title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C11_ad006


title: GFP_MV_II

status: Public on Dec 02 2020

type: SRA

city: BOSTON

first: Francois

last: Cherbonneau

state: MA

address: 185 CAMBRIDGE STREET, CPZN3200

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
Reads were aligned to hg19 using STAR module
counting reads associated genes were detected with the FeatureCounts module and generate a count matrix text file
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Microvesicles control

growth_protocol: Cell were cultured in Exo-media: Dulbeccco’s modified Eagle’s media, supplemented with 10% exosome depleted fetal bovine serum (Exosome-Depleted FBS), 1% penicillin/streptomycin and RNAse A at a final concentration of 30µg/mL.

extract_protocol:
Microvesicles were isolated by serial steps of ultracentrifugation and a 0.8µm filtration. Both MVs and cell pelets were resuspend in PBS and RNAse inhibitor and treated with phenol chloroform followed by RNA isolation with the RNeasy MinElute Cleanup column from Qiagen.
RNA libraries were prepared from isolated total RNA in reference of the SMART-Seq2 protocol was use (Superscript II RT focus on specific mRNA RT, and KAPA Hifi pre-amplification) in complement with the Nextera kit from illumina (illumina cat no: FC-131-1001 and FC-131-1096).

treatment_protocol: Cell transfected with the two constructs with lipofectamine 3000 reagent in 10cm dishes as recomemded by the manufacturer

tag: cell line

value: HEK 293T

tag: status

value: Control


title: GFP_MV_I


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C11_ad002

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

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT 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 INTACT
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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: PTLp

tag: target

value: MOp

tag: gender

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C11_ad001


title: RNA_BrafSmarcb1_CKI_BS53958

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse genome assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: thyroid tumor cell line

growth_protocol: To generate mouse tumor cell lines, tumors were dissected, minced in PBS, and resuspended in 10 mL of digestion medium (minimum essential media containing 112 U/mL type I collagenase (Worthington catalog # CLS-1), 1.2 U/mL dispase (Gibco catalog # 17105-041), penicillin (50 U/mL), and streptomycin (50 mg/mL). Cells were incubated at 37oC for 60 minutes with vigorous shaking, after which cells were spun down and resuspended in Coon’s modified F12 medium with penicillin/streptomycin/L-glutamine (P/S/G; Gemini; #400-110) and 0.5% bovine brain extract and plated into CellBind plates (Corning Inc., Lowell, MA, USA) for two weeks, and then switched to Coon’s modified F12 medium with P/S/G containing 5% FBS for routine culturing and maintenance.

extract_protocol:
RNA was isolated by TRIzol extraction
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

treatment_protocol: Thyroid tumor cell lines were treated with 300 nM CKI for 8 days in the presence of bovine TSH or vehicle (40% Trappsol, Cyclo Therapeutics, Alachua, FL).

value: thyroid tumor cell line

tag: genotype

value: Braf(V600E) + Smarcb1 KO

tag: treatment


title: GFP_Cell_I

source_name: Cell lysate control


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C10_ad012

value: VIS

value: female


title: RNA_BrafSmarcb1_CKI_BS53736


title: GFP_Cell_II


title: RNA_Braf_CKI_B52482


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C10_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_C10_ad004


title: C1_MV_III

source_name: Microvesicles construct

value: Construct


title: C1_MV_II


title: C1_Cell_II

source_name: Cell lysate construct


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B9_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B9_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B9_ad004


title: RNA_BrafArid2_Veh_AB55694

value: Braf(V600E) + Arid2 KO

value: Vehicle


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B8_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B8_ad012


title: C1_Cell_III


title: RNA_BrafArid2_Veh_AB52980


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B9_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B8_ad002


title: S010: Cancerous - 010_HCC

city: Guangzhou

first: Ke

last: He

state: Guangdong

address: 466 Xingangdong Road, Guangzhou

country: China

institute: Guangdong Second Provincial General Hospital

data_processing:
Firstly, effective reads sequence is extracted, and index sequence and adapter sequence in each sequence are removed.
Thereafter, RNA-seq data was mapped to hg19 using hisat2 and cufflinks were used to calculate the gene expression level in all samples.
We analyze mRNA coverage and characteristics, including box and-whisker diagram analysis of the coverage of reads in different regions and the distribution of reads on homogenized mRNA.
Genome_build: hg19

source_name: Cancerous

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2 ml tube contain of 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3 ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1 ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25μL~100μL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
According to the manufacturer’s instructions, the first step involves the removal of ribosomal RNA (rRNA) using target-specific oligos and RNase H reagents to deplete both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA and 28S rRNA) and mitochodrial ribosomal RNA (12S rRNA and 16S rRNA) from total RNA preparations. Following SPRI beads purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. This process removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. After UDG treatment, the incorporation of dUTP quenches the second strand during amplification. The products are enriched with PCR to create the final cDNA library. The libraries were assessed quality and quantity in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe).

tag: diagnosis

value: liver hepatocellular carcinoma

value: Liver

value: Cancerous

tag: tumor stage

value: II


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B8_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B8_ad001


title: RNA_BrafArid2_CKI_AB55694


title: S009: Cancerous - 009_HCC

value: III


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B7_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B7_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B6_ad012


title: RNA_BrafArid2_Veh_AB51189


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B6_ad008


title: S008: Cancerous - 008_HCC


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B6_ad007


title: S007: Cancerous - 007_HCC


title: RNA_Braf_CKI_B47275


title: RNA_BrafArid2_CKI_AB52980


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B6_ad006


title: RNA_Braf_CKI_B48051


title: RNA_BrafArid2_CKI_AB51189


title: S006: Cancerous - 006_HCC


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B6_ad001


title: RNA_BrafArid1a_Veh_BA49112

value: Braf(V600E) + Arid1a KO


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B5_ad010

value: brain


title: S005: Para-cancerous - 005_HCC

source_name: Para-cancerous

value: Para-cancerous


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B5_ad008

value: MOp


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B5_ad002

value: PTLp

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B5_ad001


title: RNA_BrafArid1a_Veh_BA47473

value: thyroid tumor cell line


title: RNA_BrafArid1a_Veh_BA45198


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B4_ad001


title: S003: Para-cancerous - 003_HCC


title: S002: Para-cancerous - 002_HCC


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B3_ad012

value: VIS


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B3_ad010

value: female


title: RNA_BrafArid1a_CKI_BA49112


title: RNA_BrafArid1a_CKI_BA47473


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B3_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B3_ad002


title: RNA_BrafArid1a_CKI_BA45198


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B6_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B3_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B2_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B2_ad007


title: Braf_Smarcb1_53965_d12_h3k4me3

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, read overlap density was calculated with an extension of 200 bp, the signal was then normalized to the peak-based size factor from the raw counts table (DESeq2) and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to the size factor from the raw count matrix

