title: EE_SNA rep2

value: 10 days  Environmental Enrichment  plus SNA


title: IMS-M2-FA_OTX_1

status: Public on Oct 12 2020

type: SRA

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
reads were aligned using Tophat v2.1.1
differential expression was assessed using Cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated file containing FPKM values of each genes of the hg19 UCSC reference annotation

molecule: polyA RNA

organism: Homo sapiens

source_name: IMS-M2 cells cultured without FA treated with OTX

extract_protocol:
Total RNA was extracted using Qiagen RNAEasy plus mini kit
Stranded RNA-seq libraries done with barcoded TruSeq Stranded mRNA LT Sample Prep Kit

tag: cell line

tag: tissue

value: hematopoietic cells

tag: disease state

value: AML


title: EE_Sham rep2

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

country: USA

institute: University of Miami

data_processing:
Sequence reads were aligned to the mm10 mouse reference genome sequence using tophat version 2.0.12 running Bowtie2-2.2.3.
Gene structure annotations corresponding to the Ensembl annotation of the mm10 genome sequence were used to build a transcriptome index and provided to tophat during the alignment step
The aligned reads were sorted using samtools-0.1.19, then read counts per gene were obtained from mapped reads using HTSeq-0.6.0
EdgeR version 3.8.6 (using limma-3.22.7) in R-3.1.1 was used to identify differentially expressed genes.
Read-level quality checking was performed using fastqc-0.10.1 and the fastqc-aggregator (https://github.com/staciaw/fastqc_aggregator) and gene-level quality checking was performed using RSeQC-2.6.1 (Wang et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file of sequencing read counts per gene
Supplementary_files_format_and_content: tab-delimited txt file represents the normalized expression data as FPKM, produced by EdgeR

molecule: total RNA

organism: Mus musculus

source_name: sciatic L4-L6 dorsal root ganglion

extract_protocol:
For whole DRG, RNA was extracted using RNeasy kit (Qiagen), according to manufacturer’s guidelines. Residual DNA contamination was removed by treating the spin column with 40 units of RNase-free DNase I (Qiagen) for 15 min at room temperature prior to RNA elution. RNA concentrations and purity were verified for each sample following elution with Agilent 2100 Bioanalyzer (Agilent). RNA with RIN factor above 7.5 was used for library preparation.
Libraries were generated using the TruSeq mRNA Sample Preparation Kit  (Illumina, San Diego CA) at Ospedale San Raffaele according to the Sample Preparation Guide protocol. Ligation and library integrity was verified using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer (Agilent). Sample libraries ligated with unique adapter sequences were multiplexed and were sequenced using Illumina HiSeq 2500 100-cycle, pair end sequencing.

treatment_protocol: Mice (5-8 weeks old)  were housed for 10 days in EE vs SH and underwent either sciatic nerve axotomy or sham injury

value: sciatic L4-L6 dorsal root ganglion

tag: strain

tag: treatment

value: 10 days Environmental Enrichment plus Sham

tag: age

value: 5-8 weeks old


title: EE_SNA rep3


title: PR403_22_3

city: Nanning

first: Jijing

last: Luo

state: Guangxi

address: 100 Daxue Rd.(East)

country: China

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, 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.
Genome_build: MSU RGAP release 7.0
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Oryza sativa

source_name: Drought treated seedlings

growth_protocol: The seedlings were grew under normal condition in green house for 21 days

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
cDNA library

treatment_protocol: 21-day old seedlings were drought-treated to soil moisture of 20%.

value: penultimate leaves

value: 21 days

tag: line

tag: phenotype

value: Drought tolerant

tag: stress

value: Drought treated


title: SH_SNA rep2

value: 10 days Standard Housing plus SNA


title: PR403_22_2


title: VU10_Duo_R3

city: Nashville

first: E Michelle

last: Southard-Smith

state: TN

address: 2215 Garland Ave,

department: Medicine, Genetic Medicine

institute: Vanderbilt University Medical Center

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software
RNA-Seq reads were then aligned to their respective Ensembl release 76 human or mouse top-level assemblies with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned, unambiguous reads by Subread:featureCount version 1.4.5
Isoform expression of known Ensembl transcripts were estimated with Sailfish version 0.6.13.
Sequencing performance was then assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.3.
Genome_build: Ensembl release 76 human assembly
Supplementary_files_format_and_content: counts matrix

source_name: Duodenum

extract_protocol:
Total RNA was extracted using the RNeasy Micro® kit (Ambion) as described in May-Zhang et al. Jove 2018. Briefly, 1-3 Arcturus XT laser capture caps were pooled for each sample after collecting sufficient quantities of enteric ganglia. Lysates were incubated at 26C for 30 min in 250uL of Buffer RLT with repeated brief vortexing. Lysates were frozen at -80C and stored for up to 2 months before isolating RNA.
cDNA libraries were prepared using the Takara SMARTer kit according to llumina's instructions. Libraries were sequenced using the NovaSeq as 1x100bp single-end reads. Each sample had a mean depth of approximately 138 million reads and a mean alignment rate of 99.01%.

