumor

value: TIS


title: Genomic DNA from breast tissue 15779 tumor


title: Genomic DNA from breast tissue 15535 tumor


title: Genomic DNA from breast tissue 15762 tumor


title: Genomic DNA from breast tissue 15620 tumor


title: Genomic DNA from breast tissue 15429 tumor


title: Genomic DNA from breast tissue 15121 tumor


title: Genomic DNA from breast tissue 15484 tumor


title: Genomic DNA from breast tissue 15046 tumor


title: Genomic DNA from breast tissue 14851 tumor


title: Genomic DNA from breast tissue 15050 tumor


title: Genomic DNA from breast tissue 16980 tumor


title: Genomic DNA from breast tissue 15384 tumor


title: Genomic DNA from breast tissue 14810 tumor


title: Genomic DNA from breast tissue 14920 tumor


title: Genomic DNA from breast tissue 15423 tumor


title: Genomic DNA from breast tissue 14697 tumor


title: Genomic DNA from breast tissue 14617 tumor


title: Genomic DNA from breast tissue 14767 tumor


title: Genomic DNA from breast tissue 14730 tumor


title: Genomic DNA from breast tissue 14576 tumor


title: Genomic DNA from breast tissue 14591 tumor


title: Genomic DNA from breast tissue 14573 tumor


title: Genomic DNA from breast tissue 14509 tumor


title: Genomic DNA from breast tissue 14537 tumor


title: Genomic DNA from breast tissue 14505 tumor


title: Genomic DNA from breast tissue 14414 tumor


title: Genomic DNA from breast tissue 14218 tumor


title: Genomic DNA from breast tissue 14116 tumor


title: Genomic DNA from breast tissue 14043 tumor


title: Genomic DNA from breast tissue 14306 tumor


title: Genomic DNA from breast tissue 14447 tumor


title: Genomic DNA from breast tissue 14269 tumor


title: Genomic DNA from breast tissue 14593 tumor


title: Genomic DNA from breast tissue 13916 tumor


title: Genomic DNA from breast tissue 13910 tumor


title: Genomic DNA from breast tissue 14064 tumor


title: Genomic DNA from breast tissue 14059 tumor


title: Genomic DNA from breast tissue 14019 tumor


title: Genomic DNA from breast tissue 13645 tumor


title: Genomic DNA from breast tissue 13998 tumor


title: Genomic DNA from breast tissue 14001 tumor


title: Genomic DNA from breast tissue 13583 tumor

value: IV


title: Genomic DNA from breast tissue 13846 tumor


title: Genomic DNA from breast tissue 13676 tumor


title: Genomic DNA from breast tissue 13780 tumor


title: Genomic DNA from breast tissue 13417 tumor


title: Genomic DNA from breast tissue 13361 tumor


title: Genomic DNA from breast tissue 13315 tumor


title: Genomic DNA from breast tissue 17163 tumor

value: Yes


title: Genomic DNA from breast tissue 13934 tumor

value: tumor


title: Genomic DNA from breast tissue 13476 tumor


title: Genomic DNA from breast tissue 13661 tumor


title: Genomic DNA from breast tissue 14090 tumor


title: Genomic DNA from breast tissue 13152 tumor


title: Genomic DNA from breast tissue 14500 tumor


title: Genomic DNA from breast tissue 13258 tumor


title: Genomic DNA from breast tissue 13131 tumor


title: Genomic DNA from breast tissue 13120 tumor


title: Genomic DNA from breast tissue 12811 tumor


title: Genomic DNA from breast tissue 13100 tumor


title: Genomic DNA from breast tissue 12788 tumor


title: Genomic DNA from breast tissue 13017 tumor


title: Genomic DNA from breast tissue 12976 tumor


title: Genomic DNA from breast tissue 12780 tumor


title: Genomic DNA from breast tissue 13438 tumor


title: Genomic DNA from breast tissue 12887 tumor


title: Genomic DNA from breast tissue 12801 tumor


title: Genomic DNA from breast tissue 12638 tumor


title: Genomic DNA from breast tissue 12766 tumor


title: Genomic DNA from breast tissue 12600 tumor


title: Genomic DNA from breast tissue 12484 tumor


title: Genomic DNA from breast tissue 12440 tumor


title: Genomic DNA from breast tissue 12612 tumor


title: Genomic DNA from breast tissue 12716 tumor


title: Genomic DNA from breast tissue 12423 tumor


title: Genomic DNA from breast tissue 12421 tumor


title: Genomic DNA from breast tissue 12394 tumor


title: Genomic DNA from breast tissue 12933 tumor


title: Genomic DNA from breast tissue 12623 tumor


title: Genomic DNA from breast tissue 12365 tumor


title: Genomic DNA from breast tissue 12857 tumor


title: Genomic DNA from breast tissue 12364 tumor


title: Genomic DNA from breast tissue 12356 tumor


title: Genomic DNA from breast tissue 12273 tumor


title: Genomic DNA from breast tissue 13277 tumor


title: Genomic DNA from breast tissue 12249 tumor


title: Genomic DNA from breast tissue 23891 tumor


title: Genomic DNA from breast tissue 12280 tumor


title: Genomic DNA from breast tissue 12207 tumor


title: Genomic DNA from breast tissue 12197 tumor


title: Genomic DNA from breast tissue 12138 tumor


title: Genomic DNA from breast tissue 12239 tumor


title: Genomic DNA from breast tissue 12123 tumor


title: Genomic DNA from breast tissue 12109 tumor


title: Genomic DNA from breast tissue 12107 tumor


title: Genomic DNA from breast tissue 12437 tumor


title: Genomic DNA from breast tissue 12424 tumor


title: Genomic DNA from breast tissue 11982 tumor


title: Genomic DNA from breast tissue 11914 tumor


title: Genomic DNA from breast tissue 12063 tumor


title: Genomic DNA from breast tissue 11913 tumor


title: Genomic DNA from breast tissue 11989 tumor


title: Genomic DNA from breast tissue 12062 tumor


title: Genomic DNA from breast tissue 11781 tumor


title: Genomic DNA from breast tissue 11724 tumor


title: Genomic DNA from breast tissue 11904 tumor


title: Genomic DNA from breast tissue 11684 tumor


title: Genomic DNA from breast tissue 11709 tumor


title: Genomic DNA from breast tissue 11741 tumor


title: Genomic DNA from breast tissue 11688 tumor


title: Genomic DNA from breast tissue 11888 tumor


title: Genomic DNA from breast tissue 11624 tumor


title: Genomic DNA from breast tissue 11431 tumor


title: Genomic DNA from breast tissue 11462 tumor


title: Genomic DNA from breast tissue 11449 tumor


title: Genomic DNA from breast tissue 11435 tumor


title: Genomic DNA from breast tissue 11333 tumor


title: Genomic DNA from breast tissue 11117 tumor


title: Genomic DNA from breast tissue 11131 tumor


title: Genomic DNA from breast tissue 11098 tumor


title: Genomic DNA from breast tissue 11025 tumor


title: Genomic DNA from breast tissue 11043 tumor


title: Genomic DNA from breast tissue 11059 tumor


title: Genomic DNA from breast tissue 10940 tumor


title: Genomic DNA from breast tissue 11038 tumor


title: Genomic DNA from breast tissue 10608 tumor


title: Genomic DNA from breast tissue 10607 tumor


title: Genomic DNA from breast tissue 10556 tumor


title: Genomic DNA from breast tissue 11652 tumor


title: Genomic DNA from breast tissue 10391 tumor


title: Genomic DNA from breast tissue 10389 tumor


title: Genomic DNA from breast tissue 10310 tumor


title: Genomic DNA from breast tissue 10203 tumor


title: Genomic DNA from breast tissue 10197 tumor


title: Genomic DNA from breast tissue 32007 adj_norm

description:
Genomic DNA from breast tissue
adjacent normal breast tissue

source_name: frozen adjacent normal breast tissue


title: Genomic DNA from breast tissue 30823 adj_norm


title: Genomic DNA from breast tissue 30393 adj_norm


title: Genomic DNA from breast tissue 10601 tumor


title: Genomic DNA from breast tissue 29901 adj_norm


title: Genomic DNA from breast tissue 29493 adj_norm


title: Genomic DNA from breast tissue 28355 adj_norm


title: Genomic DNA from breast tissue 29483 adj_norm


title: Genomic DNA from breast tissue 29108 adj_norm


title: Genomic DNA from breast tissue 28525 adj_norm


title: Genomic DNA from breast tissue 10533 tumor


title: Genomic DNA from breast tissue 11577 tumor


title: Genomic DNA from breast tissue 10184 tumor


title: Genomic DNA from breast tissue 10330 tumor


title: Genomic DNA from breast tissue 27122 adj_norm


title: Genomic DNA from breast tissue 10360 tumor


title: Genomic DNA from breast tissue 31651 adj_norm


title: Genomic DNA from breast tissue 27113 adj_norm


