title: SM-GE5PH_S100_E1-50


title: SM-GE5PH_S108_E1-50

status: Public on Sep 08 2021

type: SRA

city: Seattle

first: Bosiljka

last: Tasic

state: WA

address: 615 Westlake Ave N.

department: Molecular Genetics

country: USA

institute: Allen Institute for Brain Science

library_source: transcriptomic

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: mm10, Mmul_10

molecule: polyA RNA

organism: Mus musculus

source_name: Mouse LP

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols 1508, 1510, and 1511 at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 14/10-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Cux2-CreERT2;Ai140 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. We excluded any animals with anophthalmia or microphthalmia. The brain tissues of two adult M. nemestrina (southern pig-tailed macaque) and one M. fascicularis  (crab-eating macaque) were obtained through the Tissue Distribution Program of the Washington  National Primate Research Center and conformed to the guidelines provided by the US National  Institutes of Health. All procedures were approved by the Institutional Animal Care and Use Commit-  tee of the University of Washington under protocol number 4277-01.

extract_protocol:
We isolated single cells and nuclei as previously described (Tasic et al., 2016, Bakken et al., 2018) with modifications. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C. For nuclei isolation, dissected regions of interest were transferred to microcentrifuge tubes, snap frozen in a slurry of dry ice and ethanol, and stored at -80°C until the time of use. To isolate nuclei, frozen tissues were placed into a homogenization buffer that consisted of 10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNasin Plus RNase inhibitor (Promega), 1X protease inhibitor (Promega), and 0.1mM DTT. Tissues were placed into a 1ml dounce homogenizer (Wheaton) and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30μm cell strainer (Miltenyi Biotech) and centrifuged at 900xg for 10 minutes to pellet nuclei. Nuclei were then resuspended in staining buffer containing 1X PBS supplemented with 0.8% nuclease-free BSA and 0.5% RNasin Plus RNase inhibitor.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

tag: donor

tag: Sex

value: M

tag: genotype

value: LP

tag: facs gating

value: RFP-positive

tag: sequencing batch

tag: cell class

value: Glut

tag: cell cluster


title: SM-GE5PH_S104_E1-50


title: SM-GE5PH_S107_E1-50


title: SM-GE5PH_S101_E1-50


title: LS-15589_S63_E1-50


title: SM-GE5PH_S103_E1-50


title: SM-GE5PH_S097_E1-50


title: SM-GE5PH_S102_E1-50


title: LS-15589_S62_E1-50

value: GABA


title: SM-GE5PH_S099_E1-50


title: LS-15589_S60_E1-50


title: LS-15589_S56_E1-50


title: SM-GE5PH_S098_E1-50


title: LS-15589_S61_E1-50


title: LS-15589_S58_E1-50


title: LS-15589_S59_E1-50


title: LS-15589_S64_E1-50


title: LS-15589_S49_E1-50


title: SM-GE5PH_S105_E1-50


title: LS-15589_S57_E1-50


title: LS-15589_S50_E1-50


title: LS-15589_S54_E1-50


title: LS-15589_S48_E1-50


title: LS-15589_S52_E1-50


title: LS-15589_S51_E1-50


title: LS-15589_S47_E1-50

value: Low Quality


title: LS-15589_S46_E1-50


title: LS-15589_S40_E1-50


title: LS-15589_S44_E1-50


title: LS-15589_S42_E1-50


title: LS-15589_S43_E1-50


title: LS-15589_S41_E1-50


title: LS-15589_S39_E1-50


title: LS-15589_S53_E1-50


title: LS-15589_S37_E1-50


title: LS-15589_S36_E1-50


title: LS-15589_S35_E1-50


title: LS-15589_S31_E1-50


title: LS-15589_S34_E1-50


title: LS-15589_S32_E1-50


title: LS-15589_S45_E1-50


title: LS-15589_S26_E1-50


title: LS-15589_S25_E1-50

value: Non-Neuronal


title: LS-15589_S29_E1-50


title: LS-15589_S27_E1-50


title: LS-15589_S33_E1-50


title: LS-15581_S93_E1-50


title: LS-15581_S90_E1-50


title: LS-15581_S92_E1-50


title: LS-15589_S38_E1-50


title: LS-15581_S89_E1-50


title: LS-15581_S88_E1-50


title: LS-15581_S91_E1-50


title: LS-15581_S87_E1-50


title: LS-15581_S83_E1-50


title: LS-15581_S86_E1-50


title: LS-15581_S84_E1-50


title: LS-15581_S85_E1-50


title: LS-15589_S30_E1-50


title: LS-15581_S82_E1-50


title: LS-15581_S80_E1-50


title: LS-15581_S79_E1-50


title: LS-15581_S78_E1-50


title: LS-15581_S95_E1-50


title: LS-15581_S94_E1-50


title: LS-15581_S77_E1-50


title: LS-15581_S75_E1-50


title: LS-15581_S73_E1-50


title: LS-15581_S76_E1-50


title: LS-15581_S74_E1-50


title: LS-15589_S28_E1-50


title: LS-15580_S79_E1-50


title: LS-15580_S78_E1-50


title: LS-15580_S75_E1-50


title: LS-15580_S72_E1-50


title: LS-15580_S73_E1-50


title: LS-15580_S77_E1-50


title: LS-15580_S71_E1-50


title: LS-15581_S81_E1-50


title: LS-15580_S69_E1-50


title: LS-15580_S67_E1-50


title: LS-15580_S55_E1-50


title: LS-15580_S68_E1-50


title: LS-15581_S96_E1-50


title: LS-15580_S53_E1-50


title: LS-15580_S52_E1-50


title: LS-15580_S51_E1-50


title: LS-15580_S80_E1-50


title: LS-15580_S66_E1-50


title: LS-15580_S50_E1-50


title: LS-15580_S54_E1-50


title: LS-15589_S96_E1-50

source_name: Mouse LGv

value: LGv


title: LS-15589_S92_E1-50


title: LS-15589_S95_E1-50


title: LS-15589_S94_E1-50


title: LS-15589_S93_E1-50


title: LS-15589_S89_E1-50


title: LS-15589_S90_E1-50


title: LS-15589_S87_E1-50


title: LS-15589_S91_E1-50


title: LS-15589_S82_E1-50


title: LS-15589_S83_E1-50


title: LS-15589_S84_E1-50


title: LS-15580_S65_E1-50


title: LS-15589_S85_E1-50


title: LS-15580_S56_E1-50


title: LS-15589_S71_E1-50


title: LS-15589_S66_E1-50


title: LS-15589_S86_E1-50


title: LS-15589_S68_E1-50


title: LS-15589_S72_E1-50


title: LS-15589_S69_E1-50


title: LS-15589_S81_E1-50


title: LS-15581_S64_E1-50


title: LS-15589_S70_E1-50


title: LS-15589_S65_E1-50


title: LS-15581_S63_E1-50


title: LS-15581_S60_E1-50


title: LS-15589_S88_E1-50


title: LS-15581_S59_E1-50


title: LS-15581_S62_E1-50


title: LS-15581_S54_E1-50


title: LS-15581_S58_E1-50


title: LS-15581_S55_E1-50


title: LS-15581_S53_E1-50


title: LS-15581_S56_E1-50


title: mec1-1991A_Pol2-HA_150

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

library_source: genomic

data_processing:
Library strategy: Slim-Chip
bowtie2 (-p8 --local --very-sensitive)
picard for duplicates
filter reads based on samflag (-F0x0400 -f2)
genomecoverage (BEDtools) "-pc -d"
Genome_build: R64-1-1 (SacCer3)
Supplementary_files_format_and_content: out file provides coverage of each base ordered by chromosome

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: exponential growth in YPD media

extract_protocol:
SLIM-ChIP [Voichek Y, Mittelman K, Gordon Y, Bar-Ziv R, Lifshitz Smit D, Shenhav R, Barkai N. Epigenetic Control of Expression Homeostasis during Replication Is Stabilized by the Replication Checkpoint. Mol Cell. 2018 Jun 21;70(6):1121-1133.e9. doi: 10.1016/j.molcel.2018.05.015. Epub 2018 Jun 14. PMID: 29910110.]
ChIPmentation (Frenkel and Jonas, 2021)

treatment_protocol: alpha factor arrest + different times in HU

tag: antibody

value: BY4741 bar1{delta}0 MEC1::Mec1(S1991A) POL2::Pol2-HA (pYm17+) MCM7::Mcm7-myc (pYM18+)

tag: treatment

value: aFactor release + 150min 200 mM HU


title: mec1-1991A_Pol2-HA_90

value: aFactor release + 90min 200 mM HU


title: LS-15581_S57_E1-50


title: mec1-1991A_Pol2-HA_60

value: aFactor release + 60min 200 mM HU


title: LS-15581_S52_E1-50


title: scRNA_seq_dI21

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes
map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: susScr11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: total RNA

organism: Sus scrofa

source_name: ileum cell

extract_protocol: Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics Inc., Pleasanton, CA, USA) following the manufacture’s introduction.

tag: age

value: 21 day

tag: tissue

value: ileum

value: male


title: mec1-1991A_Pol2-HA_15

value: aFactor release + 15min 200 mM HU


title: LS-15581_S51_E1-50


title: LS-15581_S50_E1-50


title: LS-15581_S49_E1-50


title: scRNA_seq_dI14

value: 14 day


title: LS-15581_S47_E1-50

value: M


title: LS-15581_S48_E1-50


title: scRNA_seq_dI7

value: 7 day


title: scRNA_seq_dI3

value: 3 day


title: LS-15581_S46_E1-50

value: RFP-positive


title: LS-15581_S61_E1-50

value: Glut


title: scRNA_seq_dI0

value: 0 day


title: LS-15581_S45_E1-50


title: LS-15581_S43_E1-50


title: LS-15581_S44_E1-50

value: GABA


title: WT_ZIKV_R2

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
Illumina Casava1.8.2 software was used for basecalling
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12 and then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab).
Remaining reads were aligned to the mouse genome assembly mm10 using Hisat2.
Reads mapping to genes were counted using htseq-count, version 0.9.1
Gene normalization and differential expression analysis were performed using Deseq2, version 1.16.1
Genome_build: mm10
Supplementary_files_format_and_content: deseq2 normalized reads counts

source_name: mouse embryonic fibroblasts

growth_protocol: Murine embryonic fibroblasts (WT MEF), Ajuba-/- and PINK1-/- MEFs were grown in Dulbecco’s modified enrichment medium (GIBCO; 11995-065) containing 10% fetal bovine serum (GIBCO; 16000-044) and 1% penicillin/streptomycin (GIBCO; 15140-122) in an atmosphere of 5% CO2 at 37°C.