tag: Sex

value: Male

tag: race

value: Black/African American

tag: sequencer


title: VU10_Duo_R2


title: IMS-M2-FA_DMSO_2

source_name: IMS-M2 cells cultured without FA treated with DMSO


title: IMS-M2-FA_DMSO_3


title: SH_Sham rep2

value: 10 days Standard Housing plus Sham


title: PR403_22_1


title: IMS-M2-FA_DMSO_1


title: VU10_Duo_R1


title: PY6_CK40_3

source_name: Untreated seedlings

value: Drought sensitive

value: Untreated


title: VU10_Col_R3

source_name: Colon


title: EE_SNA rep1


title: EE_Sham rep1


title: PY6_CK40_2


title: VU10_Col_R2b


title: IMS-M2+FA_OTX_3

source_name: IMS-M2 cells cultured with FA treated with OTX


title: IMS-M2+FA_OTX_1


title: SH_Sham rep1


title: IMS-M2+FA_OTX_2


title: VU10_Col_R1


title: PR403_CK40_3


title: VU1_Col_R4

value: Female

value: Caucasian


title: IMS-M2+FA_DMSO_3

source_name: IMS-M2 cells cultured with FA treated with DMSO

value: hematopoietic cells


title: C3H10T1/2, H3.3WT_H3K4me1 (ChIP-seq)

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

description: Immunoprecipitated DNA

library_source: genomic

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
Data was normalized using RPKM (1000000/aligned reads) or RX (1000000/reads aligned to drosophila genome)
Deeptools was used to generate bigwig files for visuallization
mosaics was used to identify enriched regions of the genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig, bed (peaks)

molecule: genomic DNA

source_name: mMSC C3H10T1/2

growth_protocol: Cells were grown in Dulbecco's modified Eagle's medium with 10% FBS

extract_protocol:
Cells were crosslinked with 1% PFA for 5 min. Lysed in (15 mM Tris, 1 mM CaCl2, 0.25% TritonX-100), treated with MNase to genrate mono-nucleosomes and sonicated using covaris (PIP 140, DF 5%, CPB 200 for 45 sec for 3 times). Chromatin was dialyzed against RIPA buffer (10mM Tris, 1% TritonX-100, 0.1% SDS, 0.1% Na-DOC) and supernatant was incubated with antibody overnight. Antibody was caputred using dynabeads for 3 hours. IPed material was eluted by boiling the beads in 1% SDS buffer at 65 degree C, after washing 5 times.
Libraries were constructed according to NEB Next Ultra protocol

treatment_protocol: Lentivurses for stable expression of H3.3WT or H3.3G34W were transduced in the cells.

tag: genotype

value: cells overexpressing H3.3WT

tag: chip antibody

value: H3K4me1 (Abcam, pAb Cat# ab8895)


title: VU1_Col_R3


title: IMS-M2+FA_DMSO_2

value: AML


title: PR403_CK40_2


title: IMS-M2+FA_DMSO_1


title: C3H10T1/2, H3.3G34W_H3K27ac (ChIP-seq)

description: Immunoprecipitated DNA

value: cells overexpressing H3.3G34W

value: H3K27ac (Active Motif; pAb Cat# 39133)


title: PR403_CK40_1

value: penultimate leaves

value: 21 days


title: VU1_Col_R2


title: C3H10T1/2, H3.3WT_H3K27ac (ChIP-seq)

description: Immunoprecipitated DNA


title: Miz1fl/fl AlbCre Positive 3

status: Public on Oct 11 2020

city: Shanghai

first: Guangyan

last: Zhangyuan

state: Shanghai

address: 197 Ruijin Er Road

department: Department of General Surgery, Pancreatic Disease Center

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: processed data file: Miz1.xls

data_processing:
Basecalls performed using bcl2fastq2 version 2.19.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic v0.36, then mapped to mm10 whole genome using bowtie2 v2.2.6。
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using RSEM v1.1.17
Differential expression genes were calculated using edgeR v3.18.1 and DESeq2 v1.16.1
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

source_name: Liver cancer

growth_protocol: SPF (specific pathogen free)

extract_protocol:
Pure liver tumors were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice HCC was induced by the combination of DEN (25 mg/kg i.p.) given at Week 2 postpartum followed by weekly injections of CCl4 (0.5 ml/kg i.p., dissolved in corn oil)

value: Liver

value: HCC


title: Miz1fl/fl AlbCre Positive 2

description: processed data file: Miz1.xls


title: Miz1fl/fl AlbCre negative 3

description: processed data file: Miz1.xls


title: SH_SNA rep1

value: sciatic L4-L6 dorsal root ganglion

value: 10 days Standard Housing plus SNA

value: 5-8 weeks old


title: Miz1fl/fl AlbCre negative 1

description: processed data file: Miz1.xls


title: PY6_CK40_1

value: Drought sensitive


title: Miz1fl/fl AlbCre negative 2

description: processed data file: Miz1.xls


title: Miz1fl/fl AlbCre Positive 1

description: processed data file: Miz1.xls


title: SAT_HC_HF_C116_V2_3

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: subcutaneous adipose tissue, HC/HF diet, time point 3

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Adipose tissue samples were taken at the level of the umbilicus by the needle aspiration.