title: Genomic DNA from breast tissue 11327 tumor


title: Genomic DNA from breast tissue 27103 adj_norm


title: Genomic DNA from breast tissue 10929 tumor


title: Genomic DNA from breast tissue 10968 tumor


title: Genomic DNA from breast tissue 26599 adj_norm


title: Genomic DNA from breast tissue 27101 adj_norm


title: Genomic DNA from breast tissue 25801 adj_norm


title: Genomic DNA from breast tissue 10618 tumor


title: Genomic DNA from breast tissue 28571 adj_norm


title: Genomic DNA from breast tissue 27618 adj_norm


title: Genomic DNA from breast tissue 27334 adj_norm


title: Genomic DNA from breast tissue 27130 adj_norm


title: Genomic DNA from breast tissue 27108 adj_norm


title: Genomic DNA from breast tissue 24716 adj_norm


title: Genomic DNA from breast tissue 25139 adj_norm


title: Genomic DNA from breast tissue 24508 adj_norm


title: Genomic DNA from breast tissue 24980 adj_norm


title: Genomic DNA from breast tissue 27115 adj_norm


title: Genomic DNA from breast tissue 24471 adj_norm


title: Genomic DNA from breast tissue 25692 adj_norm


title: Genomic DNA from breast tissue 25412 adj_norm


title: Genomic DNA from breast tissue 25388 adj_norm


title: Genomic DNA from breast tissue 25649 adj_norm


title: Genomic DNA from breast tissue 27107 adj_norm


title: Genomic DNA from breast tissue 26432 adj_norm


title: Genomic DNA from breast tissue 23969 adj_norm


title: Genomic DNA from breast tissue 25330 adj_norm

value: Asian


title: Genomic DNA from breast tissue 24242 adj_norm


title: Genomic DNA from breast tissue 20874 adj_norm


title: Genomic DNA from breast tissue 26130 adj_norm


title: Genomic DNA from breast tissue 24834 adj_norm

value: European American


title: Genomic DNA from breast tissue 23964 adj_norm

value: F


title: Genomic DNA from breast tissue 24243 adj_norm

value: POS


title: Genomic DNA from breast tissue 19943 adj_norm


title: Genomic DNA from breast tissue 24576 adj_norm

value: HR+


title: Genomic DNA from breast tissue 19842 adj_norm

value: African American

value: Low grade


title: Genomic DNA from breast tissue 25300 adj_norm


title: Genomic DNA from breast tissue 24231 adj_norm

value: NEG

value: II


title: Genomic DNA from breast tissue 23891 adj_norm


title: Genomic DNA from breast tissue 25373 adj_norm


title: Genomic DNA from breast tissue 20805 adj_norm


title: Genomic DNA from breast tissue 19826 adj_norm

value: TNBC


title: Genomic DNA from breast tissue 19576 adj_norm


title: Genomic DNA from breast tissue 19526 adj_norm


title: Genomic DNA from breast tissue 18973 adj_norm


title: Genomic DNA from breast tissue 18395 adj_norm

value: I


title: Genomic DNA from breast tissue 19075 adj_norm


title: Genomic DNA from breast tissue 17952 adj_norm


title: Genomic DNA from breast tissue 18084 adj_norm


title: Genomic DNA from breast tissue 17351 adj_norm


title: Genomic DNA from breast tissue 16387 adj_norm


title: Genomic DNA from breast tissue 17014 adj_norm


title: Genomic DNA from breast tissue 16163 adj_norm

value: No


title: Genomic DNA from breast tissue 15878 adj_norm


title: Genomic DNA from breast tissue 15842 adj_norm


title: Genomic DNA from breast tissue 15121 adj_norm


title: Genomic DNA from breast tissue 16047 adj_norm


title: Genomic DNA from breast tissue 15429 adj_norm

value: III


title: Genomic DNA from breast tissue 14920 adj_norm

value: TIS


title: Genomic DNA from breast tissue 15050 adj_norm


title: Genomic DNA from breast tissue 14697 adj_norm


title: Genomic DNA from breast tissue 15046 adj_norm


title: Genomic DNA from breast tissue 19566 adj_norm


title: Genomic DNA from breast tissue 14573 adj_norm


title: Genomic DNA from breast tissue 14576 adj_norm


title: Genomic DNA from breast tissue 14591 adj_norm


title: Genomic DNA from breast tissue 14509 adj_norm


title: Genomic DNA from breast tissue 17163 adj_norm


title: Genomic DNA from breast tissue 16666 adj_norm


title: Genomic DNA from breast tissue 16404 adj_norm


title: Genomic DNA from breast tissue 14090 adj_norm


title: Genomic DNA from breast tissue 14306 adj_norm


title: Genomic DNA from breast tissue 14064 adj_norm


title: Genomic DNA from breast tissue 13676 adj_norm


title: Genomic DNA from breast tissue 14019 adj_norm


title: Genomic DNA from breast tissue 13645 adj_norm


title: Genomic DNA from breast tissue 13916 adj_norm


title: Genomic DNA from breast tissue 13361 adj_norm


title: Genomic DNA from breast tissue 13120 adj_norm


title: Genomic DNA from breast tissue 13315 adj_norm


title: Genomic DNA from breast tissue 14810 adj_norm


title: Genomic DNA from breast tissue 13152 adj_norm


title: Genomic DNA from breast tissue 12976 adj_norm


title: Genomic DNA from breast tissue 13100 adj_norm


title: Genomic DNA from breast tissue 14447 adj_norm


title: Genomic DNA from breast tissue 13017 adj_norm


title: Genomic DNA from breast tissue 12887 adj_norm


title: Genomic DNA from breast tissue 14537 adj_norm


title: Genomic DNA from breast tissue 12788 adj_norm


title: Genomic DNA from breast tissue 12716 adj_norm


title: Genomic DNA from breast tissue 12424 adj_norm


title: Genomic DNA from breast tissue 12638 adj_norm


title: Genomic DNA from breast tissue 12600 adj_norm


title: Genomic DNA from breast tissue 12423 adj_norm


title: Genomic DNA from breast tissue 12421 adj_norm


title: Genomic DNA from breast tissue 12394 adj_norm


title: Genomic DNA from breast tissue 12437 adj_norm


title: Genomic DNA from breast tissue 12138 adj_norm


title: Genomic DNA from breast tissue 12109 adj_norm


title: Genomic DNA from breast tissue 11989 adj_norm


title: Genomic DNA from breast tissue 11982 adj_norm


title: Genomic DNA from breast tissue 12364 adj_norm


title: Genomic DNA from breast tissue 12280 adj_norm


title: Genomic DNA from breast tissue 12273 adj_norm


title: Genomic DNA from breast tissue 11688 adj_norm


title: Genomic DNA from breast tissue 12239 adj_norm


title: Genomic DNA from breast tissue 12207 adj_norm


title: Genomic DNA from breast tissue 11435 adj_norm


title: Genomic DNA from breast tissue 12197 adj_norm


title: Genomic DNA from breast tissue 12123 adj_norm

value: IV


title: Genomic DNA from breast tissue 11117 adj_norm


title: Genomic DNA from breast tissue 12107 adj_norm


title: Genomic DNA from breast tissue 12623 adj_norm


title: Genomic DNA from breast tissue 11781 adj_norm


title: Genomic DNA from breast tissue 11462 adj_norm


title: Genomic DNA from breast tissue 11904 adj_norm

value: Yes


title: Genomic DNA from breast tissue 11913 adj_norm


title: Genomic DNA from breast tissue 11059 adj_norm


title: Genomic DNA from breast tissue 11449 adj_norm


title: Genomic DNA from breast tissue 11724 adj_norm


title: Genomic DNA from breast tissue 10608 adj_norm


title: Genomic DNA from breast tissue 11043 adj_norm


title: Genomic DNA from breast tissue 10940 adj_norm


title: Genomic DNA from breast tissue 10391 adj_norm


title: Genomic DNA from breast tissue 10929 adj_norm


title: Genomic DNA from breast tissue 10618 adj_norm


title: Genomic DNA from breast tissue 11577 adj_norm


title: Genomic DNA from breast tissue 10533 adj_norm


title: Genomic DNA from breast tissue 16832 normal

description:
Genomic DNA from breast tissue
normal breast tissue

source_name: frozen normal breast tissue

value: normal


title: Genomic DNA from breast tissue 16194 normal


title: Genomic DNA from breast tissue 16031 normal


title: Genomic DNA from breast tissue 15608 normal


title: Genomic DNA from breast tissue 10330 adj_norm


title: Genomic DNA from breast tissue 10184 adj_norm


title: Genomic DNA from breast tissue 16594 normal


title: Genomic DNA from breast tissue 15585 normal


title: Genomic DNA from breast tissue 15490 normal


title: Genomic DNA from breast tissue 10601 adj_norm


title: Genomic DNA from breast tissue 11333 adj_norm


title: Genomic DNA from breast tissue 16028 normal


title: Genomic DNA from breast tissue 15380 normal


title: Genomic DNA from breast tissue 14931 normal


title: Genomic DNA from breast tissue 14848 normal