extract_protocol:
Cells were harvested in Trizol and frozen on dry ice. Each sample lysate was combined with additional Trizol to bring the final volume to 1000l in each sample, 200ml of 1-Bromo-3-chloropropane (MilliporeSigma) was added, samples mixed, and centrifuged at 16,000 x g for 15 min at 4°C.  RNA containing aqueous phase of 600l was collected from each sample and passed through Qiashredder column (Qiagen) at 21,000 x g for 2 min to homogenize any remaining genomic DNA in the aqueous phase. Aqueous phase was combined with 600mL of RLT lysis buffer (Qiagen) with 1%  mercaptoethanol and RNA was extracted using Qiagen AllPrep DNA/RNA 96-well system. An additional on-column Dnase I treatment was performed during RNA extraction. Standard RNeasy extraction protocol resulted in RNAs larger than 200nt. All sample processing was performed using amplicon-free reagents and tools in aerosol resistant vials. RNA was quantitated by spectrophotometry and RNA yield ranged from 0.6 to 8.5µg. RNA quality was analyzed using Agilent 2100 Bioanalyzer (Agilent Technologies) and RNA integrity number (RIN) ranged from 7.6 to 9.9 (showing an overall exceptional RNA quality).
500 ng RNA was used as input for the TruSeq Stranded mRNA-Seq Sample Preparation Kit (Illumina). The protocol was followed without modification. Final library size distribution was assessed on a BioAnalyzer DNA 1000 chip (Agilent Technologies). The average size of the libraries was on target at around 310 bp. Libraries were quantified using the Kapa SYBR FAST Universal qPCR kit for Illumina sequencing on the CFX384 Real-Time PCR Detection System (Bio-Rad Laboratories). The libraries were diluted to 4 nM stocks and pooled equitably for sequencing.

treatment_protocol: Cells were either mock infected or infected with ZIKV PRABC59 strain (MOI 1). Virus was allowed to adsorb for 1 hour at 37oC followed by a media change and incubation for the indicated time.

tag: infection

value: zika virus

value: WildType


title: PINK1_KO_ZIKV_R1

value: Pink1 -/-


title: Ajuba_KO_ZIKV_R3

value: Ajuba -/-


title: PINK1_KO_Mock_R2

value: mock


title: LS-15581_S42_E1-50

value: LGv


title: PINK1_KO_Mock_R1


title: LS-15580_S94_E1-50


title: LS-15580_S95_E1-50


title: LS-15580_S96_E1-50

value: Non-Neuronal


title: LS-15580_S92_E1-50


title: LS-15580_S93_E1-50


title: WT_ZIKV_R1


title: Ajuba_KO_ZIKV_R2


title: WT_ZIKV_R3


title: LS-15580_S90_E1-50


title: LS-15580_S89_E1-50


title: LS-15580_S91_E1-50


title: Ajuba_KO_Mock_R2


title: WT_Mock_R3


title: WT_Mock_R2


title: LS-15580_S85_E1-50


title: LS-15580_S84_E1-50


title: LS-15580_S86_E1-50


title: Ajuba_KO_ZIKV_R1


title: scRNA_seq_dI1

value: 1 day

value: ileum

value: male


title: LS-15580_S82_E1-50

value: M


title: PINK1_KO_ZIKV_R3


title: LS-15580_S48_E1-50


title: WT_Mock_R1


title: PINK1_KO_Mock_R3


title: Ajuba_KO_Mock_R3


title: LS-15580_S83_E1-50


title: LS-15580_S88_E1-50


title: LS-15580_S87_E1-50


title: MCT rats- Losartan [Los_965]

city: Durham

first: Gayathri

last: Viswanathan

state: NC

address: 0150, Carl building, 130 Research Drive

department: Cardiology

institute: Duke University

data_processing:
Received FPKM data sets for each treatment groups of rats from Novogene
The gene expression log2 values of test group rats (Angiotensin 2, TRV023 and Losartan) that are normalized with control rat (PBS) are used to identify the differentially expressed genes
In-silico analysis or literature search was performed to identify those differentially expressed genes that play role in pulmonary hypertension and vascular remodelling and vascular cell proliferation.
Data represented as FPKM values using GraphPad Prism
Supplementary_files_format_and_content: FPKM

organism: Rattus norvegicus

source_name: MCT rats- Losartan-lung tissue

extract_protocol:
Total RNA is isolated using Qiagen Rneasy Mini kit from Lung tissues isolated from MCT rats
Novogene RNA sequencing

tag: strain/genotype

value: MCT model

value: 9 weeks old

value: Losartan

value: Lung tissue


title: MCT rats- Losartan [Los_925]


title: LS-15580_S42_E1-50

value: RFP-positive


title: LS-15580_S81_E1-50


title: PINK1_KO_ZIKV_R2


title: MCT rats- Losartan [Los_964]


title: MCT rats- TRV023 [Trv_930]

source_name: MCT rats- TRV023-lung tissue


title: MCT rats- TRV023 [Trv_918]


title: MCT rats- Angiotensin 2 [Ang2_933]

source_name: MCT rats- Angiotensin 2-lung tissue

value: Angiotensin 2


title: Ajuba_KO_Mock_R1


title: LS-15580_S38_E1-50

value: GABA


title: LS-15580_S43_E1-50


title: LS-15580_S40_E1-50


title: LS-15580_S39_E1-50


title: LS-15580_S35_E1-50


title: LS-15580_S44_E1-50


title: Stroma

type: RNA

city: Beijing

first: Wujiang

last: Liu

address: 8 Xishiku Xicheng

department: Urology

institute: Peking University

hyb_protocol: The chip was placed in the hybridization furnace in balance and hybridized at 45 ℃, 60 rpm for 16 hr

scan_protocol: Put the chip into the scanner, start scanning, and check the autofocus to ensure that the high spots do not interfere with the focus. If the prompt focusing error message is observed, discard the spots and replace it with a new one. Be sure to make it flat. If the focus is normal, the chip starts scanning.

data_processing: The scanning intensity of each point is used as the expression level of the gene; Fold change ≥2 or Fold change≤0.5

label: biotin

organism: Homo sapiens

source_name: stromal tissue

label_protocol: In vitro transcription and synthesis of biotin labeled cRNA

growth_protocol: Clinical sample was colleceted from a patient with benign prostatic hyperplasia with informed consent

extract_protocol: RNA was isolated with Invitrogen Ambion rna isolate kit

treatment_protocol: Stroma and epithelium were isolated by laser microdissection

tag: subject status

value: pateint with benign prostatic hyperplasia

value: Stroma


title: MCT rats- Angiotensin 2 [Ang2_922]


title: MCT rats- TRV023 [Trv_917]


title: LS-15580_S33_E1-50


title: LS-15580_S34_E1-50


title: MCT rats- PBS [Veh_963]

source_name: MCT rats- PBS-lung tissue

value: PBS


title: MCT rats- Angiotensin 2 [Ang2_931]


title: MCT rats- PBS [Veh_924]


title: LS-15580_S45_E1-50


title: LS-15580_S27_E1-50


title: L_fraction_siNat10_RepliSeq

first: wenhui

address: 5 Yiheyuan Road, Haidian District

data_processing:
library strategy: Replication-seq
Reads were aligned to the hg19 human genome with Bowtie2 2.1.0
Coverage data are calculated from mapped reads using samtools and bedtools.  Data are smoothed using R Loess function (“*_T_Loess.bg” files)
Base 2 log of control to treatment group coverage ratio is calculated on 40kb windows (“*_T_.bg” files)
Log Ratio data are quantile normalized using R package preprocessCore (“*_T_qnorm.bg” files)
Genome_build: hg19
Supplementary_files_format_and_content: processed data are coverage data on hg19, they can be visualized using a genome viewer. To visualize them using UCSC genome viewer, add a bedgraph file header

source_name: U2OS cells

extract_protocol:
Lysates were clarified from sonicated nuclei from early-S phase and late-S phase cells and biotin-EdU labeled DNA  were isolated with streptavidin.
Replication-seq libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: NAT10 knockdown

value: untreated


title: LS-15580_S32_E1-50

value: LGv

value: Non-Neuronal


title: L_fraction_siNat10_BHB_RepliSeq

value: β-hydroxybutyrate treated


title: LS-15580_S47_E1-50


title: LS-15580_S29_E1-50


title: E_fraction_siCtrl_RepliSeq

value: control


title: LS-15580_S26_E1-50

value: M


title: LS-15580_S28_E1-50


title: L_fraction_siCtrl_RepliSeq


title: LS-15580_S37_E1-50


title: CTCF_ChIPseq_siNAT10_BHB

data_processing:
Reads were aligned to the hg19 human genome with Bowtie2 2.1.0
MACS2 2.1.1 was used for peak calling (p value threshold = 10-5) with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: all the locally  enriched peaks were determined by MACS2 2.1.1

extract_protocol:
Lysates were clarified from sonicated nuclei and NAT10-DNA or CTCF-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: U2OS cells

value: beta-hydroxybutyrate treated

value: CTCF


title: MCT rats- PBS [Veh_923]

value: MCT model

value: 9 weeks old

value: Lung tissue


title: E_fraction_siNat10_RepliSeq


title: Epitheliun

source_name: epithelial tissue

value: Epitheliun


title: LS-15580_S30_E1-50

value: RFP-positive

value: GABA


title: CTCF_ChIPseq_siNAT10


title: E_fraction_siCtrl_BHB_RepliSeq


title: LS-15580_S25_E1-50


title: CTCF_ChIPseq_siCtrl_BHB


title: CTCF_ChIPseq_siCtrl


title: LS-15048_S94_E1-50

source_name: Mouse LGN - Core

value: dLGN - Core


title: LS-15048_S93_E1-50


title: E_fraction_siNat10_BHB_RepliSeq

value: NAT10 knockdown


title: LS-15048_S96_E1-50


title: NAT10_ChIPseq_Control

value: untreated


title: CTCF_Input_ChIPseq


title: LS-15580_S36_E1-50

value: LGv


title: NAT10_Input_ChIPseq


title: L_fraction_siCtrl_BHB_RepliSeq


title: NAT10_ChIPseq_BHB


title: LS-15048_S91_E1-50


title: LS-15048_S87_E1-50


title: LS-15048_S85_E1-50


title: LS-15048_S95_E1-50


title: LS-15048_S89_E1-50


title: LS-15048_S92_E1-50

value: Non-Neuronal


title: LS-15048_S88_E1-50


title: mec1-S1991A.HU

data_processing:
fastq files were mapped on genome reference using the R (version 3.3.2) package QuasR v1.14.0 (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html), with the included aligner bowtie allowing multiple mapping reads (100) for tDNA.
The command qAlign ('samples.txt, BSgenome.Scerevisiae.SCSC.sacCer3') instructs bowtie to align using the parameters 'auxiliaryFile="NULL", splicedAlignment=false, maxHits=100'
read counts for each annotated feature in the annotation file were obtained using qCount v1.1.9
readcounts were normalized using edgeR 3.6.0 to obtain count-per-million (cpm) densities
Genome_build: S288C_reference_genome_R64-2-1_20150113 (www.yeastgenome.org)
Supplementary_files_format_and_content: Normalized_read_counts_mec1-S1991A_tdNA.csv: with identifier and width of annotated tDNA used in the analysis, read count and densities for each sample

growth_protocol: Growth medium : SC + 2% glucose

extract_protocol:
Total RNA was extracted from asynchronous or HU-treated cells using standard hot phenol procedure.
Strand-specific total RNA-seq libraries from rRNA-depleted total RNA with Illumina’s TruSeq kit

treatment_protocol: Exponentially growing MATa cells were grown at 25°C. For hydroxyurea treatment, asynchronous cells were treated with 200mM hydroxyurea for 1h.

