title: ATAC_Activated_2D2_Egr2KO_Th17_rep3

city: Arlington

first: Vanja

last: Lazarevic

address: 1820 N Tuckahoe Street,

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads were mapped to the mouse genome (mm10 assembly) using Bowtie 0.12.8. In all cases, redundant reads were removed using FastUniq (Xu et al., 2012), and customized Python scripts were used to calculate the fragment length of each pair of uniquely mapped paired-end (PE) reads. Only one mapped read to each unique region of the genome that was less than 175 bp was kept and used in peak calling.
Regions of open chromatin were identified by MACS (version 1.4.2) using a p-value threshold of 1 × 10−5.
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: Spleen

growth_protocol: Naïve sorted (CD4+ CD62Lhi CD25-) CD4+ T cells were activated and differentiated under non-pathogenic (Th17(b)) condition for 48 hours.

extract_protocol:
1 X 10^4 cells were pelleted and washed with 50 μl 1× PBS. After pelleting the nuclei by centrifuging at 500 × g for 10 min, the pellets were re-suspended in 50 μl transposase mixture (25 µl of 2x TD buffer, 2.5 µl of TDE1, 0.5 µl of 1% digitonin, 22 µl of nuclease-free water) (#FC-121-1030, Illumina; #G9441, Promega). The reaction was incubated at 37°C with shaking at 300 rpm for 30 min. The fragmentalized DNAs were then purified using a QIAGEN MinElute kit and amplified with 10 or 11 cycles of PCR based on the amplification curve, and the paired-end libraries were purified using a QIAGEN PCR cleanup kit
Indexed libraries were multiplexed and sequenced for 50 paired-end read cycles on NextSeq 550 instrument according to the manufacturer's instructions

treatment_protocol: WT or Egr2-/- naïve sorted (CD4+ CD62Lhi CD25-) CD4+ T cells  and activated CD4 T cells under non-pathogenic (Th17(b) condition for 48 hours

value: Spleen

value: Primary cells

value: CD4 T cells

value: anti-CD3/CD28+IL-6+TGFb1 (aIFN-g + aIL-4)


title: EOMA _Empty- pLC5-ciR_rep2 [ncRNA-Seq]

status: Public on Jun 28 2023

type: SRA

city: chengdu

first: shuaijie

last: qian

state: sichuan

address: NO. 1, 4th Keyuan Road, Chengdu,

country: China

institute: West China Hospital, Sichuan University

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing 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 from raw data. At the same time, Q20, Q30, and GC-content of the raw dataswere calculated.
For known miRNA alignment, the acquired clean data were mapped to miRBase20.0 using modified software mirdeep2 and srna-tools-cli to obtain the potential miRNA and draw the secondary structures.
For novel miRNA prediction,  miREvo  and mirdeep2 were used to predict novel miRNA through exploring the secondary structure.
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
Differential expression analysis of two groups was performed using the DESeq R package (3.0.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach.
Assembly: miRBase20.0
Supplementary files format and content: Matrix table with miRNA TPM (transcript per million) for each sample

molecule: total RNA

organism: Mus musculus

source_name: EOMA

extract_protocol:
Total RNA was extracted from EOMA cells using TRIzol reagent (Thermo Fisher Scientific, USA).
Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations

tag: cell line

value: EOMA

tag: treatment

value: Empty- pLC5-ciR


title: ATAC_Activated_2D2_Egr2KO_Th17_rep2

state: VA

country: USA

library_source: genomic

molecule: genomic DNA

tag: tissue

tag: cell type

tag: genotype


title: ATAC_Activated_2D2_Egr2KO_Th17_rep1


title: EOMA _Empty- pLC5-ciR_rep1 [ncRNA-Seq]


title: pituitaries of hpg mice, Male, placebo, 13

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw data were processed using bcl2fastq Conversion Software (Illumina) to obtain FASTQ files, and the FASTQ files were aligned to the mm10 genome using STAR (Dobin et al., 2013).
Gene expression was quantified with featureCounts (Liao et al., 2014).
Assembly: mm10
Supplementary files format and content: tab delimited file including the counts of reads for all genes and for all samples

molecule: polyA RNA

source_name: pituitaries of hpg mice

extract_protocol:
Mouse pituitary tissues were homogenized in a Bead Ruptor Elite bead mill homogenizer (Omni International, Kennesaw, GA) cooled by liquid nitrogen and homogenized for 2 x 20 seconds at 4.2 m/s. Pituitary tissue homogenates were processed for RNA extraction using the Agencourt RNAdvance Tissue Kit (Beckman Coulter, Indianapolis, IN) on a BioMek FXP Laboratory Automation Workstation (Beckman Coulter, Indianapolis, IN) according to the manufacturer’s instructions. The purity and concentration of the RNA samples were evaluated on a NanoDrop One/One spectrophotometer (ThermoFisher Scientific) and quantified using Quant-iT RiboGreen RNA Assay Kit (ThermoFisher Scientific). The RNA integrity was assessed with an RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA, United States). RNA integrity numbers (RINs) for all samples were above 8.2 with a median RIN of 9.1. A total of 250 ng total RNA per sample was used as input material for the cDNA library preparation.
cDNA libraries were constructed from total RNA using the Universal Plus mRNA-Seq kit (Tecan Genomics, San Carlos, CA, United States) in a Biomek i7 Automated Workstation (Beckman Coulter). Briefly, mRNA was isolated from purified 300 ng total RNA using oligo-dT beads and used to synthesize cDNA following the manufacturer’s instructions. The transcripts for ribosomal RNA (rRNA) and globin were further depleted using the AnyDeplete kit (Tecan Genomics) prior to the amplification of libraries. Library concentration was assessed fluorometrically using the Qubit dsDNA HS Kit (Thermo Fisher), and quality was assessed with the Genomic DNA 50Kb Analysis Kit (DNF-467, Agilent Technologies). Following library preparation, samples were pooled, preliminary sequencing of cDNA libraries (average read depth of 90,000 reads) was performed using a MiSeq system (Illumina) to confirm library quality and concentration. Deep sequencing was subsequently performed using an S4 flow cell in a NovaSeq sequencing system (Illumina) (average read depth ~30 million pairs of 2×100 bp reads). In addition to the 8-base i5 and i7 barcodes, the i7 adaptor contains 8 random bases immediately following the library index. The additional 8 bases are used for duplicate read determination using the Duplicate Marking Tool. To take advantage of this feature, the libraries were sequenced using 16 cycles for the i7 index read.

treatment_protocol: Hypogonadal mice (hpg/hpg) were injected once daily i.p. with GnRH (1 µg) or saline for a total of 10 days. One hour after the last injection, animals were sacrificed, and pituitaries were snap frozen for bulk RNA-seq and qPCR analyses.

value: pituitaries

value: hpg

tag: Sex

value: Male

tag: group

value: placebo


title: pituitaries of hpg mice, Male, placebo, 12


title: pituitaries of hpg mice, Male, placebo, 16


title: HEK293T, Q226E PU.1

city: Bronx

first: Samuel

middle: John

last: Taylor

address: 1300 Morris Park Ave, Chanin building 601

institute: Albert Einstein College of Medicine

data_processing:
library strategy: CUT&Tag
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Sequencing reads passing quality control criteria were aligned to the Homo Sapiens transcriptome (hg38) using bowtie2 aligner using the options --end-to-end --very-sensitive --no-mixed --no-discordant --phred -I 10 -X 700.
Normalized bedgraphs were generated using genomecov with a normalization factor of 1,000,000/ number of total reads.
Assembly: hg38
Supplementary files format and content: Bedgraph of each sample

organism: Homo sapiens

source_name: fetal kidney

growth_protocol: HEK293T cells were maintained in 10% FBS, 1% Pen Strep, DMEM media

extract_protocol:
CUT&Tag was performed as follows, 5 × 10^5 cells per cell line were harvested and lightly fixed with 2% formaldehyde for 2 minutes. The cells were bound to Concavalin A-coated beads (Bangs laboratories) and incubated with the primary antibody (anti-PU.1 (Santa Cruz, sc-352) at 4°C overnight. Samples were then incubated with a secondary antibody (guinea pig α-rabbit (Antibodies Online, ABIN101961)) followed by adding pre-loaded pA-Tn5 adapter complex (generated in house). Tagmentation buffer with magnesium was used to induce transposase fragmentation. And PCR based library preparation was conducted (see below).
DNA was extracted by phenol/chloroform/isoamyl alcohol and fragments were amplified with NEBNext HiFi 2x PCR Master mix and universal i5 and barcoded i7 primers for 13 cycles. AMPure XP beads (#A63880) were used for post-PCR clean-up of the libraries. Libraries were subject to 35 bp paired-end sequencing using Illumina NextSeq 500 platform with 35bp paired end reads on high output mode at the Einstein Epigenomics core. Fastq files were generated using Picard tools v2.17.1 with adapter trimming by TrimGalore v0.3.7 and QC assessment using FASTQC v0.11.4.

treatment_protocol: Cells were transduced with WT PU.1 or Q226E PU.1 expression vector (pcDNA3.1 backbone) using lipofetamine, and were harvested for CUT&Tag after 48hrs

value: fetal kidney

value: Human embryonic kidney

value: PU.1 antibody

value: VEH


title: ATAC_Activated_2D2_WT_Th17_rep3

value: WT


title: ATAC_Activated_2D2_WT_Th17_rep2


title: Patient 12 Slide D18 ROI 041

type: RNA

city: Seattle

first: Rich

middle: A

last: Klinghoffer

state: WA

address: 530 Fairview Ave N

institute: Presage Biosciences

scan_protocol: Nanostring GeoMx Digital Spatial Profiling (DSP) Platform

data_processing: Raw probe level counts from the NanoString DSP machine were subjected to QC and normalization as follows. ROIs with deduplicated read counts of <10,000 were excluded. Count data was then normalized using TMM normalization(26) prior to performing limma analysis