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: 15 non-diabetic non-obese men participated in the cross-over study. We compared effects of two 4-week isocaloric diets – (1) HC/HF diet consisted of a carbohydrate-rich breakfast and lunch (65 EN% carbohydrates, 20 EN% fat, 15 EN% protein) and a fat-rich snack and dinner (35 EN% carbohydrates, 50 EN% fat, 15 EN% protein) and (2) HF/HC diet consisted of a fat-rich breakfast and lunch and a carbohydrate-rich snack and dinner, with a 4-week washout phase between intervention periods. At the end of each intervention period, subcutaneous adipose tissue biopsies (300-400mg) were collected three times during the investigation day (at 8.40, 12.20 and 19.00) at the level of the umbilicus by the needle aspiration. Samples were shock-frozen in liquid nitrogen and stored at -80°C until the RNA extraction.

tag: patient no

tag: gender

value: male

tag: diet

tag: time point

value: SAT


title: SAT_HC_HF_C116_V2_2

description: subcutaneous adipose tissue, HC/HF diet, time point 2

tag: tissue


title: SAT_HF_HC_C119_V4_3

description: subcutaneous adipose tissue, HF/HC diet, time point 3


title: SAT_HC_HF_C119_V2_3

source_name: subcutaneous adipose tissue, HC/HF diet, time point 3


title: SAT_HC_HF_C118_V2_1

description: subcutaneous adipose tissue, HC/HF diet, time point 1


title: SAT_HC_HF_C115_V4_3


title: SAT_HC_HF_C115_V4_2

source_name: subcutaneous adipose tissue, HC/HF diet, time point 2


title: SAT_HC_HF_C115_V4_1

source_name: subcutaneous adipose tissue, HC/HF diet, time point 1


title: SAT_HC_HF_C118_V2_2


title: SAT_HF_HC_C119_V4_1

description: subcutaneous adipose tissue, HF/HC diet, time point 1


title: SAT_HF_HC_C118_V4_1

source_name: subcutaneous adipose tissue, HF/HC diet, time point 1


title: SAT_HC_HF_C116_V2_1


title: SAT_HC_HF_C114_V4_3


title: SAT_HC_HF_C118_V2_3


title: SAT_HC_HF_C119_V2_2


title: SAT_HF_HC_C118_V4_3

source_name: subcutaneous adipose tissue, HF/HC diet, time point 3


title: SAT_HC_HF_C119_V2_1


title: SAT_HF_HC_C116_V4_3


title: SAT_HF_HC_C118_V4_2

description: subcutaneous adipose tissue, HF/HC diet, time point 2


title: SAT_HF_HC_C119_V4_2

source_name: subcutaneous adipose tissue, HF/HC diet, time point 2


title: SAT_HF_HC_C116_V4_1


title: SAT_HF_HC_C115_V2_2


title: SAT_HF_HC_C116_V4_2


title: SAT_HF_HC_C115_V2_3


title: SAT_HF_HC_C114_V2_2


title: SAT_HF_HC_C115_V2_1


title: SAT_HC_HF_C114_V4_1


title: SAT_HF_HC_C114_V2_1


title: SAT_HF_HC_C114_V2_3


title: SAT_HF_HC_C113_V4_3


title: SAT_HF_HC_C113_V4_2


title: SAT_HF_HC_C111_V4_2


title: SAT_HC_HF_C114_V4_2


title: SAT_HF_HC_C113_V4_1


title: SAT_HC_HF_C112_V4_2


title: SAT_HC_HF_C112_V4_1


title: SAT_HC_HF_C112_V4_3


title: SAT_HF_HC_C112_V2_2


title: SAT_HF_HC_C112_V2_1


title: SAT_HF_HC_C111_V4_3


title: SAT_HC_HF_C113_V2_1


title: SAT_HC_HF_C113_V2_2


title: SAT_HF_HC_C112_V2_3


title: SAT_HC_HF_C113_V2_3


title: SAT_HC_HF_C111_V2_1


title: SAT_HC_HF_C111_V2_3


title: SAT_HC_HF_C111_V2_2


title: SAT_HC_HF_C110_V4_3


title: SAT_HF_HC_C108_V4_3


title: SAT_HF_HC_C110_V2_2


title: SAT_HF_HC_C110_V2_1


title: SAT_HF_HC_C108_V4_2


title: SAT_HF_HC_C111_V4_1


title: SAT_HC_HF_C110_V4_2


title: SAT_HC_HF_C108_V2_2


title: SAT_HF_HC_C108_V4_1


title: SAT_HF_HC_C110_V2_3


title: SAT_HC_HF_C110_V4_1


title: SAT_HC_HF_C108_V2_1


title: SAT_HC_HF_C108_V2_3


title: SAT_HC_HF_C107_V4_3


title: SAT_HF_HC_C107_V2_3


title: SAT_HC_HF_C107_V4_1


title: SAT_HC_HF_C107_V4_2


title: SAT_HC_HF_C104_V4_ZP3


title: SAT_HF_HC_C107_V2_1


title: SAT_HC_HF_C105_V2_ZP3


title: SAT_HF_HC_C104_V2_ZP2


title: SAT_HC_HF_C105_V2_ZP2


title: SAT_HF_HC_C105_V4_ZP2


title: SAT_HC_HF_C104_V4_ZP1


title: SAT_HC_HF_C104_V4_ZP2


title: SAT_HF_HC_C107_V2_2


title: SAT_HF_HC_C104_V2_ZP3


title: SAT_HC_HF_C105_V2_ZP1


title: SAT_HF_HC_C105_V4_ZP1


title: SAT_HF_HC_C104_V2_ZP1


title: SAT_HF_HC_C105_V4_ZP3


title: C57BL/6 WT soleus 5 months 10X snRNA-seq

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: Muscles combined from 4 mice