tag: strain

tag: cell-cycle phase

value: S phase

value: hydroxyurea 200mM


title: wt_pol2-HA_150

description: Raw data from two models (NextSeq 500/550).

value: BY4741 bar1{delta}0 POL2::Pol2-HA (pYm17+) MCM7::Mcm7-myc (pYM18+)

value: aFactor release + 150min 200 mM HU


title: LS-15580_S31_E1-50

tag: donor

tag: Sex

value: M


title: WT.async

tag: genotype

value: WT

value: asynchronous


title: mec1-S1991A.async


title: wt_pol2-HA_60

value: aFactor release + 60min 200 mM HU


title: wt_pol2-HA_90

value: aFactor release + 90min 200 mM HU


title: LS-15048_S84_E1-50

tag: facs gating

tag: sequencing batch


title: LS-15048_S86_E1-50

tag: cell class

tag: cell cluster


title: wt_pol2-HA_15

tag: antibody

tag: treatment

value: aFactor release + 15min 200 mM HU


title: LS-15048_S83_E1-50

value: RFP-positive


title: LS-15048_S82_E1-50

value: GABA


title: WT.HU


title: LS-15048_S78_E1-50

value: dLGN - Core


title: LS-15048_S90_E1-50


title: LS-15048_S80_E1-50


title: SM-GE67B_S044_E1-50

organism: Macaca nemestrina

source_name: Macaque LGN Magnocellular

tag: age

value: 2.3 yrs

value: MC

value: NeuN-positive

value: Glut


title: SM-GE67B_S043_E1-50


title: SM-GE67B_S042_E1-50


title: LS-15048_S79_E1-50


title: LS-15048_S81_E1-50


title: LS-15048_S77_E1-50


title: SM-GE67B_S041_E1-50


title: LS-15048_S76_E1-50


title: SM-GE67B_S039_E1-50


title: SM-GE67B_S040_E1-50


title: LS-15048_S75_E1-50


title: LS-15048_S74_E1-50


title: LS-15048_S72_E1-50


title: SM-GE67B_S037_E1-50


title: SM-GE67B_S036_E1-50


title: SM-GE67B_S038_E1-50


title: SM-GE67B_S035_E1-50


title: LS-15048_S71_E1-50


title: SM-GE67B_S034_E1-50


title: LS-15048_S70_E1-50


title: LS-15048_S73_E1-50


title: LS-15048_S68_E1-50


title: SM-GE67B_S032_E1-50

value: Low Quality


title: SM-GE67B_S029_E1-50


title: SM-GE67B_S028_E1-50


title: LS-15048_S67_E1-50


title: SM-GE67B_S026_E1-50


title: SM-GE67B_S031_E1-50


title: LS-15048_S69_E1-50


title: LS-15048_S66_E1-50


title: LS-15048_S65_E1-50


title: LS-15034_S94_E1-50


title: LS-15034_S92_E1-50


title: SM-GE67B_S033_E1-50


title: SM-GE67B_S025_E1-50


title: SM-GE67B_S027_E1-50


title: LS-15034_S96_E1-50


title: LS-15034_S93_E1-50


title: LS-15034_S91_E1-50


title: LS-15034_S95_E1-50


title: SM-GE67A_S189_E1-50

source_name: Macaque LGN Parvocellular

value: PC

value: P


title: SM-GE67A_S192_E1-50


title: LS-15034_S90_E1-50


title: SM-GE67B_S030_E1-50


title: LS-15034_S87_E1-50


title: SM-GE67A_S188_E1-50


title: LS-15034_S88_E1-50


title: SM-GE67A_S191_E1-50


title: LS-15034_S86_E1-50


title: SM-GE67A_S187_E1-50


title: LS-15034_S89_E1-50


title: LS-15034_S85_E1-50


title: SM-GE67A_S184_E1-50


title: SM-GE67A_S186_E1-50


title: SM-GE67A_S190_E1-50


title: LS-15034_S84_E1-50


title: SM-GE67A_S185_E1-50


title: LS-15034_S83_E1-50


title: LS-15034_S82_E1-50


title: SM-GE67A_S181_E1-50


title: SM-GE67A_S180_E1-50


title: LS-15034_S81_E1-50


title: SM-GE67A_S183_E1-50


title: LS-15034_S80_E1-50


title: LS-15034_S77_E1-50


title: SM-GE67A_S179_E1-50


title: SM-GE67A_S177_E1-50


title: LS-15034_S78_E1-50


title: LS-15034_S79_E1-50


title: LS-15034_S76_E1-50


title: LS-15034_S75_E1-50


title: SM-GE67A_S176_E1-50


title: SM-GE67A_S175_E1-50


title: SM-GE67A_S174_E1-50


title: SM-GE67A_S173_E1-50


title: LS-15034_S73_E1-50


title: SM-GE67A_S172_E1-50


title: LS-14686_S80_E1-50

source_name: Mouse LGN - Shell

value: dLGN - Shell


title: SM-GE67A_S170_E1-50

value: M


title: LS-14686_S78_E1-50


title: LS-14686_S76_E1-50


title: SM-GE67A_S168_E1-50


title: SM-GE67A_S169_E1-50


title: LS-14686_S74_E1-50


title: LS-14686_S75_E1-50


title: SM-GE67A_S165_E1-50


title: SM-GE67A_S166_E1-50


title: SM-GE67A_S167_E1-50


title: SM-GE67A_S164_E1-50


title: LS-15034_S74_E1-50


title: LS-14686_S72_E1-50


title: SM-GE67A_S162_E1-50


title: SM-GE67A_S171_E1-50


title: SM-GE67A_S161_E1-50


title: LS-14686_S71_E1-50


title: LS-14686_S70_E1-50


title: LS-14686_S68_E1-50


title: SM-GE67A_S160_E1-50


title: LS-14686_S69_E1-50


title: LS-14686_S67_E1-50


title: SM-GE67A_S156_E1-50


title: SM-GE67A_S159_E1-50


title: SM-GE67A_S157_E1-50


title: LS-14686_S73_E1-50


title: LS-14686_S44_E1-50


title: LS-14686_S46_E1-50


title: SM-GE67A_S163_E1-50


title: LS-14686_S41_E1-50


title: SM-GE67A_S152_E1-50


title: SM-GE67A_S155_E1-50


title: SM-GE67A_S154_E1-50


title: LS-14686_S40_E1-50


title: LS-14686_S39_E1-50


title: SM-GE67A_S149_E1-50


title: SM-GE67A_S151_E1-50


title: SM-GE67A_S158_E1-50


title: LS-14686_S79_E1-50


title: SM-GE67A_S150_E1-50


title: LS-14686_S38_E1-50


title: SM-GE67A_S147_E1-50


title: SM-GE67A_S148_E1-50


title: LS-14686_S42_E1-50


title: SM-GE67A_S146_E1-50


title: LS-14686_S36_E1-50


title: LS-14686_S43_E1-50


title: SM-GE67A_S143_E1-50


title: LS-14686_S77_E1-50


title: SM-GE67A_S141_E1-50


title: LS-14686_S33_E1-50


title: LS-14686_S32_E1-50


title: LS-14686_S37_E1-50


title: SM-GE67A_S142_E1-50


title: LS-14686_S31_E1-50


title: LS-14686_S34_E1-50


title: LS-14686_S28_E1-50


title: SM-GE67A_S139_E1-50


title: LS-14686_S30_E1-50


title: LS-14686_S29_E1-50


title: SM-GE67A_S136_E1-50


title: SM-GE67A_S138_E1-50


title: LS-14686_S24_E1-50


title: SM-GE67A_S137_E1-50


title: SM-GE67A_S144_E1-50


title: SM-GE67A_S135_E1-50


title: SM-GE67A_S133_E1-50


title: SM-GE67A_S134_E1-50


title: SM-GE67A_S131_E1-50


title: SM-GE67A_S132_E1-50


title: LS-14686_S35_E1-50


title: LS-14686_S25_E1-50


title: LS-14686_S21_E1-50


title: LS-14686_S23_E1-50


title: LS-14686_S20_E1-50


title: SM-GE67A_S130_E1-50


title: LS-14686_S26_E1-50


title: SM-GE67A_S128_E1-50


title: SM-GE67A_S140_E1-50


title: LS-14685_S88_E1-50

value: LGd


title: LS-14685_S86_E1-50


title: SM-GE67A_S127_E1-50


title: LS-14686_S17_E1-50


title: LS-14686_S27_E1-50


title: LS-14685_S84_E1-50


title: SM-GE67A_S123_E1-50


title: SM-GE67A_S121_E1-50


title: SM-GE67A_S129_E1-50


title: SM-GE67A_S125_E1-50


title: SM-GE67A_S124_E1-50


title: SM-GE67A_S122_E1-50


title: LS-14685_S85_E1-50


title: LS-14686_S19_E1-50


title: LS-14685_S81_E1-50


title: SM-GE91M_S095_E1-50

value: 2.8 yrs


title: SM-GE91M_S096_E1-50


title: LS-14685_S83_E1-50


title: LS-14685_S82_E1-50


title: SM-GE91M_S094_E1-50


title: SM-GE67A_S126_E1-50


title: LS-14685_S78_E1-50


title: LS-14685_S79_E1-50


title: SM-GE91M_S092_E1-50


title: LS-14685_S77_E1-50


title: LS-14685_S76_E1-50


title: LS-14685_S75_E1-50


title: SM-GE91M_S093_E1-50


title: SM-GE91M_S089_E1-50


title: SM-GE91M_S087_E1-50


title: LS-14685_S87_E1-50


title: SM-GE91M_S088_E1-50


title: LS-14685_S72_E1-50


title: LS-14685_S73_E1-50


title: SM-GE91M_S091_E1-50


title: SM-GE91M_S090_E1-50


title: LS-14685_S74_E1-50


title: LS-14685_S71_E1-50


title: SM-GE91M_S085_E1-50


title: SM-GE91M_S086_E1-50


title: LS-14685_S69_E1-50


title: LS-14685_S70_E1-50


title: LS-14685_S66_E1-50


title: LS-14685_S67_E1-50


title: LS-14685_S80_E1-50