source_name: head and neck carcinoma

label_protocol: Nanostring

extract_protocol: Tissue sections were baked, deparaffinized, washed in PBS, and targets were retrieved for 20 minutes in 1x Tris-EDTA pH 9.0 buffer (Invitrogen #00-4956-58) at 100 °C. Next, tissues were washed in PBS, incubated in 0.1 μg/ml proteinase K (Thermo Fisher Scientific, #AM2546) in PBS for 15 minutes at 37 °C and washed again in PBS. Protein targets were post-fixed in 10% neutral-buffered formalin for 5 minutes, followed by two 5-minute incubations in 12.25 mg/ml Tris base, 7.5 mg/ml Glycine stop buffer diluted in DEPC-treated water. Tissues were incubated overnight at 37 °C with hybridization solution (Human Cancer Transcriptome Atlas probe mix (NanoString #121400101), Buffer R (NanoString #121300313), and DEPC-treated water). During incubation, slides were covered with HybriSlip hybridization covers (Grace BioLabs #714022). After incubation, HybriSlip covers were gently removed by soaking in 2x SSC buffer. Two 25 minute stringent washes were performed using 50% formamide in 2x SSC at 37 °C. Tissues were washed for 5 minutes in 2× SSC and incubated in blocking buffer W (NanoString #121300313) for 30 minutes at room temperature in a humidity chamber. Primary antibody targeted against MIL113 was diluted in buffer W and incubated with the tissues for 1 hour followed by a 1 hour incubation with fluorescently-labeled secondary antibody diluted in buffer W. After the slides were washed twice for 5 minutes in 5x SSC buffer they were incubated for 1 hour in SYTO13 (50 nM) and fluorescently conjugated antibody targeting PanCK in blocking  8  buffer. Following staining the sections were washed for 5 minutes in fresh 2x SSC. Following whole slide imaging, multiple geometric ROIs of 400 μm2 were placed in regions of subasumstat drug exposure according to MIL113 signal intensity and regions of vehicle or background. Indexing oligonucleotides were then cleaved and quantified via next gen sequencing on a NovaSeq 6000 Illumina sequencer as previously described(25)

value: head and neck carcinoma

tag: gender

tag: anatomical location

value: Left lateral tongue

tag: age

tag: tumor level

value: negative


title: Patient 12 Slide D18 ROI 035

value: Vehicle


title: Patient 12 Slide D18 ROI 034


title: pituitaries of hpg mice, Female, GnRH, 11

value: Female

value: GnRH


title: Patient 12 Slide D18 ROI 033


title: HEK293T, WT PU.1


title: pituitaries of hpg mice, Female, GnRH, 10


title: ATAC_Activated_2D2_WT_Th17_rep1

value: Spleen

value: Primary cells

value: CD4 T cells

value: anti-CD3/CD28+IL-6+TGFb1 (aIFN-g + aIL-4)


title: Patient 12 Slide D18 ROI 032

value: Male


title: ATAC_Naïve_2D2_Egr2KO_CD4T_rep3


title: ATAC_Naïve_2D2_Egr2KO_CD4T_rep2


title: pituitaries of hpg mice, Female, GnRH, 9

value: pituitaries

value: hpg


title: ATAC_Naïve_2D2_Egr2KO_CD4T_rep1


title: pituitaries of hpg mice, Female, GnRH, 8


title: Patient 12 Slide D18 ROI 031


title: pituitaries of hpg mice, Female, GnRH, 7


title: Patient 12 Slide D18 ROI 030

value: Background


title: Patient 12 Slide D18 ROI 029


title: Patient 12 Slide D18 ROI 028


title: pituitaries of hpg mice, Female, placebo, 5

value: placebo


title: ATAC_Naïve_2D2_WT_CD4T_rep2


title: ATAC_Naïve_2D2_WT_CD4T_rep1


title: T3 10nM+Irisin 3

city: Botucatu

first: Miriane

last: Oliveira

address: District of Rubião Jr

country: Brazil

institute: Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.

data_processing:
Steps for adapter removal and low quality read filtering were performed using Cutadapt and Trimmomatic software.
The reads were aligned and quantified in Kallisto (version 0.43.0) using the Gh38 human genome index (GRCh38.p12 release-92) as a reference.
The abundance data (Counts) generated were imported using the Bioconductor Tximport package from R  and used for the analysis of differential gene expression with the Deseq2 package. Multifactor design analysis was used to control the effect of biological variation between samples from the same condition.
Assembly: GRCh38.p12 release-92
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human subcutaneous adipocytes

growth_protocol: Human subcutaneous preadipocytes (HPAd - 802S-05A; Cell Applications, Inc., San Diego, CA, USA) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Cultured HPAd were differentiated into mature adipocytes according to the manufacturer's instructions. In brief, preadipocytes were cultured in preadipocyte basal medium (Cat No. 811-500; Sigma-Aldrich). After reaching approximately 70%–80% confluence, preadipocytes were transferred to 6-well plates (approximately 1.7 × 105 cells/well) and maintained in the basal medium for 48 h. After 48 h (day 0), cells differentiation was initiated using a human adipocyte differentiation medium (Cat No. 811D-250; Sigma-Aldrich). The differentiation medium was renewed every 3 days for 16 days, according to protocol . Differentiated adipocytes were deprived of pre-existing hormones using a human adipocyte starvation medium (Cat No. 811S-250; Sigma-Aldrich) one day before application of treatments.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA samples were quantified in Qubit and the integrity of the RNA was analyzed using a  Bioanalyzer 2100® (Agilent, Santa Clara, CA, USA). Three RNA samples from each group were used to build each of the libraries.
The libraries were constructed using the TruSeq1 RNA Sample Prep kit v2 (Illumina, San Diego, CA, USA) following the protocol suggested by the manufacturer. Runs were performed on the Illumina HiSeq2500 platform with 100 bp paired end reads.

treatment_protocol: After 16d of growth in differentiation medium, adipocytes were treated with 10 nM triiodothyronine (T3 group; Sigma- Aldrich St. Louis, MO, USA) or 1 μg/ml (20 nM) irisin (I group; Sigma- Aldrich St. Louis, MO, USA); control cells were allowed to grow in the same culture conditions, but in the absence of test hormones.

value: Subcutaneous adipocytes cell

value: treated with T3 10nM+Irisin 20nM


title: THP-1 EVs, M1-like GAM, rep3

city: Chongqing

first: Chao

last: Xu

address: 118 Xingguang Boulevard, Liang Jiang New Area

institute: Chongqing General Hospital

description: EVs RNA

data_processing:
The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt. After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2 (2 2.2.9). Particularly, cmsearch (1.1.2) was performed for Rfam mapping. The software miRDeep2 (2.0.0.8) was used to predict novel miRNA by exploring the secondary structure. The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. Differential expression analysis was performed using the DEGseq, Q value≤ 0.001 and the absolute value of Log2Ratio ≥ 1 as the default threshold to judge the significance of expression difference.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read count and expression for each Sample

source_name: peripheral blood

growth_protocol: THP-1 was cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS; Gibco), 200 mM glutamine, 50 units/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
M1- and M2- EVs were extracted by ultracentrifugation.  Total RNA of EVs was extracted with exoRNeasy Maxi Kit (Qiagen, Hilden, Germany)according to the handbook instructment.
miRNA libraries were prepared for sequencing using BGI DNA nanoball sequencing protocols.

treatment_protocol: THP-1 cells were pretreated with 100 ng/ml phorbol myristate acetate (PMA; Sigma‒Aldrich, St. Louis, USA) for 48 h to obtain differentiated macrophage-like cells. GAM activation was conducted in accordance with previously reported procedures with some modifications (21). In brief, to obtain M1-GAMs, PMA-stimulated THP-1 cells were cultured with 50 ng/mL granulocyte-macrophage colony stimulating factor (GM-CSF; PeproTech, Cranbury, USA) for 3 days, while IL-4 and IL-13 (PeproTech) were applied to stimulate the generation of M2-GAMs.

value: peripheral blood

value: monocytes

value: WT

value: PMA and GM-CSF stimulated


title: E15.5 heart_Dp16+JAKi-3

city: Aurora

first: Kunhua

last: Song

state: Colorado

institute: University of Colorado Anschutz Medical Campus

description: RNA-seq_counts_normalized_18_mice_E15.5_hearts_by_gene.xlsx

data_processing:
FastQC was used for the raw RNA-seq reads for the control of sequence quality, GC content, the presence of adaptor sequences and duplicated reads and ensure homogeneity of sequencing reads between samples.
Reads that passed quality control were aligned to NCBI GRCh38 human reference genome or GRCm38/mm10 mouse reference genome using the splice-aware STAR aligner v2.7.
The read counts were generated from the aligned reads with featureCounts function in the RsubRead package.
The read counts were normalized with DESeq2 R package.
Assembly: NCBI GRCh38 or GRCm38/mm10
Supplementary files format and content: Excel files include normalized RPKM values for each sample

source_name: Embryonic heart

extract_protocol:
Total RNA from cells or mouse tissues was isolated by using TRIzol reagent (Invitrogen) according to manufacturer’s instructions. 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by BGI Genomics or Novogene Corporation.

value: Embryonic heart

value: JAKi, 10 mg/kg/day IP injection


title: Patient 12 Slide D18 ROI 074

value: head and neck carcinoma

value: Left lateral tongue

value: high


title: Patient 12 Slide D18 ROI 073

value: negative


title: Patient 12 Slide D18 ROI 072

value: Male


title: ATAC_Naïve_2D2_WT_CD4T_rep3

value: Spleen

value: Primary cells

value: CD4 T cells


title: pituitaries of hpg mice, Female, GnRH, 6

value: pituitaries

value: hpg

value: Female

value: GnRH


title: pituitaries of hpg mice, Female, placebo, 2

value: placebo


title: pituitaries of hpg mice, Female, placebo, 4


title: E15.5 heart_Dp16+JAKi-1


title: pituitaries of hpg mice, Female, placebo, 3


title: E15.5 heart_Dp16+JAKi-2


title: pituitaries of hpg mice, Female, placebo, 1


title: P120-CT 3

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from rat hippocampal ventral CA3

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 and hybridized to Rat Gene Expression 4x44K v3 Microarray Kit (G2519F-028282, Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering none NA.

organism: Rattus norvegicus

source_name: rat hippocampal ventral CA3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: CA3 explants (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Fresh ex-vivo explants of rat hippocampal ventral CA3 were obtained from dissected brain and collected after animal sacrifice following 110 days (P120) from the hyperthermic insult. CA3 samples were immediately kept in 600uL of RNAlater (Qiagen) until RNA extraction.

tag: age (days)

value: Control


title: P120-CT 1


title: P120-CT 2


title: P120-CT 4


title: P120-HS 5

value: animal with seizure


title: E15.5 heart_WT+JAKi-3

value: Embryonic heart

value: WT


title: Patient 12 Slide D18 ROI 070

value: head and neck carcinoma

value: Background


title: P120-HS 6


title: P120-CT 5


title: E15.5 heart_WT+JAKi-2

value: JAKi, 10 mg/kg/day IP injection


title: P120-HS 3


title: RD7-3

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using featureCounts function from Rsubread (v1.30.7) and rpkm function of edgeR (v3.24.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: prostate basal cell organoids

growth_protocol: Mouse prostate basal cells were flow-sorted and cultured as organoids using published protocol (Drost et al, Nature Protocol 2016) for 5 days before harvest.