data_processing:
Raw sequencing data of all samples were processed using the cellRanger workflow (version 3.1.0), using a combined intron-exon reference produced as described using the vendor-provided “Generating a Cell Ranger compatible "pre-mRNA" Reference Package” guidelines (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references). In brief, the “pre-mRNA” reference was derived using the default exon-level GTF file provided by 10x Genomics ( http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-mm10-3.0.0.tar.gz). Using the below awk command, this exon-level GTF file into “pre-MRNA” GTF containing intron transcript definitions). Next, the below mkref command was run to produce the final “pre-MRNA” GTF and genome fasta file ($ cellranger mkref --genome=Mmpre --fasta=genome.fa --genes=genes.premrna.gtf). For each dataset, we corrected for ambient background RNA by filtering with the R package SoupX (version 0.3.0), using the inferNonExpressedGenes() function to determine which genes had the highest probability of being ambient mRNA, and the strainCells() function in order to transform count matrices.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5

source_name: Soleus muscle

extract_protocol:
Nuclei were isolated from skeletal muscle immediately following euthanasia. Muscle was homogenized and then filtered, and nuclei were purified from the homogenate by staining with Hoechst dye and then FACS sorting for DAPI+ nuclei.
Isolated nuclei were loaded into the 10X Chromium system (targeting ~12,000-13,000 loading count) using the Single Cell 3’ Reagent Kit v3, and libraries were constructed according to the manufacturer’s protocol.

value: Whole skeletal muscle

value: Wild-type

value: 5 months

tag: sequencing parameters

value: 356 million reads


title: C57BL/6 WT tibialis anterior postnatal day 21 10X snRNA-seq

description: Muscles combined from 2 mouse pups

source_name: Tibialis anterior muscle

tag: strain

value: day 21

value: 433 million reads


title: SAT_HF_HC_C102_V4_ZP3


title: C57BL/6 WT tibialis anterior postnatal day 10 10X snRNA-seq

description: Muscles combined from 4 mouse pups

value: day 10

value: 1,013 million reads


title: C57BL/6 WT tibialis anterior 30 months 10X snRNA-seq

value: 30 months

value: 474 million reads


title: C57BL/6 WT tibialis anterior 5 months 10X snRNA-seq

value: 419 million reads


title: WT tibialis anterior 24 months 10X snRNA-seq

value: 24 months

value: 434 million reads


title: SAT_HC_HF_C102_V2_ZP2


title: SAT_HC_HF_C101_V4_ZP3


title: SAT_HC_HF_C102_V2_ZP1


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H8_ad006

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACA,PL,ILA


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H9_ad002

tag: age


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H8_ad001


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H9_ad004


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H9_ad007


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H8_ad010


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H9_ad010


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H9_ad006


title: SAT_HF_HC_C101_V2_ZP3


title: SAT_HC_HF_C101_V4_ZP2


title: SAT_HF_HC_C102_V4_ZP2


title: SAT_HF_HC_C102_V4_ZP1


title: SAT_HC_HF_C102_V2_ZP3


title: SAT_HC_HF_C101_V4_ZP1


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H8_ad002


title: SAT_HF_HC_C101_V2_ZP1


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H8_ad008


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H9_ad001


title: SAT_HF_HC_C101_V2_ZP2


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H7_ad001


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H7_ad012


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H7_ad007


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H7_ad010


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H7_ad004


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H8_ad012


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H7_ad006


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H6_ad001


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H6_ad010


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H7_ad002


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H6_ad002


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H5_ad001


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H6_ad006


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H6_ad004


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H6_ad008


title: CEMBA190307_5A_3_CEMBA190307_5A_4_H6_ad007


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title: CEMBA190307_5A_1_CEMBA190307_5A_2_F11_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F12_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F11_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F12_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F11_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F11_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F11_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F11_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F10_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F10_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F10_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F10_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F10_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F1_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F1_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F1_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F1_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F1_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F1_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F1_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F1_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E9_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E9_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E9_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E9_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E9_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E8_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E9_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E9_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E9_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E8_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F11_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E8_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E8_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E8_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_F10_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E8_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E7_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E7_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E7_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E7_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E8_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E7_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E6_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E7_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E6_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E6_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E6_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E8_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E5_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E6_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E6_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E5_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E4_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E5_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E5_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E4_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E6_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E5_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E6_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E5_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E4_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E4_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E3_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E4_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E7_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E4_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E3_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E3_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E2_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E2_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E2_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E2_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E12_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E2_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E3_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E12_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E12_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E12_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E12_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E12_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E11_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E10_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E12_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E11_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E10_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E11_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E10_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E10_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E11_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E11_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E10_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E10_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E3_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E1_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E1_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E12_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E10_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E1_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E1_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E1_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E1_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D9_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D9_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D9_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D9_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_E11_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D9_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D8_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D9_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D9_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D8_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D8_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D8_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D7_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D7_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D7_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D7_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D7_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D7_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D7_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D6_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D6_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D6_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D6_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D6_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D6_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D5_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D5_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D5_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D6_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D5_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D5_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D8_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D9_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D5_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D5_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D5_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D4_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D4_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D4_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D4_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D8_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D6_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D4_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D4_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D4_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D3_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D3_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D3_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D3_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D3_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D3_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D3_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D3_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D2_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D2_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D2_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D2_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D2_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D12_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D2_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D12_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D12_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D2_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D12_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D11_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D12_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D12_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D12_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D11_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D11_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D10_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D10_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D10_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D10_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D10_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D10_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D1_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D1_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D10_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D1_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D1_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D1_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C9_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C9_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C9_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C9_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C9_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C9_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C9_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C8_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C9_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C8_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C8_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C8_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C8_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C8_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C7_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C7_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C8_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C8_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C7_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C7_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_D1_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C6_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C7_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C7_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C6_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C6_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C6_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C6_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C6_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C6_ad002