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

value: Braf(V600E) + Smarcb1 KO

tag: chip antibody

value: H3K4me3 (Cell Signaling Technology catalog # 9751S)


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B2_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B5_ad007


title: S004: Para-cancerous - 004_HCC


title: Braf_Smarcb1_53965_c12_h3k4me1

value: H3K4me1 (Abcam catalog # ab8895)


title: 2-Rep2-input

city: Memphis

first: Aseem

last: Ansari

state: TN

address: 262 Danny Thomas Place

department: Chemical Biology & Therapeutics

institute: St. Jude Children's Research Hospital

data_processing:
library strategy: crosslinking of small molecules to isolate chromatin (COSMIC)-seq
Alignment to genome hg19 using bowtie-0.12.8
Peak calling using SPP
Genome_build: hg19
Supplementary_files_format_and_content: regionpeak files contains the peaks called from SPP

growth_protocol: LNCaP cells were maintained in RPMI 1640 (Invitrogen) with 10% Fetal Bovine Serum (FBS) (Irvine Scientific) at 37°C under 5% CO2. LNCaP cells were purchased from ATCC (Manassas, VA, USA).

extract_protocol:
COSMIC was performed as previously described (Erwin,G.S., Bhimsaria,D., Eguchi,A. and Ansari,A.Z. (2014) Mapping Polyamide–DNA Interactions in Human Cells Reveals a New Design Strategy for Effective Targeting of Genomic Sites. Angew. Chemie Int. Ed., 53, 10124.).  Briefly, cells or nuclei were centrifuged at 500 × g and re-suspended in COSMIC buffer [20 mM Tris·Cl (pH 8.1), 2 mM EDTA, 150 mM NaCl, 1mM PMSF, 1mM benzamidine, 1.5 μM pepstatin,1% Triton X-100, 0.1% SDS]. Samples were sonicated at 3 °C for 36 min with a cycle of 10 s ON and 10 s OFF, at HIGH setting (Bioruptor Plus, Diagenode). Samples were centrifuged 10 min at 12,000 × g and 10% of the sample was saved as input DNA and stored at -80 °C until reversal of cross-linking.  The rest of the sample was used for the affinity purification. Streptavidin-coated magnetic beads (100 μL per sample, Dynabeads MyOne C1) were washed in COSMIC buffer and incubated with samples for 16 h at 4°C.  All washes were performed at room temperature unless otherwise noted. For 1 and 2, 1A and 2A were added (5 μM), respectively, in the washes. Samples were washed twice with COSMIC buffer (once 12 h and once 4 h). Samples were then washed once with washing buffer 1 [10 mM Tris·Cl (pH 8.0), 1 mM EDTA, 3% (v/v) SDS], once with washing buffer 2 [10 mM Tris·Cl (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet P-40, 1% sodium deoxycholate], twice with freshly prepared washing buffer 3 [4 M urea, 10 mM Tris·Cl (pH 7.5) at 50 °C, 1 mM EDTA, 0.1% Nonidet P-40], and twice with TE buffer [10 mM Tris·Cl (pH 8.0), 1 mM EDTA]. Samples were re-suspended in TE and labelled as AP DNA.  Input and AP samples were re-suspended in cross-link reversal buffer [10 mM Tris (pH 7.6), 0.4 mM EDTA, 100 mM KOH]. Crosslinks were reversed, and DNA was eluted from beads at the same time by heating samples for 30 min at 90 °C. Input and AP samples were neutralized with 6N HCl, and incubated first with RNase A (0.2 μg/μL) for 1 h at 37 °C and then with Proteinase K (0.2 μg/μL) for 1 h at 55 °C. Samples were purified with the MinElute PCR Purification Kit (Qiagen).
Sequencing libraries for Input and AP DNA were labeled with a DNA barcode for multiplexing, and prepared for sequencing with the TruSeq ChIP Sample Prep Kit (Illumina, Inc., San Diego, CA) per manufacturer’s directions.

treatment_protocol: LNCaP nuclei were treated with molecule for 24 h. At 24 h after treatment, nuclei were irradiated for 30 min with a UV lamp (2.4 mW/cm2; CalSun) through a Pyrex filter.

tag: cell type

value: LNCaP


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B2_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B2_ad001


title: 2-Rep2-ap

tag: structure

tag: target sequence

value: PB-GGWC


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B1_ad010


title: 2-Rep1-input


title: Braf_Smarcb1_53965_a12_h3k27ac

value: H3K27ac (Abcam catalog # ab4729)


title: Braf_Smarcb1_53958_d10_h3k4me3


title: 2-Rep1-ap


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B1_ad007


title: S001: Para-cancerous - 001_HCC

value: liver hepatocellular carcinoma

value: Liver

value: II


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B1_ad001

value: brain


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B12_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B11_ad008


title: 1-Rep4-input


title: 1-Rep4-ap

value: PB-GWWC


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B1_ad004

value: MOp


title: Braf_Smarcb1_53958_a10_h3k27ac


title: Braf_Smarcb1_53958_c10_h3k4me1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B10_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B12_ad002

value: PTLp


title: 1-Rep3-input


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B10_ad006


title: Braf_Smarcb1_53736_d11_h3k4me3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_B10_ad002

value: male


title: 1-Rep3-ap


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A9_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A9_ad010


title: Braf_Smarcb1_53736_c11_h3k4me1

value: thyroid tumor cell line


title: Braf_Smarcb1_53736_a11_h3k27ac


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A9_ad006


title: 1-Rep2-input


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A9_ad001


title: 1-Rep2-ap


title: 1-Rep1-input


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A8_ad012

value: VIS


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A8_ad007


title: Braf_Arid2_55694_c8_h3k4me1

value: Braf(V600E) + Arid2 KO


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A8_ad008

value: female


title: 1-Rep1-ap


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A8_ad006


title: Braf_Arid2_52980_d9_h3k4me3

value: H3K4me3 (Cell Signaling Technology catalog # 9751S)


title: ESC26

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

data_processing:
We used RUM to align the scRNAseq data to the human genome (Hg19).  In total, we obtained 213,348,824 and 217,094,429 reads for 96 cells in hESCs and hDiffs, respectively.  Cells with less than 1 million mapped reads were removed. RPKM values were calculated using RUM over UCSC gene annotation (Hg19).
Genome_build: Hg19
Supplementary_files_format_and_content: RPKM

source_name: human female embryonic stem cell

extract_protocol: sinlge cell RNAseq protocol: The Fluidigm C1 requires at least 1000 cells to be loaded (5 ml), of which about 10% fill the 96 wells of the 5-10mm diameter chip. Capture efficiency was briefly evaluated and then the chip was loaded onto the C1 for cDNA preparation using Clontech SMARTer kit (Takara-Clontech, CA). Cell debris or clusters of 2 or more cells were excluded. Hence, RNA libraries for the remaining cells were generated using the low throughput Nextera XT SNA library prep kit (Illumina, CA). Individual bar-coded libraries were sequenced by the University of Pennsylvania Functional Genomic Core using Illumina HiSeq 2500

tag: agent


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A7_ad012


title: Braf_Arid2_52980_c9_h3k4me1

tag: cell line

value: H3K4me1 (Abcam catalog # ab8895)


