title: treated axon_Rep5


status: Public on Mar 07 2022

type: SRA

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

country: Japan

institute: NARO

description:
Pv11_42C_24h_rep1
Transcriptome sequencing of Pv11 cells submitted to 42C and sampled at 24h, replicate number 1

library_source: transcriptomic

data_processing:
Gene expression was quantified with RSEM using the Trinity utility
Mapped counts were statistically tesed with DESeq2 and transcripts with FDR < 0.05 and absolute fold change > 2 were determined as differentially expressed genes.
Genome_build: Pv11_5.2 (SUB8069519)
Supplementary_files_format_and_content: TPM expression matrix.

molecule: total RNA

organism: Polypedilum vanderplanki

source_name: Pv11 cell line

growth_protocol: Pv11 cells were cultured in IPL-41 medium (Thermo Fisher Scientific, Waltham, MA) supplemented with 2.6 g/L tryptone phosphate broth (Becton, Dickinson and Company, Franklin Lakes, NJ), 10% (v/v) fetal bovine serum (MP Biomedicals, Santa Ana, CA), and 0.05% (v/v) of an antibiotic and antimycotic mixture (penicillin, amphotericin B, and streptomycin; Merck KGaA, Darmstadt, Germany).

extract_protocol:
At each time point cells were collected at each time point by centrifugation at 8,000g for 2 minutes (4˚C), and the culture medium was removed. Cells were suspended in 500µL of RNAiso Plus (Takara) and incubated for 5 minutes.
The total RNA was extracted with Nucleospin RNA clean-up and the TruSeq RNA Sample Prep Kit -v8 following the manufacturer's protocol.

treatment_protocol: 5x10^6 Pv11 cells were resuspended in 2mL IPL-41 medium and were submitted to the following stresses; 0.5% (V/W) NaCl, 600mM Mannitol, 600mM Trehalose, 20µM Paraquat, and 15 minute 42˚C heat shock and was sampled at for 1, 3 and 24 hours post exposure.

tag: cell line

tag: stress


title: Darmouth092107_ReCirc

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

country: USA

institute: moffitt cancer center

description:
CD8 TILs
Darmouth_AD_CD103_CD69

data_processing:
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt (https://doi.org/10.14806/ej.17.1.200) (version 1.8.1), and mapped to hg19 reference genome using star v2.5.3a with default settings.
Uniquely mapped reads were counted at gene-level by featureCounts (version 1.5.3) using RefSeq transcript annotations for human
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each sample

organism: Homo sapiens

source_name: Surgically removed High Grade Serous Ovarian Cancer tumor tissue

extract_protocol:
Tissue pieces from the ovarian tumors were mechanically dissociated and single cell suspensions were prepared after debris removal. TRM and re-circulating CD8+ TILs were FACs sorted in Aria-sort
RNA libraries were prepared for sequencing using Ovation® Human FFPE RNA-Seq kit

tag: cancer type

value: HGSOC

tag: cell type

value: Re-circulating CD8+ TILs


title: Darmouth092107_TRM

description:
CD8 TILs
Darmouth_AD_CD103

value: TRM CD8+ TILs


title: control soma_Rep3

city: Pisa

first: Vittoria

last: Raffa

state: Please Select

address: S.S. 12 Abetone e Brennero, 4

department: Department of Biology

country: Italy

institute: Università di Pisa

data_processing:
Library QC: Library preparation was checked by calculating ribosomal content
Raw data quality: Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw data set was determined using third-party (FastQC v0.11.9, MultiQC v1.12)  QC tools
Data trimming: Sequence reads were trimmed to remove possible adapter sequences using fastp v0.20.1
Mapping of reads: The reads were mapped to the reference sequence using a short read aligner STAR v2.7.08a with default settings
Feature counting: Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a gene was determined with HTSeq v0.13.5
Genome_build: mm10
Supplementary_files_format_and_content: text file with raw counts of the overlap of reads with annotation features/genes obtained using HTSeq v0.13.5

organism: Mus musculus

source_name: cells dissociated from hippocampi

growth_protocol: Newborn animals (P1) were sacrificed and both hippocampi were harvested in a solution of D-glucose 6.5 mg/ml in D-PBS (Cell isolation was performed by chemical digestion and mechanical dissociation. After this step, cells were seeded in high-glucose DMEM with 10% fetal bovine serum, 100 IU ml-1 penicillin, 100 µg ml-1 streptomycin and 2 mM Glutamax (DIV0). The medium was replaced four hours later by cell culture medium (Neurobasal-A medium modified with B27, 2 mM Glutamax, 50 IU ml-1 penicillin, 50 µg ml-1 streptomycin, 2.5 μM. Half of the medium was replaced every 2-3 days.

extract_protocol:
NucleoSpin RNA PLUS XS Kit was used for RNA extraction. Samples from axonal compartment and somatodendritic compartment were collected in lysis solution and incubated at 4° (protocol adapted from Bio-protocol 9(14): e3312, DOI:10.21769/BioProtoc.3312). Then, lysed samples were treated to digest the DNA and the RNA that was eluted in RNAse-free water. Quant-iT RiboGreen RNA Kit was used for the quantification of total RNA. RQN was >=9.7 for all samples.
The NEBNext Low Input RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Low Inputr RNA Library Prep Kit for Illumina" (NEB #E6420S/L). Briefly, cDNA was syntesized and amplified from poly A tailed mRNA. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a peak between 200-400 bp).
Low input sample preparations including unique dual indexing and unique molecular identifiers (UMIs). RNA sequencing (polyA enriched) of 24 totalRNA samples (mouse), using Illumina NovaSeq6000 sequencing, Paired-End, 150 bp. Per sample ~9 Gb, 30 million Paired-End reads.

treatment_protocol: Cells we seeded on Poly-D-Lysine and laminin coated microfluidic chambers (XONA, #RD150). A differential coating was performed (poly-D-Lysine 100 ug/ml and laminin 1 ug/ml in the soma side; poly-D-Lysine 500 ug/ml and laminin 10 ug/ml in the axonal side). At DIV0, 200.000 cells were seeded in the soma side. Four hours later, the medium was replaced with cell growth medium modified with 5 µg ml-1 MNPs. In the stretched growth, the stimulus was applied from DIV1 to DIV6.

value: total cell culture

tag: treatment

value: MNP + null magnetic field gradient

tag: genotype


description:
Pv11_42C_1h_rep3
Transcriptome sequencing of Pv11 cells submitted to 42C and sampled at 1h, replicate number 3


title: 092608M_ReCirc

description:
CD8 TILs
Moffitt_BH_CD103_CD69


title: control soma_Rep2


description:
Pv11_42C_1h_rep2
Transcriptome sequencing of Pv11 cells submitted to 42C and sampled at 1h, replicate number 2


title: Darmouth080609_TRM

description:
CD8 TILs
Darmouth_Z_CD103


title: Darmouth033009_ReCirc

description:
CD8 TILs
Darmouth_W_CD103_CD69


title: T082219-TRM-VDJ

description: CD8 TILs

data_processing:
Library strategy: TCR-seq
Raw sequencing reads from scRNA-seq were processed using Cell Ranger (v3.0, 10X Genomics). Cell barcodes and UMIs associated with the aligned reads were subjected to correction and filtering. Filtered gene-barcodes matrices containing only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.0 for downstream analysis.
Barcodes with fewer than 200 genes expressed, or more than 10% UMIs originated from mitochondrial genes, were excluded filtered out; genes expressed in fewer than 3 barcodes were also excluded. This process resulted in 43,368 cells for TRM+re-circ scRNA-seq from 4 tumors, and 60,010 cells for TRM scRNA-seq from 8 tumors.
TCR reads sequenced by V(D)J assay were aligned to GRCh38 reference transcriptome using Cell Ranger VDJ. T cells were assigned with productive CDR3 regions for TCR alpha and TCR beta chains.
Each clonotype was assigned with a unique identifier based on amino acid sequences of the CDR3 regions and V(D)J genes of the two chains, which was then used to match clonotypes across samples
Genome_build: GRCH38
Supplementary_files_format_and_content: csv files include assembled TCR heavy chain and light chain sequences and VDJ annotation for each T cell
Supplementary_files_format_and_content: csv files include the number of UMIs associated with a gene (row) and a cell (column) measured from single-cell RNA-seq

extract_protocol:
Tissue pieces from the ovarian tumors were mechanically dissociated and single cell suspensions were prepared after debris removal. TRM and re-circulating CD8+ TILs were FACs sorted in Aria-sort
The scRNA-Seq libraries were prepared following the protocol provided by the 10X genomics. The cDNA and VDJ-enriched libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell 5’ v 1.1 and V(D)J Reagent Kits.  50,000 or 5,000 sequencing reads per cell for scRNA-seq or VDJ libraries, respectively, were generated on the Illumina NextSeq 500 instrument.


title: 042017M_ReCirc

description:
CD8 TILs
Moffitt_AC_CD103_CD69


description:
Pv11_42C_1h_rep1
Transcriptome sequencing of Pv11 cells submitted to 42C and sampled at 1h, replicate number 1


title: control soma_Rep1


title: T072817-TRM-VDJ

description: CD8 TILs


title: T022719-TRM-VDJ

description: CD8 TILs


title: control axon_Rep7

value: pure axonal preparation


title: T041218-TRM-VDJ

description: CD8 TILs


title: macaque2_ventralS1_rep1_atac

city: Pittsburgh

first: Morgan

last: Wirthlin

state: Pennsylvania

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

description: transposase-accessible DNA

library_source: genomic

data_processing:
ATAC-seq alignment: Macaque, rat, and mouse reads were mapped to the Mmul_8.0.1, rn6, and mm10s genomes, respectively, with Bowtie2 using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) with default parameters except for "atac.multimapping" : 0 (read filtering), "atac.cap_num_peak" : 300000 (peak calling), "atac.smooth_win" : 150 (peak calling), "atac.enable_idr" : true (peak calling), and "atac.idr_thresh" : 0.1 (peak calling).
ATAC-seq filtering: Duplicate reads, mitochondrial reads, and multi-mapping reads were filtered out as a part of the ENCODE ATAC-seq pipeline.  The pipeline also created signal tracks using MACS2.
ATAC-seq peak calling: Within the ENCODE ATAC-seq pipeline workflow, peaks were called on each sample individually, on the pool of biological replicates, on pooled pseudo-replicates, and on self pseudo-replicates using MACS2 and reproducible peaks were determined on biological replicates with an IDR threshold of 0.1.
Other: More information on all data processing and conclusions can be found in the publication.
Genome_build: Mmul_8.0.1, rn6, mm10
Supplementary_files_format_and_content: ATAC-seq peaks called in each sample
Supplementary_files_format_and_content: MACS2 pval signal tracks for each sample in bigwig format

molecule: genomic DNA

organism: Macaca mulatta

source_name: adult male macaque primary somatosensory cortex, ventral portion (ventralS1)

extract_protocol:
Nuclei were extracted from fresh tissue with Dounce homogenization in lysis buffer. The nuclei were pelleted by centrifugation and filtered through 70µm and 40µm strainers.
ATAC-seq libraries were constructed with standard amplification and size selection methods. See publication for more details.