title: Mouse Alignment PDX-biopsy - surface layer - rep2

city: Rockville

first: David

last: Morse

state: Maryland

address: 9800 Medical Center Drive

department: National Center for Advancing Translational Sciences

institute: National Institutes of Health

description:
inDrops Transcriptome libraries
mouse_align_biopsy_surface_TR2_TCTTACGC

data_processing:
For Raw Fastq Files: R1 biological read, R2 first half of the gel barcode, R3 library index, and R4 second half of the gel barcode (8 cycles) and the UMI (6 cycles).
indropv3 filtering and demultiplexing
indropv3 identify abundant barcodes
indropv3 quantify expression
indropv3 sort
indropv3 aggregate
demultiplexed and sorted fastq files for each sample are provided as output from the indop pipeline
Matrices are coverted into 10X format and loaded into R for processing
Genome_build: Homo_sapiens.GRCh38.85 and Mus_musculus.GRCm38.85
Supplementary_files_format_and_content: processed data provided in a sparse raw counts matrix

growth_protocol: spheroids were cultured in 96-well ultra-low attachemnt plates for 14 days; Organoids were derived from patient ascites and miantained in a matrigel solution; PDX tumors were derived from patient ascites and grown subcutaneously in mice.

extract_protocol: Indrop v3

treatment_protocol: samples were stained using the SEEP protocol, dissociated using accutase (spheroid/organoid) or gentleMACS (PDX biopsy), and sorted by fluorescent intensity via FACS.

value: biopsy of PDX solid tumor

tag: cell type

value: ascites-derived HGSOC cells

tag: layer

value: surface

tag: disease state

value: HGSOC


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C5_ad001

tag: Sex

value: male


title: Mouse Alignment PDX-biopsy - middle layer - rep2

description:
inDrops Transcriptome libraries
mouse_align_biopsy_middle_TR2_ACTCTAGG

value: middle


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C5_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C7_ad012


title: Mouse Alignment PDX-biopsy - center layer - rep1

description:
inDrops Transcriptome libraries
mouse_align_biopsy_central_TR1_ATAGAGAG

value: center


title: Mouse Alignment PDX-biopsy - middle layer - rep1

description:
inDrops Transcriptome libraries
mouse_align_biopsy_middle_TR1_AGAGGATA


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C5_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C4_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C4_ad004


title: VMH_refeed_WT_1

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

description: reverb_ARC_VMH_fasting_refeeding_leptin_counts.txt

data_processing:
#genome alignment single read: STAR --genomeDir ~/STAR_mm10_GENOME_DIR  --runThreadN 20 --readFilesIn $i --outFileNamePrefix ${i/.fastq.gz/}_ --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMstrandField intronMotif
#counting reads: featureCounts -t exon -g gene_id -a ~/mm10/mm10_genes.gtf -T 20
#DGE with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts read counts for all samples

source_name: Hypothalamic nuclei

extract_protocol:
2-4 independents hypothalamic nuclei punches were pooled together per biological replicate. Hypothalamus punches were homogenized manually by Pellet-Pestle (Kimble, 749515) for 1 minutes with 1mL QIAzol Lysis Reagent (Qiagen). Samples were then centrifuged at 4°C for 10min at 15,000 x g. In a new tube, 200uL chloroform was added to homogenate and mixed thoroughly before repeating the previous centrifugation. The aqueous chloroform phases were pipetted into new tubes, followed by addition of one volume of 70% EtOH to each sample. Total RNA was purified and collected from RNeasy Mini spin columns according to RNeasy Lipid Mini Kit (Qiagen, 74804).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 8-12 weeks

value: control

value: VMH

tag: treatment

value: Refeeding


title: Mouse Alignment PDX-biopsy - center layer - rep2

description:
inDrops Transcriptome libraries
mouse_align_biopsy_central_TR2_AGCTAGAA