title: Genomic DNA from breast tissue 14795 normal


title: Genomic DNA from breast tissue 14638 normal


title: Genomic DNA from breast tissue 14658 normal


title: Genomic DNA from breast tissue 14618 normal


title: Genomic DNA from breast tissue 14547 normal


title: Genomic DNA from breast tissue 14594 normal


title: Genomic DNA from breast tissue 14477 normal


title: Genomic DNA from breast tissue 14522 normal


title: Genomic DNA from breast tissue 14474 normal


title: Genomic DNA from breast tissue 14389 normal


title: Genomic DNA from breast tissue 16427 normal


title: Genomic DNA from breast tissue 14268 normal


title: Genomic DNA from breast tissue 14368 normal


title: Genomic DNA from breast tissue 14404 normal


title: Genomic DNA from breast tissue 16136 normal


title: Genomic DNA from breast tissue 15669 normal


title: Genomic DNA from breast tissue 14165 normal


title: Genomic DNA from breast tissue 14215 normal


title: Genomic DNA from breast tissue 14111 normal


title: Genomic DNA from breast tissue 14152 normal


title: Genomic DNA from breast tissue 14071 normal


title: Genomic DNA from breast tissue 14008 normal


title: Genomic DNA from breast tissue 13974 normal


title: Genomic DNA from breast tissue 13959 normal


title: Genomic DNA from breast tissue 13885 normal


title: Genomic DNA from breast tissue 26361 normal


title: Genomic DNA from breast tissue 13847 normal


title: Genomic DNA from breast tissue 13843 normal


title: Genomic DNA from breast tissue 13856 normal


title: Genomic DNA from breast tissue 13837 normal


title: Genomic DNA from breast tissue 13774 normal


title: Genomic DNA from breast tissue 13725 normal


title: Genomic DNA from breast tissue 13618 normal


title: Genomic DNA from breast tissue 13637 normal


title: Genomic DNA from breast tissue 13682 normal


title: Genomic DNA from breast tissue 13654 normal


title: Genomic DNA from breast tissue 13459 normal


title: Genomic DNA from breast tissue 13601 normal


title: Genomic DNA from breast tissue 13570 normal


title: Genomic DNA from breast tissue 13571 normal


title: Genomic DNA from breast tissue 13500 normal


title: Genomic DNA from breast tissue 13407 normal


title: Genomic DNA from breast tissue 13450 normal


title: Genomic DNA from breast tissue 13382 normal


title: Genomic DNA from breast tissue 13355 normal


title: Genomic DNA from breast tissue 13208 normal


title: Genomic DNA from breast tissue 13368 normal


title: Genomic DNA from breast tissue 13279 normal


title: Genomic DNA from breast tissue 14178 normal


title: Genomic DNA from breast tissue 13341 normal


title: Genomic DNA from breast tissue 13310 normal


title: Genomic DNA from breast tissue 13381 normal


title: Genomic DNA from breast tissue 13255 normal


title: Genomic DNA from breast tissue 13135 normal


title: Genomic DNA from breast tissue 13191 normal


title: Genomic DNA from breast tissue 13118 normal


title: Genomic DNA from breast tissue 13156 normal


title: Genomic DNA from breast tissue 13189 normal


title: Genomic DNA from breast tissue 13105 normal


title: Genomic DNA from breast tissue 13090 normal


title: Genomic DNA from breast tissue 13082 normal


title: Genomic DNA from breast tissue 13053 normal


title: Genomic DNA from breast tissue 13049 normal


title: Genomic DNA from breast tissue 13038 normal


title: Genomic DNA from breast tissue 13024 normal


title: Genomic DNA from breast tissue 12812 normal


title: Genomic DNA from breast tissue 12919 normal


title: Genomic DNA from breast tissue 12886 normal


title: Genomic DNA from breast tissue 12863 normal


title: Genomic DNA from breast tissue 12924 normal


title: Genomic DNA from breast tissue 12616 normal


title: Genomic DNA from breast tissue 12588 normal


title: Genomic DNA from breast tissue 12791 normal


title: Genomic DNA from breast tissue 12590 normal


title: Genomic DNA from breast tissue 12657 normal


title: Genomic DNA from breast tissue 12572 normal


title: Microbiota of paraffin negative control_2

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 8 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose >Log_di_cutadapt.txt
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 261 --p-trunc-len-r 198 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: rep_sequences.fasta: representative ASV sequences in fasta fomat (sequence names correspond to row names of the feature_table.tsv file)
Supplementary files format and content: feature_table.tsv: TSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence

organism: unidentified

source_name: None (paraffin)

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

tag: tissue

value: None (paraffin)

tag: patient id

tag: time

tag: condition

tag: crc site

tag: crc sex

tag: tumor grading

tag: tumor stage


title: Genomic DNA from breast tissue 12501 normal

tag: methylation id (basenames)

tag: sample type

value: European American

tag: Sex

tag: diabetes


title: Microbiota of paraffin negative control_1


title: Genomic DNA from breast tissue 12493 normal

tag: race

value: F

tag: ndi continuous

tag: dichtomized ndi status


title: Genomic DNA from breast tissue 12428 normal

tag: ndi quartiles


title: Genomic DNA from breast tissue 12489 normal


title: Genomic DNA from breast tissue 12433 normal


title: Genomic DNA from breast tissue 13013 normal


title: Genomic DNA from breast tissue 12914 normal


title: NMP peptides APV rep3

city: Baltimore

first: Fulya

last: Turker

address: 725 N. Wolfe Street

institute: Johns Hopkins School of Medicine

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Pep-APV_3

data_processing:
Illumina HiSeq reads were processed through Illumina’s Real-Time Analysis (RTA) software generating base calls and corresponding base call quality scores.  CIDRSeqSuite 7.1.0 was used to convert compressed bcl files into compressed FASTQ files.
FASTQ files were imported into CLC Genomics Server 9.1.1
Sequences aligned as paired reads to Mus May-19 NCBI transcriptome GRCm38_p6: Mismatch cost 2, Insertion cost 3, Deletion cost 3, Length fraction 0.8, Similarity fraction 0.8.
Alignments expressed as Quantile-normalized log2 values.
Assembly: GRCm38_p6 May-19
Supplementary files format and content: Margolis_NoNonStim_1-LogMeanQuant-Signals.txt is tab-delimited file of Quantile normalized Log2 FPKM RNA-Seq data used for analyses, containing Nulls for zero FPKM.

source_name: primary mouse cortical neuronal culture

growth_protocol: Primary mouse cortical neuronal culture were maintained in Neurobasal media supplemented with 2% B-27 (ThermoFisher; 17504044), penicillin/streptomycin (100 U/ml and 100 µg/ml, respectively) (Millipore; 15140122), and 2 mM glutamine (ThermoFisher; 25030081) at 37°C/5% CO2. Culture media were changed to Neurobasal media without serum 3 days after plating and supplemented with fresh media every 4-5 days. Experiments were performed at days in vitro (DIV) 12.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
Illumina’s TruSeq Total RNA V2 protocol was used to generate libraries.  Specifically, ribosomal depleted RNA is converted to cDNA and size selected to 150 to 200 bp in length with 3' or 5' overhangs. End repair is performed where 3' to 5' exonuclease activity of enzymes removes 3' overhangs and the polymerase activity fills in the 5' overhangs. An ‘A’ base is then added to the 3' end of the blunt phosphorylated DNA fragments which prepares the DNA fragments for ligation to the sequencing adapters, which have a single ‘T’ base overhang at their 3' end. Ligated fragments are subsequently size selected through purification using SPRI beads and undergo PCR amplification techniques to prepare the ‘libraries’. The BioAnalyzer is used for quality control of the libraries to ensure adequate concentration and appropriate fragment size.  The resulting library insert size is 120-200bp with a median size of 150bp. Libraries were uniquely barcoded and pooled for sequencing.DNA Sequencing: DNA sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.