treatment_protocol: Mice processed for liver samples were injected intravenously with an fluorescent AAV related to tissues for a different study. The procedure was minimally invasive and did not affect the health of the animals. No other animals processed in this study received any treatments.

tag: tissue

value: bulk tissue

tag: Sex

value: M

tag: age

value: 4 years


title: T051110-TRM-VDJ

description: CD8 TILs


title: T021518-TRM-VDJ

description: CD8 TILs


title: control axon_Rep5


title: T082219-TRM-GEX

description: CD8 TILs

data_processing:
Raw sequencing reads from scRNA-seq were processed using Cell Ranger (v3.0, 10X Genomics). Cell barcodes and UMIs associated with the aligned reads were subjected to correction and filtering. Filtered gene-barcodes matrices containing only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.0 for downstream analysis.
Barcodes with fewer than 200 genes expressed, or more than 10% UMIs originated from mitochondrial genes, were excluded filtered out; genes expressed in fewer than 3 barcodes were also excluded. This process resulted in 43,368 cells for TRM+re-circ scRNA-seq from 4 tumors, and 60,010 cells for TRM scRNA-seq from 8 tumors.
TCR reads sequenced by V(D)J assay were aligned to GRCh38 reference transcriptome using Cell Ranger VDJ. T cells were assigned with productive CDR3 regions for TCR alpha and TCR beta chains.
Each clonotype was assigned with a unique identifier based on amino acid sequences of the CDR3 regions and V(D)J genes of the two chains, which was then used to match clonotypes across samples
Genome_build: GRCH38
Supplementary_files_format_and_content: csv files include assembled TCR heavy chain and light chain sequences and VDJ annotation for each T cell
Supplementary_files_format_and_content: csv files include the number of UMIs associated with a gene (row) and a cell (column) measured from single-cell RNA-seq


title: macaque2_ventralM1_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque primary motor cortex, ventral portion (ventralM1)


title: control axon_Rep2


title: macaque2_SMA_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque supplementary motor area (SMA)

value: supplementary motor area (SMA)


title: macaque2_Putamen_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque putamen

value: putamen


title: T051209-TRM-VDJ

description: CD8 TILs


title: T021518-TRM-GEX

description: CD8 TILs


title: T022719-TRM-GEX

description: CD8 TILs


title: Darmouth080609_ReCirc

description:
CD8 TILs
Darmouth_Z_CD103_CD69


title: control axon_Rep1


title: macaque2_NAcc_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque nucleus accumbens (NAcc)

value: nucleus accumbens (NAcc)


title: T042718-TRM-GEX

description: CD8 TILs


title: T072817-TRM-GEX

description: CD8 TILs


title: macaque2_Muscle_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque muscle

value: muscle


title: T051209-TRM-GEX

description: CD8 TILs


title: T042718-TRM-VDJ

description: CD8 TILs


title: T051110-TRM-GEX

description: CD8 TILs


title: Darmouth033009_TRM

description:
CD8 TILs
Darmouth_W_CD103


title: macaque2_Liver_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque liver

value: liver


title: 18mo BUMC M Het 4

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from humerus of BUMC male Brd2wt/lo animal at 18 months.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor R package and the Brainarray mogene10stv1mmentrezgcdf R package (version 14.0.0).

label: biotin

source_name: humerus

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Thermo Fisher, Waltham, MA).

growth_protocol: Animals were allowed to age for 3 to 18 months and were maintained under standard feeding and light dark cycle conditions at BUMC.

extract_protocol: RNA was purified from whole mouse humerus flash frozen under liquid nitrogen and stored at -80C until processed for total RNA.  Total bones were powdered with a mortar and pestle under liquid nitrogen and placed in Qiagen Tissue Lyzer tubes with 1 ml of Qiazol reagent per humerus. After extraction aqueous solutions for the Qiazol were applied to a miRNA RNeasy column (catalog #217004).

value: humerus

tag: animal

tag: batch

value: batch 2

tag: colony

value: BUMC

tag: timepoint

value: 18 months

value: male

tag: brd2 genotype

value: wt/lo


title: T042719CD8_3 [VDJ]

extract_protocol:
Tissue pieces from the ovarian tumors were mechanically dissociated and single cell suspensions were prepared after debris removal. TRM and re-circulating CD8+ TILs were FACs sorted in Aria-sort
The scRNA-Seq libraries were prepared following the protocol provided by the 10X genomics. The cDNA and VDJ-enriched libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell 5’ v 1.1 and V(D)J Reagent Kits.  50,000 or 5,000 sequencing reads per cell for scRNA-seq or VDJ libraries, respectively, were generated on the Illumina NextSeq 500 instrument.
10X genomics Chromium 5' Single Cell RNA-seq + VDJ Single Cell T Cell Receptor Sequencing

tag: disease

value: High Grade Serous Ovarian Cancer tumor

value: CD8+ TILs


title: macaque2_dorsalS1_rep1_atac

description: transposase-accessible DNA

source_name: adult male macaque primary somatosensory cortex, dorsal portion (dorsalS1)


title: control axon_Rep3

value: pure axonal preparation

value: MNP + null magnetic field gradient


title: T041218-TRM-GEX

description: CD8 TILs

value: HGSOC

value: TRM CD8+ TILs


title: T042719CD8_2 [VDJ]


title: macaque2_dorsalM1_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque primary motor cortex, dorsal portion (dorsalM1)

value: bulk tissue

value: M

value: 4 years


title: T082219_ReCir [VDJ]

value: Re-circulating CD8+ TILs


title: macaque2_Caudate_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque caudate

value: caudate


title: macaque2_Cerebellum_rep1_atac

description: transposase-accessible DNA

source_name: adult male macaque cerebellum

value: cerebellum


title: T021518_ReCir [VDJ]


title: macaque2_6V_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque premotor area 6V

value: premotor area 6V


title: Input

city: Beijing

first: Xiaohan

last: Yang

address: 38 Xueyuan road

department: Biochemistry and Biophysics

country: China

institute: Peking Unversity Health Science Center

data_processing:
The raw fastq data were preprocessed for the removal of adapter and low-quality reads by using fastp version0.19.6.
The processed data were aligned to the reference genome using Bowtie2.
Peak calling was performed by using MACS2.
Genome_build: hg38 and DM6
Supplementary_files_format_and_content: bigwig, signal value

source_name: HeLa cells

extract_protocol:
Chromatin DNAs were precipitated with polyclonal antibodies and purified with the Qiagen PCR purification kit.
The DNA library was prepared using a Next Ultra DNA Library Prep Kit (NEB, E7645) according to the manufacturer’s instructions. The libraries were purified with AMPure  beads (Beckman, A63881) according to the manufacturer’s instructions, and  sequenced using Illumina platforms.

treatment_protocol: HeLa cells were synchronized in G1/S boundary through double thymidine block, and released in fresh medium for 0.5 or 2.5 h before being harvested. Approximately 5 × 10^7cells were used for each ChIP-seq assay.

value: HeLa

value: Double thymidine block


title: T082219_TRM [VDJ]


title: H3K4me2 of HeLa cells at 2.5h

tag: chip antibody

value: H3K4me2 (Active motif, Cat.# 39142)


title: 18mo BUMC M Het 2

value: humerus

value: batch 1

value: BUMC

value: 18 months

value: male

value: wt/lo


title: macaque2_2A_rep2_atac

description: transposase-accessible DNA

source_name: adult male macaque secondary auditory cortex (2A)

value: secondary auditory cortex (2A)


title: T022719_TRM [VDJ]

source_name: Surgically removed High Grade Serous Ovarian Cancer tumor tissue

value: High Grade Serous Ovarian Cancer tumor

value: TRM CD8+ TILs


title: macaque1_ventralM1_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque primary motor cortex, ventral portion (ventralM1)

value: bulk tissue

value: F

value: 12 years


title: H3K4me2 of HeLa cells at 0.5h


title: T021518_TRM [VDJ]


title: MOLM.14.72hr.Combination.treatment.

city: Baltimore

first: Michael

middle: Jonathan

last: Topper

state: MD

address: 1650 Orleans St., Suite 530

department: Oncology

institute: Johns Hopkins University

description: Gene expression after 72 hours in-vitro exposure 10nM Decitabine + 5nM Talazoparib

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Microarrays were scanned using an Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MOLM14 (TP53 WT) cells were cultured in RPMI1640 + L-Glutamine supplemented with 10% FBS and maintained in 37oC incubators with 5% CO2 and passaged every 3- 5 days

extract_protocol: Total RNA was isolated from cultured cells using the NucleoSpin RNA Plus kit (Macherey-Nagel).

treatment_protocol: The DNTMi decitabine (DAC, Sigma-Aldrich) was prepared as a stock solution of 10 mM in DMSO and stored at -80 ̊C in single-use vials. Cell lines were treated daily with 10 nM DAC. The PARPi talazoparib (Tal, Pfizer) was prepared as a stock solution of 5mM in DMSO and stored at -80 ̊C. Cell lines were treated with 5nM Tal every 72h. For combination treatments, cells were treated with 10nM DAC and 5nM Tal on day 1 and DAC was added to cells at the appropriate concentration on days 2 and 3 for a final concentration of 10nM. Cells were harvested after 72h.


title: 18mo BUMC M Het 3

value: batch 2


title: 18mo BUMC M WT 2

description: Gene expression data from humerus of BUMC male Brd2wt/wt animal at 18 months.

value: wt/wt


title: macaque1_SMA_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque supplementary motor area (SMA)

value: supplementary motor area (SMA)


title: 18mo BUMC M WT 3


title: T022719_ReCir [VDJ]

value: Re-circulating CD8+ TILs


title: MOLM.14.Control

description: Gene expression after 72 hours in-vitro control

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software.


title: 18mo BUMC M WT 4


title: 18mo BUMC M Het 1


title: 18mo BUMC M WT 1


title: MOLM.14.72hr.5nM.Talazoparib.treatment.

description: Gene expression after 72 hours in-vitro exposure 5nM Talazoparib


title: MOLM.14.72hr.10nM.Decitabine.treatment.

description: Gene expression after 72 hours in-vitro exposure 10nM Decitabine


title: T042719CD8_3 [GEX]

value: CD8+ TILs


title: 18mo BUMC F Het 4

description: Gene expression data from humerus of BUMC female Brd2wt/lo animal at 18 months.

value: humerus

value: female


title: 18mo BUMC F Het 3

value: BUMC


title: Repli-seq of LSD1 knockdown HeLa cells at 3 h

data_processing:
Library strategy: Repli-seq
The raw fastq data were preprocessed for the removal of adapter and low-quality reads by using fastp version0.19.6.
The processed data were aligned to the reference genome using Bowtie2.
RepliScan was used for the calculation of the replication signal.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph, replication signal.