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C4_ad002


title: VMH_refeed_WT_3


title: VMH_refeed_KO_3

value: REV-ERBS DKO


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C5_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C4_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C4_ad006


title: VMH_refeed_KO_4


title: VMH_refeed_KO_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C3_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C4_ad008


title: VMH_leptin_WT_3

value: Leptin


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C3_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C3_ad010


title: VMH_leptin_WT_2


title: Mouse Alignment PDX-biopsy - surface layer - rep1

description:
inDrops Transcriptome libraries
mouse_align_biopsy_surface_TR1_CTCCTTAC


title: VMH_leptin_WT_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C3_ad006


title: VMH_refeed_WT_4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C4_ad001


title: VMH_refeed_WT_2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C3_ad004


title: VMH_leptin_KO_3


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C5_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C2_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C2_ad012


title: VMH_leptin_KO_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C2_ad010


title: VMH_refeed_KO_2


title: VMH_leptin_KO_4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C2_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C3_ad002


title: VMH_fasting_KO_3

value: Fasting


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C2_ad004


title: VMH_fasting_KO_2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C2_ad002


title: VMH_fasting_WT_2


title: VMH_fasting_WT_3


title: ARC_refeed_WT_3

value: ARC


title: VMH_fasting_WT_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C2_ad008


title: ARC_refeed_WT_2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C12_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C12_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C12_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C12_ad001


title: VMH_leptin_KO_2


title: ARC_refeed_WT_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C12_ad002


title: ARC_refeed_KO_4


title: VMH_fasting_KO_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C11_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C11_ad012


title: ARC_refeed_KO_3


title: ARC_refeed_WT_4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C11_ad006


title: ARC_refeed_KO_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C11_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C11_ad004


title: ARC_refeed_KO_2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C11_ad002


title: ARC_leptin_WT_2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C10_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C10_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C10_ad006


title: ARC_leptin_KO_4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C10_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C11_ad010


title: PCI-35-Vec_exp1

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression in PCI-35 vector plasmid (pcDNA6) transfection

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PCI-35_Vec, experiment 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The pancreatic cancer cell lines were grown in RPMI-1640 medium (Sigma-Aldrich, St.Louis, MO, USA) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA) in a humidified atmosphere containing 5% CO2 at 37℃.

extract_protocol: The RNAs from each transfected cell line were prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Nine pancreatic cancer cell lines, PK-1, PK-8, PK-9, PK-45P, PK-45H, PK-59, PCI-6, PCI-35, and BxPC-3 were seeded in 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6/myc-His vector or pcDNA6-3xFLAG-NFkB (AD)-MBD using Lipofectamine 2000 reagent (Invitrogen).

tag: cell line

value: pancreas


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C11_ad001

value: ACA,PL,ILA


title: BxPC-3-MeTA_exp1

description: Gene expression in BxPC-3 MeTA inducible plasmid (NFkB (AD)-MBD) transfection

source_name: BxPC-3_MeTA, experiment 1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C10_ad001


title: BxPC-3-Vec_exp1

description: Gene expression in BxPC-3 vector plasmid (pcDNA6) transfection

source_name: BxPC-3_Vec, experiment 1


title: ARC_leptin_WT_3

tag: genotype


title: ARC_leptin_KO_3


title: PCI-6-MeTA_exp1

description: Gene expression in PCI-6 MeTA inducible plasmid (NFkB (AD)-MBD) transfection

source_name: PCI-6_MeTA, experiment 1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C1_ad001


title: ARC_leptin_KO_2


title: ARC_leptin_KO_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C1_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C1_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C10_ad008


title: ARC_fasting_WT_3


title: ARC_leptin_WT_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C1_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C1_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C10_ad007


title: PCI-35-MeTA_exp1

description: Gene expression in PCI-35 MeTA inducible plasmid (NFkB (AD)-MBD) transfection

source_name: PCI-35_MeTA, experiment 1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C1_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C1_ad008


title: PCI-6-Vec_exp1

description: Gene expression in PCI-6 vector plasmid (pcDNA6) transfection

source_name: PCI-6_Vec, experiment 1


title: PK-45H-MeTA_exp1

description: Gene expression in PK-45H MeTA inducible plasmid (NFkB (AD)-MBD) transfection

source_name: PK-45H_MeTA, experiment 1


title: ARC_fasting_WT_2


title: PK-59-Vec_exp1

description: Gene expression in PK-59 vector plasmid (pcDNA6) transfection

source_name: PK-59_Vec, experiment 1


title: PK-59-MeTA_exp1

description: Gene expression in PK-59 MeTA inducible plasmid (NFkB (AD)-MBD) transfection

source_name: PK-59_MeTA, experiment 1


title: PK-45H-Vec_exp1

description: Gene expression in PK-45H vector plasmid (pcDNA6) transfection

source_name: PK-45H_Vec, experiment 1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_C1_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B9_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B9_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B9_ad010


title: ARC_fasting_WT_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B9_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B9_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B9_ad008


title: PK-45P-MeTA_exp1

description: Gene expression in PK-45P MeTA inducible plasmid (NFkB (AD)-MBD) transfection

source_name: PK-45P_MeTA, experiment 1


title: ARC_fasting_KO_3


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B8_ad007


title: ARC_fasting_KO_2


title: ARC_fasting_KO_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B8_ad006


title: PK-45P-Vec_exp1

description: Gene expression in PK-45P vector plasmid (pcDNA6) transfection

source_name: PK-45P_Vec, experiment 1


title: PK-9-MeTA_exp1

description: Gene expression in PK-9 MeTA inducible plasmid (NFkB (AD)-MBD) transfection

source_name: PK-9_MeTA, experiment 1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B8_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B8_ad004


title: HFD_VMH_ZT4_DKO_5

description: hypothalamus_reverb_HFD_circadian_RNA_seq.txt

value: HFD


title: HFD_VMH_ZT4_DKO_4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B8_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B8_ad008


title: HFD_VMH_ZT4_DKO_2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B7_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B8_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B7_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B7_ad001