title: SM-GE91M_S083_E1-50


title: LS-14685_S65_E1-50


title: LS-14685_S64_E1-50


title: SM-GE91M_S084_E1-50


title: LS-14685_S63_E1-50


title: SM-GE91M_S079_E1-50


title: SM-GE91M_S082_E1-50


title: SM-GE91M_S081_E1-50


title: LS-14685_S62_E1-50


title: SM-GE91M_S078_E1-50


title: LS-14685_S58_E1-50


title: SM-GE91M_S064_E1-50


title: SM-GE91M_S073_E1-50


title: LS-14685_S56_E1-50


title: SM-GE91M_S074_E1-50


title: SM-GE91M_S075_E1-50


title: SM-GE91M_S063_E1-50


title: LS-14685_S68_E1-50


title: LS-14685_S59_E1-50


title: LS-14685_S61_E1-50


title: LS-14685_S57_E1-50


title: LS-14685_S60_E1-50


title: SM-GE91M_S076_E1-50


title: SM-GE91M_S080_E1-50


title: LS-14685_S54_E1-50


title: LS-14685_S52_E1-50


title: LS-14685_S49_E1-50


title: SM-GE91M_S056_E1-50


title: SM-GE91M_S062_E1-50


title: SM-GE91M_S055_E1-50


title: SM-GE91M_S077_E1-50


title: LS-14685_S53_E1-50


title: SM-GE91M_S058_E1-50


title: SM-GE91M_S059_E1-50


title: LS-14685_S47_E1-50


title: SM-GE91M_S060_E1-50


title: SM-GE91M_S061_E1-50


title: LS-14685_S51_E1-50


title: SM-GE91M_S049_E1-50


title: LS-14685_S42_E1-50


title: LS-14685_S41_E1-50


title: LS-14685_S50_E1-50


title: LS-14685_S48_E1-50


title: SM-GE91M_S053_E1-50


title: LS-14685_S46_E1-50


title: LS-14685_S55_E1-50


title: SM-GE91M_S054_E1-50


title: SM-GE91M_S057_E1-50


title: SM-GE67U-Q_S192_E1-50


title: SM-GE91M_S052_E1-50


title: SM-GE91M_S051_E1-50


title: LS-14685_S44_E1-50


title: SM-GE91M_S050_E1-50


title: LS-14686_S94_E1-50


title: LS-14685_S45_E1-50


title: LS-14685_S43_E1-50


title: SM-GE67U-Q_S190_E1-50


title: LS-14686_S95_E1-50


title: SM-GE67U-Q_S189_E1-50


title: LS-14686_S93_E1-50


title: SM-GE67U-Q_S188_E1-50


title: LS-14686_S91_E1-50


title: SM-GE67U-Q_S191_E1-50


title: SM-GE67U-Q_S186_E1-50


title: LS-14686_S90_E1-50


title: SM-GE67U-Q_S185_E1-50


title: LS-14686_S89_E1-50


title: LS-14686_S96_E1-50


title: SM-GE67U-Q_S183_E1-50


title: LS-14686_S87_E1-50


title: LS-14686_S88_E1-50


title: SM-GE67U-Q_S182_E1-50


title: SM-GE67U-Q_S180_E1-50


title: LS-14686_S86_E1-50


title: LS-14686_S84_E1-50


title: SM-GE67U-Q_S181_E1-50


title: LS-14686_S85_E1-50


title: SM-GE67U-Q_S179_E1-50


title: SM-GE67U-Q_S178_E1-50


title: LS-14686_S92_E1-50


title: SM-GE67U-Q_S187_E1-50


title: LS-14686_S82_E1-50


title: LS-14686_S55_E1-50


title: SM-GE67U-Q_S173_E1-50


title: LS-14686_S56_E1-50


title: SM-GE67U-Q_S174_E1-50


title: SM-GE67U-Q_S176_E1-50


title: LS-14686_S83_E1-50


title: SM-GE67U-Q_S172_E1-50


title: SM-GE67U-Q_S184_E1-50


title: SM-GE67U-Q_S171_E1-50


title: LS-14686_S54_E1-50


title: SM-GE67U-Q_S177_E1-50


title: SM-GE67U-Q_S170_E1-50


title: SM-GE67U-Q_S169_E1-50


title: LS-14686_S52_E1-50


title: LS-14686_S53_E1-50


title: LS-14686_S51_E1-50


title: SM-GE67U-Q_S168_E1-50


title: LS-14686_S49_E1-50


title: LS-14686_S15_E1-50


title: SM-GE67U-Q_S165_E1-50


title: LS-14686_S50_E1-50


title: SM-GE67U-Q_S167_E1-50


title: SM-GE67U-Q_S164_E1-50


title: LS-14686_S14_E1-50


title: LS-14686_S81_E1-50


title: SM-GE67U-Q_S163_E1-50


title: LS-14686_S08_E1-50


title: SM-GE67U-Q_S161_E1-50


title: SM-GE67U-Q_S160_E1-50


title: SM-GE67U-Q_S162_E1-50


title: LS-14686_S10_E1-50


title: LS-14686_S11_E1-50


title: LS-14686_S06_E1-50


title: LS-14686_S07_E1-50


title: LS-14686_S09_E1-50


title: SM-GE67U-Q_S157_E1-50


title: LS-14686_S05_E1-50


title: SM-GE67U-Q_S158_E1-50


title: LS-14686_S04_E1-50


title: SM-GE67U-Q_S156_E1-50


title: SM-GE67U-Q_S159_E1-50


title: SM-GE67U-Q_S166_E1-50


title: SM-GE67U-Q_S155_E1-50


title: SM-GE67U-Q_S153_E1-50


title: SM-GE67U-Q_S152_E1-50


title: SM-GE67U-Q_S154_E1-50


title: LS-14686_S02_E1-50


title: LS-14686_S01_E1-50


title: LS-14685_S38_E1-50


title: LS-14685_S40_E1-50


title: SM-GE67U-Q_S151_E1-50


title: SM-GE67U-Q_S150_E1-50


title: SM-GE67U-Q_S147_E1-50


title: LS-14685_S36_E1-50


title: LS-14685_S37_E1-50


title: SM-GE67U-Q_S146_E1-50


title: LS-14686_S03_E1-50


title: SM-GE67U-Q_S148_E1-50


title: LS-14685_S39_E1-50


title: LS-14685_S32_E1-50


title: LS-14685_S31_E1-50


title: SM-GE67U-Q_S141_E1-50


title: LS-14685_S30_E1-50


title: SM-GE67U-Q_S145_E1-50


title: LS-14685_S33_E1-50


title: SM-GE67U-Q_S144_E1-50


title: SM-GE67U-Q_S143_E1-50


title: LS-14685_S34_E1-50


title: SM-GE67U-Q_S142_E1-50


title: LS-14685_S29_E1-50


title: SM-GE67U-Q_S140_E1-50


title: LS-14685_S28_E1-50


title: SM-GE67U-Q_S138_E1-50


title: LS-14685_S35_E1-50


title: LS-14685_S25_E1-50


title: SM-GE67U-Q_S137_E1-50


title: LS-14686_S13_E1-50


title: LS-14685_S23_E1-50


title: LS-14685_S27_E1-50


title: SM-GE67U-Q_S134_E1-50


title: SM-GE67U-Q_S139_E1-50


title: LS-14685_S21_E1-50


title: SM-GE67U-Q_S136_E1-50


title: LS-14685_S26_E1-50


title: SM-GE67U-Q_S132_E1-50


title: LS-14685_S24_E1-50


title: SM-GE67U-Q_S135_E1-50


title: SM-GE67U-Q_S133_E1-50


title: LS-14685_S22_E1-50


title: SM-GE67U-Q_S131_E1-50


title: SM-GE67U-Q_S130_E1-50


title: LS-14685_S20_E1-50


title: LS-14685_S19_E1-50


title: SM-GE67U-Q_S064_E1-50


title: LS-14685_S15_E1-50


title: LS-14685_S17_E1-50


title: LS-14685_S14_E1-50


title: SM-GE67U-Q_S063_E1-50


title: SM-GE67U-Q_S129_E1-50


title: LS-14685_S16_E1-50


title: SM-GE67U-Q_S062_E1-50


title: SM-GE67U-Q_S061_E1-50


title: LS-14685_S13_E1-50


title: SM-GE67U-Q_S059_E1-50


title: LS-14685_S10_E1-50


title: SM-GE67U-Q_S060_E1-50


title: LS-14685_S09_E1-50


title: LS-14685_S12_E1-50


title: SM-GE67U-Q_S058_E1-50


title: SM-GE67U-Q_S056_E1-50


title: SM-GE67U-Q_S055_E1-50


title: SM-GE67U-Q_S052_E1-50


title: SM-GE67U-Q_S054_E1-50


title: LS-14684_S70_E1-50


title: LS-14684_S72_E1-50


title: LS-14684_S71_E1-50


title: LS-14684_S69_E1-50


title: SM-GE67U-Q_S050_E1-50


title: LS-14684_S68_E1-50


title: SM-GE67U-Q_S051_E1-50


title: LS-14684_S67_E1-50


title: LS-14684_S65_E1-50


title: SM-GE67U-Q_S046_E1-50


title: SM-GE67U-Q_S047_E1-50


title: LS-14684_S66_E1-50


title: LS-14685_S11_E1-50


title: SM-GE67U-Q_S045_E1-50


title: LS-14684_S64_E1-50


title: LS-14684_S63_E1-50


title: SM-GE67U-Q_S043_E1-50


title: SM-GE67U-Q_S042_E1-50


title: SM-GE67U-Q_S044_E1-50


title: LS-14684_S62_E1-50


title: SM-GE67U-Q_S053_E1-50


title: LS-14684_S59_E1-50


title: SM-GE67U-Q_S040_E1-50


title: LS-14684_S60_E1-50


title: SM-GE67U-Q_S039_E1-50


title: LS-14684_S56_E1-50


title: SM-GE67U-Q_S038_E1-50


title: SM-GE67U-Q_S037_E1-50


title: LS-14684_S54_E1-50


title: LS-14684_S57_E1-50


title: SM-GE67U-Q_S049_E1-50


title: LS-14684_S53_E1-50


title: SM-GE67U-Q_S036_E1-50


title: SM-GE67U-Q_S035_E1-50


title: LS-14684_S52_E1-50


title: SM-GE67U-Q_S034_E1-50


title: SM-GE67U-Q_S033_E1-50


title: LS-14684_S50_E1-50


title: LS-14684_S51_E1-50


title: SM-GE67U-Q_S032_E1-50


title: LS-14684_S49_E1-50


title: SM-GE67U-Q_S041_E1-50


title: SM-GE67U-Q_S030_E1-50


title: LS-14684_S55_E1-50


title: SM-GE67U-Q_S031_E1-50


title: LS-14672_S25_E1-50