extract_protocol:
Organoid mRNA was isolated using the RNeasy Micro Kit (Qiagen) based on the kit instructions.
RNA was reverse transcribed and amplified into cDNA using the Takara SmartSeq kit. Libraries were subsequently constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB,E7645L).

treatment_protocol: To make the basement medium (BM), the following components were added to advanced DMEM/F12: B27 (50× diluted), HEPES 1 M (100× diluted), GlutaMAX (100× diluted), Penicillin-streptomycin (100× diluted), N-acetylcysteine (1.25 mM), EGF (50 ng/ml), A83-01 (200 nM), Noggin (100 ng/ml), and Y-27632 dihydrochloride (10 μM). For R samples, 500 ng/ml R-spondin1 were added to BM. For RD7 samples, 500 ng/ml R-spondin1 and 10-7 M DHT were added to BM.

tag: strain

value: prostate basal cell organoids

value: basement medium plus R-spondin (500 ng/ml) and DHT (10-7M)


title: RD7-1


title: Patient 12 Slide D18 ROI 069

value: Male

value: Left lateral tongue

value: negative


title: E15.5 heart_WT+JAKi-1


title: Patient 12 Slide D18 ROI 068


title: Patient 12 Slide D18 ROI 071


title: P120-HS 4


title: E15.5 heart_Dp16-8 (low p-STAT1)

value: low


title: R-3

value: basement medium plus R-spondin (500 ng/ml)


title: P120-HS 1


title: P120-HNS 5

value: animal without seizure


title: E15.5 heart_Dp16-7 (low p-STAT1)


title: Patient 12 Slide D18 ROI 066


title: P120-HS 2


title: R-2


title: R-1


title: E15.5 heart_Dp16-6 (low p-STAT1)


title: Patient 12 Slide D18 ROI 064

value: med


title: E15.5 heart_Dp16-5 (low p-STAT1)


title: RD7-2


title: P120-HNS 4


title: Patient 12 Slide D18 ROI 067


title: P120-HNS 3


title: E15.5 heart_Dp16-4 (high p-STAT1)

value: high


title: BM-3

value: basement medium


title: Patient 12 Slide D18 ROI 063


title: BM-2


title: BM-1


title: E15.5 heart_Dp16-3 (high p-STAT1)


title: P60-CT 5

treatment_protocol: Fresh ex-vivo explants of rat hippocampal ventral CA3 were obtained from dissected brain and collected after animal sacrifice following 50 days (P60) from the hyperthermic insult. CA3 samples were immediately kept in 600uL of RNAlater (Qiagen) until RNA extraction.

value: Control


title: Patient 12 Slide D18 ROI 062


title: Patient 12 Slide D18 ROI 060


title: E15.5 heart_Dp16-2 (high p-STAT1)

value: Embryonic heart


title: Patient 12 Slide D18 ROI 065


title: Patient 12 Slide D18 ROI 061


title: P120-HNS 2


title: P120-HNS 1


title: E15.5 heart_Dp16-1 (high p-STAT1)


title: EOMA _circRNA-007371-pLC5-ciR_rep2

data_processing:
Raw data were firstly processed through in-house perl scripts to remove reads containing adapter, reads containing ploy-N and low quality reads, and were then filtered by Q20, Q30 and GC contents.
The acquired clean data were mapped to the mouse reference genome (mm10) using HISAT2 (v2.0.4).
For each sample, read counts for each gene were obtained with HTSeq(v0.6.1) and were standardized as fragments per kilobase million (FPKM).
Differential expression analysis of two groups was performed using the DESeq R package (1.10.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: mm10
Supplementary files format and content: Matrix table with mRNA FPKM for each sample

extract_protocol:
Total RNA was extracted from EOMA cells using TRIzol reagent (Thermo Fisher Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: EOMA


title: E15.5 heart_WT-4

value: WT


title: Patient 12 Slide D18 ROI 059

value: head and neck carcinoma


title: EOMA _circRNA-007371-pLC5-ciR_rep1


title: P60-CT 4


title: E15.5 heart_WT-3


title: P60-CT 3


title: EOMA _Empty- pLC5-ciR_rep3

value: Empty- pLC5-ciR


title: E15.5 heart_WT-2


title: EOMA _Empty- pLC5-ciR_rep2


title: Patient 12 Slide D18 ROI 058


title: Patient 12 Slide D18 ROI 057


title: E15.5 heart_WT-1


title: EOMA _circRNA-007371-pLC5-ciR_rep3


title: EOMA _Empty- pLC5-ciR_rep1


title: Patient 12 Slide D18 ROI 056


title: PD-L1 knockout TRAMP-C2 after 8hr of oncolytic virus infection (MOI 0.1; rep 3) [PDL1_KO_MOI_01_3]

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Transcript quantification for each sample was performed using Kallisto (v0.45.0) (74) with the GRCm38 transcriptome reference and the -b 50 bootstrap option. The R package Sleuth (v0.30.0) (75) was then used to construct general linear models for the log-transformed expression of each gene across experimental conditions. Wald’s test was used to test for differential expression between groups and the resultant p-values were adjusted to q-values using the Benjamini‑Hochberg false discovery rate method.
Assembly: GRCm38
Supplementary files format and content: Gene-level transcripts per million (TPM) quantifications for all samples

growth_protocol: Cell lines were cultured at 37°C in a humidified atmosphere containing 5% CO2. TRAMP-C2 were maintained in DMEM supplemented with 5% FBS, 5% NuSerum, 0.005 mg/mL bovine insulin, 10 nM dehydroisoandrosterone, 100 U/mL penicillin, 100 ug/mL streptomycin, 10 ug/mL gentamicin sulfate, and 20 mM HEPES. 786-0, Hs746, HEK293T, L929-ISRE, and Vero cells were maintained in DMEM supplemented with 10% FBS, 100 U/mL penicillin, 100 ug/mL streptomycin, 10 ug/mL gentamicin sulfate, and 20 mM HEPES.

extract_protocol:
RNA was isolated using GenElute RNA Miniprep Kit (Sigma) as per manufacturer’s protocol
Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed on a 2100 Bioanalyzer (Agilent Technologies). Libraries were generated from 250 ng of total RNA as follows: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was performed using the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. Libraries were then sequenced on a NovaSeq6000 S4 200 cycle (2 x 100bp) flow cell to an approximate depth of 30M reads per sample.

value: Adenocarcinoma of mouse prostate

value: PD-L1 knockout

value: VSV-delta51 infection (MOI 0.1; 8hr)


title: P60-CT 2

value: Male


title: Patient 12 Slide D18 ROI 054

value: Left lateral tongue

value: Background

value: negative


title: P60-HS 5

value: animal with seizure


title: PD-L1 knockout TRAMP-C2 after 8hr of oncolytic virus infection (MOI 0.1; rep 2) [PDL1_KO_MOI_01_2]


title: PB-TSC-24h-con-1

city: Xiamen

first: Jinhua

last: Lu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

institute: Xiamen University

data_processing:
Zebracall  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Genome_build: mm10

source_name: Mouse trophoblast stem cells

growth_protocol: Advanced DMEM/F12 supplemented with: 64mg/l L-ascorbic acid-2-phosphate magnesium, 1% ITS-X supplement,2mM L-glutamine,0.5% B27,0.05%BSA,1% P/S,25ng/ml FGF4,2ng/ml TGF-β,1μg/ml Heparin

extract_protocol:
mTSCs were harvested and extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mTSCs were treated with or without Dox for 48h

value: Placenta


title: P60-HS 4


title: Patient 12 Slide D18 ROI 053


title: PD-L1 knockout TRAMP-C2 after 8hr of oncolytic virus infection (MOI 0.1; rep 1) [PDL1_KO_MOI_01_1]


title: PD-L1 knockout TRAMP-C2 without oncolytic virus infection (rep 3) [PDL1_KO_Mock_3]

value: Mock infection (8hr)


title: PB-TSC-24h-Dox-1

value: Set8 KO


title: P60-HS 2


title: Patient 10 Slide C18 ROI 061

value: Left anterior neck

value: low


title: Patient 12 Slide D18 ROI 027


title: P60-HS 1


title: PD-L1 knockout TRAMP-C2 without oncolytic virus infection (rep 2) [PDL1_KO_Mock_2]


title: Patient 10 Slide C18 ROI 060


title: 3-mTSC_Dox-48h

description: Set8KO_Mouse_48h_FPKM_10-2-2021_two_duplicate.txt


title: P60-CT 1

value: Control


title: P60-HNS 5

value: animal without seizure


title: PB-TSC-24h-Dox-2


title: Patient 10 Slide C18 ROI 057

value: head and neck carcinoma

value: high


title: Patient 10 Slide C18 ROI 058


title: P60-HNS 4


title: PB-TSC-24h-con-2

value: WT


title: PD-L1 knockout TRAMP-C2 without oncolytic virus infection (rep 1) [PDL1_KO_Mock_1]

value: Adenocarcinoma of mouse prostate

value: PD-L1 knockout


title: P60-HS 3

value: Male


title: PD-L1 wildtype TRAMP-C2 after 8hr of oncolytic virus infection (MOI 0.1; rep 3) [Thy1_MOI_01_3]

value: PD-L1 wild type

value: VSV-delta51 infection (MOI 0.1; 8hr)


title: 2-mTSC_Con


title: Patient 10 Slide C18 ROI 056

value: negative


title: 4-mTSC_Dox-48h


title: PD-L1 wildtype TRAMP-C2 after 8hr of oncolytic virus infection (MOI 0.1; rep 2) [Thy1_MOI_01_2]


title: P60-HNS 2


title: P60-HNS 3


title: PD-L1 wildtype TRAMP-C2 after 8hr of oncolytic virus infection (MOI 0.1; rep 1) [Thy1_MOI_01_1]


title: Patient 10 Slide C18 ROI 059

value: med


title: Patient 10 Slide C18 ROI 054


title: PD-L1 wildtype TRAMP-C2 without oncolytic virus infection (rep 3) [Thy1_Mock_3]


title: Patient 10 Slide C18 ROI 053


title: PD-L1 wildtype TRAMP-C2 without oncolytic virus infection (rep 2) [Thy1_Mock_2]


title: Patient 10 Slide C18 ROI 048

value: Vehicle


title: Patient 10 Slide C18 ROI 047


title: 1-mTSC_Con

value: Placenta


title: P60-HNS 1


title: Patient 10 Slide C18 ROI 046


title: P120-HS 5

description: miRNA expression from rat hippocampal ventral CA3

hyb_protocol: Dried Cy3-labelled miRNA sample was resuspended with 17uL of nuclease-free water and mixed to Hyb Spike-In and 10x GE Blocking Agent solutions, and 2x Hi-RPM Hybridization buffer. The final volume was incubated at 100°C for 5 minutes and hybridized to Rat miRNA Microarray slides (8x15K) (G4471A-070154) - Agilent Technologies, for 20 hours at 55°C in a rotating Agilent hybridization oven (20rpm).