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A8_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A8_ad002


title: ESC28


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A7_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A7_ad004


title: ESC25


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A9_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A6_ad012


title: ESC31


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A6_ad007


title: Braf_Arid2_52980_a9_h3k27ac


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A6_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A6_ad002


title: Braf_Arid2_55694_d8_h3k4me3


title: ESC27


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A5_ad004


title: Braf_Arid2_51189_a7_h3k27ac


title: Braf_Arid2_55694_a8_h3k27ac


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A5_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A5_ad002


title: ESC29


title: ESC24


title: Braf_Arid1a_49112_d6_h3k4me3

value: Braf(V600E) + Arid1a KO


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A4_ad004


title: ESC30


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A4_ad008


title: Braf_Arid1a_49112_c6_h3k4me1


title: ESC42


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A4_ad002


title: Braf_Arid2_51189_d7_h3k4me3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A4_ad001


title: ESC40


title: Braf_Arid2_51189_c7_h3k4me1


title: Braf_Arid1a_49112_a6_h3k27ac


title: ESC44


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A3_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A3_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A2_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A5_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A1_ad004


title: Braf_Arid1a_47473_a5_h3k27ac


title: Braf_Arid1a_45198_d4_h3k4me3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A1_ad002


title: ESC43


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A3_ad007


title: Braf_Arid1a_45198_c4_h3k4me1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A3_ad006


title: ESC45


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A12_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A2_ad002


title: Braf_Arid1a_45198_a4_h3k27ac


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A1_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A12_ad007


title: ESC46


title: Braf_52482_d3_h3k4me3


title: Braf_Arid1a_47473_d5_h3k4me3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A11_ad008


title: ESC47


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A11_ad006


title: Braf_52482_c3_h3k4me1


title: ESC0


title: Braf_Arid1a_47473_c5_h3k4me1


title: ESC41


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A1_ad012


title: ESC2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H9_ad007

value: RSP


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H9_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H9_ad006

value: AUD


title: Braf_52482_a3_h3k27ac

value: H3K27ac (Abcam catalog # ab4729)


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H9_ad012


title: Braf_48051_d1_h3k4me3


title: ESC4


title: ESC1


title: Braf_48051_c1_h3k4me1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H8_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H8_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H7_ad012


title: ESC7


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H7_ad010


title: Braf_48051_a1_h3k27ac


title: Braf_47275_d2_h3k4me3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H9_ad004


title: ESC3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H7_ad006


title: ESC5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H7_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H6_ad008


title: Braf_47275_c2_h3k4me1


title: ESC6


title: ESC90


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H6_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A11_ad012


title: Braf_47275_a2_h3k27ac


title: ATAC_CL_Braf_Vehicle_rep3

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, read overlap density was calculated with an extension of 0 bp, the signal was then normalized to the peak-based size factor from the raw counts table (DESeq2) and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to the size factor from the raw count matrix

extract_protocol:
Cells were lysed and incubated with transposition reaction mix containing PBS, 1% Digitonin, Tween-20, and Transposase (llumina). Samples were incubated for 30 minutes at 37C in a thermomixer at 1000rpm. Prior to amplification, samples were concentrated with the DNA Clean and Concentrator Kit-5 (Zymo).
Samples were eluted in 20uL of elution buffer and PCR-amplified using the NEBNext 2X Master Mix (NEB) for 10 cycles and sequenced on a HiSeq 2500 (Illumina).

value: Vehicle


title: ESC88


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H5_ad008


title: ATAC_CL_Braf_Vehicle_rep2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H4_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H7_ad004


title: ESC92


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H3_ad012


title: ATAC_CL_Braf_Vehicle_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H4_ad004


title: ESC89


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H3_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H3_ad006


title: ATAC_CL_BrafSmarcb1_Vehicle_rep3

value: Braf(V600E) + Smarcb1 KO


title: ATAC_CL_BrafSmarcb1_Vehicle_rep2


title: ESC91


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H2_ad012

value: brain


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H2_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H2_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H2_ad004


title: ESC94


title: ESC93


title: ATAC_CL_BrafSmarcb1_Vehicle_rep1


title: ATAC_CL_BrafSmarcb1_CKI_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H12_ad010


title: ESC36


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H12_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H1_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H12_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H4_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H2_ad001


title: ATAC_CL_Braf_CKI_rep2


title: ATAC_CL_BrafSmarcb1_CKI_rep2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H1_ad006


title: ESC34


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H12_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H1_ad004


title: ESC32


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H12_ad004


title: ATAC_CL_Braf_CKI_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H11_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H12_ad001


title: ESC33


title: ESC95


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H3_ad004


title: ATAC_CL_BrafArid2_Vehicle_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H11_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H10_ad007


title: ATAC_CL_Braf_CKI_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H10_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_H10_ad002


title: ATAC_CL_BrafArid2_CKI_rep3


title: ESC37


title: ESC38


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G9_ad010


title: ATAC_CL_BrafArid2_Vehicle_rep2


title: ATAC_CL_BrafArid2_Vehicle_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G9_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G9_ad008


title: ESC66


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G9_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G9_ad001


title: ATAC_CL_BrafArid1a_Vehicle_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G8_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G8_ad001


title: ESC68


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G8_ad002


title: ATAC_CL_BrafArid2_CKI_rep2


title: ESC64


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G7_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G7_ad012


title: ESC39


title: ESC65


title: ESC35


title: ATAC_CL_BrafArid2_CKI_rep1


title: ATAC_CL_BrafArid1a_Vehicle_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G8_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G7_ad007


title: ESC67


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G6_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G6_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G7_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G5_ad004