title: PK-8-Vec_exp1

description: Gene expression in PK-8 vector plasmid (pcDNA6) transfection

source_name: PK-8_Vec, experiment 1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B6_ad012


title: HFD_VMH_ZT4_DKO_1


title: HFD_VMH_ZT4_Ctrl_4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B6_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B6_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B7_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B6_ad004


title: HFD_VMH_ZT4_Ctrl_3


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B5_ad010


title: HFD_VMH_ZT4_Ctrl_2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B5_ad008


title: HFD_VMH_ZT4_DKO_3


title: PK-1-Vec_exp1

description: Gene expression in PK-1 vector plasmid (pcDNA6) transfection

source_name: PK-1, Vec, experiment 1


title: PK-8-MeTA_exp1

description: Gene expression in PK-8 MeTA inducible plasmid (NFkB (AD)-MBD) transfection

source_name: PK-8_MeTA, experiment 1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B7_ad012

source_name: C57BL/6J Male P56 Mouse Brain


title: HFD_ARC_ZT4_DKO_5

source_name: Hypothalamic nuclei


title: HFD_VMH_ZT4_Ctrl_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B5_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B5_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B4_ad012


title: HFD_ARC_ZT4_DKO_4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B4_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B4_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B4_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B4_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B6_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B4_ad004


title: PK-9-Vec_exp1

description: Gene expression in PK-9 vector plasmid (pcDNA6) transfection

source_name: PK-9_Vec, experiment 1


title: HFD_ARC_ZT4_DKO_3


title: HFD_ARC_ZT4_DKO_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B4_ad002


title: HFD_ARC_ZT4_DKO_2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B5_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B4_ad008


title: HFD_ARC_ZT4_Ctrl_4


title: HFD_ARC_ZT4_Ctrl_3


title: HFD_ARC_ZT4_Ctrl_2


title: PK-1-MeTA_exp1

description: Gene expression in PK-1 MeTA inducible plasmid (NFkB (AD)-MBD) transfection

source_name: PK-1, MeTA, experiment 1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B3_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B3_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B2_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B3_ad010


title: HFD_ARC_ZT4_Ctrl_1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B3_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B3_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B3_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B3_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B2_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B2_ad010


title: NC_VMH_DKO4

value: Normal chow


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B2_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B2_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B2_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B12_ad012


title: NC_VMH_DKO2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B12_ad010


title: NC_VMH_DKO1


title: NC_VMH_dc4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B12_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B12_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B12_ad006


title: NC_VMH_dc3


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B12_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B12_ad001


title: NC_ARC_DKO4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B11_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B11_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B10_ad008


title: NC_VMH_dc2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B11_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B11_ad006


title: NC_VMH_DKO3


title: NC_ARC_DKO3


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B10_ad012


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B2_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B11_ad004


title: NC_VMH_dc1


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B10_ad010


title: NC_ARC_DKO1


title: NC_ARC_DKO2


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B10_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B12_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B1_ad012


title: NC_ARC_dc4


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B1_ad001


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B10_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B10_ad004


title: metastasis_27

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in quasR
Genome_build: mm10
Supplementary_files_format_and_content: txt file and contains counts for each sample

source_name: MMTV-PyMT

growth_protocol: The outgrowth of clonal cell populations has been analysed when the maximum allowed tumour volume comprising all stages (normal, hyperplasia, adenoma, carcinoma, pulmonary metastases) had been reached in colour-induced MMTV-PyMT; R26-CBW; K8-CreERT2 mice.

extract_protocol:
By combining the recently published Geo-seq protocol using SmartSeq2 for laser capture microdissected samples with a recent report for parallel DNA and RNA sequencing from single cells, representative cDNA libraries of laser-captured regions from fixed tumour sections were generated. In brief, 7 µm thick cryosections were mounted onto Menzel Superfrost Plus slides and placed in decreasing and increasing ethanol solutions. Zonal patches of clonal populations of various stages in the primary tumour as well as monochromatic metastases were microdissected by using a Zeiss Laser Capture Microscope (energy: 49, focus: 67, delta-energy: 15, delta-focus: 5; CFP (474/23), GFP (510/20), YFP (535/22) and RFP (620/60)) in Auto LPC mode. Clonal populations of normal mammary glands were pooled to obtain a sufficient sample size. Collected laser capture microdissected samples were first lysed at 37 °C for 30 minutes by using a digestion buffer containing proteinase K (150 mM NaCl, 100 mM Tris pH 7.5, 0.5% Igepal, 0.5 µg/µl proteinase K) to reverse the cross-linking of formalin fixation and for further 30 minutes at 42 °C by using a 4M GuSCN solution (Thermo Fisher). Biotinylated oligo-dT30VN beads were used to discard gDNA in the supernatant and specifically start the reverse-transcriptase reaction and cDNA preamplification on poly-adenylated mRNA (exception to GeoSeq protocol: dNTP mix contained 10mM each of dATP, dCTP, dGTP, dTTP and SmartSeq2 ISPCR oligos were used, 5′-AAGCAGTGGTATCAACGCAGAGT-3′). cDNA quality was assessed by a Qubit Fluorometer with a dsDNA HS assay kit (Thermo Fisher), an Agilent high-sensitivity DNA chip for cDNA size distribution and quantitative real-time PCR to check for the expression of housekeeping genes and the absence of gDNA. Laser capture microdissected samples with best quality were subjected to RNA sequencing.
For library preparation, 500 pg cDNA was amplified using the Nextera XT DNA library preparation kit (Illumina). 12 PCR cycles were carried out, DNA was purified using AMPure XP beads in a 0.8:1 ratio and cDNA was sequenced on a NextSeq 500 platform (Illumina) with a 75-bp single-read mode (Index1:8, Index2: 8).