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 8x15k miRNA microarrray slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The expression values transformed in Log (base 2) and normalized with limma package.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 ug RNA using the microRNA Complete Labeling and Hyb Kit (Agilent Technologies), without column purification, according to the manufacturer's instructions.

treatment_protocol: Fresh ex-vivo explants of rat hippocampal ventral CA3 were obtained from dissected brain and collected after animal sacrifice following the hyperthermic insult. CA3 samples from the animal with seizure (HS) were immediately kept in 600uL of RNAlater (Qiagen) until RNA extraction.

value: animal with seizure (P120)


title: P120-HS 4


title: P120-HS 3


title: P120-HS 1


title: mouse68_PDGFA_4days

city: Calgary

first: Gregory

last: Cairncross

state: AB

address: 3330 Hospital Dr NW

department: Clinical Neurosciences

institute: University of Calgary

data_processing:
quality control: fastqc
alignment and reads counting: STAR
Differential gene expression analysis: DESeq2
Assembly: mm10 reference genome (GRCm38; Genome Reference Consortium)
Supplementary files format and content: Normalized read counts from DESeq2

source_name: Neural Progenitor Cells

growth_protocol: Stem cell media with EGF, FGF and heparin or PDGFA (20ug/ml)

extract_protocol:
Qiagen RNEasy kit.  1.3 ug of total RNA was used for the construction of sequencing libraries.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®, NEB #E7770

value: Neural Progenitor Cells

value: PDGFA


title: Patient 10 Slide C18 ROI 045

value: Left anterior neck


title: P30-CT 4

treatment_protocol: Fresh ex-vivo explants of rat hippocampal ventral CA3 were obtained from dissected brain and collected after animal sacrifice following 20 days (P30) from the hyperthermic insult. CA3 samples were immediately kept in 600uL of RNAlater (Qiagen) until RNA extraction.

value: Control


title: P30-CT 3


title: mouse62_PDGFA_4days


title: Patient 10 Slide C18 ROI 043

value: head and neck carcinoma

value: low


title: P30-HS 5

value: animal with seizure


title: mouse69_EF_4days

value: EGF/FGF


title: mouse69_PDGFA_4days


title: Patient 10 Slide C18 ROI 042

value: high


title: PD-L1 wildtype TRAMP-C2 without oncolytic virus infection (rep 1) [Thy1_Mock_1]

value: Adenocarcinoma of mouse prostate

value: Mock infection (8hr)


title: P30-HS 4

value: Male


title: P60-HS 3

value: animal with seizure (P60)


title: P120-HS 2


title: P30-CT 5


title: P30-CT 2


title: P60-HS 2


title: mouse68_EF_4days


title: Patient 10 Slide C18 ROI 041


title: P30-HS 3


title: P30-CT 1


title: P60-HS 4


title: mouse62_EF_4days


title: P30-HS 2


title: P60-HS 1


title: Patient 10 Slide C18 ROI 040

value: med


title: P30-HS 5

value: animal with seizure (P30)


title: P30-HS 4


title: Quadriceps wildtype D2-mdx

city: Leiden

first: Pietro

last: Spitali

state: Zuid Holland

address: Postzone S4-P, Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: affected DMD mouse model

data_processing:
spaceranger pipeline mkfastq wraps Illumina's bcl2fastq to demultiplex Visium-prepared sequencing runds and convert barcode and read data to fastq files
spaceranger pipeline count akes a microscope slide image and FASTQ files from spaceranger mkfastq and performs alignment, tissue detection, fiducial detection, and barcode/UMI counting. Outputs are delivered in BAM, MEX, CSV, HDF5, TIFF, PNG, JPEG and HTML formats.
Assembly: mm10
Supplementary files format and content: Processed output from spaceranger pipelines mkfastq and count (filtered barcode-feature matrices along with spatial output data such as tissue positions list) which can be inputted to analyse the data further

source_name: Quadriceps

extract_protocol:
Quadriceps were isolated and fresh-frozen in LN-cooled isopentane, sectioned on the cryostat in 10µm thick sections that were placed on the Visium slide (n=1 per mouse model), methanol fixation, H&E staining, imaging, after permeabilization, reverse transcription, second strand synthesis and denaturation occurred, hereafter cDNA was amplified and finally, to generate a sequencing ready indexed library, P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 were added via end repair, A-tailing, adaptor ligation and PCR amplification. The spatial gene expression libraries were sequenced on an Illumina NovaSeq6000 with a target of ~125 million Paired-End reads per sample, or 50,000 reads per spot for each sample.
Libraries were prepared following the standard processing protocol of 10x Genomics, using a Dual Index Kit TT Set for Illumina sequencing
Next generation whole transcriptome sequencing (RNA-seq)

value: skeletal muscle (quadriceps)

value: 10 weeks


title: P30-HS 1


title: Quadriceps wildtype mdx

description: affected DMD mouse model

value: mdx


title: Patient 10 Slide C18 ROI 055

value: negative


title: Quadriceps wildtype DBA/2J

description: wildtype


title: P30-HS 3


title: Quadriceps wildtype C57BL10

description: wildtype


title: Patient 10 Slide E18 ROI 021

value: Left anterior neck


title: P30-HS 2


title: Patient 10 Slide E18 ROI 020


title: Patient 10 Slide C18 ROI 039


title: RNAseq_AML12_Mus1_rep2

city: Shanghai

first: Xuan

last: Cao

address: 320 Yueyang Road

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

data_processing:
Reads were mapped to mouse reference genome (mm10) using HISAT2 v2.1.0 , with parameters: --rna-strandness RF.
FPKM values were calculated using StringTie v1.3.5 (Pertea et al., 2015) based on Refgene annotation from the UCSC genome browser, with parameters: --rf.
Read counts were generated using HTSeq-count v0.6.1.
Differentially expressed genes (DEGs) were calculated using the R package DESeq2 v1.26.0 .
Assembly: mm10
Supplementary files format and content: bw

source_name: AML12 cells

growth_protocol: The mouse hepatocyte cell line alpha mouse liver 12 (AML12; CRL-2254, ATCC, Manassas, VA) were cultured in DMEM/F12 (11320033, Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (16140071, Gibco, Grand Island, NY), ITS Liquid Media Supplement (100×, 41400045, Gibco), and 40 ng/ml dexamethasone (D4902, Sigma, Darmstadt, Germany) at 37℃ and 5% CO2.

extract_protocol:
The RNA samples were extracted with Trizol
The libraries were prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, NRM603-01)

treatment_protocol: Cells were adherently cultured to about 60% confluency, then the antisense oligonucleotides were added to the culture medium using Lipofectamine™ RNAiMAX transfection regent (13778030, Thermo Fisher Scientific). The final concentration of ASOs is 50mM. ASO target for AS L1 RNA was chose on the consensus sequence on antisense L1_Mus1 RNAs.

value: AML12 cells

value: hepatocyte

value: wild-type

value: antisense Mus1_L1 ASO treatment


title: P30-HS 1


title: RNAseq_AML12_Scramble_rep2

value: Scramble ASO treatment


title: P12-HS 6

value: animal with seizure (P12)


title: P30-HNS 3

value: animal without seizure


title: P30-HNS 4


title: Patient 10 Slide C18 ROI 038

value: head and neck carcinoma


title: Patient 10 Slide E18 ROI 019

value: Male


title: Patient 10 Slide E18 ROI 018


title: P12-HS 5


title: P12-HS 4


title: P30-HNS 2


title: P30-HNS 1


title: P30-HNS 5


title: P12-CT 5

treatment_protocol: Fresh ex-vivo explants of rat hippocampal ventral CA3 were obtained from dissected brain and collected after animal sacrifice following 1-day the hyperthermic insult. CA3 samples were immediately kept in 600uL of RNAlater (Qiagen) until RNA extraction.

value: Control


title: P12-CT 2


title: RNAseq_AML12_Scramble_rep1


title: P12-HS 3


title: RNAseq_AML12_Mus1_rep1


title: Patient 10 Slide E18 ROI 016


title: P12-CT 4


title: P12-HS 2


title: SAMMY_AML12_shMatr3_S4_rep2

data_processing:
SAMMY-Seq reads were mapped to mouse genome (mm10) using Bowtie. Duplicate reads were excluded and kept only one read for each genomic site.
Duplicate reads were excluded and kept only one read for each genomic site.
To visualize the SAMMY signals, the log2 ratio of S4 vs S2 was calculated for each 10kb bin using bedtools (v2.29.2).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: SAMMY-seq

extract_protocol:
The DNA samples were extracted with phenol chloroform
The libraries were prepared using the VAHTS Universal DNA Library Prep Kit for MGI (Vazyme, NDM607-01)

treatment_protocol: For Dox-inducible MATR3-Knock down system, plasmids were constructed by cloning the target sequences to the pLKO-Tet-On vector and then transfect AML12 cells by lentivirus-based system. To generate stable cell lines, AML12 cells were selected in the presence of 1 ug/ml puromycin for 1 day. 1 ug/ml dox was used to induce MATR3 depletion.

value: MATR3 Knock-down


title: P12-CT 3


title: SAMMY_AML12_shMatr3_S4_rep1


title: Patient 10 Slide E18 ROI 015


title: SAMMY_AML12_shMatr3_S3_rep2


title: Patient 10 Slide E18 ROI 014

value: low


title: Patient 10 Slide E18 ROI 013

value: Vehicle


title: SAMMY_AML12_shMatr3_S3_rep1


title: SAMMY_AML12_shMatr3_S2_rep2


title: Patient 10 Slide E18 ROI 017


title: Patient 10 Slide E18 ROI 012


title: Patient 10 Slide E18 ROI 011


title: SAMMY_AML12_shMatr3_S2_rep1


title: P12-HS 5

value: animal with seizure


title: P120-HNS 6

treatment_protocol: Fresh ex-vivo explants of rat hippocampal ventral CA3 were obtained from dissected brain and collected after animal sacrifice following the hyperthermic insult. CA3 samples from the rats without seizure after insult (HNS) group were immediately kept in 600uL of RNAlater (Qiagen) until RNA extraction.