title: SM-GE67U-Q_S027_E1-50


title: LS-14672_S20_E1-50


title: SM-GE67U-Q_S016_E1-50


title: LS-14672_S26_E1-50


title: SM-GE67U-Q_S026_E1-50


title: SM-GE67U-Q_S029_E1-50


title: LS-14672_S24_E1-50


title: SM-GE67U-Q_S025_E1-50


title: SM-GE67U-Q_S028_E1-50


title: LS-14672_S22_E1-50


title: LS-14672_S21_E1-50


title: SM-GE67U-Q_S015_E1-50


title: LS-14672_S17_E1-50


title: SM-GE67U-Q_S014_E1-50


title: LS-14672_S18_E1-50


title: SM-GE67U-Q_S013_E1-50


title: LS-14672_S16_E1-50


title: LS-14672_S27_E1-50


title: SM-GE67U-Q_S010_E1-50


title: SM-GE67U-Q_S011_E1-50


title: LS-14672_S15_E1-50

value: Non-Neuronal


title: LS-14672_S23_E1-50


title: SM-GE67U-Q_S009_E1-50


title: LS-14672_S13_E1-50


title: SM-GE67U-Q_S008_E1-50


title: LS-14672_S14_E1-50


title: LS-14684_S61_E1-50


title: LS-14672_S19_E1-50


title: SM-GE67U-Q_S006_E1-50


title: LS-14672_S11_E1-50


title: LS-14672_S10_E1-50


title: LS-14672_S12_E1-50


title: SM-GE67U-Q_S005_E1-50


title: SM-GE67U-Q_S012_E1-50


title: SM-GE67U-Q_S004_E1-50


title: LS-14672_S09_E1-50


title: SM-GE67U-Q_S003_E1-50


title: LS-14672_S07_E1-50


title: SM-GE67U-Q_S002_E1-50


title: LS-14672_S04_E1-50


title: LS-14672_S05_E1-50


title: SM-GE67R-Q_S094_E1-50


title: SM-GE67R-Q_S095_E1-50


title: LS-14672_S06_E1-50


title: LS-14672_S03_E1-50


title: SM-GE67R-Q_S096_E1-50


title: SM-GE67U-Q_S001_E1-50


title: SM-GE67R-Q_S093_E1-50


title: SM-GE67R-Q_S092_E1-50


title: LS-14672_S01_E1-50


title: SM-GE67U-Q_S007_E1-50


title: LS-14671_S96_E1-50


title: SM-GE67R-Q_S091_E1-50


title: SM-GE67R-Q_S090_E1-50


title: LS-14671_S95_E1-50


title: LS-14671_S94_E1-50


title: SM-GE67R-Q_S088_E1-50


title: SM-GE67R-Q_S089_E1-50


title: LS-14671_S91_E1-50


title: LS-14671_S92_E1-50


title: LS-14671_S90_E1-50


title: SM-GE67R-Q_S086_E1-50


title: LS-14672_S02_E1-50


title: LS-14671_S89_E1-50


title: SM-GE67R-Q_S085_E1-50


title: SM-GE67R-Q_S084_E1-50


title: SM-GE67R-Q_S083_E1-50


title: SM-GE67R-Q_S087_E1-50


title: SM-GE67R-Q_S080_E1-50


title: SM-GE67R-Q_S079_E1-50


title: SM-GE67R-Q_S081_E1-50

value: Pulv


title: SM-GE67R-Q_S076_E1-50


title: LS-14671_S77_E1-50


title: LS-14671_S79_E1-50


title: LS-14672_S08_E1-50


title: LS-14671_S76_E1-50


title: LS-14671_S80_E1-50


title: LS-14671_S75_E1-50


title: LS-14671_S73_E1-50


title: LS-14671_S74_E1-50


title: LS-14671_S78_E1-50


title: SM-GE67R-Q_S075_E1-50


title: LS-14671_S72_E1-50


title: SM-GE67R-Q_S074_E1-50


title: SM-GE67R-Q_S073_E1-50


title: LS-14671_S71_E1-50


title: LS-14671_S93_E1-50


title: SM-GE67R-Q_S072_E1-50


title: SM-GE67R-Q_S071_E1-50


title: LS-14671_S70_E1-50


title: SM-GE67R-Q_S070_E1-50


title: LS-14671_S67_E1-50


title: LS-14671_S68_E1-50


title: SM-GE67R-Q_S077_E1-50


title: LS-14671_S69_E1-50


title: SM-GE67R-Q_S067_E1-50


title: SM-GE67R-Q_S068_E1-50


title: LS-14671_S66_E1-50


title: LS-14671_S65_E1-50


title: SM-GE67R-Q_S066_E1-50


title: SM-GE67R-Q_S065_E1-50


title: LS-14671_S45_E1-50


title: LS-14671_S46_E1-50


title: LS-14671_S43_E1-50


title: LS-14671_S48_E1-50


title: SM-GE67H_S186_E1-50


title: SM-GE67H_S188_E1-50


title: SM-GE67H_S190_E1-50


title: LS-14671_S47_E1-50


title: LS-14671_S41_E1-50


title: LS-14671_S42_E1-50


title: SM-GE67H_S187_E1-50


title: SM-GE67H_S189_E1-50


title: LS-14671_S40_E1-50


title: LS-14671_S44_E1-50


title: SM-GE67H_S185_E1-50


title: SM-GE67H_S183_E1-50


title: LS-14671_S37_E1-50


title: SM-GE67H_S182_E1-50


title: LS-14671_S38_E1-50


title: SM-GE67H_S180_E1-50


title: SM-GE67H_S192_E1-50


title: SM-GE67H_S179_E1-50


title: SM-GE67H_S191_E1-50


title: LS-14671_S34_E1-50


title: LS-14671_S33_E1-50


title: SM-GE67H_S177_E1-50


title: SM-GE67H_S178_E1-50


title: SM-GE67H_S167_E1-50


title: SM-GE67H_S164_E1-50


title: LS-14671_S16_E1-50


title: SM-GE67H_S184_E1-50


title: LS-14671_S11_E1-50


title: LS-14671_S10_E1-50


title: LS-14671_S39_E1-50


title: LS-14671_S15_E1-50


title: SM-GE67H_S168_E1-50


title: LS-14671_S36_E1-50


title: LS-14671_S13_E1-50


title: SM-GE67H_S165_E1-50


title: LS-14671_S09_E1-50


title: SM-GE67H_S181_E1-50


title: LS-14671_S12_E1-50


title: LS-14671_S35_E1-50


title: SM-GE67H_S166_E1-50


title: LS-14671_S07_E1-50


title: LS-14671_S14_E1-50


title: SM-GE67H_S162_E1-50


title: SM-GE67H_S160_E1-50


title: SM-GE67H_S159_E1-50


title: SM-GE67H_S163_E1-50


title: LS-14671_S05_E1-50


title: SM-GE67H_S157_E1-50


title: SM-GE67H_S156_E1-50


title: SM-GE67H_S158_E1-50


title: SM-GE67H_S161_E1-50


title: LS-14671_S06_E1-50


title: SM-GE67H_S153_E1-50


title: LS-14671_S08_E1-50


title: SM-GE67H_S151_E1-50


title: LS-14670_S95_E1-50


title: LS-14670_S93_E1-50


title: SM-GE67H_S150_E1-50


title: LS-14671_S01_E1-50


title: SM-GE67H_S149_E1-50


title: LS-14671_S03_E1-50


title: SM-GE67H_S154_E1-50


title: LS-14671_S02_E1-50


title: LS-14670_S92_E1-50


title: LS-14670_S96_E1-50


title: SM-GE67H_S152_E1-50


title: LS-14670_S94_E1-50


title: LS-14670_S91_E1-50


title: LS-14671_S04_E1-50


title: SM-GE67H_S148_E1-50


title: SM-GE67H_S146_E1-50


title: LS-14670_S90_E1-50


title: SM-GE67H_S144_E1-50


title: LS-14670_S88_E1-50


title: SM-GE67H_S145_E1-50


title: LS-14670_S87_E1-50


title: SM-GE67H_S143_E1-50


title: SM-GE67H_S155_E1-50


title: LS-14670_S83_E1-50


title: SM-GE67H_S147_E1-50


title: LS-14670_S81_E1-50


title: SM-GE67H_S140_E1-50


title: SM-GE67H_S139_E1-50


title: SM-GE67H_S142_E1-50


title: SM-GE67H_S141_E1-50


title: SM-GE67H_S138_E1-50


title: LS-14670_S82_E1-50


title: LS-14670_S46_E1-50


title: LS-14670_S85_E1-50


title: SM-GE67H_S094_E1-50


title: SM-GE67H_S137_E1-50


title: LS-14670_S89_E1-50


title: SM-GE67H_S095_E1-50


title: LS-14670_S47_E1-50


title: SM-GE67H_S096_E1-50


title: LS-14670_S48_E1-50


title: LS-14670_S45_E1-50


title: LS-14670_S84_E1-50


title: SM-GE67H_S093_E1-50


title: LS-14670_S86_E1-50


title: LS-14670_S44_E1-50


title: LS-14670_S43_E1-50


title: SM-GE67H_S092_E1-50


title: LS-14670_S42_E1-50


title: LS-14670_S41_E1-50


title: LS-14670_S40_E1-50


title: SM-GE67H_S089_E1-50


title: SM-GE67H_S091_E1-50


title: LS-14670_S38_E1-50


title: SM-GE67H_S088_E1-50


title: SM-GE67H_S087_E1-50


title: LS-14670_S39_E1-50


title: SM-GE67H_S090_E1-50


title: SM-GE67H_S086_E1-50


title: SM-GE67H_S084_E1-50


title: SM-GE67H_S085_E1-50


title: SM-GE67H_S082_E1-50


title: LS-14670_S35_E1-50


title: LS-14670_S36_E1-50


title: LS-14670_S34_E1-50


title: LS-14670_S37_E1-50


title: SM-GE67H_S080_E1-50


title: SM-GE67H_S083_E1-50


title: SM-GE67H_S076_E1-50


title: SM-GE67H_S079_E1-50


title: SM-GE67H_S078_E1-50


title: LS-14670_S30_E1-50


title: LS-14670_S31_E1-50


title: SM-GE67H_S074_E1-50


title: LS-14670_S29_E1-50


title: SM-GE67H_S081_E1-50


title: SM-GE67H_S077_E1-50


title: SM-GE67H_S062_E1-50


title: SM-GE67H_S061_E1-50


title: LS-14670_S22_E1-50


title: LS-14670_S28_E1-50


title: LS-14670_S23_E1-50


title: LS-14670_S33_E1-50