title: ESC71


title: ESC70


title: ATAC_CL_BrafArid1a_CKI_rep2


title: ATAC_CL_BrafArid1a_Vehicle_rep2


title: ATAC_CL_BrafArid1a_CKI_rep1


title: ESC69


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G4_ad008


title: WT activation rep 3

city: Rochester

first: Hu

last: Zeng

state: MN

address: 200 First ST SW

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (mm10) using Tophat (v2.0.6) with default parameters
FPKM were calculated using RSeQC (v2.3.6)
Genome_build: mm10
Supplementary_files_format_and_content: Xian Cell Reports genes fpkm

source_name: B cells

extract_protocol:
Splenic follicular B cells were flow sorted.They were activated by LPS/IL-4 for 72 hours. Total RNA was extracted using Rneasy micro kit (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

tag: strains

tag: passage

value: Splenic follicular B cells

value: spleen


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G3_ad008

tag: strain

tag: age

value: MOp


title: WT activation rep 2

tag: tissue


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G3_ad012

tag: source

tag: target


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G3_ad010

tag: gender

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G3_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G5_ad002


title: ESC50


title: ESC48


title: WT activation rep 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G7_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G3_ad004


title: WT rest rep 3


title: ESC52


title: ESC49


title: WT rest rep 2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G3_ad001


title: ATAC_CL_BrafArid1a_CKI_rep3

value: thyroid tumor cell line

tag: genotype

tag: treatment


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P5_CEMBA190826_RS2_P6_A1_ad001

value: PTLp


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G2_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G2_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G1_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G2_ad004


title: WT rest rep 1


title: ESC55


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G1_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G1_ad007


title: ESC53


title: P0 Lhx6-GFP bulk-ATAC-Seq-Hypothalamus-2

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description:
bulk ATAC-Seq
P0-Hypothalamus-ATAC.csv

data_processing:
ATAC-Sequencing: Illumina adapters of sequenced libraries were trimmed using Cutadapt (v1.18)/TrimGalore (v0.5.0) and library qualities were assessed using FastQC (v0.11.7)/MultiQC. Libraries were aligned to mm10 using Bowtie 2 (v2.25) (Langmead and Salzberg, 2012) using --very-sensitive parameter, and Samtools (v1.9) (Li et al., 2009) was used to check the percentage of mitochondria DNA reads. Picard (v2.18) was used to remove PCR duplicates, and MACS2 (v2.1.2) (Zhang et al., 2008) was used to capture narrow peaks (open chromatin regions) with --shift 100, --extsize 200, --nolambda, --nomodel parameters. ENCODE blacklist regions of the genome were removed using Bedtools (v2.27) intersect function (Amemiya et al., 2019; Quinlan and Hall, 2010; Zhang et al., 2008). Bedtools intersect function was used to find matching peaks between replicates, which the distance of peak ends were less than 10 base pairs. ChIPseeker (v1.18.0) (Yu et al., 2015) was then used to identify regions that were within 3 kb of the transcription start site (TSS). Footprinting was done using pyDNase (v0.24) (Piper et al., 2015) wellington_footprints function to find transcription factor binding sites and motif analysis was done on footprinting sites with HOMER (v4.11) (Heinz et al., 2010) with default parameters. Peaks between groups were compared as previously described (Buenrostro et al., 2014; Wang et al., 2018) to visualize changes in chromatin accessibility between different ages and brain regions using DiffBind (v.2.10.0) (Ross-Innes et al., 2012) and edgeR using default parameters. Differential peaks were compared to bulk RNA-Seq, and open chromatin peaks in promoter regions that correspond to gene expression were identified to obtain a positive correlation between promoter accessibility and gene expression. Peaks and differential gene expressions were then cross-matched to scRNA-Seq to identify potential different regions within Lhx6 hypothalamic cells that are demarcated by expression of specific transcription factors.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM-generated counts (bulk RNA-seq samples),  count matrix/barcode/genes (scRNA-seq samples),  individual peak files (ATAC-seq samples)

source_name: P0 Lhx6-GFP bulk-ATAC-Seq-Hypothalamus

extract_protocol: ATAC-Sequencing: Cortex and hypothalamus of E15 and P0 Lhx6-GFP mice were collected, dissociated with papain-based enzymatic reaction, and GFP cells were flow-sorted. Between 60,000 and 70,000 cells were collected. Flow-sorted cells were prepared for ATAC libraries as previously described (Buenrostro et al., 2014; Wang et al., 2018). Libraries were sequenced with Illumina NextSeq500, paired-end read of 75 bp, 50 million reads per library. Each sample was run in duplicates.

value: Hypothalamus

tag: Sex

value: pooled male and female

tag: flow-sorting

value: GFP+


title: ESC51


title: ESC54


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G1_ad001


title: P0 Lhx6-GFP bulk-ATAC-Seq-Hypothalamus-1

description:
bulk ATAC-Seq
P0-Hypothalamus-ATAC.csv


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G1_ad004

value: female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G12_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G12_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G12_ad004


title: P0 Lhx6-GFP bulk-ATAC-Seq-Cortex-1

description:
bulk ATAC-Seq
P0-Cortex-ATAC.csv

source_name: P0 Lhx6-GFP bulk-ATAC-Seq-Cortex

value: Cortex


title: ESC10


title: P0 Lhx6-GFP bulk-ATAC-Seq-Cortex-2

description:
bulk ATAC-Seq
P0-Cortex-ATAC.csv


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G12_ad002


title: ESC8


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G12_ad001


title: E15.5 Lhx6-GFP bulk-ATAC-Seq-Hypothalamus-2

description:
bulk ATAC-Seq
E15-Hypothalamus-ATAC.csv


title: ESC12


title: E15.5 Lhx6-GFP bulk-ATAC-Seq-Hypothalamus-1

description:
bulk ATAC-Seq
E15-Hypothalamus-ATAC.csv


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G11_ad004


title: E15.5 Lhx6-GFP bulk-ATAC-Seq-Cortex-2

description:
bulk ATAC-Seq
E15-Cortex-ATAC.csv

source_name: E15.5 Lhx6-GFP bulk-ATAC-Seq-Cortex


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G11_ad007

value: RSP


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G11_ad002

value: AUD


title: ESC9


title: ESC15


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G10_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G12_ad012


title: E15.5 Lhx6-GFP bulk-ATAC-Seq-Cortex-1

description:
bulk ATAC-Seq
E15-Cortex-ATAC.csv


title: ESC11


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G10_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F9_ad012