value: animal without seizure (P120)


title: P120-HNS 4


title: P120-HNS 5


title: P12-HS 6


title: P12-CT 1


title: SAMMY_AML12_Ctrl_S4_rep2

value: control


title: P120-HNS 3


title: Patient 10 Slide E18 ROI 010

value: Left anterior neck

value: negative


title: P120-HNS 2


title: SAMMY_AML12_Ctrl_S4_rep1

value: hepatocyte


title: P12-HS 3


title: P12-HS 1


title: P12-HS 2


title: P120-HNS 1


title: SAMMY_AML12_Ctrl_S3_rep2


title: Patient 10 Slide E18 ROI 08

value: high


title: P12-HS 1


title: P60-HNS 4

value: animal without seizure (P60)


title: SAMMY_AML12_Ctrl_S3_rep1


title: P12-HS 4


title: P12-HNS 5


title: Patient 10 Slide E18 ROI 07


title: P12-HNS 4


title: P12-HNS 6


title: P60-HNS 3


title: Patient 10 Slide C18 ROI 068

value: med


title: SAMMY_AML12_Ctrl_S2_rep1


title: SAMMY_AML12_Ctrl_S2_rep2


title: Patient 10 Slide C18 ROI 065

value: Background


title: Patient 10 Slide E18 ROI 09


title: RIPseq-IgG_ESC_Ctrl_rep2

data_processing:
RIP-Seq reads were mapped to mouse reference genome (mm10) using HISAT2 (v2.1.0),with parameters: --rna-strandness RF --dta.
Peaks were called using MACS (v1.4.2)
BedGraph files were generated using genomecov from bedtools (v2.29.2)

source_name: ES cells

growth_protocol: The mouse ES cell line (E14TG2a) were cultured in 2i/LIF conditions

treatment_protocol: No treatment

value: Embryonic Stem Cell

tag: disease

value: Normal


title: P60-HNS 1

value: Male


title: RIPseq-IgG_ESC_Ctrl_rep1


title: P12-HNS 3

value: animal without seizure


title: Patient 10 Slide C18 ROI 064

value: head and neck carcinoma


title: P30-HNS 5

value: animal without seizure (P30)


title: RIPseq-MATR3_ESC_Ctrl_rep2


title: Patient 10 Slide C18 ROI 063


title: F5R7Sept2017

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

data_processing:
Fastq files (R1, R2) were assembled using FLAsH (Fast Length Adjustment of SHort reads) version 1.2.11
Annotation of the consensus with the IMGT HighV-QUEST tools v3.6.0. Parameters : Locus:IGH, species: Mus muris, other parameters as default values.
Supplementary files format and content: IMGT HighV-QUEST output archive, containing tabular files

source_name: spleen B cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (ThermoFisher) from 5 millions of CD43- spleen B cells
For each sample, 500 ng total RNA was reverse-transcribed to cDNA by a 5’RACE PCR using ProtoScript II (New England Biolabs) and a cap race primer associated with consensus reverse primers for each mouse IgH Cm, Cg and Ca CH1 region or the human Cµ CH1

value: spleen B cells

tag: disease state

value: MmCu

tag: timepoint

value: Day 0


title: F5R8Sept2017


title: F5R6Sept2017


title: P30-HNS 3


title: P30-HNS 4


title: F5R5Sept2017


title: P30-HNS 2


title: HiC_ESC_M3AID_rep2

data_processing:
For Hi-C data, paired-end reads were mapped, processed, and iterative correction (ICE) using HiC-Pro software.Read pairs were mapped to the mouse mm10 reference genome with end-to-end algorithm and “-very-sensitive” option.
Singleton, multi-mapped, dumped, dangling, self-circle paired-end reads, and PCR duplicates were removed after mapping.
To eliminate the possible effects on data analyses of variable sequencing depths, we randomly sampled equal numbers read pairs from each sample for downstream analyses.
Valid read pairs were used to generate raw contact matrices at 100-kb, 250-kb and 1-Mb resolutions and applied iterative correction (ICE) on them.

extract_protocol:
The DNA samples were extracted with phenol chloroform
Cells (2.5 billions/sample) were crosslinked by 1% formaldehyde at 25℃ for 10 minutes. Then the cell chromatin was digested with 100U MboI at 37℃ overnight. Subsequently, filled in the restriction fragment overhangs with biotin at 37℃ for 1.5 hours and performed proximity ligation at room temperature for 4 hours. After protein degradation and crosslink reversal, DNA was purified by ethanol precipitation and were sheared to a size of 300-500bp. After size selection, the biotinylated DNA was pulled-down by streptavidin beads and then prepared for Illumine sequencing.

treatment_protocol: The auxin (IAA) inducible MATR3 degradation system was developed in mouse ESCs according to the rapid proteins depletion methods established by Natsume et al (Natsume et al., 2016). Firstly, the parental cells were generated by introducing the vector encoding constitutive cytomegalovirus-controlled auxin responsive F-box protein (CMV-OsTIR1) at the safe harbor ROSA26 using CRISPR/Cas (Nakao, Harada et al., 2016). Cells were further selected in the presence of 1 ug/ml puromycin. After 7 days, colonies were picked for further selection in a 96-well plate and the genotype was checked by genomic PCR. Based on this parental cell line, an in-frame mAID cassette was introduced after the last codon of MATR3 gene by CRISPR/Cas9. Plasmids were transfected with Lipofectamine™ 3000 Transfection Reagent (L3000150, Thermo Fisher Scientific, Waltham, MA). To ensure AID-tagging on both alleles, two short homology donor vectors containing neomycin and hygromycin resistance markers were transfected simultaneously into cells. Cells were further selected in the presence of 2 mg/ml neomycin and 200 ug/ml hygromycin. After 7 days, colonies were picked for further selection in a 96-well plate and the genotype was checked by genomic PCR. 0.5mM IAA (dissolved in alcohol) was used to induce MATR3 degradation.

value: MATR3 acute-degradation


title: P60-HNS 2


title: P30-HNS 1


title: Patient 10 Slide C18 ROI 030

data_processing: Raw probe level counts from the NanoString DSP machine were subjected to QC and normalization as follows. ROIs with deduplicated read counts of <10,000 were excluded. Count data was then normalized using TMM normalization(26) prior to performing limma analysis

value: Left anterior neck

value: Vehicle


title: Patient 10 Slide C18 ROI 031

value: negative


title: P12-HNS 1


title: HiC_ESC_M3AID_rep1


title: Patient 10 Slide C18 ROI 037


title: Patient 10 Slide C18 ROI 036


title: HiC_ESC_Alchol_rep2

value: no


title: RIPseq-MATR3_ESC_Ctrl_rep1


title: Patient 10 Slide C18 ROI 062


title: HiC_ESC_Alchol_rep1


title: F5R4Sept2017


title: F5R3Jan2018

value: VDJ-hCu


title: P12-HNS 4

value: animal without seizure (P12)


title: F5R3Sept2017


title: F5R2Sept2017


title: Patient 10 Slide C18 ROI 029


title: P12-HNS 2


title: RNAseq_AML12_shMatr3_rep1

data_processing:
Reads were mapped to mouse reference genome (mm10) using HISAT2 v2.1.0 , with parameters: --rna-strandness RF.
FPKM values were calculated using StringTie v1.3.5 (Pertea et al., 2015) based on Refgene annotation from the UCSC genome browser, with parameters: --rf.
Read counts were generated using HTSeq-count v0.6.1.
Differentially expressed genes (DEGs) were calculated using the R package DESeq2 v1.26.0 .

extract_protocol:
The RNA samples were extracted with Trizol
The library was constructed by VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2

value: hepatocyte

value: MATR3 Knock-down


title: Patient 10 Slide C18 ROI 028


title: RNAseq_AML12_shMatr3_rep2


title: Patient 1 Slide C410 ROI 021

value: Female

value: Oral cavity

value: high


title: F5R2Jan2018


title: F5R1Sept2017


title: P12-HNS 2

value: Male


title: RNAseq_AML12_Ctrl_rep2


title: F5R4Jan2018


title: P12-HNS 3


title: P12-HNS 1


title: P12-HNS 5


title: RNAseq_AML12_Ctrl_rep1


title: F5R1Jan2018


title: Patient 1 Slide C410 ROI 019

value: head and neck carcinoma


title: RIPseq-IgG_AML12_Ctrl_rep2

source_name: AML15 cells

value: Normal


title: F4R8Jan2018

value: spleen B cells

value: MmCu


title: Patient 1 Slide C410 ROI 018

value: Background


title: P120-Control 4

treatment_protocol: Fresh ex-vivo explants of rat hippocampal ventral CA3 were obtained from dissected brain and collected after animal sacrifice following the hyperthermic insult. CA3 samples from the Control (CT) group were immediately kept in 600uL of RNAlater (Qiagen) until RNA extraction.

value: Control (P120)


title: P120-Control 5


title: P120-Control 3


title: RIPseq-IgG_AML12_Ctrl_rep1

source_name: AML14 cells


title: F4R6Jan2018

value: Day 0


title: RIPseq-MATR3_AML12_Ctrl_rep2

source_name: AML13 cells


title: Patient 1 Slide C410 ROI 020

value: negative


title: F4R5Jan2018


title: F4R5Sept2017


title: P120-Control 1


title: Patient 1 Slide C410 ROI 016

value: med


title: RIPseq-MATR3_AML12_Ctrl_rep1


title: HiC_AML12_shMatr3_rep1

extract_protocol: Cells (2.5 billions/sample) were crosslinked by 1% formaldehyde at 25℃ for 10 minutes. Then the cell chromatin was digested with 100U MboI at 37℃ overnight. Subsequently, filled in the restriction fragment overhangs with biotin at 37℃ for 1.5 hours and performed proximity ligation at room temperature for 4 hours. After protein degradation and crosslink reversal, DNA was purified by ethanol precipitation and were sheared to a size of 300-500bp. After size selection, the biotinylated DNA was pulled-down by streptavidin beads and then prepared for Illumine sequencing.