extract_protocol:
The cells were collected and lysed immediately in lysis buffer (50 mM Tris-HCl, pH 8.0, 10mM EDTA, 1 M NaCl, 0.5% SDS, 0.1mg/ml RNase A, 0.2mg/ml protease K), and the lysates were incubated at 37 °C for 3 h and then at 55 °C for 8 h before being sonicated for 5 cycles using Bioruptor with 30s on and 30s off for 30 cycles. DNA fragments ranging from 200 bp to 400 bp was selected with AMPure beads (0.6 × to 1.0 ×) (Beckman, A63881). Biotin was conjugated to EdU-labeled DNAs by Click-iT reaction
DNAs were purified with MinElute PCR purification kit (Qiagen, 28004), end-repaired, dA-tailed, and adapter-ligated before being dissolved in 1× TE buffer and incubated with M280 streptavidin beads. After rinsing in binding/washing buffer containing 0.5% IGEPAL CA-630 (Sigma, I3021) for 6 times, recovered DNAs from beads.

treatment_protocol: HeLa cells were transfected with control siRNA or LSD1 siRNA and synchronized to G1/S phase by thymidine and aphidicolin double treatments. Cells were cultured with 20 μmol of EdU for 10 min after release into S phase by washing out aphidicolin for 0, 3, and 5 h.

value: HeLa

tag: genotype/variation

value: aphidicolin washout 3 h

value: M-280 streptavidin Dynabeads (Life Technologies)


title: 18mo BUMC F Het 2

value: batch 1

value: 18 months

value: wt/lo


title: macaque1_Putamen_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque putamen

value: putamen

value: bulk tissue


title: Repli-seq of LSD1 knockdown HeLa cells at 0 h

tag: cell line

value: aphidicolin washout 0 h


title: macaque1_NAcc_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque nucleus accumbens (NAcc)

value: nucleus accumbens (NAcc)

value: F

value: 12 years


title: T042719CD8_2 [GEX]

value: High Grade Serous Ovarian Cancer tumor


title: macaque1_Muscle_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque muscle

value: muscle


title: T082219_ReCir [GEX]

value: Re-circulating CD8+ TILs


title: 18mo BUMC F Het 1

value: humerus

value: female


title: Repli-seq of control HeLa cells at 3h

value: HeLa

value: siCTR


title: Repli-seq of control HeLa cells at 0h

value: M-280 streptavidin Dynabeads (Life Technologies)


title: 18mo BUMC F WT 4

description: Gene expression data from humerus of BUMC female Brd2wt/wt animal at 18 months.

value: batch 2

value: BUMC

value: wt/wt


title: T022719_ReCir [GEX]


title: 18mo BUMC F WT 3

value: 18 months


title: macaque1_dorsalM1_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque primary motor cortex, dorsal portion (dorsalM1)

value: bulk tissue


title: Repli-seq of LSD1 knockdown HeLa cells at 5 h

value: aphidicolin washout 6 h


title: T082219_TRM [GEX]

value: TRM CD8+ TILs


title: H3K4me2_2.5h

data_processing:
The raw sequencing data were firstly conducted quality control via Fastx toolkit for the reliable of the following analysis with the default parameters, i.e. only retain sequences with at least 90% base pair with quality score > 20.
Remaining sequences were aligned to the unmasked human reference genome (hg38) using Bowtie Version 2(26) with only one mismatch allowed.
MACS Version 2 (Model-based Analysis for ChIP-Seq) was used for the identification of LSD1, Cdc45 or H3K4me2 specific binding peaks with all default settings except q < 0.05.
Supplementary_files_format_and_content: Bigwig files

growth_protocol: HeLa cells were synchronized in G1/S boundary through double thymidine block, and released in fresh medium for 0.5 or 2.5 h before being harvested. Approximately 5 × 107cells were used for each ChIP-seq assay.

extract_protocol:
The chromatin DNA precipitated by polyclonal antibodies against LSD1, Cdc45 and H3K4me2. The DNA was purified with the Qiagen PCR purification kit. Deep DNA sequencing was performed by the BGI Corporation (Beijing Genomics Institute).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: Double thymidine block

value: H3K4me2 (Active motif, Cat.# 39142)


title: H3K4me2_0.5h


title: macaque1_Liver_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque liver

value: liver

value: F

value: 12 years


title: 18mo BUMC F WT 1

value: humerus

value: batch 1


title: macaque1_Caudate_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque caudate

value: caudate


title: T021518_ReCir [GEX]

value: High Grade Serous Ovarian Cancer tumor

value: Re-circulating CD8+ TILs


title: T022719_TRM [GEX]


title: HeLa_GSK-LSD1_LSD1 inhibitor treatment

data_processing:
Deep DNA sequencing was performed by the Jiayin biotechnology (shanghai) co., ltd. Raw sequencing reads in fastq format were preprocessed using fastp for adapter trimming and removal of low-quality (Phred score < 20) bases followed by mapping of remained high-quality reads to Ensembl GRCh37/hg19 reference genome through bowtie2 with discard of unpaired, discordant and multiple alignments.
The read coverage across genome is calculated in genomic windows of 50 kb and normalized through quantile method across samples with loess smoothing for noise reduction.
Supplementary_files_format_and_content: BedGraph; BigWig

extract_protocol:
Cells were washed with ice-cold PBS and then fixed for 12 minutes at RT. Fixed cells were permeabilized, clicked, resuspended in lysis buffer and sonicated with Bioruptor with the following setting: 30 seconds on, 30 seconds off, 30 cycles. After reserving an aliquot for input, dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl [pH 8.1], 3 mM CaCl2) at 10 times the volume of lysis buffer was added and mixed well, and biotinylated DNA was pulled down using M-280 streptavidin Dynabeads. After being extensively washed, the beads were resuspended in 0.1 × TE (10 mM Tris-HCl pH [8.0], 1 mM ethylenediaminetetraacetic acid), and RNase A was added and incubated at 37℃ for 60 min. SDS was added to a final concentration of 1% and proteinase K (Thermo Fisher Scientific) was added to a final concentration of 20 mg per ml, and the suspension was incubated at 55℃ for 2 h and then 65 ℃ overnight to reverse cross-links and degrade proteins. After incubation, phenol-chloroform-isoamyl alcohol extraction was performed, and the DNA in the aqueous phase was precipitated using 70% isopropanol, 30 mM sodium acetate, and 150 mg/ml glycogen at -80℃ for at least 30 min followed by centrifugation at 4℃, 16,000 × g for 30 min. The DNA pellet was washed with 75% ethanol and resuspended in 20 ml TE buffer.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Briefly, HeLa cells were transfected with LSD1 siRNAs or FLAG-LSD1 plasmids, or treated with GSK-LSD1, and synchronized in S phase by double thymidine block. Cells were released for 2 h representing early S phase, and before being harvested cells were pulse-labeled with 10 mM EdU for 10 min.

value: HeLa

value: LSD1 inhibitor treatment

value: M-280 streptavidin Dynabeads (Life Technologies)


title: 18mo BUMC F WT 2

source_name: humerus

value: BUMC

value: 18 months

value: female

value: wt/wt


title: T021518_TRM [GEX]

value: TRM CD8+ TILs


title: 041218M-ReCir [ATAC-seq]

data_processing:
Raw sequencing reads generated from 10X multimode assay were processed by cellranger-arc workflow with default settings to generate mapping and chromatin accessibility data for ATAC and filtered UMI count data for GEX. The UMI count data for gene expression was imported to Seurat v4.0 for downstream analysis.
Barcodes with fewer than 200 genes expressed, or more than 10% UMIs originated from mitochondrial genes, were excluded filtered out; genes expressed in fewer than 3 barcodes were also excluded. This process resulted in 20,866 cells.
The mapping and chromatin accessibility data generated from Multiome ATAC were imported to R package Signac v1.3.0  for downstream analysis. The low-quality cells with total number of fragments in peaks < 3000 or > 20,000, fraction of fragments in peaks < 15%, ratio of mononucleosomal to nucleosome-free fragments > 4, or transcriptional start site (TSS) enrichment score < 2 were filtered out.
Genome_build: GRCH38
Supplementary_files_format_and_content: csv files include the number of UMIs associated with a gene (row) and a cell (column) measured from single-cell RNA-seq
Supplementary_files_format_and_content: csv files include peaks( local enrichment of transposase cut-sites) identified from ATAC data

source_name: Surgically removed Ovarian Cancer tumor tissue

extract_protocol:
Tissue pieces from the ovarian tumors were mechanically sissociated and single cell suspensions were prepared after debris removal. B cells were sorted using anti-human CD19 antibodies.
The scRNA-Seq libraries were prepared following the protocol provided by the 10X genomics. The cDNA and ATAC-seq libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell Multiome ATAC + Gene Expression Reagent Kit.  50,000 or 25,000 sequencing reads per cell for scRNA-seq or ATAC-seq libraries, respectively, were generated on dedicated Illumina NextSeq 500 sequencing runs according to the vendor protocol.

value: HGSOC

value: CD8 TILs


title: 12mo BUMC M Het 3

description: Gene expression data from humerus of BUMC male Brd2wt/lo animal at 12 months.

value: batch 2

value: 12 months

value: male

value: wt/lo


title: 12mo BUMC M Het 4

value: humerus


title: Over_3

city: New York

first: Jessica

middle: E.

last: Treisman

state: NY

address: 540 First Ave, Skirball Institute

department: Cell Biology

institute: NYU Grossman School of Medicine

data_processing:
RNA-seq data were analyzed by sns/rna-star pipeline
Sequencing reads were mapped to the reference genome (dm6) using the STAR aligner (v2.6.1d)
Alignments were guided by a Gene Transfer Format (GTF) file.
The mean read insert sizes and their standard deviations were calculated using Picard tools (v.2.18.20)
The read count tables were generated using subread (v1.6.3),normalized based on their library size factors using DEseq2
Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.26.0), and bedGraphToBigWig tool (v4)
Genes were considered significantly changed and included in the heat map if the log2 fold change for either overexpression or knock-down was >1, p<0.05, and standard deviation/mean of the three replicates was <0.5
Genome_build: dm6
Supplementary_files_format_and_content: Excel spreadsheet with FPKM for each sample, log fold change between control and Blimp-1 gain or loss of function samples, adjusted p values, predicted gene functions, peak expression times and predicted binding sites for  Blimp-1 and Slbo.

organism: Drosophila melanogaster

source_name: 48hr APF retinas and optic lobes

growth_protocol: White prepupae grown in uncrowded conditions were aged for 48 hrs at 25 degrees C.

extract_protocol:
48hr APF pupal retinas and optic lobes were dissected out and other brain tissue removed. Total RNA was extracted using Trizol.
Libraries were constructed using Illumina TruSeq Stranded mRNA (Cat #20020595),  with 250ng of total RNA as input.