treatment_protocol: To stochastically express one of the four Confetti reporter fluorescent proteins, female MMTV-PyMT; R26-CBW; K8-CreERT2 mice of five weeks of age were induced intraperitoneally with five mg tamoxifen (Sigma-Aldrich) dissolved in 200 µl sunflower oil (Sigma-Aldrich) containing 10% EtOH (Scharlau).

tag: tumour stage

value: Metastasis

tag: image

value: GFP

value: Center of the lung


title: NC_ARC_dc3


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B1_ad007

value: male


title: metastasis_58

value: RFP

value: Border of the lung


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B1_ad006


title: NC_ARC_dc2

value: 8-12 weeks

value: control


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B1_ad010


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B1_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B1_ad002


title: CEMBA190307_5A_1_CEMBA190307_5A_2_B1_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A9_ad001


title: metastasis_56


title: ARC_HFD_HA_ChIP

data_processing:
All the reads were aligned to mouse genome, mm10, using Bowtie2 with option (--p 12 -N 1 -x ~/mm10/mm10).
All the redundant tags were eliminated except one per each genomic position before downstream analysis.
Peak calling was done using Homer and 1 rpm cutoff was further applied for peak tag counts within 200bp window.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig  of  HA-tag IP for REVERB in ARC and VMH hypothalamic nuclei and corresponding input

extract_protocol:
ChIP was performed with anti-HA magnetic beads (Pierce 888367). 10 independents hypothalamic nuclei punches were pooled together per biological replicate. Hypothalamic nuclei punches were directly thawed in cross-linking solution during 20min at room temperature (1% formaldehyde in 1X PBS) , quenched with 0.125M of glycine during 5min and washed three times with 1XPBS at 4°C. Cross-linked hypothalamic nuclei punches were re-suspended un ChIP dilution buffer (50 mM HEPES pH7.5, 155 mM NaCl, 1 mM EDTA, 1.1% Triton X-100, 0.11% Sodium-deoxycholate, 0.1% SDS) on ice and re-suspend during chromatin fragmentation at 4°C (Fischer Scientific, FB705 Sonic Dismembrator : three cycles at 10% amplitude, three cycles of at 15% amplitude). Lipid-cleared samples were resuspended in 1mL with ChIP dilution buffer and input was saved before incubation with BSA blocked HA magnetic beads (Pierce, 888367) overnight at 4°C with rotation. Immunoprecipitation were washed on rotation at 4°C with ChIP dilution buffer twice (1min and 5min), ChIP dilution buffer with 500mM NaCl (5min), ChIP wash buffer (5min, 10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium-deoxycholate, 1 mM EDTA) and Tris-EDTA buffer (5min, 10 mM Tris-HCl pH 8.0, 1 mM EDTA). Cross-linking was reversed overnight at 65°C in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) and DNA was isolated using phenol/chloroform before precipitation by NaCl/EtOH overnight at -20°C with 20ug of glycogen carrier (Thermo Fisher Scientic, AM9515).
ChIP DNA was prepared for sequencing according to the amplification protocol provided by Illumina

value: arcuate nucleus

tag: chromatin

value: anti-HA magnetic beads


title: Input_VMH

description: used for peak calling

value: ventromedial nucleus


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A9_ad007


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A9_ad010


title: VMH_HFD_HA_ChIP


title: metastasis_57


title: metastasis_42


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A9_ad002


title: metastasis_40


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A9_ad008


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A9_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A8_ad001


title: metastasis_02

value: YFP


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A8_ad007


title: Input_ARC

description: used for peak calling


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A8_ad012


title: Miz1(POZ)fl/fl AlbCre Positive 3

description: processed data file: Miz1(POZ).xls

source_name: Liver cancer

value: Liver

value: HCC


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A8_ad010

value: ACA,PL,ILA


title: carcinoma_39

value: Carcinoma

value: Tumor border


title: Miz1(POZ)fl/fl AlbCre Positive 2

description: processed data file: Miz1(POZ).xls


title: NC_ARC_dc1

value: ARC

value: Normal chow


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A8_ad004


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A8_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A8_ad008


title: Miz1(POZ)fl/fl AlbCre Positive 1

description: processed data file: Miz1(POZ).xls


title: carcinoma_08


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A7_ad012


title: Miz1(POZ)fl/fl AlbCre negative 3

description: processed data file: Miz1(POZ).xls


title: carcinoma_54

value: Tumor core


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A7_ad007

value: male


title: carcinoma_38

value: RFP


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A7_ad001


title: carcinoma_07


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A7_ad006


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A7_ad002


title: carcinoma_53


title: carcinoma_55


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A6_ad001


title: Miz1(POZ)fl/fl AlbCre negative 2

description: processed data file: Miz1(POZ).xls


title: Miz1(POZ)fl/fl AlbCre negative 1

description: processed data file: Miz1(POZ).xls


title: CEMBA190307_5A_1_CEMBA190307_5A_2_A6_ad010