treatment_protocol:
For Dox-inducible MATR3-Knock down system, plasmids were constructed by cloning the target sequences to the pLKO-Tet-On vector and then transfect AML12 cells by lentivirus-based system. To generate stable cell lines, AML12 cells were selected in the presence of 1 ug/ml puromycin for 1 day. 1 ug/ml dox was used to induce MATR3 depletion.
The DNA samples were part2cted with phenol chloroform


title: HiC_AML12_shMatr3_rep2


title: P120-Control 2


title: P60-Control 2

value: Control (P60)


title: P60-Control 3


title: P60-Control 4


title: F4R4Jan2018

value: VDJ-hCu


title: P60-Control 1


title: F4R7Jan2018


title: HiC_AML12_shCtrl_rep2

value: hepatocyte

value: no


title: F4R3Sept2017


title: HiC_AML12_shCtrl_rep1


title: F4R3Jan2018


title: F4R2Sept2017


title: P30-Control 4

value: Control (P30)


title: P30-Control 2


title: Patient 1 Slide C410 ROI 014

extract_protocol: Tissue sections were baked, deparaffinized, washed in PBS, and targets were retrieved for 20 minutes in 1x Tris-EDTA pH 9.0 buffer (Invitrogen #00-4956-58) at 100 °C. Next, tissues were washed in PBS, incubated in 0.1 μg/ml proteinase K (Thermo Fisher Scientific, #AM2546) in PBS for 15 minutes at 37 °C and washed again in PBS. Protein targets were post-fixed in 10% neutral-buffered formalin for 5 minutes, followed by two 5-minute incubations in 12.25 mg/ml Tris base, 7.5 mg/ml Glycine stop buffer diluted in DEPC-treated water. Tissues were incubated overnight at 37 °C with hybridization solution (Human Cancer Transcriptome Atlas probe mix (NanoString #121400101), Buffer R (NanoString #121300313), and DEPC-treated water). During incubation, slides were covered with HybriSlip hybridization covers (Grace BioLabs #714022). After incubation, HybriSlip covers were gently removed by soaking in 2x SSC buffer. Two 25 minute stringent washes were performed using 50% formamide in 2x SSC at 37 °C. Tissues were washed for 5 minutes in 2× SSC and incubated in blocking buffer W (NanoString #121300313) for 30 minutes at room temperature in a humidity chamber. Primary antibody targeted against MIL113 was diluted in buffer W and incubated with the tissues for 1 hour followed by a 1 hour incubation with fluorescently-labeled secondary antibody diluted in buffer W. After the slides were washed twice for 5 minutes in 5x SSC buffer they were incubated for 1 hour in SYTO13 (50 nM) and fluorescently conjugated antibody targeting PanCK in blocking  8  buffer. Following staining the sections were washed for 5 minutes in fresh 2x SSC. Following whole slide imaging, multiple geometric ROIs of 400 μm2 were placed in regions of subasumstat drug exposure according to MIL113 signal intensity and regions of vehicle or background. Indexing oligonucleotides were then cleaved and quantified via next gen sequencing on a NovaSeq 6000 Illumina sequencer as previously described(25)

value: Female

value: Oral cavity


title: Patient 1 Slide C410 ROI 015


title: ChIPseq_Input_AML12_Ctrl

data_processing:
ChIP-Seq reads were mapped to mouse genome (mm10) using Bowtie. Duplicate reads were excluded and kept only one read for each genomic site.
BedGraph files were normalized for total mapped read counts using genomecov from bedtools v2.29.2
To generate the ChIP-Seq signal distribution for interested regions, we calculated the average ChIP-Seq signal across these regions.


title: Patient 1 Slide C410 ROI 013


title: Patient 1 Slide C410 ROI 012

value: low


title: F4R2Jan2018


title: ChIPseq_Input_AML12_shMatr3_rep1

value: MATR3 Knock-down


title: ChIPseq_Input_AML12_shMatr3_rep2


title: 134-2-2D

city: Bath

first: William

last: Monteith

address: Claverton Down

country: United Kingdom

institute: University of Bath

data_processing:
Reads were mapped to a reference transcriptome index created using Salmon (version 1.9.0) against a genome reference F2365.
Gene expression was calculated in units of transcripts per million (TPM), a relative abundance measure used for downstream analysis.
DESeq2 in Bioconductor was used for differential expression analysis.
Hypothesis testing was applied using the Wald’s test across the negative binomial distribution. Differences in fold-change values were calculated by determining the log2 fold-change (LFC). A stringent cut-off of LFC <-2 and/or >2 was used to identify differentially expressed genes. An adjusted p-value was calculated for every gene with those p<0.05 being considered significant.
Assembly: F2365
Supplementary files format and content: comma-separated text file includes normalised abundance measurments for each Sample

organism: Listeria monocytogenes

source_name: Listeria monocytogenes

extract_protocol:
RNA was isolated using the SV RNA isolation kit (Promega). 23S and 16S rRNA was depleted using a MicrobExpress kit (Ambion) and genomic DNA digested using amplification-grade DNase I (Invitrogen). RNA was reverse-transcribed using random primers (Invitrogen) and Superscript III (Invitrogen) at 45 °C for 3 h and denatured at 70 °C for 15 min.
Nextera XT libraries were constructed and sequenced with over 30,000 reads per sample (min estimated coverage above x107).

value: Listeria monocytogenes

value: shaken 48 hours


title: 134-2-0h

value: shaken 0 hours


title: 134-2-1D

value: shaken 24 hours


title: 134-2-PC

value: stationary 24 hours


title: P30-Control 1

value: Male


title: ChIPseq_H3K27me3_AML12_shMatr3_rep2


title: F4R1Sept2017

value: spleen B cells

value: Day 0


title: 134-1-2D


title: 134-1-1D


title: ChIPseq_H3K27me3_AML12_shMatr3_rep1


title: P12-Control 5

value: Control (P12)


title: F4R1Jan2018

value: VDJ-hCu


title: 134-1-0h


title: P12-Control 4


title: 134-1-PC


title: ChIPseq_H3K27me3_AML12_Ctrl_rep2

value: hepatocyte


title: P12-Control 3


title: F3R8Sept2017

value: MmCu


title: P30-Control 3

value: Control (P30)


title: 132-2-PC


title: ChIPseq_H3K27me3_AML12_Ctrl_rep1

value: no


title: 132-2-2D


title: s4-mTSC-H4K20me3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 with default parameters
MACS2 was used to call the peaks of these antibodies binding using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: pileup peaks

source_name: TSC

growth_protocol: Advanced DMEM/F12 supplemented with: 64mg/l L-ascorbic acid-2-phosphate magnesium, 1% ITS-X supplement, 2mM L-glutamine, 0.5% B27, 0.05%BSA, 1% P/S, 25ng/ml FGF4, 2ng/ml TGF-β, 1μg/ml Heparin

extract_protocol:
ChIP was performed according to the reported previousl with slight modification. Briefly, about 2x106 TS cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified. The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150 using standard Illumina protocols

value: Mouse trophoblast stem cells

tag: chip antibody

value: Anti-Histone H4 (tri methyl K20), Abcam, catalog number:ab9053


title: F3R7Sept2017


title: 132-2-1D


title: wild type bacterium, rep 2

city: Wuerzburg

first: Martin

middle: J

last: Fraunholz

address: Theodor-Boveri-Weg

department: Chair of Microbiolgy

country: Germany

institute: University of Wuerzburg

description:
Sa_WT_10h_2
RAW_COUNT_TABLE_SA.csv

data_processing:
To assure high sequence quality, Illumina reads were quality and adapter-trimmed via Cutadapt v2.5
Reads were first filtered with FastQScreen and then subsequently mapped to the human and bacterial genomes
Differential Expression analysis with DESeq2 v1.24.0
Assembly: GRCh38.p13 for human and GCF_000013465.1_ASM1346v1 for bacteria
Supplementary files format and content: DESeq2_intracell_Mut_vs_RPMI_Mut_BACTERIA.xlsx - DESeq2 Comparison of S. aureus transcripts (brnQ1 mutant in infected macrophages vs growth in RPMI1640)
Supplementary files format and content: DESeq2_intracell_Mut_vs_intracell_WT_BACTERIA.xlsx - DESeq2 Comparison of S. aureus transcripts (brnQ1 mutant in infected macrophages vs JE2 WT in infected macrophages)
Supplementary files format and content: DESeq2_intracell_Mut_vs_intracell_WT_HUMAN.xlsx - DESeq2 Comparison of human transcripts (brnQ1 mutant in infected macrophages vs JE2 WT in infected macrophages)
Supplementary files format and content: DESeq2_intracell_WT_vs_RPMI_WT_BACTERIA.xlsx - DESeq2 Comparison of S. aureus transcripts (JE2 WT in infected macrophages vs growth in RPMI1640)

organism: Staphylococcus aureus

source_name: bacteria

extract_protocol:
RNAprotect Cell Reagent was added immediately to the infected samples. RNA of bacteria or infected macrophages was prepared using RNeasy Mini Kit (Qiagen).
DNA libraries suitable for sequencing were prepared using CORALL Total RNA-Seq Library Prep protocol according to manufacturer’s recommendation.
libraries were sequenced on an Illumina NextSeq platform (1*75 bp single-end run)

value: bacteria

value: wild type bacterium


title: 132-2-0h

value: Listeria monocytogenes


title: F3R5Sept2017


title: s1-mTSC-H4K20me1

value: Histone H4K20me1 antibody(Active motif),catalog number:#39727


title: P12-Control 2

extract_protocol: CA3 explants (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)


title: wild type bacterium, rep 1

description:
Sa_WT_10h_1
RAW_COUNT_TABLE_SA.csv


title: F3R4Sept2017


title: mTSC-H3K4me3-Dox24h

value: Anti-Histone H3 (tri methyl K4), Abcam, catalog number:ab8580


title: wild type bacterium, rep 3

description:
Sa_WT_10h_3
RAW_COUNT_TABLE_SA.csv


title: F4R4Sept2017


title: F3R3Sept2017


title: mTSC-H3K4me3-Con


title: 132-1-2D

value: shaken 48 hours


title: P12-Control 1

value: Male


title: 3-mTSC-H4K20me3


title: F3R2Sept2017

value: spleen B cells


title: bacterial brnQ1 mutant, rep 2

description:
Sa_Mut_10h_2
RAW_COUNT_TABLE_SA.csv

value: bacterial brnQ1 mutant


title: 132-1-1D

value: shaken 24 hours


title: 2-mTSC-H4K20me1


title: F3R1Sept2017

value: Day 0


title: 132-1-0h

value: shaken 0 hours


title: bacterial brnQ1 mutant, rep 1

description:
Sa_Mut_10h_1
RAW_COUNT_TABLE_SA.csv


title: F3R6Sept2017

value: MmCu


title: 132-1-PC

value: stationary 24 hours


title: PDO #46, Non-conditioned media, Fulvestrant, rep 2, batch1

status: Public on Jun 27 2023

city: Boston

first: Laura

last: Selfors

state: MA

address: 240 Longwood Avenue

institute: Harvard Medical School

data_processing:
Reads were aligned to the human genome using Star 2.7.0f. Differential expression was assessed using an additive model that included a ‘batch’ variable using edgeR v3.30.3.
Assembly: GRCh38
Supplementary files format and content: allData_tpm_human.txt includes TPM values for each Sample

source_name: breast

growth_protocol: PDOs were grown in BC organoid media or CAF-conditioned media

extract_protocol:
Cells were lysed in quanidine-isothiocyanate buffer and RNA was isolated using the RNeasy Fibrous Tissue Mini Kit according to manufacturer’s instructions. Prior to library preparation, the quality of RNA was assessed with Bioanalyzer (Agilent technologies).
mRNA libraries were generated by BGI and bulk RNA sequencing was performed using BGISEQ

treatment_protocol: For treated samples, 500 nM Fulvestrant was added to the growth media for 4 days.