title: P8 Lhx6-GFP GFP+ bulK-RNA-Seq Hypothalamus-2

description:
bulk RNA-Seq
Replicate 2

data_processing:
Lhx6 pulse-chase sample sequencingLhx6 pulse-chase sample sequencing: Libraries were sequenced with Illumina NextSeq500, paired-end read of 75 bp, 50 million reads per library. Illumina adapters of sequenced libraries were trimmed using Cutadapt (v1.18)/TrimGalore (v0.5.0) (Martin, 2011) with default parameters, library qualities were assessed using FastQC (v0.11.7)/MultiQC (Ewels et al., 2016). Libraries were then aligned to mm10 using STAR (v2.54b) (Dobin et al., 2013) with --twopassMode Basic, and RSEM (v1.3.0) was used for quantification (Li and Dewey, 2011) with rsem-calculate-expression (--forward-prob 0.5). Expected counts value from RSEM was used to perform differential expression using edgeR (v3.24.3) (Robinson et al., 2010) using default parameters except calcNormFactors (method = “TMM”).  Lhx6CreER/+;Ai9 or Lhx6CreER/+;Lhx6lox/+;Baxlox/lox;Ai9 enriched genes (fold change > 2 consistent gene value across replicates), were used with EnrichR (Kuleshov et al., 2016). Lhx6lox/+;Baxlox/lox;Ai9 enriched genes were compared to Mouse Cells and Tissues (MESA) dataset available ascot.cs.jhu.edu (Ling et al., 2020), relying in robustness of expression (NAUC >20) and specificity, as many of enriched genes were not commonly expressed in the developing brain. We reasoned that the enriched genes in Lhx6CreER/+;Ai9.compare to Lhx6CreER/+;Lhx6lox/+;Baxlox/lox;Ai9 would be either a result of an absence of Lhx6 and/or Bax. Furthermore, since tdTomato expression is detected in blood vessels due to weak Lhx6 expression in endothelial cells during development (Liu et al., 2017), we wanted to enrich expression from Lhx6+ cells of the hypothalamus. P8 Lhx6-GFP, in which GFP expression is absent in endothelial cells, were used to generate bulk RNA-Sequencing (bulk RNA-Seq) from the cortex and hypothalamus (method described below). Hypothalamus-enriched genes from P8 Lhx6-GFP bulk RNA-Seq data was used to enrich genes that are highly expressed in the hypothalamus Lhx6 cells. After enrichment, the gene lists were compared to single-cell RNA-Sequencing (scRNA-Seq) data from P8 Lhx6-GFP hypothalamus using the method described below to further cross-check specificity of expression and remove any possible contamination that may occurred during flow-sorting from bulk RNA-Seq. EnrichR was used to identify gene pathways, and pathways that are involved with neuronal survival across literature were selected.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM-generated counts (bulk RNA-seq samples),  count matrix/barcode/genes (scRNA-seq samples),  individual peak files (ATAC-seq samples)

extract_protocol: Lhx6 pulse-chase sample sequencing: Lhx6CreER/+;Ai9 and Lhx6CreER/+;Lhx6lox/+;Baxlox/lox;Ai9 P1 pups were treated with 4-OHT, and collected at P10. Between 4 and 6 pups from 2 different litters were pooled per sample without regard to the sex, and papain-based enzymatic dissociation was performed on the dissected hypothalamus as previously described (D. W. Kim et al., 2019). Dissociated cells were flow-sorted for tdTomato signal, and between 25,000 and 30,000 cells were collected directly into TRIzolTM LS reagent. RNA was extracted using Direct-zol RNA kits (Zymo Research) and RNA-Sequencing libraries were made using stranded Total RNASeq library prep. 2 libraries were made for Lhx6CreER/+;Ai9 and 3 libraries were made for Lhx6CreER/+;Lhx6lox/+;Baxlox/lox;Ai9. Libraries were sequenced with Illumina NextSeq500, paired-end read of 75 bp, 50 million reads per library. Illumina adapters of sequenced libraries were trimmed using Cutadapt (v1.18)/TrimGalore (v0.5.0) (Martin, 2011) with default parameters, library qualities were assessed using FastQC (v0.11.7)/MultiQC (Ewels et al., 2016).


title: ESC13


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F9_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G10_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F9_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F9_ad002


title: ESC14


title: P8 Lhx6-GFP GFP- bulK-RNA-Seq Hypothalamus-2

description:
bulk RNA-Seq
Replicate 2

value: GFP-


title: ESC74


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F9_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G10_ad008


title: P8 Lhx6-GFP GFP- bulK-RNA-Seq-Hypothalamus-1

description:
bulk RNA-Seq
Replicate 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F8_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F8_ad004


title: ESC72


title: P8 Lhx6-GFP GFP+ bulK-RNA-Seq-Cortex-1

description: bulk RNA-Seq

source_name: P8 Lhx6-GFP GFP+ bulK-RNA-Seq-Cortex


title: ESC73


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F7_ad012


title: P8 Lhx6-GFP GFP- bulK-RNA-Seq-Cortex-1

description: bulk RNA-Seq

source_name: P8 Lhx6-GFP GFP- bulK-RNA-Seq-Cortex


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F8_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F8_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F7_ad008


title: ESC79


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F7_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F7_ad002


title: ESC75


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F6_ad012


title: P8 Lhx6-GFP GFP+ bulK-RNA-Seq-Hypothalamus-1

description:
bulk RNA-Seq
Replicate 1


title: P0 Lhx6-GFP GFP+ bulK-RNA-Seq-Hypothalamus-1

description:
bulk RNA-Seq
Replicate 1


title: P0 Lhx6-GFP GFP- bulK-RNA-Seq Hypothalamus-2

description:
bulk RNA-Seq
Replicate 2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_G11_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F6_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F6_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F6_ad006


title: ESC78


title: P0 Lhx6-GFP GFP- bulK-RNA-Seq-Hypothalamus-1

description:
bulk RNA-Seq
Replicate 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F5_ad012


title: ESC76


title: ESC58


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F5_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F7_ad007


title: P0 Lhx6-GFP GFP+ bulK-RNA-Seq-Cortex-1

description:
bulk RNA-Seq
Replicate 1

source_name: P0 Lhx6-GFP GFP+ bulK-RNA-Seq-Cortex


title: P0 Lhx6-GFP GFP+ bulK-RNA-Seq-Cortex-2

description:
bulk RNA-Seq
Replicate 2


title: ESC56


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F6_ad002


title: P0 Lhx6-GFP GFP- bulK-RNA-Seq-Cortex-2

description:
bulk RNA-Seq
Replicate 2

source_name: P0 Lhx6-GFP GFP- bulK-RNA-Seq-Cortex


title: P0 Lhx6-GFP GFP+ bulK-RNA-Seq Hypothalamus-2

description:
bulk RNA-Seq
Replicate 2


title: ESC57


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F5_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F4_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F5_ad007