tag: gennotype

value: lGMR GAL4>UAS Blimp-1

value: retinas, optic lobes

tag: Stage

value: 48hr APF pupa


title: 041218M-TRM [ATAC-seq]

tag: cancer type

tag: cell type


title: Repli-seq of control HeLa cells at 5h

value: HeLa

value: siCTR

tag: treatment

value: aphidicolin washout 6 h


title: HeLa_FLAG-LSD1_Double thymidine block

value: FLAG-LSD1 plasmid

value: Double thymidine block

value: M-280 streptavidin Dynabeads (Life Technologies)


title: macaque1_6V_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque premotor area 6V

tag: tissue

value: premotor area 6V

value: bulk tissue

value: F

value: 12 years


title: 041218M-ReCir [scRNA-seq]

value: HGSOC

value: Re-circulating CD8+ TILs

value: CD8 TILs


title: 12mo BUMC M Het 2

value: humerus

value: batch 1

value: BUMC

value: 12 months

tag: Sex

value: male

value: wt/lo


title: 041218M-TRM [scRNA-seq]

value: TRM CD8+ TILs


title: HeLa_Vector_Double thymidine block

value: HeLa

value: Vector


title: Over_2

value: lGMR GAL4>UAS Blimp-1

value: retinas, optic lobes

value: 48hr APF pupa


title: RNAi_2

value: lGMR GAL4>Blimp-1 RNAi


title: HeLa_Control_DMSO treatment

value: Control

value: DMSO treatment

value: M-280 streptavidin Dynabeads (Life Technologies)


title: 12mo BUMC M Het 1

value: batch 2


title: HeLa_Input_No treatment

value: No treatment


title: macaque1_2A_rep1_atac

description: transposase-accessible DNA

source_name: adult female macaque secondary auditory cortex (2A)

value: secondary auditory cortex (2A)

value: bulk tissue

value: F

tag: age

value: 12 years


title: 042718M-ReCir [scRNA-seq]

value: HGSOC

value: Re-circulating CD8+ TILs

value: CD8 TILs


title: HeLa_siCTR_Double thymidine block

value: HeLa

value: siCTR

value: Double thymidine block


title: RNAi_3

value: retinas, optic lobes

value: 48hr APF pupa


title: 042718M-ReCir [ATAC-seq]


title: HeLa_Input


title: WT_2

value: lGMR GAL4/+


title: 12mo BUMC M WT 1

description: Gene expression data from humerus of BUMC male Brd2wt/wt animal at 12 months.

value: humerus

tag: animal

value: batch 1

value: BUMC

value: 12 months

value: male

value: wt/wt


title: 12mo BUMC M WT 2

tag: batch


title: 100809M-ReCir [ATAC-seq]


title: 042718M-TRM [ATAC-seq]

value: TRM CD8+ TILs


title: HeLa_CDC45

value: Cdc45 (Protein Tech Group, Cat.# 15678-1-AP


title: 042718M-TRM [scRNA-seq]

value: HGSOC


title: 100809M-ReCir [scRNA-seq]

value: Re-circulating CD8+ TILs


title: Over

value: lGMR GAL4>UAS Blimp-1


title: HeLa_LSD1

value: HeLa

value: LSD1 (Abcam, Cat.# ab17721)


title: 12mo BUMC F Het 3

description: Gene expression data from humerus of BUMC female Brd2wt/lo animal at 12 months.

value: batch 2

tag: colony

value: female

value: wt/lo


title: HeLa_siLSD1_Double thymidine block

value: LSD1 siRNA

value: Double thymidine block

value: M-280 streptavidin Dynabeads (Life Technologies)


title: FJH3 rep3

city: Nanjing

first: HD

last: Guo

address: Weigang NO.1

institute: Nanjing Agricultural University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: fetal jejunum

extract_protocol:
Placenta, fetal duodenum and jejunum were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: ICR

value: Fetal jejunum

tag: developmental stage

value: gestation 18.5


title: Sample_106047 [FR3-2]

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

description: FACS-sorted, tamoxifen at E12.5

data_processing:
We downloaded the reads files and  concatenated those into a single .fastq file for each sample.
We checked the quality of the raw reads data for each sample using FastQC [1] (version v0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content).
We used the Tuxedo Suite software package for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference genome including both mRNAs and lncRNAs (UCSC mm10)  [5] using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We ran two different, popular techniques for differential expression analysis: Cufflinks/CuffDiff and HTSeq/DESeq2 [9], using UCSC mm10.fa as the reference genome sequence.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2: depth_normalized_counts, raw_counts, rlog_normalized_counts, Tuxedo: Fpkm, RawCounts, ScaledCounts

source_name: Bone/bone marrow (femur)

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated.  GFP+tdTomato+ cells were FACS-isolated from postnatal day 21 (P21) femurs of Cxcl12-GFP; Dlx5-creER; R26R-tdTomato and Cxcl12-GFP; Fgfr3-iCreER; R26R-tdTomato mice, both pulsed with a single dose of tamoxifen at embryonic day 12.5 (E12.5).
Nextera XT DNA Library Preparation Kit

tag: genotype

tag: cells

value: Fgfr3-derived CAR cells (GFP+tdTomato+)

value: Postnatal day 21

value: Bone/bone marrow (femur)


title: Sample_106048 [FR3-3]

description: FACS-sorted, tamoxifen at E12.5


title: 100809M-TRM [ATAC-seq]

value: HGSOC

value: TRM CD8+ TILs

value: CD8 TILs


title: WT_3

value: lGMR GAL4/+

value: retinas, optic lobes

value: 48hr APF pupa


title: 12mo BUMC M WT 4

value: humerus

value: batch 2

value: BUMC

tag: timepoint

value: 12 months

value: male

tag: brd2 genotype

value: wt/wt


title: 12mo BUMC F Het 4

value: batch 1

value: female

value: wt/lo


title: FJH2 rep2

value: ICR

value: Fetal jejunum

value: gestation 18.5


title: 12mo BUMC F Het 2


title: 12mo BUMC M WT 3


title: 12mo BUMC F Het 1


title: 12mo BUMC F WT 4

description: Gene expression data from humerus of BUMC female Brd2wt/wt animal at 12 months.


title: FJH1 rep1


title: RNAi

tag: gennotype

value: lGMR GAL4>Blimp-1 RNAi


title: Sample_2281.YM.3 [Dlx5-3]

description: FACS-sorted, tamoxifen at E12.5

value: Dlx5-derived CAR cells (GFP+tdTomato+)

value: Postnatal day 21

value: Bone/bone marrow (femur)


title: 100809M-TRM [scRNA-seq]

value: HGSOC

value: TRM CD8+ TILs

value: CD8 TILs


title: 12mo BUMC F WT 3

value: humerus

value: batch 2

value: BUMC


title: Sample_2281.YM.2 [Dlx5-2]

description: FACS-sorted, tamoxifen at E12.5


title: 012320M-ReCir [ATAC-seq]

value: Re-circulating CD8+ TILs


title: FJC3 rep3


title: 012320M-ReCir [scRNA-seq]


title: WT

value: lGMR GAL4/+

value: retinas, optic lobes

tag: Stage

value: 48hr APF pupa


title: Sample_2281.YM.1 [Dlx5-1]

description: FACS-sorted, tamoxifen at E12.5


title: FJC1 rep1

value: ICR


title: 012320M-TRM [ATAC-seq]

tag: cancer type


title: 12mo BUMC F WT 2

value: batch 1

value: 12 months

value: female

value: wt/wt


title: KO_Female_iWAT_3

city: Seoul

first: Kyung-Mi

last: Choi

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Raw sequence reads were preprocessed using HTStream.
The remaining reads were then aligned to the GRCm39 mouse genome.
A gene counts table for each tissue was then generated using featureCounts.
Using R and the limma voom pipeline, differential expression analysis was conducted.

source_name: iWAT

extract_protocol: Total RNA was extracted from iWAT and BAT and purified using Zymo RNA clean & concentrate kit. The purified RNA was analyzed by using Bioanalyzer for quality control and used for library preparation.

value: iWAT

value: Female

value: KO


title: KO_Female_iWAT_2


title: FDH3 rep3

source_name: fetal duodenum

value: Fetal duodenum

value: gestation 18.5


title: 012320M-TRM [scRNA-seq]

value: HGSOC

tag: cell type

value: TRM CD8+ TILs

value: CD8 TILs


title: myeloid cells, WT3

first: Hao

last: Zuo

address: P&S 7-401, 630 WEST 168th STREET

institute: Columbia University

data_processing:
Quality control was performed with FastQC (v0.11.2) and FastQ Screen (v0.4.4)
Reads were trimmed to remove adapter sequences using fastq-mcf (ea-utils/1.1.2-806), then mapped to mm10 genome using TopHat (v2.0.12) with duplicated reads marked by Picard tools (v1.127).
RNA counts were generated from Subread/FeatureCounts. After TMM normalization, differentially expressed genes (DEGs) were identified using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each Sample

source_name: Bone marrow

growth_protocol: Bone marrow cells were filtered with a 40 μm cell strainer, and differentiated with 40 ng/mL of mouse M-CSF in α-MEM containing 10% FBS for 3 days

extract_protocol:
Total RNA was extracted with Trizol and miRNeasy Mini Kit (Qiagen #217004).
RNA library for sequencing was constructed from 4 μg of each DNase-treated RNA sample by using the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina (Illumina #RS-122). RNA was purified and fragmented before strand-specific cDNA synthesis. cDNA was then A-tailed, ligated with indexed adapters, PCR amplified and purified with Ampure XP beads. Library quality was validated on the Agilent 2100 Bioanalyzer.

value: myeloid cells

value: PD-L1 flox/flox

value: 2 months

value: Bone marrow


title: FDH2 rep2

value: ICR


title: KO_Female_iWAT_1


title: FDH1 rep1


title: 9mo BUMC M Het 4

description: Gene expression data from humerus of BUMC male Brd2wt/lo animal at 9 months.

value: humerus

value: batch 2

value: BUMC

value: 9 months

value: male

value: wt/lo


title: myeloid cells, WT2


title: 12mo BUMC F WT 1

value: batch 1

value: 12 months

value: female

value: wt/wt


title: 9mo BUMC M Het 3


title: WT_Female_iWAT_3

value: iWAT

value: Female

value: WT


title: 9mo BUMC M Het 2


title: myeloid cells, WT1

value: myeloid cells

value: PD-L1 flox/flox


title: WT_Female_iWAT_2


title: FDC3 rep3

value: Fetal duodenum

value: gestation 18.5


title: myeloid cells, CKO3

value: PD-L1 flox/flox +lysozyme-Cre

value: 2 months

value: Bone marrow


title: WT_Female_iWAT_1


title: 9mo BUMC M WT 4

description: Gene expression data from humerus of BUMC male Brd2wt/wt animal at 9 months.

value: humerus

value: batch 2

value: BUMC

value: 9 months


title: myeloid cells, CKO2


title: myeloid cells, CKO1


title: FDC1 rep1

value: ICR


title: 9mo BUMC M WT 3

value: male


title: PH3 rep3

source_name: placenta

value: Placenta


title: KO_Male_iWAT_2

value: iWAT

value: Male

value: KO


title: TRX_CP_3 [6_TRXtr-Vim_4_4]

city: Amsterdam

first: Judy

last: van Beijnum

state: Noord Holland

address: CCA rm 2.52, De Boelelaan 1118

department: Medical Oncology

country: Netherlands

institute: VUMC

description: 6245_6_TRXtr-Vim_4_4_GAGTCATA-GTGTGGCGCT_S50

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using HiSat2
Hisat2 was supplied with a known set of gene models (Ensembl version 87).
In order to count the number of reads per gene, a custom script, Itreecount (https://github.com/NKI-GCF/itreecount), has been used. This script is based on the same ideas as HTSeq-count. A list of the total number of uniquely mapped sequencing reads for each gene that is present in the provided Gene Transfer Format (GTF) file was generated.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

source_name: B16F10 tumor

extract_protocol:
Tumors were excised and snap frozen. RNA was isolated using Rneasy mini columns according to the manufacturers' instructions
Libraries preparation was performed using the TruSeq Stranded Total RNA with Illumina Ribo-Zero Plus kit (Illumina Inc., 20040525) in combination with IDT for Illumina RNA UD Indexes, Set A (Illumina Inc., 20040553) according to the manufacturer's instructions (Illumina Inc, Part # 1000000092426 v01). The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA).