value: breast

tag: cell line

value: PDO #46

value: patient derived organoid

tag: media

value: Control media

value: Fulvestrant


title: PDO #46, Conditioned-media, Fulvestrant, rep 2, batch1

tag: tissue

value: Cancer associated fibroblast conditioned medium

tag: treatment


title: PDO #46, Non-conditioned media, DMSO, rep 2, batch1

tag: cell type

value: DMSO control


title: PDO #46, Non-conditioned media, Fulvestrant, rep 1, batch1


title: PDO #46, Non-conditioned media, DMSO, rep 1, batch1


title: PDO #46, Conditioned-media, DMSO, rep 2, batch1


title: PDO #30, Non-conditioned media, Fulvestrant, rep 4, batch2

value: PDO #30


title: bacterial brnQ1 mutant, rep 3

description:
Sa_Mut_10h_3
RAW_COUNT_TABLE_SA.csv

value: bacteria

tag: genotype


title: PDO #46, Conditioned-media, DMSO, rep 1, batch1


title: PDO #30, Non-conditioned media, Fulvestrant, rep 3, batch2


title: PDO #30, Non-conditioned media, DMSO, rep 3, batch2


title: PDO #30, Non-conditioned media, Fulvestrant, rep 2, batch1


title: PDO #30, Non-conditioned media, DMSO, rep 4, batch2


title: PDO #30, Non-conditioned media, Fulvestrant, rep 1, batch1


title: PDO #30, Non-conditioned media, DMSO, rep 1, batch1


title: PDO #30, Conditioned-media, Fulvestrant, rep 3, batch2


title: PDO #30, Non-conditioned media, DMSO, rep 2, batch1


title: PDO #30, Conditioned-media, Fulvestrant, rep 1, batch1


title: PDO #30, Conditioned-media, Fulvestrant, rep 4, batch2


title: PDO #30, Conditioned-media, DMSO, rep 4, batch2


title: PDO #30, Conditioned-media, Fulvestrant, rep 2, batch1


title: PDO #30, Conditioned-media, DMSO, rep 1, batch1


title: PDO #30, Conditioned-media, DMSO, rep 2, batch1


title: PDO #46, Conditioned-media, Fulvestrant, rep 1, batch1


title: PDO #30, Conditioned-media, DMSO, rep 3, batch2


title: PDO #28, Non-conditioned media, Fulvestrant, rep 3, batch2

value: PDO #28


title: PDO #28, Non-conditioned media, Fulvestrant, rep 2, batch1


title: PDO #28, Non-conditioned media, Fulvestrant, rep 1, batch1


title: PDO #28, Non-conditioned media, DMSO, rep 3, batch2


title: PDO #28, Non-conditioned media, DMSO, rep 1, batch1


title: PDO #28, Conditioned-media, Fulvestrant, rep 4, batch2


title: PDO #28, Non-conditioned media, DMSO, rep 4, batch2


title: PDO #28, Non-conditioned media, Fulvestrant, rep 4, batch2


title: PDO #28, Conditioned-media, Fulvestrant, rep 1, batch1


title: PDO #28, Non-conditioned media, DMSO, rep 2, batch1


title: PDO #28, Conditioned-media, Fulvestrant, rep 3, batch2


title: PDO #28, Conditioned-media, DMSO, rep 3, batch2


title: 2907 cells, shCXCL81

city: Nanjing

first: Wei

last: Yuan

address: No. 101, Longmian Avenue, Jiangning District, Nanjing City, Jiangsu Province, China

institute: Nanjing Medical University

data_processing:
RNA sequencing was performed using BGISEQ-500 platforms. FASTQ sequencing reads were trimmed using Trim Galore (RRID:SCR_011847), and transcript quantification was performed using Salmon with the quasi-mapping mode
Assembly: hg38
Supplementary files format and content: core_table_gene.xls.gz include FPKM values for each Sample

source_name: glioblastoma

extract_protocol:
Total RNA was extracted with Trizol reagent (Takara) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: glioblastoma

value: glioma stem cells

value: CXCL8 knockdown


title: 839 cells, shCXCL81


title: 839 cells, shCXCL82


title: PDO #28, Conditioned-media, DMSO, rep 4, batch2


title: 839 cells, shControl2

value: WT


title: 2907 cells, shCXCL82


title: 839 cells, shControl1


title: PDO #28, Conditioned-media, Fulvestrant, rep 2, batch1


title: U29_1_mir

city: New York

first: Sofie

last: Delbare

address: 435 East 30th Street

institute: NYU Langone

data_processing:
We removed adapters using Cutadapt and kept reads with a length between 19 and 25 bp (Martin 2011).
Reads were aligned to dm6 using bowtie2 (Langmead and Salzberg 2012)
FeatureCounts (Liao, Smyth, and Shi 2014) was used to obtain counts for annotated microRNAs.
Assembly: dm6
Supplementary files format and content: The processed data file contains raw read counts for each sample (output from featureCounts).

organism: Drosophila melanogaster

source_name: female reproductive tract, unmated, 29C, biol rep 1

growth_protocol: D. melanogaster stocks were maintained at 21 or 29C on yeast/glucose food in a 12 hour light/dark cycle.

extract_protocol:
RNA was extracted from on average 64 female reproductive tracts per sample. For males, RNA was extracted from 3 whole males. RNA was extracted using the Direct-zol RNA microprep kit according to the manufacturer's instructions (Zymo, CA)
To sequence small RNAs, we used the NEBnext Small RNA library prep (New England Biolabs, MA), starting from 1 ug of total RNA (we used RNA from the same samples that were also used for long RNA-seq; small RNA-seq was not done for male samples). We adjusted the NEB protocol at particular steps: 1) We ran the 3’ ligation reaction overnight at 16°C to improve detection of any piRNAs that could be present in our samples. 2) We modified the protocol to remove abundant small rRNAs. To remove eight abundant small rRNA fragments, we used blocking oligos designed by (Fowler et al. 2019). We incorporated these in the library preparation using a slightly modified method from (Wickersheim and Blumenstiel 2013). Specifically, we added 1 ul of an oligo cocktail (each oligo at a concentration of 10 uM) to the 3’ ligation reaction. We incubated this reaction for 2 minutes at 70°C and for 5 minutes at 60°C, before proceeding to the reverse transcriptase primer hybridization step. We purified the resulting libraries using the Monarch PCR & DNA cleanup kit (New England Biolabs, MA) and size selected using Pippin Prep (Sage Science, MA), selecting fragments of 120-250 bp.

treatment_protocol: Females either remained virgin or were collected 10-15 after mating with a wildtype control male (w1118 or esgts F/O w1118), or Dad male (esgts F/O UAS-Dad). Reproductive tracts of females were dissected in 1X PBS. The digestive system and the upper part of the common ovidcut were removed.

value: female reproductive tract

tag: Sex

value: female

value: unmated

tag: time

value: collected in parallel with mated samples

tag: temperature


title: PDO #28, Conditioned-media, DMSO, rep 1, batch1

value: breast


title: U29_2_mir

source_name: female reproductive tract, unmated, 29C, biol rep 2


title: U29_3_mir

source_name: female reproductive tract, unmated, 29C, biol rep 3


title: U21_1_mir

source_name: female reproductive tract, unmated, 21C, biol rep 1


title: U21_2_mir

source_name: female reproductive tract, unmated, 21C, biol rep 2


title: MW21_3_mir

source_name: female reproductive tract, mated to w1118 male, 21C, biol rep 3

value: mated to w1118 male

value: 10-15 min post-mating


title: 2907 cells, shControl1


title: U21_3_mir

source_name: female reproductive tract, unmated, 21C, biol rep 3


title: MW21_2_mir

source_name: female reproductive tract, mated to w1118 male, 21C, biol rep 2


title: 2907 cells, shControl2


title: PDO #28, Conditioned-media, DMSO, rep 2, batch1

value: patient derived organoid


title: MW21_1_mir

source_name: female reproductive tract, mated to w1118 male, 21C, biol rep 1


title: MC29_3_mir

source_name: female reproductive tract, mated to control male, 29C, biol rep 3

value: mated to control male


title: MC29_2_mir

source_name: female reproductive tract, mated to control male, 29C, biol rep 2


title: D29_2

data_processing:
We used Trimmomatic to remove overrepresented sequences and to filter reads (Bolger, Lohse, and Usadel 2014). Specifically, bases at the end of a read with a Phred quality score less than 20 were clipped off. The read was also clipped once, in a window of 5 bases, the average read quality dropped below a Phred score of 20. After trimming, we kept only reads with a minimum length of 30 bases.
Reads were aligned to dm6 using STAR (Dobin et al. 2013).
Read counts were obtained using HTSeq (Anders, Pyl, and Huber 2015).
Assembly: dm6
Supplementary files format and content: The processed data files contains raw read counts for each sample (output from HTSeq).

source_name: whole Dad male, 29C, biol rep 2

extract_protocol:
RNA was extracted from on average 64 female reproductive tracts per sample. For males, RNA was extracted from 3 whole males. RNA was extracted using the Direct-zol RNA microprep kit according to the manufacturer's instructions (Zymo, CA)
To sequence mRNAs and non-polyadenylated long noncoding RNAs, we used the Ovation Universal Drosophila RNA-Seq Kit, which allows for the depletion of abundant ribosomal RNAs (Tecan, CA). We prepared the libraries according to the manufacturer’s instructions (Tecan, CA). For the optional fragmentation step in the protocol, we fragmented cDNA using Covaris to obtain a fragment size of 400 bases.