treatment_protocol: DIV12 neuronal cultures were treated with corresponding drugs/compounds for 1 hr.

tag: strain

value: C57BL/6 mice

tag: cell line

value: primary mouse cortical neuronal culture

tag: cell type

value: cortical neurons

tag: genotype

value: WT

tag: treatment

value: 4% (v/v) purified NMP peptide in the presence of 100 µM APV treatment for 1 hr


title: Genomic DNA from breast tissue 12598 normal

tag: er status

value: NEG

tag: grade

tag: ajcc stage

value: II

tag: molecular subtype


title: NMP peptides APV rep2

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Pep-APV_2


title: NMP peptides (PK) rep3

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Pep-PK_3

value: 4% (v/v) purified proteinase K (PK)-cleaved NMP peptide treatment for 1 hr


title: Genomic DNA from breast tissue 12403 normal

tag: methylation id (basenames)

value: African American


title: Genomic DNA from breast tissue 12412 normal

tag: sample type

value: No


title: Genomic DNA from breast tissue 13918 normal

tag: Sex


title: NMP peptides (PK) rep1

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Pep-PK_1


title: Genomic DNA from breast tissue 12379 normal


title: Genomic DNA from breast tissue 12368 normal


title: NMP peptides rep1

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Pep_1

value: 4% (v/v) purified NMP peptide treatment for 1 hr


title: NMP peptides rep3

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Pep_3


title: NMP peptides rep2

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Pep_2


title: Genomic DNA from breast tissue 12367 normal

tag: diabetes


title: NMP peptides APV rep1

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Pep-APV_1


title: Genomic DNA from breast tissue 12338 normal

tag: race


title: Bic rep3

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Bic_3

value: 20 µM bicuculline (Tocris) treatment for 1 hr


title: Genomic DNA from breast tissue 12258 normal

tag: ndi continuous


title: Bic rep1

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Bic_1


title: Genomic DNA from breast tissue 12327 normal

tag: dichtomized ndi status


title: Bic rep2

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Bic_2


title: DMSO rep3

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Nostim_3

value: 1% dimethyl sulfoxide (DMSO; Sigma) treatment for 1 hr


title: E5_nogln: 7x10^6 cells,  -glutamine, replicate 3

city: Boston

first: Raul

last: Mostoslavsky

state: MA

address: 185 Cambridge St.

institute: The Massachusetts General Hospital Cancer Center-Harvard University

description: shRNA cassette amplicon

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 2500 Real-Time Analysis (RTA) software (Illumina)
Samples were demultiplexed using fastx_barcode_splitter from the fastx_toolkit (v0.0.13.2), allowing 2 mismatches.
FASTQC v0.11.2 was used to assess sequence data quality.
Sequences were trimmed using fastx_trimmer from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -f 22 -l 42. This keeps only the section of each read corresponding to the unique shRNA sequences (positions 22-42 inclusive).
Bases with qual ≥10 were removed with fastx_quality_filter from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -q 10 -p 94.
Trimmed and filtered sequences were mapped with Bowtie2 v2.2.3 using the following options (--phred33 --end-to-end --very-sensitive).
High-quality TRC2-alignments were filtered using Samtools view and tabulated using Samtools idxstats.
Genome_build: A reference index was generated for Bowtie2 using only the unique shRNA sequences from the mouse TRC2 library annotation (PMID 16564017).
Supplementary_files_format_and_content: Tab delimited text file containing raw shRNA counts for each sample

source_name: MycER MEF cells

growth_protocol: 7x10^6 cells were cultured in DMEM supplemented with 10% fetal bovine serum + 1% penicillin streptomycin, and were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
shRNA screen protocol: 6x10^6 cells were transduced with the mouse TRC2 library and propogated for 7 days to clear shRNAs targeting essential genes. The resulting cell populations were treated in triplicate with 2mM GLN or no GLN for 4-5 weeks.
Genomic DNA was extracted using a DNeasy Blood and Tissue kit (Qiagen)

treatment_protocol: Cells were cultured with or without 2mM Glutmaine to select for cells able to overcome nutrient starvation.

value: MycER MEF

value: p53 immortalized Mouse Embryonic Fibroblasts

tag: stable expression

value: cells stably express a tamoxifen-inducible Myc-Estrogen Receptor fusion protein

tag: shRNA library

value: mouse TRC2

tag: culture condition

value: no glutamine + 200uM 4-OHT


title: Genomic DNA from breast tissue 12254 normal

value: normal

value: F

tag: ndi quartiles


title: Genomic DNA from breast tissue 12166 normal

value: European American


title: DMSO rep2

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Nostim_2

tag: strain

value: C57BL/6 mice

tag: cell line

value: primary mouse cortical neuronal culture

tag: cell type

value: cortical neurons

tag: genotype

value: WT


title: E4_nogln: 7x10^6 cells,  -glutamine, replicate 2

description: shRNA cassette amplicon

tag: treatment


title: NMP peptides (PK) rep2

description:
Sequencing was performed on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 100bp sequencing.
Pep-PK_2

value: 4% (v/v) purified proteinase K (PK)-cleaved NMP peptide treatment for 1 hr


title: E3_nogln: 7x10^6 cells,  -glutamine, replicate 1

description: shRNA cassette amplicon


title: Genomic DNA from breast tissue 12141 normal

value: African American

value: No


title: Genomic DNA from breast tissue 12145 normal


title: E5_gln: 7x10^6 cells,  +glutamine, replicate 3

description: shRNA cassette amplicon

value: 2mM glutamine + 200uM 4-OHT


title: Genomic DNA from breast tissue 12376 normal


title: E4_gln: 7x10^6 cells,  +glutamine, replicate 2

description: shRNA cassette amplicon


title: Genomic DNA from breast tissue 12132 normal


title: Genomic DNA from breast tissue 12130 normal


title: Genomic DNA from breast tissue 12264 normal


title: E3_gln: 7x10^6 cells,  +glutamine, replicate 1

description: shRNA cassette amplicon


title: Genomic DNA from breast tissue 12136 normal


title: vp9_Monocytes_Enhancer_DMSO

city: Nijmegen

first: Cheng

last: Wang

address: Geert Grooteplein 28

department: Molecular biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

data_processing:
Library strategy: 4C-seq
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Library strategy:Kapa hyperprep.
Fastq data was processed with 4Cseqpipe
DpnII read primer was removed, the fastq was mapping to hg19 using bwa, DpnII fragments around the viewpoint were qualitied using peakstats
the viewpoint +/- 5 kb counts were ingnored, CPM(counts per million) counts for bedgraph for UCSC genome browser visualization
Genome_build: hg19

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were obtained by depletion of CD3, CD19 and CD56 positive cells from PBMCs obtained upon Ficoll isolation of a buffycoat. HeLa cells were cultured in DMEM + 10% FBS. THP1 cells were cultured in RPMI 1640 +10% FBS.

extract_protocol:
The cells were fixed with formaldehyde and then lysised. Isolated nuclei were then fully digested by DpnII followed by overnight ligation. Ligated cycle DNA were purified after de-crosslinking incubation with proteinase K at 65 degree for 4 hours, followed by further digestion by NlaIII.  The digested DNA were ligated again and purified.
The 4C library was  amplified with the viewpoint specific primers with inverse PCR. For each viewpoint, 8 PCR reactions products were pooled to enhance the library complexity.
Kapa hyperprep kit

treatment_protocol: The cells were treated with 1 uM triamcinolone acetonide(TA) for 4 hours.

value: Monocytes

value: DMSO(Veh control) for 4 hours


title: Genomic DNA from breast tissue 12073 normal


title: vp9_FKBP5_THP1_Enhancer_DMSO

source_name: Human acute monocytic leukemia cell line


title: Genomic DNA from breast tissue 12071 normal


title: Genomic DNA from breast tissue 12069 normal

value: Yes


title: vp9_FKBP5_THP1_Enhancer_TA

value: 100 nM triamcinolone acetonide(TA) for 4 hours.