title: LS-14670_S18_E1-50


title: LS-14670_S26_E1-50


title: SM-GE67H_S059_E1-50


title: LS-14670_S17_E1-50


title: SM-GE67H_S058_E1-50


title: LS-14670_S24_E1-50


title: SM-GE67H_S075_E1-50


title: LS-14670_S25_E1-50


title: LS-14670_S07_E1-50

value: LP


title: SM-GE67H_S073_E1-50


title: SM-GE67H_S057_E1-50


title: SM-GE67H_S064_E1-50


title: SM-GE67H_S063_E1-50


title: LS-14670_S08_E1-50

value: RFP-positive


title: LS-14670_S20_E1-50


title: LS-14670_S19_E1-50


title: LS-14670_S05_E1-50


title: SM-GE67H_S056_E1-50

value: GABA


title: SM-GE67H_S060_E1-50


title: LS-14670_S27_E1-50

value: dLGN - Core


title: SM-GE67H_S055_E1-50


title: LS-14670_S06_E1-50


title: LS-14670_S04_E1-50


title: SM-GE67H_S050_E1-50


title: SM-GE67H_S051_E1-50


title: SM-GE67H_S052_E1-50


title: SM-GE67H_S053_E1-50


title: SM-GE67H_S049_E1-50


title: LS-14670_S02_E1-50


title: LS-14668_S94_E1-50


title: LS-14668_S96_E1-50


title: LS-14670_S01_E1-50


title: LS-14668_S95_E1-50


title: SM-GE67H_S044_E1-50


title: LS-14670_S03_E1-50


title: SM-GE67H_S045_E1-50


title: LS-14668_S92_E1-50


title: SM-GE67H_S046_E1-50


title: SM-GE67H_S048_E1-50


title: LS-14668_S93_E1-50


title: SM-GE67H_S047_E1-50


title: LS-14668_S90_E1-50


title: LS-14668_S91_E1-50


title: SM-GE67H_S054_E1-50


title: SM-GE67H_S042_E1-50


title: SM-GE67H_S041_E1-50


title: SM-GE67H_S043_E1-50


title: LS-14668_S89_E1-50


title: LS-14668_S88_E1-50


title: SM-GE67G_S192_E1-50


title: LS-14668_S85_E1-50


title: LS-14668_S86_E1-50


title: LS-14668_S84_E1-50


title: SM-GE67G_S189_E1-50


title: SM-GE67G_S191_E1-50


title: SM-GE67G_S190_E1-50


title: SM-GE67G_S188_E1-50


title: LS-14668_S82_E1-50


title: SM-GE67G_S185_E1-50


title: SM-GE67G_S187_E1-50


title: SM-GE67G_S183_E1-50


title: SM-GE67G_S186_E1-50


title: LS-14668_S70_E1-50


title: SM-GE67G_S184_E1-50


title: LS-14668_S69_E1-50


title: LS-14668_S71_E1-50


title: LS-14668_S87_E1-50


title: SM-GE67G_S181_E1-50


title: SM-GE67G_S182_E1-50


title: SM-GE67G_S179_E1-50


title: LS-14668_S67_E1-50


title: LS-14668_S68_E1-50


title: LS-14670_S32_E1-50


title: LS-14668_S66_E1-50


title: LS-14668_S83_E1-50


title: LS-14668_S65_E1-50


title: SM-GE67G_S178_E1-50


title: LS-14668_S64_E1-50


title: LS-14668_S63_E1-50


title: LS-14668_S72_E1-50


title: LS-14668_S81_E1-50


title: LS-14668_S62_E1-50


title: SM-GE67G_S175_E1-50


title: SM-GE67G_S174_E1-50


title: LS-14668_S61_E1-50


title: SM-GE67G_S173_E1-50


title: SM-GE67G_S172_E1-50


title: LS-14668_S59_E1-50


title: LS-14668_S58_E1-50


title: SM-GE67G_S171_E1-50


title: LS-14668_S57_E1-50


title: SM-GE67G_S170_E1-50


title: SM-GE67G_S096_E1-50


title: LS-14668_S40_E1-50


title: SM-GE67G_S176_E1-50


title: SM-GE67G_S177_E1-50


title: SM-GE67G_S169_E1-50


title: LS-14668_S37_E1-50


title: SM-GE67G_S094_E1-50


title: SM-GE67G_S093_E1-50


title: LS-14668_S60_E1-50


title: SM-GE67G_S091_E1-50


title: LS-14668_S36_E1-50


title: LS-14668_S33_E1-50


title: LS-14668_S39_E1-50


title: SM-GE67G_S088_E1-50


title: SM-GE67G_S090_E1-50


title: LS-14668_S35_E1-50


title: LS-14668_S30_E1-50


title: LS-14668_S29_E1-50


title: LS-14668_S32_E1-50


title: LS-14668_S31_E1-50


title: SM-GE67G_S089_E1-50


title: LS-14668_S34_E1-50


title: SM-GE67G_S086_E1-50


title: SM-GE67G_S087_E1-50


title: LS-14668_S28_E1-50


title: LS-14668_S26_E1-50


title: SM-GE67G_S092_E1-50


title: LS-14668_S27_E1-50


title: SM-GE67G_S095_E1-50


title: SM-GE67G_S084_E1-50


title: SM-GE67G_S083_E1-50


title: SM-GE67G_S085_E1-50


title: SM-GE67G_S081_E1-50


title: LS-14668_S23_E1-50


title: SM-GE67G_S082_E1-50


title: LS-14668_S25_E1-50


title: LS-14668_S24_E1-50


title: SM-GE67G_S080_E1-50


title: SM-GE67G_S078_E1-50


title: LS-14668_S20_E1-50


title: LS-14668_S22_E1-50


title: SM-GE67G_S076_E1-50


title: LS-14668_S19_E1-50


title: LS-14668_S21_E1-50


title: SM-GE67G_S074_E1-50


title: LS-14668_S16_E1-50


title: LS-14668_S17_E1-50


title: SM-GE67G_S073_E1-50


title: LS-14668_S18_E1-50


title: SM-GE67G_S075_E1-50


title: SM-GE67G_S072_E1-50


title: LS-14668_S14_E1-50


title: LS-14668_S13_E1-50


title: LS-14668_S12_E1-50


title: SM-GE67G_S079_E1-50


title: SM-GE67G_S069_E1-50


title: SM-GE67G_S067_E1-50


title: LS-14668_S11_E1-50


title: LS-14668_S10_E1-50


title: SM-GE67G_S077_E1-50


title: SM-GE67G_S068_E1-50


title: SM-GE67G_S071_E1-50


title: LS-14668_S08_E1-50


title: SM-GE67G_S066_E1-50


title: LS-14668_S09_E1-50


title: LS-14668_S07_E1-50


title: LS-14668_S05_E1-50


title: LS-14668_S06_E1-50


title: SM-GE67G_S064_E1-50


title: SM-GE67G_S063_E1-50


title: LS-14668_S04_E1-50


title: SM-GE67G_S061_E1-50


title: SM-GE67G_S062_E1-50


title: LS-14668_S02_E1-50


title: SM-GE67G_S060_E1-50


title: SM-GE67G_S070_E1-50


title: LS-14668_S01_E1-50


title: SM-GE67G_S058_E1-50


title: SM-GE67G_S057_E1-50


title: LS-14667_S87_E1-50


title: SM-GE67G_S059_E1-50


title: SM-GE67G_S048_E1-50


title: SM-GE67G_S065_E1-50


title: LS-14667_S86_E1-50


title: LS-14667_S88_E1-50


title: SM-GE67G_S046_E1-50


title: LS-14667_S84_E1-50


title: LS-14667_S83_E1-50


title: LS-14667_S85_E1-50


title: SM-GE67G_S045_E1-50


title: LS-14667_S82_E1-50


title: LS-14667_S81_E1-50


title: SM-GE67G_S044_E1-50


title: LS-14667_S71_E1-50


title: LS-14668_S03_E1-50


title: SM-GE67G_S047_E1-50


title: SM-GE67G_S043_E1-50


title: SM-GE67G_S041_E1-50


title: LS-14667_S69_E1-50


title: LS-14667_S70_E1-50


title: SM-GE67G_S040_E1-50


title: SM-GE67G_S039_E1-50


title: LS-14667_S68_E1-50


title: SM-GE67G_S038_E1-50


title: LS-14667_S67_E1-50


title: LS-14667_S63_E1-50


title: SM-GE67G_S035_E1-50


title: LS-14667_S65_E1-50


title: SM-GE67G_S033_E1-50


title: SM-GE67G_S032_E1-50


title: SM-GE67G_S042_E1-50


title: LS-14667_S61_E1-50


title: SM-GE67G_S030_E1-50


title: SM-GE67G_S029_E1-50


title: LS-14667_S56_E1-50


title: SM-GE67G_S034_E1-50


title: SM-GE67G_S028_E1-50


title: SM-GE67G_S037_E1-50


title: LS-14667_S58_E1-50


title: SM-GE67G_S031_E1-50


title: LS-14667_S59_E1-50


title: SM-GE67G_S036_E1-50


title: LS-14667_S64_E1-50


title: SM-GE67G_S025_E1-50


title: LS-14667_S62_E1-50


title: LS-14667_S53_E1-50


title: LS-14667_S57_E1-50


title: SM-GE67G_S027_E1-50


title: SM-GE67F_S190_E1-50


title: LS-14667_S60_E1-50


title: LS-14667_S55_E1-50


title: LS-14667_S66_E1-50


title: SM-GE67F_S192_E1-50


title: LS-14667_S54_E1-50


title: SM-GE67F_S191_E1-50


title: SM-GE67F_S189_E1-50


title: LS-14667_S52_E1-50


title: SM-GE67F_S188_E1-50


title: SM-GE67F_S187_E1-50


title: SM-GE67F_S186_E1-50


title: LS-14667_S49_E1-50


title: LS-14667_S50_E1-50


title: SM-GE67F_S185_E1-50


title: LS-14667_S47_E1-50


title: LS-14667_S46_E1-50


title: SM-GE67F_S184_E1-50


title: LS-14667_S44_E1-50


title: LS-14667_S51_E1-50


title: SM-GE67F_S183_E1-50


title: SM-GE67F_S182_E1-50


title: LS-14667_S45_E1-50


title: SM-GE67F_S180_E1-50


title: LS-14667_S42_E1-50