title: P0 Lhx6-GFP GFP- bulK-RNA-Seq-Cortex-1

description:
bulk RNA-Seq
Replicate 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F5_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F5_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F4_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F2_ad012


title: ESC77


title: E15.5 Lhx6-GFP GFP+ bulK-RNA-Seq-Hypothalamus-2

description:
bulk RNA-Seq
Replicate 2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F3_ad010


title: ESC63


title: E15.5 Lhx6-GFP GFP+ bulK-RNA-Seq-Hypothalamus-1

description:
bulk RNA-Seq
Replicate 1


title: E15.5 Lhx6-GFP GFP- bulK-RNA-Seq-Hypothalamus-2

description:
bulk RNA-Seq
Replicate 2


title: ESC61


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F2_ad006


title: E15.5 Lhx6-GFP GFP- bulK-RNA-Seq-Hypothalamus-1

description:
bulk RNA-Seq
Replicate 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F1_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F2_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F12_ad008


title: ESC18


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F1_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F12_ad007


title: ESC60


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F12_ad001


title: E15.5 Lhx6-GFP GFP+ bulK-RNA-Seq-Cortex-2

description:
bulk RNA-Seq
Replicate 2

source_name: E15.5 Lhx6-GFP GFP+ bulK-RNA-Seq-Cortex


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F12_ad012

source_name: C57BL/6J P56 Mouse Brain


title: E15.5 Lhx6-GFP GFP- bulK-RNA-Seq-Cortex-2

description:
bulk RNA-Seq
Replicate 2

source_name: E15.5 Lhx6-GFP GFP- bulK-RNA-Seq-Cortex


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F12_ad002


title: E15.5 Lhx6-GFP GFP+ bulK-RNA-Seq-Cortex-1

description:
bulk RNA-Seq
Replicate 1


title: ESC59


title: E15.5 Lhx6-GFP GFP- bulK-RNA-Seq-Cortex-1

description:
bulk RNA-Seq
Replicate 1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F12_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F11_ad006


title: ESC17


title: ESC20


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F11_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F11_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F1_ad012


title: ESC62


title: ESC23


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F11_ad001


title: RNA_Braf_Veh_5

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: thyroid tissue

growth_protocol: For WT, Arid2, and Smarcb1 mice, thyroids were removed, flash frozen on dry ice, and RNA was isolated using TRIzol reagent.

extract_protocol:
Thyroids were dissociated into single cells and YFP+ cells were collected by flow cytometry into TRIzol LS reagent on ice for RNA isolation.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

treatment_protocol: Mice were treated with vehicle or CKI for 8 days, and euthanized ~2 hr from the last dose.

value: thyroid

value: Vehicle


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F10_ad012

value: brain


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F10_ad008


title: RNA_Braf_Veh_4


title: ESC16


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E9_ad012


title: ESC19


title: RNA_Braf_Veh_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_F10_ad001


title: RNA_Braf_CKI_5


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E9_ad010


title: ESC22


title: ESC82


title: RNA_Braf_CKI_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E9_ad001


title: ESC80


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E9_ad007


title: RNA_Braf_CKI_4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E8_ad008


title: ESC84


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E8_ad004


title: RNA_BrafSmarcb1_Veh_2

value: Braf(V600E) + Smarcb1 KO


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E8_ad001


title: RNA_BrafSmarcb1_Veh_3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E7_ad008


title: ESC21


title: RNA_BrafSmarcb1_Veh_1


title: ESC87


title: ESC81


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E7_ad007


title: ESC83


title: RNA_BrafSmarcb1_CKI_4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E7_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E9_ad008


title: RNA_BrafSmarcb1_CKI_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E8_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E7_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E6_ad010


title: RNA_BrafSmarcb1_CKI_1


title: ESC86


title: RNA_BrafArid2_Veh_4

value: Braf(V600E) + Arid2 KO


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E7_ad012

value: MOp


title: BMP122

source_name: BMP4 treated cells


title: RNA_BrafArid2_Veh_2


title: BMP120


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E6_ad007

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E6_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E6_ad002


title: RNA_BrafArid2_Veh_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E5_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E7_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E6_ad001


title: BMP124


title: BMP121


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E5_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E5_ad004


title: RNA_BrafArid2_CKI_4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E5_ad001


title: ESC85


title: RNA_BrafArid2_CKI_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E6_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E4_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E5_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E4_ad008


title: RNA_BrafArid2_CKI_3


title: RNA_BrafArid1a_Veh_3

value: Braf(V600E) + Arid1a KO


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E4_ad007


title: BMP127


title: BMP125


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E4_ad006


title: BMP123


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E4_ad012


title: RNA_BrafArid1a_CKI_5


title: BMP138


title: RNA_BrafArid1a_Veh_2


title: RNA_BrafArid1a_CKI_4


title: BMP126


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E4_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E9_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E3_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E2_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E2_ad006


title: RNA_BrafArid1a_Veh_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E3_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E1_ad007


title: BMP140


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E3_ad008


title: RNA_WT3

value: Wildtype


title: BMP143


title: RNA_WT2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E1_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E2_ad010


title: BMP139


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E1_ad002


title: RNA_WT1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E2_ad004


title: BMP141


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E12_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E12_ad007


title: RNA_BrafArid1a_CKI_2


title: RNA_Arid1a3

value: Arid1a KO


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E12_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E12_ad001


title: BMP137


title: BMP96


title: BMP142


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E11_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E11_ad002


title: RNA_Wildtype_WT45105


title: BMP100


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E1_ad006


title: RNA_Arid1a1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E10_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E10_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E10_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E10_ad001


title: BMP97


title: RNA_Wildtype_WT44970


title: RNA_Wildtype_WT45127


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E11_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D9_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E10_ad004


title: RNA_Arid1a2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D9_ad008


title: BMP98


title: BMP99


title: BMP103


title: RNA_Smarcb1_S47009

value: Smarcb1 KO


title: RNA_Smarcb1_S46994


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D9_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D9_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D9_ad002


title: BMP136


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_E1_ad001


title: RNA_Smarcb1_S46993


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D9_ad001


title: BMP102


title: RNA_Arid2_A251185A

value: Arid2 KO


title: BMP186


title: RNA_Arid2_A251181A


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D8_ad008

value: female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D8_ad006


title: BMP184


title: RNA_Arid2_A251180A


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D8_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D7_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D7_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D7_ad004


title: BMP188


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D7_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D7_ad002


title: BMP185


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D6_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D6_ad007


title: BMP191


title: ATAC_Braf_VEH_2_rep2

growth_protocol: Thyroids were dissociated into single cells and YFP+ cells were collected by flow cytometry into F-12 Coon’s media containing 5% FBS, 0.5% bovine brain extract, 100 units/ml Pencillin, and 0.1mg/ml Streptomycin, on ice.