title: vp9_FKBP5_HeLa_S9_Enhancer_TA

source_name: Human cervical cancer cell line

value: HeLa


title: Genomic DNA from breast tissue 12092 normal


title: vp9_FKBP5_HeLa_S8_Enhancer_TA


title: Genomic DNA from breast tissue 12044 normal


title: vp9_FKBP5_HeLa_S9_Enhancer_DMSO


title: Genomic DNA from breast tissue 12020 normal


title: Genomic DNA from breast tissue 11990 normal


title: vp9_FKBP5_HeLa_S8_Enhancer_DMSO


title: Genomic DNA from breast tissue 11985 normal


title: vp9_FKBP5_HeLa_S6_Enhancer_TA


title: Genomic DNA from breast tissue 11978 normal


title: vp9_FKBP5_HeLa_S6_Enhancer_DMSO


title: vp8_monocytes_CTCF20_DMSO


title: Genomic DNA from breast tissue 11977 normal


title: vp8_FKBP5_HeLa_s10b_CTCF20_DMSO


title: Genomic DNA from breast tissue 11912 normal


title: Genomic DNA from breast tissue 11930 normal


title: vp8_FKBP5_HeLa_s10b_CTCF20_TA


title: vp7_FKBP5_HeLa_S9_Downstream_TA


title: Genomic DNA from breast tissue 11909 normal


title: vp8_FKBP5_HeLa_s10a_CTCF20_DMSO


title: Genomic DNA from breast tissue 11895 normal


title: vp7_FKBP5_HeLa_S9_Downstream_DMSO


title: Genomic DNA from breast tissue 11865 normal


title: Genomic DNA from breast tissue 11881 normal


title: Genomic DNA from breast tissue 11866 normal


title: Genomic DNA from breast tissue 11844 normal


title: Genomic DNA from breast tissue 11834 normal


title: Genomic DNA from breast tissue 11889 normal


title: vp7_FKBP5_HeLa_s10a_downstream_TA


title: vp8_FKBP5_HeLa_s10a_CTCF20_TA


title: vp7_FKBP5_HeLa_s10a_downstream_DMSO


title: Genomic DNA from breast tissue 11829 normal


title: vp4_RPL10A_HeLa_CTCF16_RPL10a_intron4


title: vp1b_ZNF76ii_HeLa_s10b_TA


title: vp3_RPL10A_HeLa_CTCF16_RPL10A_promoter


title: Genomic DNA from breast tissue 11953 normal


title: vp1b_ZNF76ii_HeLa_s10a_TA


title: Genomic DNA from breast tissue 11740 normal


title: vp1a_ZNF76i_HeLa_s10b_TA


title: vp2_RPL10A_HeLa_PPARD_intron2


title: vp1b_ZNF76ii_HeLa_s10a_DMSO


title: Genomic DNA from breast tissue 11825 normal


title: vp6_HeLa_CTCF17_DMSO


title: vp6_HeLa_CTCF17_TA


title: vp1b_ZNF76ii_HeLa_s10b_DMSO


title: Genomic DNA from breast tissue 11734 normal


title: Genomic DNA from breast tissue 11811 normal


title: vp5_RPL10A_HeLa_CTCF16_TEAD3_intron12


title: Genomic DNA from breast tissue 11696 normal


title: Genomic DNA from breast tissue 11663 normal


title: Genomic DNA from breast tissue 11826 normal


title: vp1a_ZNF76i_HeLa_s10b_DMSO


title: Genomic DNA from breast tissue 11707 normal


title: vp1a_ZNF76i_HeLa_s10a_DMSO


title: vp14_FKBP5_HeLa_S9_Upstream_TA


title: vp15_SRPK1i_HeLa_s10b_DMSO


title: vp1a_ZNF76i_HeLa_s10a_TA


title: vp15_SRPK1i_HeLa_s10a_TA


title: Genomic DNA from breast tissue 11782 normal


title: vp15_SRPK1i_HeLa_s10a_DMSO


title: vp14_FKBP5_HeLa_S9_Upstream_DMSO


title: vp14_FKBP5_HeLa_s10a_Upstream_DMSO


title: Genomic DNA from breast tissue 11703 normal


title: Genomic DNA from breast tissue 11594 normal


title: vp13_Monocytes_CTCF27-28_TA


title: Genomic DNA from breast tissue 11582 normal


title: vp14_FKBP5_HeLa_s10a_Upstream_TA


title: Genomic DNA from breast tissue 11634 normal


title: Genomic DNA from breast tissue 11504 normal


title: Genomic DNA from breast tissue 11737 normal


title: Genomic DNA from breast tissue 11599 normal


title: vp13_Monocytes_CTCF27-28_DMSO


title: Genomic DNA from breast tissue 11591 normal


title: Genomic DNA from breast tissue 11603 normal

value: M


title: vp13_FKBP5_THP1_CTCF27-28_TA


title: Genomic DNA from breast tissue 11436 normal

value: normal


title: vp13_FKBP5_THP1_CTCF27-28_DMSO


title: vp13_FKBP5_HeLa_s10b_CTCF27-28_TA


title: Genomic DNA from breast tissue 11423 normal

value: F


title: Genomic DNA from breast tissue 11421 normal

value: European American


title: vp12_FKBP5_HeLA_S9_Distal_promoter_TA


title: vp13_FKBP5_HeLa_s10b_CTCF27-28_DMSO


title: vp13_FKBP5_HeLa_s10a_CTCF27-28_TA


title: Genomic DNA from breast tissue 11517 normal


title: Genomic DNA from breast tissue 11359 normal


title: Genomic DNA from breast tissue 11495 normal


title: vp12_FKBP5_HeLa_S9_Distal_promoter_DMSO


title: Genomic DNA from breast tissue 11390 normal


title: Genomic DNA from breast tissue 11353 normal


title: Genomic DNA from breast tissue 11349 normal


title: Genomic DNA from breast tissue 11422 normal


title: vp12_FKBP5_HeLa_S8_Distal_promoter_TA


title: Genomic DNA from breast tissue 11347 normal


title: vp12_FKBP5_HeLa_S6_Distal_promoter_TA


title: vp12_FKBP5_HeLa_S8_Distal_promoter_DMSO


title: vp13_FKBP5_HeLa_s10a_CTCF27-28_DMSO


title: Genomic DNA from breast tissue 11289 normal


title: Genomic DNA from breast tissue 11263 normal


title: vp11_FKBP5_HeLa_S9_promoter_TA


title: vp11_FKBP5_HeLa_S8_promoter_TA


title: Genomic DNA from breast tissue 11244 normal


title: vp11_FKBP5_HeLa_S9_promoter_DMSO


title: vp11_Monocytes_promoter_DMSO


title: Genomic DNA from breast tissue 11226 normal


title: Genomic DNA from breast tissue 11310 normal


title: Genomic DNA from breast tissue 11218 normal


title: vp11_FKBP5_HeLa_S6_promoter_DMSO


title: Genomic DNA from breast tissue 11206 normal


title: vp12_FKBP5_HeLa_S6_Distal_promoter_DMSO


title: vp11_FKBP5_HeLa_S8_promoter_DMSO


title: Genomic DNA from breast tissue 11250 normal

tag: er status

value: NEG

tag: grade

tag: ajcc stage

value: II

tag: molecular subtype

value: TNBC


title: vp10_FKBP5_HeLa_S9_Middle_DMSO


title: vp10_FKBP5_HeLa_S9_Middle_TA


title: vp10_Monocytes_Middle_DMSO


title: Genomic DNA from breast tissue 11202 normal

tag: methylation id (basenames)