tag: strain background

tag: treatment

value: vaccinated against a tumor vascular target

value: tumor


title: KO_Male_iWAT_1

tag: tissue

tag: Sex


title: FJC2 rep2

value: Fetal jejunum


title: PH2 rep2

value: gestation 18.5


title: WT_Male_iWAT_3

value: WT


title: TRX_CP_2 [5_TRXtr-Vim_4_3]

description: 6245_5_TRXtr-Vim_4_3_CCGTATGT-CATACACTGT_S49


title: 9mo BUMC M WT 2

tag: animal

value: batch 1

value: wt/wt


title: PC3 rep3


title: TRX_CP_1 [4_TRXtr-Vim_3_5]

description: 6245_4_TRXtr-Vim_3_5_AGTCAGAC-ACCAGCGACA_S48


title: PH1 rep1


title: WT_Male_iWAT_2


title: 9mo BUMC F Het 4

description: Gene expression data from humerus of BUMC female Brd2wt/lo animal at 9 months.

value: humerus

tag: batch

value: female

value: wt/lo


title: 9mo BUMC M WT 1

tag: colony

value: BUMC

value: 9 months


title: PC2 rep2

tag: strain

value: ICR


title: TRX_3 [3_TRXtr_1_4]

description: 6245_3_TRXtr_1_4_GACTGAGT-GTTGATAGTG_S47

value: control vaccinated


title: WT_Male_iWAT_1

value: iWAT


title: TRX_2 [2_TRXtr_1_2]

description: 6245_2_TRXtr_1_2_GATCAAGG-CCTTGTTAAT_S46


title: FDC2 rep2

value: Fetal duodenum

tag: developmental stage


title: 9mo BUMC F Het 1


title: 9mo BUMC M Het 1

value: male


title: PC1 rep1

value: Placenta


title: 9mo BUMC F Het 3

value: batch 2


title: KO_Male_iWAT_3

value: Male

tag: genotype

value: KO


title: 9mo BUMC F Het 2


title: UUO2_scRNAseq

city: philadelphia

first: tomohito

last: doke

address: smilow, 3400 Civic Center Blvd STRC 12-188

department: Medicine

institute: University of Pennsylvania

description: processed data files include count matrix, metadata and umap files

data_processing:
Cell Ranger 6.0.1 (https://10xgenomics.com) was used to process Chromium single cell 3' RNA-seq output.
"cellranger count" aligned the Read2 to the mouse reference genome (mm10).
Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (mm10).
The output files for 8 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell duplets). Cells were also discarded if their mitochondrial gene percentages were over 50%.
Genome_build: mm10
Supplementary_files_format_and_content: EXPORT_counts.rds: combined count matrix of all 8 samples; EXPORT_metadata.txt: combined metadata; EXPORT_umap.txt: UMAP embedding values for all non-PT cells.

source_name: whole kidney tissue

extract_protocol:
10X Genomics Chromium Prep. Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
The cDNA libraries were constructed using the 10x ChromiumTM Single cell 3’ Library Kit according to the manufacturer’s original protocol.

treatment_protocol: mice underwent ligation of the left ureter and were sacrificed on day 7

value: adult kidney

tag: age

value: 7 weeks

tag: disease

value: unilateral ureteric obstruction


title: UUO1_scRNAseq


title: TRX_1 [1_TRXtr_1_1]

description: 6245_1_TRXtr_1_1_CTAGTGCT-TGGAACAGTA_S45

value: tumor


title: 9mo BUMC F WT 4

description: Gene expression data from humerus of BUMC female Brd2wt/wt animal at 9 months.

value: humerus

tag: timepoint

value: female

tag: brd2 genotype

value: wt/wt


title: 9_old_ctrl_pancreas

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Reads were trimmed with Trim Galore (version 0.5.0). Trimmed reads were aligned to the mouse genome (GRCm38) with Bismark (version 0.20.0). Aligned reads were deduplicated based on UMI sequence and chromosomal position with Umibam (version 0.0.1). Bismark coverage files were generated from the deduplicated bam files using Bismark Methylation Extractor.
Genome_build: GRCm38
Bismark coverage file: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

source_name: Pancreas

growth_protocol: We used the reprogrammable mice known as i4F-B which carries a ubiquitous doxycycline-inducible OSKM transgene, abbreviated as i4F, and inserted into the Pparg gene (Abad et al., 2013). Mice of both sexes were used, and of different ages; young (females, 13 weeks), old (females, 55 weeks) and very old (males and females, 100 weeks). 0.2 mg/ml of Doxycycline hyclate BioChemica (PanReac) was administered in the drinking water supplemented with 7.5% sucrose for a period of 7 days. Mice were sacrificed two or four weeks after doxycycline removal.

extract_protocol:
All pancreas, liver and spleen tissues were snap-frozen directly after collection. Genomic DNA was extracted from frozen tissues using the DNeasy Blood & Tissue Kit (Qiagen). All samples were collected, processed for their methylation status and further analyzed.
RRBS libraries were prepared as described previously (Stubbs et al., 2017). 500ng of genomic DNA was digested with MspI (Thermo Scientific). Following digestion, DNA fragments were end-repaired and T-tailed with Klenow fragment lacking 5’ ® 3’ and 3’ ® 5’ exonuclease activity (NEB). In-house adapters containing 8-nucleotide unique molecular identifier (UMI) sequences were ligated onto the DNA fragments with T4 DNA ligase (NEB). Excess adapters were removed by AMPure XP beads (Agencourt, 0.8X ratio). Libraries were bisulfite converted with the EZ-96 DNA Methylation-Direct MagPrep kit and cleaned up using an automated liquid handling platform (Agilent Bravo). The bisulfite converted libraries were amplified for 12 cycles with KAPA HiFi HotStart Uracil+ ReadyMix (Roche). The amplified libraries were cleaned up with AMPure beads (0.8X ratio) and quality checked using an Agilent High Sensitivity DNA kit on an Agilent 2100 Bioanalyzer system. Libraries passing quality checks were sequenced on an Illumina HiSeq 2500 sequencer for 75 bp paired-end sequencing.

value: Pancreas

value: Old control pancreas

tag: time after dox removal

value: 54 weeks

value: Female


title: Control5_scRNAseq

value: control


title: 7_old_ctrl_pancreas


title: 9mo BUMC F WT 3

value: BUMC

value: 9 months


title: 8_old_ctrl_pancreas


title: Control4_scRNAseq


title: 75_old_OSKM_liver

source_name: Liver

value: Liver

value: Old OSKM liver

value: 2 weeks


title: Control3_scRNAseq

value: adult kidney


title: 9mo BUMC F WT 2

value: batch 1


title: 74_old_OSKM_liver


title: Control2_scRNAseq

value: 7 weeks


title: 9mo BUMC F WT 1


title: 6mo BUMC M Het 4

description: Gene expression data from humerus of BUMC male Brd2wt/lo animal at 6 months.

value: batch 2

value: 6 months

value: male

value: wt/lo


title: 73_old_OSKM_liver


title: Control1_scRNAseq


title: 6mo BUMC M Het 3

value: humerus


title: Sample_67819_HSC.F.HF.4

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
The Tuxedo Suite of software was used for alignment, differential expression analysis, and post-analysis diagnostics.
Reads were aligned to the reference genome  using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.), with default parameter settings for alignment,  except: “--b2-very-sensitive” was set.
Cufflinks/CuffDiff (version 2.1.1) for expression quantitation, normalization, and differential expression analysis.
For normalization of expression values,  “--multi-read-correct” was used to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile–norm”.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text - raw reads quantified by Cufflinks

growth_protocol: C57Bl/6 male and female mice were left on control or 60% HFD at 6 weeks of age for 16 weeks.

extract_protocol:
RNA prepared using QIAGEN kits
Clontech's SMARTer , ribodepleted, stranded.

treatment_protocol: After 16 weeks adipose tissue was isolated and stromal vascular fraction isolated and cells sorted for DAPI-CD45+CD64+ ATMs and bone marrow isolated and single cell suspension stained and HSCs sorted (DAPI-, Lineage-Sca+Kit+CD150-CD48-.

value: F

tag: diet

value: HF

value: hematopoetic stem cells (HSC)


title: 72_old_OSKM_liver

tag: cell type

value: 54 weeks

value: Female


title: 6mo BUMC M Het 2

extract_protocol: RNA was purified from whole mouse humerus flash frozen under liquid nitrogen and stored at -80C until processed for total RNA.  Total bones were powdered with a mortar and pestle under liquid nitrogen and placed in Qiagen Tissue Lyzer tubes with 1 ml of Qiazol reagent per humerus. After extraction aqueous solutions for the Qiazol were applied to a miRNA RNeasy column (catalog #217004).

value: BUMC


title: 71_old_OSKM_liver

value: Liver


title: 6mo BUMC M Het 1


title: Sample_67818_HSC.F.HF.3


title: 6_old_ctrl_pancreas

value: Pancreas

value: Old control pancreas


title: Sample_67817_HSC.F.HF.2


title: 6mo BUMC M WT 4

description: Gene expression data from humerus of BUMC male Brd2wt/wt animal at 6 months.

value: wt/wt


title: 60_old_ctrl_liver

value: Old control liver

value: 52 weeks


title: 6mo BUMC M WT 3

value: batch 2


title: Control6_scRNAseq

value: adult kidney

value: 7 weeks

value: control


title: 5_young_ctrl_pancreas

value: Young control pancreas

value: 13 weeks


title: 6mo BUMC M WT 2

value: humerus

value: batch 1

value: 6 months

value: male


title: Sample_67815_HSC.F.ND.4

value: F

value: ND

value: hematopoetic stem cells (HSC)


title: Sample_67814_HSC.F.ND.3


title: 6mo BUMC M WT 1

value: BUMC


title: 59_old_ctrl_liver

value: Liver

value: 54 weeks

value: Female


title: 58_old_ctrl_liver

value: Old control liver


title: Sample_67813_HSC.F.ND.2


title: 57_old_ctrl_liver


title: Sample_67812_HSC.F.ND.1


title: 6mo BUMC F Het 4

description: Gene expression data from humerus of BUMC female Brd2wt/lo animal at 6 months.

value: batch 2

value: female

value: wt/lo


title: 56_old_ctrl_liver


title: 6mo BUMC F Het 3


title: Sample_67811_HSC.M.HF.4

value: M

value: HF


title: 55_young_ctrl_liver

value: Young control liver

value: 13 weeks


title: Sample_67809_HSC.M.HF.2


title: 6mo BUMC F Het 2

value: humerus

value: batch 1

value: 6 months


title: Sample_67810_HSC.M.HF.3


title: 54_young_ctrl_liver


title: 53_young_ctrl_liver


title: 6mo BUMC F WT 4

description: Gene expression data from humerus of BUMC female Brd2wt/wt animal at 6 months.