title: LS-14667_S41_E1-50


title: SM-GE67F_S179_E1-50


title: LS-14667_S39_E1-50


title: SM-GE67F_S181_E1-50


title: LS-14667_S48_E1-50


title: LS-14667_S38_E1-50


title: SM-GE67F_S174_E1-50


title: SM-GE67F_S176_E1-50


title: LS-14667_S40_E1-50


title: SM-GE67F_S177_E1-50


title: LS-14667_S34_E1-50


title: LS-14667_S33_E1-50


title: LS-14667_S36_E1-50


title: LS-14667_S37_E1-50


title: LS-14667_S32_E1-50


title: SM-GE67F_S171_E1-50


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title: LS-14667_S35_E1-50


title: SM-GE67F_S172_E1-50


title: LS-14667_S43_E1-50


title: LS-14667_S30_E1-50


title: SM-GE67F_S168_E1-50


title: LS-14667_S31_E1-50


title: SM-GE67F_S175_E1-50


title: SM-GE67F_S167_E1-50


title: SM-GE67F_S165_E1-50


title: SM-GE67F_S166_E1-50


title: SM-GE67F_S173_E1-50


title: LS-14667_S29_E1-50


title: SM-GE67F_S163_E1-50


title: LS-14667_S28_E1-50


title: LS-14667_S27_E1-50


title: SM-GE67F_S164_E1-50


title: SM-GE67F_S162_E1-50


title: LS-14667_S25_E1-50


title: SM-GE67F_S161_E1-50


title: LS-14665_S88_E1-50


title: SM-GE67F_S160_E1-50


title: SM-GE67F_S170_E1-50


title: LS-14665_S87_E1-50


title: SM-GE67F_S159_E1-50


title: LS-14665_S86_E1-50


title: LS-14665_S85_E1-50


title: LS-14665_S84_E1-50


title: SM-GE67F_S157_E1-50


title: SM-GE67F_S158_E1-50


title: LS-14667_S26_E1-50


title: LS-14665_S83_E1-50


title: SM-GE67F_S155_E1-50


title: SM-GE67F_S156_E1-50


title: LS-14665_S81_E1-50


title: LS-14665_S82_E1-50


title: LS-14665_S80_E1-50


title: SM-GE67F_S154_E1-50


title: SM-GE67F_S151_E1-50


title: LS-14665_S77_E1-50


title: SM-GE67F_S150_E1-50


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title: LS-14665_S79_E1-50


title: LS-14665_S78_E1-50


title: LS-14665_S72_E1-50


title: LS-14665_S76_E1-50


title: SM-GE67F_S153_E1-50


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title: SM-GE67F_S134_E1-50


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title: SM-GE67F_S146_E1-50


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title: LS-14665_S68_E1-50


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title: LS-14665_S73_E1-50


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title: LS-14665_S65_E1-50


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title: LS-14665_S63_E1-50


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title: LS-14665_S62_E1-50


title: SM-GE67F_S126_E1-50


title: SM-GE67F_S127_E1-50


title: SM-GE67F_S131_E1-50


title: LS-14665_S60_E1-50


title: LS-14665_S61_E1-50


title: LS-14665_S59_E1-50


title: SM-GE67F_S124_E1-50


title: SM-GE67F_S125_E1-50


title: LS-14665_S57_E1-50


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title: SM-GE67F_S094_E1-50


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title: SM-GE67F_S089_E1-50


title: SM-GE67F_S088_E1-50


title: SM-GE67F_S090_E1-50


title: LS-14665_S38_E1-50


title: LS-14665_S39_E1-50


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title: SM-GE67F_S083_E1-50


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title: SM-GE67F_S070_E1-50


title: LS-14665_S06_E1-50


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title: LS-14665_S02_E1-50


title: LS-14665_S01_E1-50


title: SM-GE67F_S081_E1-50


title: R8-15101204_S87_E1-50


title: SM-GE67F_S072_E1-50


title: SM-GE67F_S071_E1-50


title: SM-GE67F_S063_E1-50


title: R8-15101204_S85_E1-50


title: LS-14665_S03_E1-50


title: LS-14665_S05_E1-50


title: SM-GE67F_S077_E1-50


title: SM-GE67F_S074_E1-50


title: SM-GE67F_S069_E1-50


title: SM-GE67F_S061_E1-50


title: R8-15101204_S81_E1-50


title: SM-GE67F_S067_E1-50


title: SM-GE67F_S068_E1-50


title: R8-15101204_S88_E1-50


title: SM-GE67F_S065_E1-50


title: SM-GE67F_S056_E1-50


title: SM-GE67F_S066_E1-50


title: R8-15101204_S78_E1-50


title: R8-15101204_S77_E1-50


title: SM-GE67F_S062_E1-50


title: R8-15101204_S83_E1-50


title: R8-15101204_S86_E1-50


title: R8-15101204_S84_E1-50


title: SM-GE67F_S059_E1-50


title: SM-GE67F_S055_E1-50


title: R8-15101204_S75_E1-50


title: SM-GE67F_S058_E1-50


title: R8-15101204_S79_E1-50


title: R8-15101204_S80_E1-50


title: SM-GE67F_S051_E1-50


title: R8-15101204_S39_E1-50


title: R8-15101204_S76_E1-50


title: SM-GE67F_S057_E1-50


title: SM-GE67F_S049_E1-50


title: SM-GE67F_S054_E1-50


title: R8-15101204_S74_E1-50


title: SM-GE67F_S060_E1-50


title: SM-GE67F_S046_E1-50


title: SM-GE67F_S053_E1-50


title: SM-GE67F_S045_E1-50


title: R8-15101204_S35_E1-50


title: R8-15101204_S34_E1-50


title: R8-15101204_S73_E1-50


title: R8-15101204_S82_E1-50


title: SM-GE67F_S052_E1-50


title: R8-15101204_S33_E1-50


title: R8-15101204_S40_E1-50


title: R8-15101204_S36_E1-50


title: SM-GE67F_S064_E1-50


title: SM-GE67F_S047_E1-50


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title: R8-15101204_S31_E1-50


title: SM-GE67F_S044_E1-50


title: R8-15101204_S32_E1-50


title: SM-GE67F_S041_E1-50


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title: R8-15101204_S29_E1-50


title: SM-GE67F_S031_E1-50


title: SM-GE67F_S030_E1-50


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title: R8-15101204_S25_E1-50


title: SM-GE67F_S032_E1-50


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title: R8-15101204_S16_E1-50


title: SM-GE67F_S027_E1-50


title: R8-15101204_S27_E1-50


title: R8-15101204_S15_E1-50


title: SM-GE67D_S048_E1-50


title: SM-GE67D_S047_E1-50


title: R8-15101204_S14_E1-50


title: R8-15101204_S13_E1-50


title: R8-15101204_S11_E1-50


title: SM-GE67D_S046_E1-50


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title: SM-GE67D_S042_E1-50


title: SM-GE67D_S044_E1-50


title: SM-GE67D_S045_E1-50


title: R8-15101203_S88_E1-50


title: R8-15101204_S10_E1-50


title: SM-GE67D_S043_E1-50


title: R8-15101203_S87_E1-50


title: R8-15101203_S86_E1-50


title: R8-15101203_S85_E1-50


title: R8-15101203_S84_E1-50


title: R8-15101203_S82_E1-50


title: SM-GE67D_S041_E1-50


title: SM-GE67D_S037_E1-50


title: SM-GE67D_S040_E1-50


title: SM-GE67D_S039_E1-50


title: R8-15101204_S12_E1-50


title: R8-15101203_S83_E1-50


title: SM-GE67D_S038_E1-50


title: SM-GE67D_S036_E1-50


title: R8-15101203_S40_E1-50


title: R8-15101203_S81_E1-50


title: R8-15101204_S09_E1-50


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title: SM-GE67D_S035_E1-50


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title: R8-15101203_S36_E1-50


title: SM-GE67D_S031_E1-50


title: R8-15101203_S38_E1-50


title: SM-GE67D_S030_E1-50


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title: R8-15101203_S33_E1-50


title: R8-15101203_S35_E1-50


title: R8-15101203_S14_E1-50


title: SM-GE67D_S024_E1-50


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title: R8-15101203_S12_E1-50


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title: SM-GE67D_S021_E1-50


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title: R8-15101203_S10_E1-50


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title: R8-15101203_S37_E1-50