title: BMP101


title: ATAC_Braf_VEH_1_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D6_ad004


title: BMP187


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D6_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D5_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D5_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D5_ad007


title: BMP189


title: BMP190


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D4_ad010


title: ATAC_Braf_CKI_5_rep2


title: ATAC_Braf_CKI_4_rep1


title: ATAC_Braf_VEH_3_rep3


title: BMP130


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D4_ad004


title: BMP128


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D4_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D4_ad008


title: BMP132


title: ATAC_BrafSmarcb1_VEH_20_rep2


title: ATAC_BrafSmarcb1_VEH_19_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D3_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D3_ad006


title: ATAC_BrafSmarcb1_CKI_23_rep2


title: BMP129


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D3_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D2_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D2_ad004


title: ATAC_Braf_CKI_6_rep3


title: BMP135


title: ATAC_BrafSmarcb1_CKI_22_rep1


title: ATAC_BrafArid2_VEH_15_rep3


title: BMP131


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D5_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D12_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D12_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D12_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D12_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D3_ad010


title: ATAC_BrafArid2_VEH_14_rep2


title: BMP133


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D11_ad008


title: BMP134


title: ATAC_BrafArid2_CKI_18_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D11_ad006


title: ATAC_BrafArid2_VEH_13_rep1


title: BMP162


title: BMP160


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D11_ad001


title: ATAC_BrafArid2_CKI_17_rep2


title: BMP164


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D10_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D10_ad001


title: ATAC_BrafArid1a_VEH_9_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D10_ad012


title: ATAC_BrafArid2_CKI_16_rep1


title: BMP161


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D10_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C8_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C9_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C9_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C9_ad002


title: ATAC_BrafArid1a_VEH_8_rep2


title: BMP167


title: ATAC_BrafArid1a_VEH_7_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C8_ad008


title: BMP163


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_D11_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C8_ad002


title: ATAC_BrafArid1a_CKI_12_rep3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C8_ad001


title: BMP165


title: ATAC_BrafArid1a_CKI_11_rep2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C7_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C7_ad010


title: ATAC_BrafArid1a_CKI_10_rep1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C7_ad007


title: BMP144


title: BMP146


title: ATAC_WT_171213

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, read overlap density was calculated with an extension of 0 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C7_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C6_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C7_ad002


title: ATAC_WT2_171130


title: BMP148


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C8_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C6_ad007


title: ATAC_WT1_171130


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C6_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C6_ad004


title: BMP145


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C5_ad012


title: BMP151


title: ATAC_Smarcb1_1


title: ATAC_Smarcb1_2


title: BMP147


title: BMP166


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C4_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C5_ad001


title: ATAC_ARID2_13


title: BMP149


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C4_ad002


title: BMP150


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C3_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C3_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C3_ad008


title: ATAC_ARID1A_S16


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C3_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C5_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C3_ad004


title: BMP106


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C5_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C2_ad006


title: BMP108


title: BMP104


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C2_ad007


title: ATAC_ARID1A_1


title: p2_ftb_4

city: Rehovot

first: Hassan

last: Massalha

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

description:
tumor_LCM
processed data file: tumor_LCM_UMItab.txt.gz

data_processing:
bcl2fastq/2.15.0.4. Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1, 66bp) and read 2 (R2, UMI 10bp)), MARSseq (R1: 66bp, R2: cell barcode 7bp + UMI 8bp)
Pooled data of scRNAseq were demultiplexed using plate specific barcode. Specific sequences for each cell were demultiplexed using well specific barcode (attached - 'marsseq_cell_barcodes.txt'). Samples analyzed with laser capture microdissection were demultiplexed using sample specific barcode (attached mcSCRBseq raw files are after demultiplexing step).
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each sample

molecule: polyA RNA

source_name: patient p2 fibrotic tumor border

extract_protocol:
Samples were collected from the surgery room immediately after isolation into sterile saline solution and processed in a sterile cabinet. Each sample was divided equally into two pieces as follows: (1) scRNAseq, samples stored in cold DMEM X1, supplemented with glutamine, (2) frozed section, sample were embedded into OCT block and kept on dry ice to be sectioned using LCM and mcSCRBseq for bulk sequencing
cell extract protocol: sample collection protocol: for scRNAseq, all samples were prepared according to Liver Dissociation Kit (GentelMAX, 130-105-807). Liberase Blendzyme3 recombinant collagenase (Roche Diagnostics) were added to the enzymatic cocktail in the first step in sample preperation protocol
for scRNAseq, 3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014). For bulk analysis, mcSCRBseq protocol was used (Bagnoli et al, Nat Commun. 2018)

value: Liver

tag: pateint tumor type

value: cholangiocarcinoma

tag: sequencing protocol

value: mcSCRBseq


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C4_ad006

value: AUD


title: p2_ftb_3


title: BMP105


title: p2_ftb_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C2_ad002


title: p2_ftb_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C2_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C1_ad012

value: RSP


title: BMP107


title: ATAC_ARID2_1

value: thyroid


title: BMP111


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C2_ad010

value: brain


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C1_ad010


title: p2_ti_4

source_name: patient p2 tumor islets


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C1_ad007


title: BMP110


title: p2_ti_3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C1_ad004


title: p2_ti_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C12_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C2_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C12_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C1_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C12_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C12_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C12_ad006


title: p2_fz_4

source_name: patient p2 fibrotic zone


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C11_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C11_ad002


title: BMP170


title: BMP172


title: p2_fz_3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C11_ad001


title: p2_fz_2


title: BMP109


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C10_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C10_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C10_ad002


title: BMP175


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_C10_ad001


title: BMP171


title: p4_tb_4

source_name: patient p4 tumor border

value: colorectal metastasis


title: p2_fz_1


title: p2_ti_1


title: BMP168


title: BMP173


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B9_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B9_ad008


title: BMP174


title: p4_tb_2


title: p4_tb_3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B9_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B9_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B8_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B8_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B8_ad012


title: BMP169


title: BMP152


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B8_ad006


title: BMP154


title: p4_ftb_4

source_name: patient p4 fibrotic tumor border


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B8_ad001


title: BMP156


title: p4_ftb_3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B7_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B9_ad010


title: BMP153


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B7_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B7_ad008