value: wt/wt


title: 52_young_ctrl_liver


title: Sample_67808_HSC.M.HF.1

value: hematopoetic stem cells (HSC)


title: Sample_67807_HSC.M.ND.4

value: ND


title: Sample_67816_HSC.F.HF.1

value: F


title: 6mo BUMC F WT 2

value: BUMC


title: 6mo BUMC F WT 3


title: Sample_67806_HSC.M.ND.3


title: 50_old_OSKM_spleen

source_name: Spleen

value: Spleen

value: Old OSKM spleen

value: 2 weeks

value: 54 weeks

value: Female


title: 6mo BUMC F WT 1

value: female


title: 3mo BUMC M Het 4

description: Gene expression data from humerus of BUMC male Brd2wt/lo animal at 3 months.

value: batch 2

value: 3 months

value: male

value: wt/lo


title: 4_young_ctrl_pancreas

value: Pancreas

value: Young control pancreas

value: 13 weeks


title: Sample_67805_HSC.M.ND.2

value: M

value: hematopoetic stem cells (HSC)


title: Sample_67804_HSC.M.ND.1

value: ND


title: Sample_67803_ATM.F.HF.4

value: F

value: HF

value: adipose tissue macrophages (ATM)


title: 3mo BUMC M Het 2

value: humerus

value: batch 1

value: BUMC


title: Sample_67802_ATM.F.HF.3


title: 48_old_OSKM_spleen

value: Spleen

value: Old OSKM spleen

value: 2 weeks

value: 54 weeks

value: Female


title: Sample_67801_ATM.F.HF.2


title: 3mo BUMC M Het 1

value: 3 months

value: male

value: wt/lo


title: 6mo BUMC F Het 1

value: 6 months

value: female


title: 49_old_OSKM_spleen


title: 46_old_OSKM_spleen


title: 3_young_ctrl_pancreas

value: Pancreas

value: Young control pancreas

value: 13 weeks


title: 3mo BUMC M WT 3

description: Gene expression data from humerus of BUMC male Brd2wt/wt animal at 3 months.

value: batch 2

value: wt/wt


title: Sample_67799_ATM.F.ND.4

value: F

value: ND

value: adipose tissue macrophages (ATM)


title: Sample_67798_ATM.F.ND.3


title: 35_old_ctrl_spleen

value: Spleen

value: Old control spleen

value: 52 weeks


title: 47_old_OSKM_spleen

value: Old OSKM spleen

value: 2 weeks

value: 54 weeks

value: Female


title: 3mo BUMC M WT 1

value: humerus

value: batch 1

value: BUMC

value: 3 months

value: male


title: 3mo BUMC F Het 4

description: Gene expression data from humerus of BUMC female Brd2wt/lo animal at 3 months.

value: batch 2

value: female

value: wt/lo


title: Sample_67797_ATM.F.ND.2

value: F

value: ND


title: 34_old_ctrl_spleen

value: Spleen


title: 33_old_ctrl_spleen

value: Old control spleen


title: 51_young_ctrl_liver

value: Liver

value: Young control liver

value: 13 weeks


title: 3mo BUMC M WT 2

value: wt/wt


title: 3mo BUMC F Het 3


title: Sample_67796_ATM.F.ND.1

value: adipose tissue macrophages (ATM)


title: 3mo BUMC M Het 3

value: humerus


title: 32_old_ctrl_spleen

value: 54 weeks

value: Female


title: Sample_67795_ATM.M.HF.4

value: M

value: HF


title: 31_old_ctrl_spleen


title: 3mo BUMC F WT 4

description: Gene expression data from humerus of BUMC female Brd2wt/wt animal at 3 months.

value: batch 2

value: BUMC

value: 3 months


title: 3mo BUMC M WT 4

value: male


title: 30_young_ctrl_spleen

value: Young control spleen


title: Sample_67793_ATM.M.HF.2


title: 2_young_ctrl_pancreas

value: Pancreas

value: Young control pancreas


title: 3mo BUMC F WT 3

value: female


title: Sample_67792_ATM.M.HF.1


title: Sample_67800_ATM.F.HF.1

value: F


title: Sample_67791_ATM.M.ND.4

value: ND


title: 28_young_ctrl_spleen

value: Spleen

value: 13 weeks


title: 29_young_ctrl_spleen


title: Sample_67790_ATM.M.ND.3

value: adipose tissue macrophages (ATM)


title: Sample_67789_ATM.M.ND.2


title: 3mo BUMC F WT 2

value: humerus

value: batch 1

value: wt/wt


title: 26_young_ctrl_spleen

value: Female


title: 3mo JAX F WT 4

description: Gene expression data from humerus of JAX female Brd2wt/wt animal at 3 months.

value: control 5

value: batch 2

value: JAX


title: 27_young_ctrl_spleen


title: 3mo BUMC F WT 1

value: BUMC

value: 3 months


title: Sample_67788_ATM.M.ND.1

value: M


title: 3mo BUMC F Het 2

value: wt/lo


title: 25_old_OSKM_pancreas

value: Pancreas

value: Old OSKM pancreas

value: 2 weeks

value: 54 weeks


title: 3mo JAX F WT 3

value: control 4

value: female


title: 3mo BUMC F Het 1

value: humerus


title: 3mo JAX F WT 2

value: control 2

value: batch 1


title: STEMI_3_B

city: Oxford

first: Robin

last: Choudhury

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

institute: University of Oxford

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
BAM to fastq file conversion using samtools v1.7 bam2fq.
Transcripts were quantified from reads using Salmon v1.2.1 with parameters --validateMappings --gcBias --seqBias -l A.
Counts were analysed using DESeq2 v1.24.0 / Bioconductor v3.8 / R v3.5.0. Transcripts with fewer than 10 counts across all samples were removed.
Variance stabilizing transformation was performed and normalized abundance values exported.
Genome_build: Ensembl 96 based on GRCh38
Supplementary_files_format_and_content: Comma-delimited matrix table with normalized abundance values for each sample and transcript

source_name: Peripheral blood neutrophils

extract_protocol:
Human peripheral blood neutrophils were isolated by diluting peripheral venous blood collected in to EDTA tubes 1:1 with PBS and neutrophils were negatively enriched using the EasySep direct human neutrophil isolation kit as per the manufacturers instructions. Isolated neutrophils were with lysed with RLT (Qiagen) and stored at -80ºC. RNA was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

value: Peripheral blood neutrophils

value: Unstimulated

tag: disease state

value: STEMI

tag: time

value: 1 month post-AMI


title: 24_old_OSKM_pancreas

tag: tissue

value: Female


title: DCIS_H4K8ac_rep1

city: Burtlington

first: Seth

last: Frietze

state: VT

address: The University of Vermont

department: Biomedical and Health Sciences

institute: The University of Vermont

data_processing:
Raw fastq files were aligned to the human genome (hg38) using STAR aligner. splicing disabled with '--alignIntronMax 1'
The peaksat R package was used to iteratively downsample bam files at 10% increments and call peaks.
peaks were called against pooled input replicates from GSM1700382 and GSM1700383 using MACS2, “callpeak -q 0.05”
Genome_build: hg38
Supplementary_files_format_and_content: peaksat_output.tar.gz is a gzipped tar file containing the output of peaksat and consists of data for analyzing peak saturation curves.  See the peaksat vignette on github for details. https://github.com/FrietzeLabUVM/peaksat

source_name: breast

growth_protocol: All cell lines were grown in DMEM: F12 supplemented with 5% (v/v) horse serum, 10 μg/ml human insulin, 20 ng/ml recombinant hEGF, 100 ng/ml cholera toxin, 0.5 μg/ml hydrocortisone 50 IU/ml penicillin/50 μg/ml streptomycin, and 2 mM glutamine.

extract_protocol:
Using 1% formaldehyde, cells were crosslinked for 10 min at room temperature, and formaldehyde crosslinking was quenched with glycine at a final concentration of 0.125M for 5 min at room temperature. Cells were washed twice with ice-cold 1X PBS, and cell pellets were flash-frozen in liquid nitrogen and stored at −80°C.
Libraries were prepared according to the NEBNext Ultra II DNA Library Prep Kit for Illumina {NEB#E7645} with NEBNext Multiplex Oligos for Illumina {NEB#7335, NEB#7500, NEB#7710, NEB#7730}.

tag: cell line

value: DCIS

tag: tumor stage

value: malignant, ductal carcinoma in situ, dervived from MCF10AT xenograft

tag: chip antibody


title: 3mo JAX F WT 1

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor R package and the Brainarray mogene10stv1mmentrezgcdf R package (version 14.0.0).

source_name: humerus

tag: animal

value: control 1

tag: batch

tag: colony

value: JAX

value: 3 months

tag: Sex

value: wt/wt


title: Sample_67794_ATM.M.HF.3

tag: strain

value: M

value: HF

value: adipose tissue macrophages (ATM)


title: double knock-out#2

city: Toronto

first: Georg

last: Zoidl

state: Ontario

address: 4700 Keele Street

department: Psychology

country: Canada

institute: York University

data_processing:
The sequencing data is in FASTQ format generated using bcl2fastq2 v2.17
The quality of the data is assessed using FastQC v.0.11.2
Adaptors are trimmed using Trim Galore v. 0.4.4.
The raw trimmed reads are aligned to the reference genome using Tophat v. 2.0.11
Tophat alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2
Genome_build: UCSC danRer11 , downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/.
Supplementary_files_format_and_content: htsqct.txt

organism: Danio rerio

source_name: whole larvae

growth_protocol: 6 day old larvae (6dpf)

extract_protocol:
Total RNAs were extracted from 6dpf larvae using RNeasy Plus Mini Kit and automated Qiacube platform (Qiagen).
The RNA library preparation was performed following the NEB NEBNext Ultra II Directional RNA Library Preparation protocol (New England Biolabs Inc., Ipswich, MA, USA). RNA libraries were loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size, quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: No treatment; larvae in light