tag: sample type

tag: Sex


title: Genomic DNA from breast tissue 11215 normal

tag: race

tag: ndi continuous

tag: dichtomized ndi status


title: Genomic DNA from breast tissue 11189 normal


title: Genomic DNA from breast tissue 11185 normal


title: Genomic DNA from breast tissue 11288 normal

tag: diabetes


title: vp10_FKBP5_HeLa_S8_Middle_DMSO


title: Genomic DNA from breast tissue 11178 normal


title: vp10_FKBP5_HeLa_S6_Middle_DMSO


title: Genomic DNA from breast tissue 11177 normal

tag: ndi quartiles


title: vp11_FKBP5_HeLa_S6_Poximal_promoter_TA


title: SRPK1ii_HeLa_s10b_TA


title: Genomic DNA from breast tissue 11165 normal


title: Genomic DNA from breast tissue 11128 normal


title: Genomic DNA from breast tissue 11141 normal


title: Genomic DNA from breast tissue 11161 normal


title: SRPK1ii_HeLa_s10a_TA


title: SRPK1ii_HeLa_s10b_DMSO


title: SRPK1ii_HeLa_s10a_DMSO


title: Genomic DNA from breast tissue 11135 normal


title: Genomic DNA from breast tissue 11093 normal


title: Genomic DNA from breast tissue 11110 normal


title: vp10_FKBP5_HeLa_S8_Middle_TA


title: Genomic DNA from breast tissue 11088 normal


title: T308A_VC_8wk_6hr_Rep7

city: Roslindale

first: Tess

last: Whitwam

address: 41 Brookdale Street

institute: Harvard University

data_processing:
Reads were trimmed with Trimmomatic (v0.36) to remove Illumina adaptors and low-quality sequence (settings: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50).
Trimmed reads were mapped to the mm10 Refseq transcriptome and genome using STAR (v2.5.2b).
Reads were counted in the full gene body (TSS to TTS of longest isoform, in order to include intronic reads) using Subread featureCounts.
Differential expression was performed with the R package edgeR (v3.34.1) or DESeq2 (v1.34.0).
Genes with low counts were filtered by keeping only genes with rowSums(cpm(y)>1) >= (number of samples per group). Differentially expressed genes were defined by an FDR < 0.05 with no fold-change cut-off. For DESeq2 analyses, shrinkage of effect sizes was performed using lfcshrink and the apeglm method following differential expression analysis
Assembly: mm10
Supplementary files format and content: tad-delimited text file with raw counts in exons for each sample

source_name: Visual Cortex

extract_protocol:
dLGN and visual cortex were dissected from littermate male mice (WT or QKI) and flash frozen. After collecting all replicates, tissue was homogenized in TRIzol reagent, and RNA was chloroform extracted and then purified using the Qiagen RNeasy Micro Kit with on-column DNase treatment according to the manufacturer’s instructions.
Total RNA (150-200 ng for dLGN libraries, 500 ng for visual cortex libraries) was used to generate libraries following rRNA depletion (NEBNext, E6310X) according to the manufacturer’s instructions (NEBNext, E7420).

tag: tissue

value: Visual Cortex

value: Male

tag: developmental stage

value: 8 weeks

tag: strain


title: T308A_VC_8wk_6hr_Rep8

tag: genotype


title: vp10_FKBP5_HeLa_S6_Middle_TA

tag: cell type

tag: treatment


title: Genomic DNA from breast tissue 11062 normal

value: No


title: T308A_VC_8wk_6hr_Rep6


title: T308A_VC_8wk_6hr_Rep4


title: T308A_VC_8wk_6hr_Rep9


title: Genomic DNA from breast tissue 11067 normal


title: Genomic DNA from breast tissue 11060 normal

value: Hispanic


title: T308A_VC_8wk_6hr_Rep5


title: T308A_VC_8wk_6hr_Rep3


title: T308A_VC_8wk_6hr_Rep2


title: Genomic DNA from breast tissue 10998 normal

value: African American


title: T308A_VC_8wk_6hr_Rep10


title: T308A_VC_8wk_6hr_Rep1


title: Genomic DNA from breast tissue 10986 normal


title: WT_VC_8wk_6hr_Rep5

value: WT


title: WT_VC_8wk_6hr_Rep4


title: Genomic DNA from breast tissue 10971 normal


title: Genomic DNA from breast tissue 10954 normal


title: Genomic DNA from breast tissue 10935 normal


title: WT_VC_8wk_6hr_Rep1


title: WT_VC_8wk_6hr_Rep3


title: WT_VC_8wk_6hr_Rep2


title: T308A_VC_8wk_0hr_Rep1


title: Genomic DNA from breast tissue 10926 normal


title: T308A_VC_8wk_0hr_Rep3


title: Genomic DNA from breast tissue 10910 normal


title: Genomic DNA from breast tissue 11010 normal


title: WT_VC_8wk_0hr_Rep1


title: T308A_VC_8wk_0hr_Rep2


title: Genomic DNA from breast tissue 10925 normal


title: WT_VC_8wk_0hr_Rep3


title: Genomic DNA from breast tissue 11749 normal


title: Genomic DNA from breast tissue 10924 normal


title: Genomic DNA from breast tissue 10922 normal


title: Genomic DNA from breast tissue 10886 normal


title: Genomic DNA from breast tissue 10898 normal


title: Genomic DNA from breast tissue 10928 normal


title: QKI_VisualCortex_LDR_4h_Rep4

value: QKI


title: Genomic DNA from breast tissue 10996 normal


title: WT_VC_8wk_0hr_Rep2


title: Genomic DNA from breast tissue 10852 normal


title: QKI_VisualCortex_LDR_0h_Rep4


title: Genomic DNA from breast tissue 10803 normal


title: Genomic DNA from breast tissue 10866 normal


title: Genomic DNA from breast tissue 10817 normal


title: WT_VisualCortex_LDR_4h_Rep3


title: WT_VisualCortex_LDR_4h_Rep4


title: QKI_VisualCortex_LDR_0h_Rep3


title: Genomic DNA from breast tissue 10861 normal


title: WT_VisualCortex_LDR_0h_Rep4


title: Genomic DNA from breast tissue 10795 normal


title: WT_VisualCortex_LDR_0h_Rep3


title: Genomic DNA from breast tissue 10776 normal


title: QKI_VisualCortex_LDR_0h_Rep2


title: Genomic DNA from breast tissue 10644 normal


title: Genomic DNA from breast tissue 10773 normal


title: QKI_VisualCortex_LDR_4h_Rep2


title: WT_VisualCortex_LDR_4h_Rep2


title: Genomic DNA from breast tissue 10434 normal


title: WT_VisualCortex_LDR_0h_Rep2


title: QKI_VisualCortex_LDR_4h_Rep3


title: Genomic DNA from breast tissue 10399 normal


title: Genomic DNA from breast tissue 10381 normal


title: Genomic DNA from breast tissue 10274 normal


title: QKI_VisualCortex_LDR_4h_Rep1


title: WT_VisualCortex_LDR_4h_Rep1


title: QKI_dLGN_LDR_4h_Rep4

source_name: dLGN

value: dLGN


title: Genomic DNA from breast tissue 10183 normal


title: Genomic DNA from breast tissue 10195 normal


title: Genomic DNA from breast tissue 10137 normal


title: WT_VisualCortex_LDR_0h_Rep1


title: Genomic DNA from breast tissue 10068 normal


title: QKI_dLGN_LDR_0h_Rep4


title: Genomic DNA from breast tissue 10029 normal


title: WT_dLGN_LDR_4h_Rep4


title: WT_dLGN_LDR_0h_Rep4


title: Genomic DNA from breast tissue 10013 normal


title: QKI_dLGN_LDR_4h_Rep3


title: QKI_dLGN_LDR_0h_Rep3


title: Genomic DNA from breast tissue 10449 normal


title: Genomic DNA from breast tissue 92-9 normal


title: Genomic DNA from breast tissue 92-6 normal


title: QKI_VisualCortex_LDR_0h_Rep1


title: WT_dLGN_LDR_0h_Rep3


title: Genomic DNA from breast tissue 92-8 normal


title: Genomic DNA from breast tissue 92-05 normal


title: Microbiota of Stool from patient HPV-1

source_name: Stool

value: Stool

tag: patient id

tag: time

tag: condition

value: CRC

tag: crc site

value: Ascending colon

tag: crc sex

value: Adenocarcinoma, NOS

tag: tumor grading

tag: tumor stage


title: QKI_dLGN_LDR_4h_Rep2

tag: Sex


title: Genomic DNA from breast tissue 92-7 normal

tag: methylation id (basenames)