title: BMP159


title: p4_tb_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B7_ad004


title: p4_ftb_1


title: p4_ftb_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B7_ad001


title: BMP157


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B6_ad008


title: BMP158


title: p4_ti_4

source_name: patient p4 tumor islets


title: BMP155


title: p4_ti_3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B6_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B6_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B5_ad001


title: BMP114


title: p4_ti_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B5_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B4_ad012


title: BMP112


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B4_ad006


title: p4_fz_4

source_name: patient p4 fibrotic zone


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B4_ad004


title: p4_fz_3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B6_ad004


title: BMP116


title: BMP113


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B3_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B6_ad001


title: p4_ti_2


title: BMP119


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B3_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B2_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B3_ad012


title: p4_fz_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B2_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B4_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B2_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B2_ad010


title: p4_tc_4

source_name: patient p4 tumor core


title: p4_fz_1


title: BMP117


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B1_ad007


title: BMP118


title: p4_tc_3


title: p4_tc_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B1_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B1_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B1_ad002


title: BMP178


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B1_ad001


title: BMP176


title: p3_tb_4

source_name: patient p3 tumor border


title: BMP115


title: BMP180


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B12_ad008


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B12_ad007


title: p4_tc_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B12_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B12_ad002


title: BMP177


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B12_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B12_ad006


title: BMP179


title: BMP183


title: p3_tb_2


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B12_ad001


title: p3_tb_1


title: p3_ftb_4

source_name: patient p3 fibrotic tumor border


title: p3_tb_3


title: BMP181


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B2_ad008


title: p3_ftb_3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B11_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B11_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B11_ad001


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B10_ad008


title: BMP182


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B10_ad002


title: p3_ftb_2


title: p3_ftb_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A9_ad004


title: TAtech3a

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
T=total, A=Adult, tech=technical replicate 3a
Sample_95731

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to verify sample quality.
The Tuxedo Suite was used to align reads to the reference transcriptome using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure only high quality data
Two different methods were used for expression quantitation, normalization, and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was one method used for expression quantitation and differential expression analysis. This analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
HTSeq (version 0.6.1)   to count non-ambiguously mapped reads only. Data were pre-filtered to remove genes with 0 counts in all samples. DESeq2 (version 1.14.1) for normalization and differential expression
Genome_build: mm10
Supplementary_files_format_and_content: text file of raw counts

source_name: Preoptic area of the hypothalamus

growth_protocol: For positive controls, GnRH CRE (homozygote) male mice were bred to floxed-stop-floxed  L10a-GFP (homozygote) female mice to generate offspring that express GFP tagged ribosomal protein L10a in GnRH neurons. For negative controls mice were either wild-type, Floxed-L10a-GFP only or GnRH CRE only as indicated in the table above. Each biological replicate is a pool of preoptic punches from 3-4 mice.

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen; 74004) with on column DNasing and assessed for quantity and quality using the Pico or Nano Chip (Agilent).
SMARTer v4 Ultra low (poly A), fragment length 120nt.

treatment_protocol: Preoptic Area hypothalamic punches were collected from female mice at either day 21 or in adulthood (70-150days). All adult female mice are in diestrus.

value: GnRH CRE x Floxed L10a-GFP

value: Preoptic area of the hypothalamus

tag: l10a gfp-expression

value: POS

value: Adult

tag: rna fraction

value: GnRH Depleted Supernatant


title: TAtech4a

description:
T=total, A=Adult, tech=technical replicate 4a
Sample_95734


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_B11_ad008

value: MOp


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A9_ad002

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A8_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A9_ad001


title: TYtech2a

description:
T=total, Y=Young, tech=technical replicate 2a
Sample_95722

value: Young


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A8_ad002


title: p3_ti_2

source_name: patient p3 tumor islets


title: p3_ti_3


title: TYtech1a

description:
T=total, Y=Young, tech=technical replicate 1a
Sample_95718


title: p3_fz_4

source_name: patient p3 fibrotic zone


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A8_ad001

source_name: C57BL/6J P56 Mouse Brain


title: TAtech4b

description:
T=total, A=Adult, tech=technical replicate 4b
Sample_122444


title: p3_fz_3


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A7_ad008

value: female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A7_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A9_ad007


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A6_ad010


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A6_ad012


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A7_ad006


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A7_ad004


title: TYtech2b

description:
T=total, Y=Young, tech=technical replicate 2b
Sample_122442


title: p3_fz_2

value: Liver


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A5_ad008


title: p3_fz_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A6_ad002


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A8_ad004


title: p3_ti_4


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A5_ad007


title: TYtech1b

description:
T=total, Y=Young, tech=technical replicate 1b
Sample_122441


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A5_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A5_ad001


title: TAtech3b

description:
T=total, A=Adult, tech=technical replicate 3b
Sample_122443


title: p3_tc_4

source_name: patient p3 tumor core


title: IPAneg1

description:
IP=Immunoprecipitate, A=Adult, neg=negative, biological repicate=1
Sample_122439

value: GnRH CRE only

value: NEG

value: Non Specific Immunoprecipitate


title: IPAneg2

description:
IP=Immunoprecipitate, A=Adult, neg=negative, biological repicate=2
Sample_122440


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A5_ad006

value: AUD


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A4_ad004


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A4_ad010

value: RSP


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A3_ad010

value: brain


title: IPYneg3

description:
IP=Immunoprecipitate, Y=Young, neg=negative, biological repicate=3
Sample_122437

value: Floxed L10a-GFP only


title: p3_tc_2

value: colorectal metastasis

value: mcSCRBseq


title: GApos1

description:
G=GnRH Immunoprecipitate, A=Adult, pos=positive control, biological replicate 1
Sample_122438

value: GnRH CRE x Floxed L10a-GFP

value: Preoptic area of the hypothalamus

value: POS

value: GnRH Enriched Immunoprecipitate


title: p3_tc_1


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A4_ad002

value: MOp

value: male


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A3_ad002


title: p1_ftb_3

source_name: patient p1 fibrotic tumor border

value: cholangiocarcinoma


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A3_ad004

value: female


title: 190826_CEMBA_mm_P56_RS2_snmC_seq2_NovaSeq_pe_150_ZZ_CEMBA190826_RS2_P3_CEMBA190826_RS2_P4_A2_ad010


title: IPYneg2

description:
IP=Immunoprecipitate, Y=Young, neg=negative, biological repicate=2
Sample_122436

value: Wild Type

value: Young


title: IPYneg1

description:
IP=Immunoprecipitate, Y=Young, neg=negative, biological repicate=1
Sample_122435

value: NEG

value: Non Specific Immunoprecipitate