tag: tag

tag: gentoype

value: TALEN mediate double knock-out


title: DCIS_H4K5ac_rep2


title: double knock-out#1


title: 23_old_OSKM_pancreas

value: Pancreas

value: Old OSKM pancreas

value: 2 weeks

tag: age

value: 54 weeks


title: STEMI_3_A

value: Peripheral blood neutrophils

tag: treatment

value: Unstimulated

value: STEMI

value: at presentation


title: DCIS_H4K5ac_rep1

value: DCIS

value: malignant, ductal carcinoma in situ, dervived from MCF10AT xenograft


title: 22_old_OSKM_pancreas

tag: time after dox removal

value: Female


title: 21_old_OSKM_pancreas

tag: cell type


title: MCF10AT1_H4K8ac_rep2

value: pre-malignant HRAS transfected cell line, dervied from MCF10A


title: NSTEMI_3_B

tag: disease state

value: NSTEMI

value: 1 month post-AMI


title: NSTEMI_3_A

tag: time


title: MCF10AT1_H4K5ac_rep2


title: MCF10AT1_H4K8ac_rep1


title: panx1b knock-out#2

value: TALEN mediate panx1b knock-out


title: panx1b knock-out#1


title: 10_old_ctrl_pancreas

tag: tissue

value: Old control pancreas

value: 52 weeks


title: 1_young_ctrl_pancreas

value: Pancreas

value: Young control pancreas

value: 13 weeks


title: DCIS_H4K8ac_rep2

tag: cell line


title: STEMI_2_B


title: MCF10AT1_H4K5ac_rep1

tag: tumor stage


title: JCX1003: Pancreas sample from untreated mouse of age 55 weeks

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

data_processing:
FastQ files were aligned against the mm10 genome with the STAR software v2.3.0e with the following parameter values: outFilterMismatchNoverLmax=0.05; outFilterMatchNmin=25
Aligned BAM files were sorted and indexed using sambamba v0.6.7
RPKM estimations per isoforms were computed with the R package casper which were then aggregated at the gene level (entrez)
RPKM matrix was log2-transformed, quantile normalized and a-priori corrected by the total number of reads in each sample using gene-wise linear models
Differential expression was performed with the R package gaga
Genome_build: mm10 from Illumina's igenomes UCSC
Supplementary_files_format_and_content: RPKM estimations per gene (entrez) as computed by the casper R package

extract_protocol:
Total RNA was extracted from pancreas samples using guanidine thiocyanate, followed by acid phenol-chloroform extraction
RNA libraries were prepared for sequencing using the kits NEBNext® rRNA depletion Kit (Human/Mouse/Rat) (New England Biolabs Cat#E6310L)  and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs Cat#E7770), following manufacturer´s instructions and 9 cycles of library amplification

treatment_protocol: old OSKM (or old reprogrammed) mice have been treated with doxycycline for 7 days to activate the OSKM cassette

tag: sample id

tag: condition


title: panx1a knock-out#3

value: TALEN mediate panx1a knock-out


title: MCF10A_H4K8ac_rep2

value: non-tumoregenic, epithelial

tag: chip antibody


title: double knock-out#3

value: TALEN mediate double knock-out


title: STEMI_1_B

value: Peripheral blood neutrophils

value: Unstimulated

value: STEMI


title: STEMI_1_A

value: at presentation


title: JCX1164: Pancreas sample from untreated mouse of age 13 weeks


title: panx1a knock-out#1


title: JCX1158: Pancreas sample from untreated mouse of age 13 weeks


title: MCF10A_H4K8ac_rep1


title: NSTEMI_2_A


title: MCF10A_H4K5ac_rep2


title: TL-control#3

value: wild-type


title: NSTEMI_2_B


title: JCX1051: Pancreas sample from untreated mouse of age 55 weeks


title: MCF10A_H4K5ac_rep1


title: panx1b knock-out#3


title: JCX1001: Pancreas sample from untreated mouse of age 55 weeks


title: ratStr_rep2_atac

first: Morgan

last: Wirthlin

institute: Carnegie Mellon University

data_processing:
ATAC-seq alignment: Reads were mapped to the mm10 or rn6 genome using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline).
ATAC-seq filtering: Duplicate reads, mitochondrial reads, and multi-mapping reads were filtered out as a part of the ENCODE ATAC-seq pipeline. We made the following read filtering changes from the pipeline defaults: "atac.multimapping" : 0.
ATAC-seq peak calling: Peaks were called on each sample individually using MACS2 within the ENCODE ATAC-seq pipeline workflow. We made the following changes from pipeline defaults: "atac.cap_num_peak" : 300000 and "atac.smooth_win" : 150.
ATAC-seq peak filtering: Reproducible peaks among replicates were determined within the ENCODE ATAC-seq pipeline workflow using IDR with the following changes from pipeline defaults: "atac.enable_idr" : true and "atac.idr_thresh" : 0.1.
Other: More information on all data processing and conclusions can be found in the publication.
Genome_build: mm10, rn6
Supplementary_files_format_and_content: ATAC-seq peaks called in each sample
Supplementary_files_format_and_content: MACS2 pval signal tracks for each sample in bigwig format

organism: Rattus norvegicus

source_name: adult female rat striatum

extract_protocol:
Nuclei were extracted from fresh tissue with Dounce homogenization in lysis buffer. The nuclei were pelleted by centrifugation and filtered through 70µm and 40µm strainers.
ATAC-seq libraries were constructed with standard amplification and size selection methods. See publication for more details.

treatment_protocol: Mice were injected intravenously with an fluorescent AAV related to tissues for a different study. The procedure was minimally invasive and did not affect the health of the animals. Rats received no treatments.

value: brown norway

value: striatum

tag: sample type

value: bulk tissue

value: F

value: 84 days

tag: sequenced molecule

value: transposase-accessible DNA


title: STEMI_2_A


title: TL-control#1


title: BC-50 (D_3)

city: Yangzhou

first: Hou

last: Zhaofeng

state: Jiangsu

address: No. 12, Wenhui East Road

institute: Yangzhou University

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads sequence, and reads with lengths shorter than 18 nt or longer than 35 nt were filtered, then mapped to Sscrofa 10.2 whole genome using bowtie-v0.12.9 with parameters -v 0 -k 1 for alignment analysis of short sequences.
Tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA and snoRNA were removed by mapping to RepeatMasker open-4.0.3, Rfam database (http://rfam.xfam.org/) or those types of data from pig.
Known miRNA were identified from the mapped sRNA tags in miRBase 20.0 (http://www.mirbase.org/), and the available software miREvo_v1.1, mirdeep2_0_0_5 and ViennaRNA-2.1.1 were integrated to predict novel miRNA
MiRNA which might have base edit could be detected by aligning all the sRNA tags to mature miRNA, allowing one mismatch
Known miRNA used miFam.dat (http://www.mirbase.org/ftp.shtml) to look for families; novel miRNA precursor was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam families.
MiRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

organism: Sus scrofa

source_name: brain

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Three individuals’ RNA samples, of the same group at each time point were equally mixed to generate an RNA pool. A total amount of 3 μg total RNA per pool was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.).

value: control

value: post inoculation day 50

value: brain


title: TL-control#2


title: NSTEMI_1_B

value: NSTEMI

value: 1 month post-AMI


title: NSTEMI_1_A


title: BI-50 (C_3)

value: infected


title: JCX1000: Pancreas sample from untreated mouse of age 55 weeks

value: Pancreas


title: ratStr_rep1_atac

city: Pittsburgh

address: 4400 Fifth Ave

source_name: adult male rat striatum

tag: strain

tag: Sex

value: M


title: BI-25 (C_2)

value: post inoculation day 25


title: ratM1_rep3_atac

source_name: adult female rat motor cortex

value: primary motor cortex M1


title: JCX1163: Pancreas sample from untreated mouse of age 13 weeks


title: panx1a knock-out#2

tag: tag

tag: gentoype

value: TALEN mediate panx1a knock-out


title: JCX1155: Pancreas sample from untreated mouse of age 13 weeks


title: ratM1_rep2_atac

source_name: adult male rat motor cortex

value: brown norway

tag: age


title: BC-10 (D_1)

value: post inoculation day 10


title: JCX1011: Pancreas sample from OSKM treated mouse of age 58 weeks (55 + 1 week treatment + 2 weeks revovery)


title: X5613711015_F_XX_E

city: Los Angeles

first: Montgomery

last: Blencowe

address: 610 Charles E Young Drive East

institute: UCLA

hyb_protocol: Individual samples were hybridized to Illumina MouseRef-8 Expression BeadChips (Illumina, San Diego, CA) by Southern California Genotyping Consortium (SCGC) at UCLA

scan_protocol: Standard Illumina scanning protocol conduced by Southern California Genotyping Consortium (SCGC) at UCLA

data_processing: The data was normalized using the Lumi R package (background substraction method: 'bgAdjust'; variance stabilization method:'vst'; normalization method: 'quantile'

label: Biotin, Cy3

label_protocol: Standard illumina label protocol

growth_protocol: We used FCG mice on a C57BL/6J B6 background (B6.Cg-TgSry2Ei Srydl1Rlb/ArnoJ, Jackson Laboratories stock 10905; backcross generation greater than 20), bred at UCLA. Gonadal females and males were housed in separate cages and maintained at 23°C with a 12:12 light: dark cycle.

extract_protocol: RNA from liver and inguinal adipose tissue was isolated using Trizol (Invitrogen, Carlsbad, CA). After homogenization and centrifugation, chloroform was applied for further RNA extraction based on the protocol provided by Invitrogen.

treatment_protocol: FCG mice were gonadectomized (GDX) at 75 days of age and implanted immediately with medical grade Silastic capsules containing Silastic adhesive only (blank control, (B) or testosterone (T) or estradiol (E). Testosterone pellets contained 5mM testosterone (Steraloids, Inc., Newport, RI, USA) in a Silastic tube with 1.57mm interior diameter, 2.41mm outside diameter (Dow Corning, Midland, MI, USA). These pellets produce testosterone levels in the high physiological range. The estradiol pellets contained 50µg of 17beta-estradiol (Steraloids) dissolved in 25 µl sesame oil within a Silastic tube with interior diameter 1.98mm and 3.17mm outside diameter, sealed on the ends with 3mm of medical grade Silastic adhesive. The estradiol pellets provide sufficient estrogen to induce progestin receptors in the brain. Mice were euthanized 3 weeks later; liver and inguinal adipose tissues were dissected, snap frozen in liquid nitrogen and stored at -80°C for RNA extraction and Illumina microarray analysis. This study design produced a total of 12 groups, with 4 groups of FCG mice (XXM, XXF, XYM, XYF), where each group was further subdivided into B or T or E based on hormonal treatment: XXM_B, XXM_T, XXM_E, XYM_B, XYM_T, XYM_E, XXF_B, XXF_T, XXF_E, XYF_B, XYF_T, XYF_E.

tag: agent

value: Estradiol

tag: genotype

value: XX

value: inguinal adipose

value: 75 days


title: X5773660094_H_XX_E

value: Testosterone


title: BI-10 (C_1)


title: X5613711014_C_XX_E


title: JXC384: Pancreas sample from OSKM treated mouse of age 58 weeks (55 + 1 week treatment + 2 weeks revovery)


title: ratM1_rep1_atac

value: sprague dawley

value: bulk tissue

value: 86 days

value: transposase-accessible DNA


title: SEXTIPrep3

first: Eduardo

last: Leyva-Diaz

address: 1212 Amsterdam Ave

department: Dept Biological Sciences

data_processing:
Alignment to WS220 using STAR
Assignment to gene feature using Featurecounts
Compare control and CUT sextuple mutant neuronal IP using DESeq2
Genome_build: WS220
Supplementary_files_format_and_content: Neuronal IP CUT DESeq2 normalized counts.txt is the normalized read counts outputted from DESeq2 after comparison of control and CUT sextuple mutant

organism: Caenorhabditis elegans

source_name: neuronal nuclei IP

growth_protocol: UPN::INTACT control worms (otIs790) as well as mutants were grown on large plates (150mm) with enriched peptone media coated with NA22 bacteria to allow for the growth of large quantities of worms. Animals were egg prepped according to standard protocol and synchronized at the L1 stage.