value: whole male

value: male

value: esgts F/O UAS-Dad


title: MD29_3_mir

source_name: female reproductive tract, mated to Dad male, 29C, biol rep 3

value: mated to Dad male


title: C29_1

source_name: whole control male, 29C, biol rep 1

value: esgts F/O w1118


title: MD29_1_mir

source_name: female reproductive tract, mated to Dad male, 29C, biol rep 1


title: MD29_2_mir

source_name: female reproductive tract, mated to Dad male, 29C, biol rep 2


title: D29_3

source_name: whole Dad male, 29C, biol rep 3


title: C29_2

source_name: whole control male, 29C, biol rep 2


title: U21_2


title: U21_3


title: U21_1


title: U29_3


title: MD29_3


title: MW21_3


title: MC29_3


title: MW21_2


title: U29_2

source_name: female reproductive tract, unmated, 29C, biol rep 2


title: MC29_2


title: MW21_1


title: MD29_1


title: MD29_2


title: MC29_1

source_name: female reproductive tract, mated to control male, 29C, biol rep 1


title: MC29_1_mir


title: C29_3

source_name: whole control male, 29C, biol rep 3


title: D29_1

source_name: whole Dad male, 29C, biol rep 1


title: RNA-Seq of mesocarp tissues from tomato fruits developed without light: 5 days after to be exposed to light, rep. 3

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

institute: UFRJ

description:
Mesocarp-5-days-Rep-3
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Mesocarp tissue was collected 5 days after light exposure.

data_processing:
The cleaning step was performed with Trimmomatic v.0.39
Read mapping step was performed against the genome using the software Star.
Mapped reads were counted using featureCounts.
Genes with low expression values (<1) were removed from differential expression analysis.
Differential expression analysis was performed using DESeq2 (FDR<0.05).
Assembly: ITAG4.1
Supplementary files format and content: Tab-delimited text file includes raw counts for each library
Supplementary files format and content: Tab-delimited text file includes TPM values for each library

organism: Solanum lycopersicum

source_name: Mesocarp

growth_protocol: Individual flowers were covered with aluminum foil at anthesis and kept for 30 days, aiming at fruit development in a complete absence of light. Subsequently, the developed fruits were exposed to light and collected at different times: immediately (0d), 2 days (2d), and 5 days (5d) after the cover was removed.

extract_protocol:
Total RNA was extracted from the epicarp and mesocarp separately using the mirVana miRNA isolation kit (Ambion, ThermoFisher) according to the manufacturer's instructions for total RNA extraction.
Library preparation and Illumina sequencing were performed at Novogene (Sacramento, CA, USA). Twenty-four cDNA libraries were prepared and then sequenced on an Illumina Novaseq 6000, with a configuration of 150-bp paired-end.

value: Mesocarp

value: fruit


title: RNA-Seq of mesocarp tissues from tomato fruits developed without light: 5 days after to be exposed to light, rep. 1

description:
Mesocarp-5-days-Rep-1
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Mesocarp tissue was collected 5 days after light exposure.


title: RNA-Seq of mesocarp tissues from tomato fruits developed without light: 5 days after to be exposed to light, rep. 2

description:
Mesocarp-5-days-Rep-2
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Mesocarp tissue was collected 5 days after light exposure.


title: RNA-Seq of mesocarp tissues from tomato fruits developed with light: control, rep. 1

description:
Mesocarp-Control-Rep-1
Tomato fruits were developed with light exposure for 30 days. Mesocarp tissue was collected and used as a control.


title: RNA-Seq of epicarp tissues from tomato fruits developed without light: 0 day after to be exposed to light, rep. 1

description:
Epicarp-0-day-Rep-1
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Epicarp tissue was collected 0 days after light exposure.

source_name: Epicarp

value: Epicarp


title: RNA-Seq of epicarp tissues from tomato fruits developed without light: 5 days after to be exposed to light, rep. 1

description:
Epicarp-5-days-Rep-1
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Epicarp tissue was collected 5 days after light exposure.


title: RNA-Seq of epicarp tissues from tomato fruits developed without light: 5 days after to be exposed to light, rep. 3

description:
Epicarp-5-days-Rep-3
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Epicarp tissue was collected 5 days after light exposure.


title: RNA-Seq of mesocarp tissues from tomato fruits developed without light: 0 day after to be exposed to light, rep. 1

description:
Mesocarp-0-day-Rep-1
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Mesocarp tissue was collected 0 days after light exposure.


title: RNA-Seq of mesocarp tissues from tomato fruits developed without light: 2 days after to be exposed to light, rep. 3

description:
Mesocarp-2-days-Rep-3
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Mesocarp tissue was collected 2 days after light exposure.


title: RNA-Seq of epicarp tissues from tomato fruits developed without light: 2 days after to be exposed to light, rep. 2

description:
Epicarp-2-days-Rep-2
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Epicarp tissue was collected 2 days after light exposure.


title: U29_1

source_name: female reproductive tract, unmated, 29C, biol rep 1

value: female reproductive tract


title: RNA-Seq of epicarp tissues from tomato fruits developed with light: control, rep. 1

description:
Epicarp-Control-Rep-1
Tomato fruits were developed with light exposure for 30 days. Epicarp tissue was collected and used as a control.


title: RNA-Seq of epicarp tissues from tomato fruits developed without light: 0 day after to be exposed to light, rep. 2

description:
Epicarp-0-day-Rep-2
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Epicarp tissue was collected 0 days after light exposure.


title: RNA-Seq of mesocarp tissues from tomato fruits developed without light: 0 day after to be exposed to light, rep. 3

description:
Mesocarp-0-day-Rep-3
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Mesocarp tissue was collected 0 days after light exposure.


title: RNA-Seq of mesocarp tissues from tomato fruits developed without light: 0 day after to be exposed to light, rep. 2

description:
Mesocarp-0-day-Rep-2
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Mesocarp tissue was collected 0 days after light exposure.


title: RNA-Seq of epicarp tissues from tomato fruits developed with light: control, rep. 3

description:
Epicarp-Control-Rep-3
Tomato fruits were developed with light exposure for 30 days. Epicarp tissue was collected and used as a control.


title: RNA-Seq of epicarp tissues from tomato fruits developed without light: 2 days after to be exposed to light, rep. 3

description:
Epicarp-2-days-Rep-3
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Epicarp tissue was collected 2 days after light exposure.


title: RNA-Seq of epicarp tissues from tomato fruits developed without light: 0 day after to be exposed to light, rep. 3

description:
Epicarp-0-day-Rep-3
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Epicarp tissue was collected 0 days after light exposure.


title: RNA-Seq of mesocarp tissues from tomato fruits developed with light: control, rep. 2

description:
Mesocarp-Control-Rep-2
Tomato fruits were developed with light exposure for 30 days. Mesocarp tissue was collected and used as a control.


title: RNA-Seq of mesocarp tissues from tomato fruits developed with light: control, rep. 3

description:
Mesocarp-Control-Rep-3
Tomato fruits were developed with light exposure for 30 days. Mesocarp tissue was collected and used as a control.


title: RNA-Seq of epicarp tissues from tomato fruits developed without light: 2 days after to be exposed to light, rep. 1

description:
Epicarp-2-days-Rep-1
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Epicarp tissue was collected 2 days after light exposure.


title: RNA-Seq of epicarp tissues from tomato fruits developed with light: control, rep. 2

description:
Epicarp-Control-Rep-2
Tomato fruits were developed with light exposure for 30 days. Epicarp tissue was collected and used as a control.


title: RNA-Seq of mesocarp tissues from tomato fruits developed without light: 2 days after to be exposed to light, rep. 2

description:
Mesocarp-2-days-Rep-2
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Mesocarp tissue was collected 2 days after light exposure.


title: RNA-Seq of epicarp tissues from tomato fruits developed without light: 5 days after to be exposed to light, rep. 2

description:
Epicarp-5-days-Rep-2
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Epicarp tissue was collected 5 days after light exposure.


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-43

city: Seattle

first: John

middle: Kenneth

last: Mich

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

library_source: transcriptomic single cell

data_processing:
Base-calling using standard Illumina software.
Alignment with STAR (https://github.com/alexdobin/STAR)
Transformed by counts per million.
Assembly: mm10
Supplementary files format and content: Processed data in counts per million (CPM) format.

source_name: VISp

extract_protocol:
Single SYFP2-expressing cells from mouse brain were flow sorted into individual tubes in SMARTerv4 collection buffer.
SMARTerv4

value: VISp


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-42


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-44


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-46


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-47


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-45


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-39


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-41


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-38


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-36


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-35


title: RNA-Seq of mesocarp tissues from tomato fruits developed without light: 2 days after to be exposed to light, rep. 1

description:
Mesocarp-2-days-Rep-1
Tomato fruits were developed in the dark for 30 days, and were then exposed to light. Mesocarp tissue was collected 2 days after light exposure.


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-37


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-31


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-29


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-34


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-30


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-33


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-26


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-27


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-25


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-24


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-21


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-20


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-40


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-32


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-48


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-14


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-17


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-18


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-12


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-8


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-19


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-15


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-11


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-10


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-9


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-7


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-2


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-42


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-5


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-23


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-4


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-6


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-22


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-16


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-3


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-1


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-40


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-43


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-13


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-38


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-37


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-34


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-35


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-36


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-41


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-31


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-29


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-33


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-30


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-26


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-23


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-32


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-27


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-20


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-24


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-28


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-18


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-25


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-16


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-21


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-22


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-39


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-17


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-14


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-15


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-12


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-11


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-10


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-9


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-8


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-7


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-4


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-5


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-6


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-19


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-13


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-3


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-1


title: BrainCell_Enhancer-eHGT_140h_MouseID-473543_Cell-2


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-45


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-38


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-34


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-43


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-41


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-40


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-39


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-42


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-32


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-33


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-35


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-37


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-31


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-30


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-29


title: BrainCell_Enhancer-eHGT_140h_MouseID-505190_Cell-28


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-28


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-26


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-46


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-36


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-27


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-44


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-23


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-24


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-25


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-21


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-22


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-19


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-18


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-12


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-20


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-17


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-10


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-7


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-16


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-14


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-15


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-8


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-13


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-6


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-4


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-2


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-3


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-11


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-5


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-9


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-47


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-42


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-46


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-45


title: BrainCell_Enhancer-eHGT_140h_MouseID-460763_Cell-1


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-40


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-44


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-38


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-39


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-43


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-41


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-36


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-35


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-32


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-30


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-34


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-31


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-33


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-28


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-27


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-26


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-25


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-24


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-22


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-21


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-19


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-20


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-17


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-40


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-18


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-33


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-38


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-35


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-39


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-36


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-34


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-29


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-32


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-30


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-29


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-28


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-24


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-31


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-25


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-27


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-16


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-26


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-37


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-12


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-23


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-15


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-13


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-11


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-10


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-9


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-37


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-7


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-6


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-8


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-4


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-3


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-5


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-2


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-23


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-22


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-21


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-1


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-20


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-19


title: BrainCell_Enhancer-eHGT_082h_MouseID-475242_Cell-14


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-8


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-12


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-11


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-17


title: BrainCell_Enhancer-eHGT_082h_MouseID-473545_Cell-10