tag: sample type

value: normal

tag: race

value: European American

value: F


title: WT_dLGN_LDR_0h_Rep2

tag: tissue


title: QKI_dLGN_LDR_0h_Rep2

tag: developmental stage


title: Microbiota of Stool from patient HPV-10


title: QKI_dLGN_LDR_4h_Rep1

tag: strain


title: Microbiota of Stool from patient HPV-8

value: Rectum


title: Microbiota of Stool from patient HPV-9

value: M


title: QKI_dLGN_LDR_0h_Rep1

value: Male

tag: genotype


title: WT_dLGN_LDR_0h_Rep1


title: Microbiota of Stool from patient HPV-7

value: Descending colon


title: WT_dLGN_LDR_4h_Rep1


title: WT_VisualCortex_P30_Rep4

value: Visual Cortex


title: WT_VisualCortex_P30_Rep5


title: Microbiota of Stool from patient HPV-3


title: Microbiota of Stool from patient HPV-6


title: WT_dLGN_LDR_4h_Rep2


title: QKI_VisualCortex_P30_Rep4


title: Microbiota of Stool from patient HPV-5


title: Microbiota of Stool from patient HPV-4


title: QKI_VisualCortex_P30_Rep5


title: Microbiota of Stool from patient HPV-2


title: WT_dLGN_LDR_4h_Rep3


title: QKI_VisualCortex_P30_Rep3


title: Microbiota of Stool from patient HPV+9

value: CRC+HPV


title: WT_VisualCortex_P30_Rep3


title: Microbiota of Stool from patient HPV+8


title: WT1_VisualCortex_P30_Rep2


title: QKI_VisualCortex_P30_Rep2


title: WT2_VisualCortex_P30_Rep2


title: Microbiota of Stool from patient HPV+6

value: rectum

value: Basaloid carcinoma


title: Microbiota of Stool from patient HPV+7


title: WT_VisualCortex_P30_Rep1

value: WT


title: Microbiota of Stool from patient HPV+4


title: QKI1_VisualCortex_P30_Rep1

value: QKI


title: Microbiota of Stool from patient HPV+3

value: Stool

value: Squamous carcinoma


title: QKI_dLGN_P30_Rep5

value: dLGN


title: Microbiota of Stool from patient HPV+2


title: Microbiota of Stool from patient HPV+1


title: WT_dLGN_P30_Rep5


title: WT_dLGN_P30_Rep3


title: QKI_dLGN_P30_Rep3


title: case [1327338]

city: WenZhou

first: Zheng

last: GongWei

address: OuHai ChaShan

country: China

institute: WenZhou Medical University

description:
otu_table.c.relative.txt
otu_table.f.relative.txt
otu_table.g.relative.txt
otu_table.k.relative.xls
otu_table.o.relative.xls
otu_table.p.relative.xls

data_processing:
library strategy: 16S_rRNA
After trimming off the barcodes and primers, paired-end sequences were assembled with FLASH (v1.2.7).
The assembled raw tags were quality controlled with Fastp (v0.23.1) to obtain high-quality clean tags
Chimeric sequences were further removed from clean tags using vsearch (v2.22.1)
Supplementary files format and content: otu_table.c.relative.txt: class level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.f.relative.txt: family level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.g.relative.txt: genus level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.k.relative.xls: kingdom level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.o.relative.xls: order level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.p.relative.xls: phylum level OTU(Operational Taxonomic Units) abundance table

source_name: fecal samples

extract_protocol:
Qiagen Gel Extraction Kit (Qiagen, Germany)
TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, USA)

value: fecal samples

tag: subject status

value: CAD patient


title: In_hiPSC_CMs

city: Wuhan

first: Saiyang

last: Xie

address: Jiefang Road 238

institute: Wuhan university

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseg output.
ChIP-seg reads were trimmed from 3' end untl the final base had a quality score > 30, using Trmmomatic v0.33, discarding reads left with < 20 bp.
ChIP-seq reads were aianed to the UCSC ho38 genome using Bowtie version 1.1.2. 0ny uniouely mapping reads wit at most two mismatches were retained.
To create ChP-se coverage plots the locations of the mapped Ch-seg reads were extended to 150 bp to represent seouenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS V2.10 with the significance cut-off g-alue <=0.01
bigWig fles were generated using the genomicRanges R package. Score represents the normalzed coverage of DNA fraaments at a given genomic coordinate.  narrowPeak files were generated using MACS v2 with default settings
Assembly: hg38
Supplementary files format and content: IP_hiPSC_CMS_vs_In_hiPSC_CMs.peak_annotation

source_name: Human induced pluripotent stem cell

extract_protocol:
Cels were fixed with 1% formaldeyde for 10 minutes. Afer quenching and cel ysis, chromafin was sonicated using a E220 focused-utrasonicator (Covaris).
ChIP-seq ibraries were prepared using the KAPAHTP Library Preparation kt complemented with NEXTfex DNA Barcodes from Bioo Scienffic.10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplicaton ibranes were sze elected at 250-450bp in length using Agecut AMPure XP beads tom Beckman Couter. Libranes were vadated sin the AaileatHioh Sensivty DWAKi.

tag: cell line

value: Human induced pluripotent stem cell

tag: cell type

value: Cardiomyocytes

tag: chip antibody


title: case [1326041]


title: case [1324765]


title: WT2_dLGN_P30_Rep2


title: QKI2_VisualCortex_P30_Rep1


title: WT1_dLGN_P30_Rep2


title: Microbiota of Stool from patient HPV+5

tag: patient id

tag: time

value: F

tag: condition

value: Ascending colon

value: Adenocarcinoma, NOS


title: case [1324273]


title: QKI_dLGN_P30_Rep2

value: Male


title: case [1324132]


title: WT_dLGN_P30_Rep1


title: QKI1_dLGN_P30_Rep1


title: case [1323238]


title: case [1323118]


title: WT_dLGN_P30_Rep4


title: case [1322935]


title: IP_hiPSC_CMs

value: PPAR alpha (Abcam, ab227074)


title: QKI_dLGN_P30_Rep4


title: case [1322533]


title: WT_VisualCortex_P15_Rep6

value: Visual Cortex


title: WT_VisualCortex_P15_Rep5


title: case [1322424]


title: QKI_VisualCortex_P15_Rep5


title: case [1321638]


title: case [1321623]


title: QKI_VisualCortex_P15_Rep3


title: case [1321612]


title: case [1320908]


title: QKI_VisualCortex_P15_Rep4


title: WT_VisualCortex_P15_Rep4


title: QKI2_dLGN_P30_Rep1


title: case [1320471]


title: case [1322936]


title: case [1319398]


title: WT_VisualCortex_P15_Rep3


title: case [1319334]


title: QKI_VisualCortex_P15_Rep2


title: WT_VisualCortex_P15_Rep2


title: QKI_VisualCortex_P15_Rep1


title: case [1315846]


title: QKI_VisualCortex_P15_Rep6


title: WT_VisualCortex_P15_Rep1


title: case [1316766]


title: case [1315658]


title: QKI_dLGN_P15_Rep6


title: WT_dLGN_P15_Rep6


title: QKI_dLGN_P15_Rep5


title: case [1313791]


title: WT_dLGN_P15_Rep5


title: case [1313438]


title: QKI_dLGN_P15_Rep4


title: case [1313636]


title: case [1311467]


title: case [1311926]


title: WT_dLGN_P15_Rep4


title: case [1309866]


title: QKI_dLGN_P15_Rep3


title: case [1308827]


title: case [1279601]


title: QKI_dLGN_P15_Rep2


title: case [1249448]


title: QKI_dLGN_P15_Rep1


title: WT_dLGN_P15_Rep2


title: case [1240831]


title: WT_dLGN_P15_Rep1


title: ID1ko_3

city: Beijing

first: Shuang

last: Shang

address: 2# NanWei Road XiCheng District

department: Pharmacology

institute: Institute of Materia Medica

data_processing:
Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MC38 cells inoculated with control TAMs isolated from tumors of Id1-Lyz-KO mice in the s.c. tumor model

growth_protocol: 6×10^5 MC38 cells were mixed with 2×10^5 control or Id1-ko TAMs  and implanted to the C57BL/6J mice.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.