extract_protocol: RNA-seq libraries were prepped using the Universal RNA-seq kit (Tecan) according to manufacter’s protocol.

tag: fractuib

value: neuronal IP

value: OH17055 [UPN INTACT;Sextuple]

value: CUT sextuple mutant (ceh-38;ceh-44;ceh-48;ceh-41,ceh-21,ceh-39 null)

tag: developmental stage


title: SEXTIPrep2


title: JCX1025: Pancreas sample from OSKM treated mouse of age 58 weeks (55 + 1 week treatment + 2 weeks revovery)

tag: tissue

value: Pancreas


title: ratLiver_rep2_atac

source_name: adult male rat liver

value: liver

value: M

value: 84 days


title: ratLiver_rep3_atac

source_name: adult female rat liver

value: brown norway

value: F


title: JCX1027: Pancreas sample from OSKM treated mouse of age 58 weeks (55 + 1 week treatment + 2 weeks revovery)


title: ratLiver_rep1_atac


title: X5773660134_E_XX_T

value: XX


title: JCX1002: Pancreas sample from untreated mouse of age 55 weeks


title: SEXTIPrep1


title: X5773660104_D_XX_T

value: inguinal adipose


title: X5613711027_A_XX_T

value: 75 days


title: X5773660094_D_XX_T

value: Testosterone


title: RPMI Tat rep 3

city: Moscow

first: Anna

last: Valyaeva

address: Leninskiye Gory, MSU, 1-73

department: Faculty of Bioengineering and Bioinformatics

country: Russia

institute: Lomonosov Moscow State University

data_processing:
Basecalling was performed using bcl2fastq v2.17.1.14.
Raw reads were aligned to GRCh38.p10 genome using HISAT2 v2.0.5 with parameters --no-softclip --dta-cufflinks; splice sites were obtained from gene annotation GENCODE v26.
Gene counts per gene were calculated using HTSeq v0.12.4 with gene annotation GENCODE v26.
Normalized counts were obtained using DESeq2 v1.30.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files with raw counts for each sample
Supplementary_files_format_and_content: Matrix table with pre-filtered and normalized gene counts for every gene and every sample

source_name: Human lymphoblastoid B cells

growth_protocol: Cells were grown at 37°C in the RPMI 1640-Gluta-Max medium (#61870-010, Gibco) with the addition of 10% embryonic serum (#SV30160.03, HyClone), sodium pyruvate (#F023 PanEco), and an antibiotic and antimycotic solution (#LS15240062, Gibco).

extract_protocol:
Cells were collected and stored in RNALater (# 76106, Quigen). Total RNA was extracted using Rneasy Mini RNA isolation kit (cat# 74134, Qiagen) following Qiagen protocol, with the following modifications: (1) lysis time is increased up to 40 min; (2) on-column DNase I treatment is performed.
cDNA libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat#E7760S/E7760L) by NEB following the manufacturer’s protocol. RNA was fragmented for 5 minutes.

tag: cell line

value: RPMI 8866

tag: exogenous expression

value: Tat protein fused with EGFP


title: Rnf149_3

first: Burcu

last: Vitrinel

address: 100 Washington Sq E

institute: New York University

description: Rnf149-CRISPR rep3

data_processing:
Bulk RNA-seq libraries were aligned using STAR 2.7.0a (Zhang et al., 2018) with the parameters ‘--runThreadN 6 --outSAMtype BAM SortedByCoordinate \ --outSAMunmapped Within \ --outSAMattributes Standard ’.
Counts were obtained using featureCounts, a function of subread (Liao et al., 2014; Liao et al., 2019).
Differential expression was calculated using DESeq2 (Love et al., 2014).
Genome_build: Ciona genome KY Gene Model(KYoto Gene Model) (http://ghost.zool.kyoto-u.ac.jp/datas/HT.KYGene.fasta.zip)
Supplementary_files_format_and_content: Gene expression read counts matrices

organism: Ciona robusta

source_name: dissociated Ciona robusta embryos

extract_protocol:
1000 cells were directly sorted in 100µl lysis buffer included in RNAqueous®-Micro Total RNA Isolation Kit (Ambion). The total RNA extraction was performed following the manufacturer’s instructions.
250-2000 pg of total RNA was loaded as template for cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) with template switching technology. RNA-Seq Libraries were prepared and barcoded using Ovation® Ultralow System V2 (NuGen)

tag: developmetal stage

value: 20 hpf

value: embryo


title: Rnf149_2

description: Rnf149-CRISPR rep2


title: RPMI Tat rep 2


title: WTIPrep3

value: neuronal IP

value: OH16748 [UPN INTACT] (otIs790)

value: wildtype


title: BC-25 (D_2)

tag: condition

value: control

tag: time

value: post inoculation day 25

value: brain


title: WTIPrep2


title: X5773660104_H_XX_B

value: Blank


title: Rnf149_1

description: Rnf149-CRISPR rep1


title: GAL71_028_193

city: Utrecht

first: Matilde

last: Galli

address: Uppsalalaan 8

institute: Hubrecht Institute

description:
Samples 73-152
CEL-seq2

data_processing:
The 50 base pair paired-end reads were aligned to the C. elegans reference transcriptome compiled from the C. elegans reference genome WS249.
Raw data was processed using R (v3.6.2). Samples were filtered to include those with sufficient counts per transcript and gene, results were filtered for batch consistency and only intestinally-expressed genes that were found at least once in every sample were included for downstream analysis.
Possibly growth-delayed or sterile outlier animals were removed from the dataset, based on spermatogenesis and oogenesis-related gene expression (Francesconi and Lehner, 2014).
The DEseq R package was used to perform differential gene expression analysis.
Genome_build: C. elegans reference genome WS249
Supplementary_files_format_and_content: Read-, UMI (Barcode)-, Transcript-, count tables for mapped reads per section as tab separated values (.tsv) per animal.

molecule: polyA RNA

source_name: Whole animal

growth_protocol: Worms were cultured on nematode growth medium (NGM) plates seeded with OP50 Escherichia coli bacteria according to standard protocols. All strains were maintained at 20°C, unless indicated otherwise. N2 Bristol were used as wildtypes.

extract_protocol:
Young adult hermaphrodites were picked using tweezers and washed in 0.5 mL sterile demineralized water before adding 200 μL trizol (Invitrogen 15596018). Samples were stored at -80 °C for a limited time.
mRNA extraction, barcoding, reverse transcription, in vitro transcription and Illumina sequencing library preparation were performed according to the robotized version of the CEL-seq2 protocol (Hashimshony T. et al., 2016) using the SuperScript II Double-Stranded cDNA synthesis kit (Thermofisher), Agencourt AMPure XP beads (Beckman Coulter) and randomhexRt for converting aRNA to cDNA using random priming.
The libraries were sequenced paired-end at 50 bp read length on an Illumina HiSeq 2500.

treatment_protocol: Worms were synchronized by isolation of eggs from adult hermaphrodites through alkaline hypochlorite treatment and hatching overnight in M9 medium in the absence of food. Next, synchronized L1 larvae were divided over two conditions: auxin control (ct) and auxin (+). Auxin worms were grown on auxin for 24 hours, after which they are transferred to control plates. Auxin control worms were grown on control plates for 24 hours, and transferred to auxin plates from 24 to 48 hours of development. Animals were grown to the young adult stage (72 hours).

tag: treatment

value: auxin or control (mixed samples)


title: RPMI Tat rep 1


title: control RPMI rep 3


title: Tyr_3

city: New York

description: Control rep3


title: GAL117_027_02

description:
Samples 41-72
CEL-seq2


title: Tyr_2

description: Control rep2


title: RPMI EGFP rep 3

value: EGFP


title: Tyr_1

description: Control rep1


title: control RPMI rep 1


title: GAL117_025_02

description:
Samples 1-20
CEL-seq2


title: WTIPrep1


title: RPMI EGFP rep 2


title: X5773660134_H_XY-_E

value: Estradiol

value: XY-


title: X5613711015_B_XX_B

value: XX

value: inguinal adipose

value: 75 days


title: GAL117_026_42

description:
Samples 21-40
CEL-seq2

value: auxin


title: X5613711014_B_XY-_E


title: X5773660094_G_XY-_E


title: HER2 L755S 2

first: Rashi

last: Kalra

state: TX

address: ABBR R531A, One Baylor Plaza, One Baylor Plaza

department: BREAST CENTER

institute: Baylor College of Medicine

data_processing:
Alignments were performed against human genome version GRCh38 using the STAR program.
Differential expression analysis was determined through edgeR.
Gene Set Enrichment Analysis was done with the pre-ranked tool on ranked gene list. Genes were ranked based on signed p value, which was calculated as the sign of log2 fold change * -log10 (adj p value).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited txt file reports expected_count, TPM, FPKM.

source_name: Lobular breast cancer cell line

growth_protocol: MM134 HER2WT and HER2L755S cells were grown in full serum media till they are 70 percent confluent. Then appropriate phenol red free media was fed to the cells supplemnted with 5 % charcoal stripped FBS for 7 days.

extract_protocol:
Cells were harvested and subjected to RNA isolation with the GE Healthcare Illustra RNA spin mini kit (Catalog # 25-0500-71)
The Genomic and RNA Profiling Core (GARP) at BCM constructed libraries with 250ng of total RNA using the TruSeq RNA Library Prep Kit (Illumina). cDNA was generated from poly(A)-selected RNA. Libraries were quantified with the KAPA Library Quantification Kit (Kapa Biosystems) and were sequenced on the NovaSeq 6000 (Illumina).

tag: cell type

value: Lobular breast cancer cells

value: estrogen deprivation


title: 107_waplko

city: Vienna

first: Bart

middle: Johan H

last: Dequeker

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechology

data_processing:
Base calling was performed by VBCF NGS unit or MPIB NGS Core facility.
Mapping: Iterative mapping (see Imakaev et al., 2012) using bwa.
Read filtering was performed as in Flyamer et al., 2017.
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

source_name: zygote pronucleus

extract_protocol:
snHi-C protocol according to Flyamer et al., 2017.
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) or MPIB NGS Core facility (https://www.biochem.mpg.de/7076201/NGS) following the standard DNA sample preparation protocol.

value: Waplfl/fl (Tg)Zp3-Cre

tag: strain

tag: parental origin

value: maternal

value: G1 zygote


title: 108_waplko_no.mcm


title: HER2 L755S 1

city: Houston


title: RPMI Cys rep 3

value: RPMI 8866

value: TatC22G mutant protein fused with EGFP


title: 106_waplko

value: paternal


title: X5773660134_D_XY-_T

value: Testosterone


title: 105_waplko_no.mcm


title: control RPMI rep 2


title: RPMI Cys rep 1


title: X5613711015_E_XY-_E


title: X5773660104_C_XY-_T


title: 104_waplko_no.mcm


title: X5613711014_F_XY-_T


title: X5613711027_H_XY-_T


title: X5773660159_D_XY-_E


title: X5773660159_A_XX_B

value: Blank