title: WT_VisualCortex_P16_Rep10


title: QKI_VisualCortex_P16_Rep10


title: QKI_VisualCortex_P16_Rep9


title: ID1ko_1


title: control [1339346]

value: matched controls


title: control [1336408]


title: QKI_VisualCortex_P16_Rep8


title: WT_VisualCortex_P16_Rep9


title: C57tumor_3

source_name: MC38 cells inoculated with control TAMs isolated from tumors of Id1f/f mice in the s.c. tumor model


title: WT_VisualCortex_P16_Rep8


title: QKI_VisualCortex_P16_Rep7


title: WT_VisualCortex_P16_Rep7


title: WT_dLGN_P15_Rep3


title: control [1332881]


title: C57tumor_1


title: control [1331868]


title: QKI_VisualCortex_P16_Rep5


title: ID1ko_2


title: QKI_VisualCortex_P16_Rep4


title: WT_LT_HSC

city: shanghai

first: xuanhui

last: wu

state: shanghai

address: yueyang road 320

department: Institute of Nutrition

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Data quality control: The quality of sequencing data is essential for reliable information analysis. Strict quality control processes are performed on the raw data to obtain high-quality sequencing data.
Genome alignment: Starting from the quality-controlled clean data, the clean data is aligned to a reference genome, and the alignment results are statistically analyzed.
Gene expression quantification: Based on the alignment results, gene expression quantification is performed. Gene quantification primarily investigates the sequencing coverage of each gene (Reads Count).
Differential gene analysis: Based on the gene expression quantification results, differential gene analysis is conducted to identify differentially expressed genes between samples or groups. This is a key focus of downstream analysis and data mining.
Functional enrichment: Using functional annotation databases such as GO, KEGG, and STRING, significant enrichment of functional information and protein interactions are obtained based on differentially expressed genes between samples or groups.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: bone morrow

growth_protocol: Isolate and amplify bone marrow HSPC cells from mice including HPC-1, HPC-2, MPP, and LT-HSC, and then perform transcriptome sequencing.

extract_protocol:
Total RNAs from HSPC of WT and AbinQ478H/Q478H mice at 5 months old were extracted with Trizol (9108, Takara). RNA samples were quantified using a Qubit 3.0 Fluorometer (Life Technologies, CA, USA), and RNA integrity was assessed using a 4200 TapeStation (Agilent Technologies, CA, USA).
(1) Most mRNA in eukaryotic organisms possess a polyA structure. Magnetic beads with oligo (dT) are used to capture mRNA with a polyA structure. (2) Fragmented mRNA serves as a template, and random oligonucleotides act as primers to synthesize the first strand of cDNA in the presence of M-MuLV reverse transcriptase. (3) RNA chains are degraded by RNaseH, and in the presence of DNA polymerase I and dNTPs, the second strand of cDNA is synthesized. (4) Double-stranded cDNA is purified and subjected to end-repair, A-tailing, and ligation of sequencing adapters. (5) cDNA fragments of approximately 200bp are selected using AMPure XP beads, followed by PCR amplification. The PCR product is further purified using AMPure XP beads to obtain the final sequencing library.

value: bone morrow

tag: treatment

value: After sorting using a flow cytometer from mouse bone marrow, the isolated cells will be cultured in Stemcell's M3434 medium for 7 days.


title: WT_VisualCortex_P16_Rep4

value: WT


title: QKI_VisualCortex_P16_Rep3

value: QKI


title: WT_HPC_2


title: WT_VisualCortex_P16_Rep5


title: control [1331432]


title: WT_VisualCortex_P16_Rep3


title: WT_MPP

value: MPP


title: control [1336037]


title: WT_VisualCortex_P16_Rep2


title: C57tumor_2


title: control [1329305]


title: control [1324576]


title: WT_VisualCortex_P16_Rep1


title: QKI_VisualCortex_P16_Rep1


title: A_LT_HSC


title: WT_HPC_1


title: control [1326212]


title: WT_VisualCortex_P16_Rep6


title: WT_dLGN_P16_Rep10

value: dLGN


title: QKI_VisualCortex_P16_Rep6


title: A_MPP


title: A_HPC_2


title: control [1321644]

value: fecal samples


title: QKI_dLGN_P16_Rep8


title: control [1322654]


title: QKI_dLGN_P16_Rep9


title: WT_dLGN_P16_Rep9


title: QKI_dLGN_P16_Rep10


title: control [1322807]


title: QKI_dLGN_P16_Rep6


title: control [1316883]


title: WT_dLGN_P16_Rep8


title: A_HPC_1


title: control [1319014]


title: WT_dLGN_P16_Rep4


title: QKI_VisualCortex_P16_Rep2


title: QKI_dLGN_P16_Rep7


title: WT_dLGN_P16_Rep7


title: control [1318973]


title: QKI_dLGN_20_Replicate-D

data_processing:
FASTQ files were created using the standard bcl2fastq pipeline from Illumina. Gene expression tables for each nuclear barcode were generated via the CellRanger 3.0.0 pipeline as designed by 10X Genomics. Samples were demultiplexed, and all QKI or WT samples were merged using the CellRanger aggr function using default parameters.
The datasets were loaded into R and analyzed using the Seurat (v3) package. Nuclei were removed from the dataset if they contained fewer than 500 detected genes, displayed more than 5% of reads mapping to mitochondrial genes, or had RNA counts detected at a level greater than 2 standard deviations higher than the mean value in their assigned cell type
Data was normalized using Seurat’s (v3) NormalizeData, and the 2,000 top variable genes across nuclei were identified using FindVariableFeatures function. Data was then integrated using FindIntegrationAnchors (16 dimensions) and IntegrateData (16 dimensions). Data was then scaled using ScaleData, and principal component analysis using the RunPCA function (npcs = 16) was performed. A shared nearest neighbor graph was constructed using the FindNeighbors function (considering the top 16 principal components), and clustering was assigned using the FindClusters function (resolution = 0.5). After, clusters with fewer than 100 nuclei were removed.
The following marker genes were used to assign cell type clusters identified: pan-neuronal (Rbfox3); pan-excitatory neurons (Slc17a7); pan-inhibitory neurons (Gad1); oligodendrocytes (Mag); oligodendrocyte precursor cells (Pdgfra); astrocytes (Aldoc); microglia (Cx3cr1); endothelial cells (Cldn5).
Differential gene expression analysis between QKI and WT cells within each cluster was conducted using Wilcoxon Rank Sum test via the FindMarkers function (default parameters), and significant genes were defined as those with an adjusted p-value less than 0.05.
Assembly: mm10
Supplementary files format and content: filtered barcode from 10x Genomics pipeline (tsv)
Supplementary files format and content: filtered feature from 10x Genomics pipleline (tsv)
Supplementary files format and content: filtered matrix from 10x Genomics pipeline (mtx)

molecule: nuclear RNA

extract_protocol:
To isolate dLGN nuclei, we combined flash-frozen dLGN tissue from 3 male mice per genotype (MeCP2-WT/Y and MeCP2-QKI/Y) for a total of 2 replicates. To the tissue, we added 1 mL of buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, supplemented with RNase inhibitors, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine) and dounced 5X with a loose pestle and 10X with a tight pestle. 5% IGEPAL CA-630 (32 μL) was added prior to douncing with a tight pestle 5 more times and filtering through a 40-μm strainer into a 50 mL conical collection tube. 1 mL working solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, supplemented with RNase inhibitors, DTT, spermine and spermidine) were added. Homogenized tissue was gently layered on top of 100 μL of 30% iodixanol on top of a layer of 100 μL of 40% iodixanol (diluted from working solution). Samples were centrifuged at 1,500 x g for 15min. Nuclei (50 μL) were collected from the 30/40% iodixanol interface. An aliquot of each sample was incubated with trypan blue, and nuclei were counted using a standard hemocytomter, for a total of ~10,000 nuclei per pooled sample.
SnRNA-seq was performed using the 10X Genomics Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) kit. Each reaction lane was loaded with up to 10,000 nuclei from each pooled dLGN sample. Subsequent steps for cDNA amplification and library preparation were conducted according to the manufacturer’s protocol
snRNA-seq


title: QKI_dLGN_P16_Rep5


title: dbdb AAV9_USP28_3

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

source_name: Left ventricular tissue

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

value: Left ventricular tissue

value: db/db


title: control [1314524]


title: control [1314353]


title: WT_dLGN_P16_Rep5


title: control [1316607]


title: WT_dLGN_P20_Replicate-C


title: QKI_dLGN_P16_Rep4


title: WT_dLGN_P20_Replicate-A


title: WT_dLGN_P16_Rep3


title: QKI_dLGN_P16_Rep3


title: QKI_dLGN_P16_Rep2


title: WT_dLGN_P16_Rep2


title: dbdb AAV9_USP28_2


title: QKI_dLGN_P20_Replicate-B


title: control [1315626]


title: control [1310251]


title: WT_dLGN_P16_Rep6


title: QKI_dLGN_P16_Rep1


title: dbdb AAV9_null_2