title: R8-15101203_S11_E1-50


title: R8-15101202_S93_E1-50


title: R8-15101202_S94_E1-50


title: SM-GE67D_S020_E1-50


title: R8-15101202_S95_E1-50


title: SM-GE67D_S014_E1-50


title: SM-GE67D_S013_E1-50


title: R8-15101202_S91_E1-50


title: SM-GE67D_S016_E1-50


title: SM-GE67D_S012_E1-50


title: R8-15101202_S90_E1-50


title: SM-GE67D_S009_E1-50


title: R8-15101202_S86_E1-50


title: SM-GE67D_S010_E1-50


title: SM-GE67D_S015_E1-50


title: SM-GE67D_S008_E1-50


title: SM-GE67D_S011_E1-50


title: R8-15101202_S85_E1-50


title: R8-15101202_S92_E1-50


title: SM-GE67D_S007_E1-50


title: R8-15101202_S83_E1-50


title: SM-GE67D_S006_E1-50


title: R8-15101202_S81_E1-50


title: SM-GE67D_S005_E1-50


title: R8-15101202_S82_E1-50


title: R8-15101202_S88_E1-50


title: SM-GE67D_S003_E1-50


title: SM-GE67D_S004_E1-50


title: R8-15101202_S87_E1-50


title: SM-GE67D_S001_E1-50


title: R8-15101202_S84_E1-50


title: R8-15101202_S64_E1-50


title: R8-15101202_S63_E1-50


title: SM-GE67B_S104_E1-50


title: SM-GE67D_S002_E1-50


title: SM-GE67B_S102_E1-50


title: R8-15101202_S62_E1-50


title: SM-GE67B_S103_E1-50


title: SM-GE67B_S101_E1-50


title: R8-15101202_S58_E1-50


title: R8-15101202_S55_E1-50


title: SM-GE67D_S028_E1-50


title: R8-15101202_S54_E1-50


title: SM-GE67B_S100_E1-50


title: SM-GE67B_S099_E1-50


title: R8-15101202_S56_E1-50


title: SM-GE67B_S098_E1-50


title: SM-GE67B_S097_E1-50


title: R8-15101202_S52_E1-50


title: SM-GE67F_S050_E1-50


title: R8-15101202_S60_E1-50


title: R8-15101202_S59_E1-50


title: R8-15101202_S50_E1-50


title: R8-15101202_S51_E1-50


title: SM-GE67B_S016_E1-50


title: R8-15101202_S49_E1-50


title: SM-GE67B_S015_E1-50


title: R8-15101202_S48_E1-50


title: SM-GE67B_S014_E1-50


title: SM-GE67B_S011_E1-50


title: SM-GE67B_S012_E1-50


title: R8-15101202_S45_E1-50


title: R8-15101202_S46_E1-50


title: SM-GE67B_S013_E1-50


title: R8-15101202_S53_E1-50


title: SM-GE67B_S010_E1-50


title: R8-15101202_S44_E1-50


title: SM-GE67B_S009_E1-50


title: R8-15101202_S42_E1-50


title: R8-15101202_S43_E1-50


title: R8-15101202_S41_E1-50


title: R8-15101201_S87_E1-50


title: SM-GE67B_S007_E1-50


title: SM-GE67B_S006_E1-50


title: R8-15101201_S86_E1-50


title: SM-GE67B_S005_E1-50


title: SM-GE67B_S004_E1-50


title: SM-GE67B_S003_E1-50


title: R8-15101201_S83_E1-50


title: SM-GE67B_S002_E1-50


title: R8-15101202_S47_E1-50


title: R8-15101201_S81_E1-50


title: SM-GE67B_S001_E1-50


title: R8-15101201_S82_E1-50


title: SM-GE67A_S120_E1-50


title: SM-GE67A_S119_E1-50


title: R8-15101201_S79_E1-50


title: R8-15101201_S76_E1-50


title: R8-15101201_S77_E1-50


title: SM-GE67A_S117_E1-50


title: SM-GE67B_S008_E1-50


title: R8-15101201_S75_E1-50


title: R8-15101201_S74_E1-50


title: SM-GE67A_S115_E1-50


title: R8-15101201_S85_E1-50


title: SM-GE67A_S113_E1-50


title: SM-GE67A_S114_E1-50


title: R8-15101201_S63_E1-50


title: R8-15101201_S64_E1-50


title: SM-GE67A_S104_E1-50


title: R8-15101201_S62_E1-50


title: R8-15101201_S61_E1-50


title: R8-15101201_S59_E1-50


title: SM-GE67A_S101_E1-50


title: R8-15101201_S48_E1-50


title: SM-GE67A_S103_E1-50


title: SM-GE67A_S102_E1-50


title: SM-GE67A_S118_E1-50


title: R8-15101201_S80_E1-50


title: SM-GE67A_S100_E1-50


title: SM-GE67A_S116_E1-50


title: SM-GE67A_S098_E1-50


title: SM-GE67A_S099_E1-50


title: R8-15101201_S47_E1-50


title: SM-GE67A_S097_E1-50


title: R8-15101201_S46_E1-50


title: SM-GE67D_S018_E1-50


title: R8-15101201_S45_E1-50


title: R8-15101201_S43_E1-50


title: R8-15101201_S44_E1-50


title: R8-15101201_S42_E1-50


title: R8-15101201_S41_E1-50


title: R8-15101201_S39_E1-50


title: SM-GE8ZI-Q_S117_E1-50

value: 2.3 yrs


title: SM-GE8ZI-Q_S120_E1-50

value: MC


title: SM-GE8ZI-Q_S116_E1-50

value: NeuN-positive


title: SM-GE8ZI-Q_S118_E1-50

value: Glut


title: R8-15101201_S37_E1-50


title: SM-GE8ZI-Q_S119_E1-50


title: SM-GE8ZI-Q_S115_E1-50


title: SM-GE8ZI-Q_S113_E1-50


title: R8-15101201_S38_E1-50


title: SM-GE8ZI-Q_S112_E1-50

value: Low Quality


title: R8-15101201_S36_E1-50


title: R8-15101201_S40_E1-50


title: SM-GE8ZI-Q_S111_E1-50


title: SM-GE8ZI-Q_S114_E1-50


title: SM-GE8ZI-Q_S109_E1-50


title: R8-15101201_S35_E1-50


title: R8-15101204_S72_E1-50


title: R8-15101201_S34_E1-50


title: R8-15101204_S71_E1-50


title: R8-15101201_S33_E1-50


title: SM-GE8ZI-Q_S110_E1-50


title: R8-15101204_S70_E1-50


title: SM-GE8ZI-Q_S108_E1-50


title: SM-GE8ZI-Q_S106_E1-50


title: SM-GE8ZI-Q_S107_E1-50


title: R8-15101204_S69_E1-50


title: SM-GE8ZI-Q_S105_E1-50


title: R8-15101204_S68_E1-50


title: SM-GE8ZC_S191_E1-50

value: PC


title: SM-GE8ZC_S192_E1-50

value: P


title: SM-GE8ZC_S190_E1-50


title: R8-15101204_S67_E1-50


title: SM-GE8ZC_S187_E1-50


title: R8-15101204_S65_E1-50


title: R8-15101204_S64_E1-50


title: R8-15101202_S96_E1-50

value: dLGN - Shell


title: SM-GE8ZC_S183_E1-50

value: M


title: R8-15101204_S66_E1-50

value: LGd


title: SM-GE8ZC_S185_E1-50


title: R8-15101204_S59_E1-50


title: R8-15101204_S62_E1-50


title: SM-GE8ZC_S188_E1-50


title: R8-15101204_S60_E1-50


title: SM-GE8ZC_S179_E1-50


title: SM-GE8ZC_S182_E1-50


title: SM-GE8ZC_S181_E1-50


title: R8-15101204_S55_E1-50


title: R8-15101204_S57_E1-50


title: R8-15101204_S63_E1-50


title: SM-GE8ZC_S180_E1-50


title: R8-15101204_S58_E1-50


title: SM-GE8ZC_S186_E1-50


title: R8-15101204_S61_E1-50


title: R8-15101204_S56_E1-50


title: R8-15101204_S53_E1-50


title: SM-GE67U-Q_S119_E1-50


title: SM-GE8ZC_S178_E1-50


title: SM-GE67U-Q_S120_E1-50


title: R8-15101204_S51_E1-50


title: R8-15101204_S54_E1-50


title: R8-15101204_S50_E1-50


title: R8-15101204_S48_E1-50


title: SM-GE67U-Q_S118_E1-50


title: R8-15101204_S47_E1-50


title: SM-GE67U-Q_S115_E1-50


title: R8-15101204_S46_E1-50


title: R8-15101204_S49_E1-50


title: SM-GE67U-Q_S117_E1-50


title: SM-GE8ZC_S189_E1-50


title: SM-GE67U-Q_S116_E1-50


title: R8-15101204_S42_E1-50


title: R8-15101204_S43_E1-50


title: SM-GE8ZC_S177_E1-50


title: R8-15101204_S44_E1-50


title: SM-GE67U-Q_S114_E1-50


title: R8-15101204_S23_E1-50


title: R8-15101204_S22_E1-50


title: R8-15101204_S24_E1-50


title: SM-GE67U-Q_S110_E1-50


title: R8-15101204_S21_E1-50


title: SM-GE67U-Q_S109_E1-50


title: SM-GE67U-Q_S111_E1-50


title: R8-15101204_S20_E1-50


title: SM-GE67U-Q_S107_E1-50


title: SM-GE67U-Q_S105_E1-50


title: R8-15101204_S19_E1-50


title: SM-GE67U-Q_S104_E1-50


title: R8-15101204_S18_E1-50


title: SM-GE67U-Q_S112_E1-50


title: SM-GE67U-Q_S102_E1-50


title: R8-15101204_S08_E1-50


title: SM-GE67U-Q_S101_E1-50


title: R8-15101204_S07_E1-50


title: SM-GE67U-Q_S100_E1-50


title: SM-GE67U-Q_S099_E1-50


title: R8-15101204_S05_E1-50


title: R8-15101204_S06_E1-50


title: SM-GE67U-Q_S108_E1-50


title: SM-GE67U-Q_S098_E1-50


title: R8-15101204_S04_E1-50


title: SM-GE67U-Q_S106_E1-50


title: R8-15101204_S03_E1-50


title: R8-15101204_S01_E1-50


title: R8-15101204_S02_E1-50


title: SM-GE67U-Q_S095_E1-50


title: SM-GE67U-Q_S097_E1-50


title: SM-GE67U-Q_S094_E1-50


title: R8-15101204_S17_E1-50


title: R8-15101203_S80_E1-50


title: SM-GE67U-Q_S103_E1-50


title: SM-GE67U-Q_S092_E1-50


title: R8-15101203_S79_E1-50


title: SM-GE67U-Q_S093_E1-50


title: R8-15101203_S77_E1-50


title: SM-GE67U-Q_S089_E1-50


title: SM-GE67U-Q_S088_E1-50


title: R8-15101203_S75_E1-50


title: SM-GE67U-Q_S091_E1-50


title: SM-GE67U-Q_S087_E1-50


title: R8-15101203_S73_E1-50


title: R8-15101203_S76_E1-50


title: SM-GE67U-Q_S090_E1-50


title: SM-GE67U-Q_S086_E1-50


title: R8-15101203_S71_E1-50


title: SM-GE67U-Q_S084_E1-50


title: SM-GE67U-Q_S113_E1-50


title: R8-15101203_S70_E1-50


title: R8-15101203_S74_E1-50


title: SM-GE67U-Q_S082_E1-50


title: SM-GE67U-Q_S096_E1-50


title: SM-GE67U-Q_S085_E1-50


title: R8-15101203_S72_E1-50


title: SM-GE67U-Q_S080_E1-50


title: SM-GE67U-Q_S079_E1-50


title: R8-15101203_S68_E1-50


title: R8-15101203_S65_E1-50


title: R8-15101203_S69_E1-50


title: SM-GE67U-Q_S081_E1-50


title: R8-15101203_S78_E1-50


title: R8-15101203_S63_E1-50


title: R8-15101203_S67_E1-50


title: SM-GE67U-Q_S076_E1-50


title: SM-GE67U-Q_S078_E1-50


title: SM-GE67U-Q_S073_E1-50


title: R8-15101203_S62_E1-50


title: R8-15101203_S61_E1-50


title: SM-GE67U-Q_S083_E1-50


title: SM-GE67U-Q_S074_E1-50


title: R8-15101203_S60_E1-50


title: R8-15101203_S64_E1-50


title: SM-GE67U-Q_S077_E1-50


title: SM-GE67U-Q_S069_E1-50


title: SM-GE67U-Q_S072_E1-50


title: SM-GE67U-Q_S068_E1-50


title: SM-GE67U-Q_S071_E1-50


title: SM-GE67U-Q_S070_E1-50


title: R8-15101203_S59_E1-50


title: R8-15101203_S57_E1-50


title: medaka98

city: Oslo

first: Khadeeja

last: siddique

address: Karl Staaffs vei 75, house 7

country: Norway

institute: Norwegian University of Life sciences (NMBU))

data_processing:
All FASTQ data were aligned against the medaka HdrR reference genome (Ensembl version 94) using STAR (version 2.7.6a). Alignments were inspected or processed using Samtools (version 1.10) and quantified using htseq-count (version 0.11.2) using the intersection-nonempty setting.
Genome_build: Hd-rR medaka reference genome (ASM223467v1, Ensembl release 94)
Supplementary_files_format_and_content: HTSEQ_Count.xlsx

organism: Oryzias latipes

source_name: Pituitary

growth_protocol: Eggs were sampled from a tank containing three females and three males. After hatching in petri dishes, fish from a single egg collection date were transferred to 1-liter tanks in a re-circulation system. After one month, fish were transferred to 3-liter tanks containing exactly 10 fish of the same age. Fish were kept at 28 °C on a 14/10h light/dark cycle, and were fed three times a day with a mix of dry food and Artemia.

extract_protocol:
RNA was isolated using a standard Trizol protocol, with minor modifications. Samples were thawed and vortexed for 10 seconds with 120 µl chloroform, incubated at room temperature for 3 minutes, and centrifuged at 14000g for 15 minutes at 4 °C. Glycoblue (Invitrogen) (17.5 µg/ml) was added to each tube to enhance precipitation and visualize the pellet. The aqueous phase (ca. 160 µl) was transferred to a new tube and RNA was precipitated in 160 µl 100% isopropanol by incubation at -20 °C for 1 hour, followed by centrifugation at 14000 g for 15 minutes at 4 °C. The pellet was then washed in 300 µl 75 % ice-cold ethanol and the sample centrifuged at 10000g for 10 minutes at 4 °C. The supernatant was removed and the RNA pellet briefly dried (approximately 5 minutes) at room temperature. The pellet was dissolved in 10 µl of RNase-free water. Samples were stored at -80 °C until use.
cDNA was generated and amplified using the Smart-SEQ HT Kit for low RNA input according to the manufacturer’s recommendations (Takara Bio), which was used for generating Illumina sequencing libraries with the Nextera XT kit.

treatment_protocol: Fish were sacrificed between 09.00–11.00h in the morning by hypothermic shock (immersion in ice water), severing of the spinal cord, and immediate dissection of the pituitary. Pituitaries were carefully dissected using fine forceps and extra care was taken to prevent cross-contamination between samples by carefully cleaning all equipment with ethanol after dissecting each fish, and also before sampling the pituitary. Each pituitary gland was put in an 0.5 ml Eppendorf tube containing 10 µl ice-cold medaka-adjusted PBS (pH 7.75 and mOsm 290 mOsm) and 5 ceramic beads of 1.4 mm, directly followed by the addition of 300 ul Trizol Reagent (Invitrogen) to each tube. The sample was vortexed at high speed for 1 minute and snap frozen in liquid nitrogen. Samples were stored at -80 °C until RNA isolation.

value: d-rR lhb:GFP

value: female

tag: age days post fertilization

tag: length in mm

tag: rin


title: medaka99

value: not determined


title: R8-15101203_S56_E1-50


title: R8-15101203_S58_E1-50


title: medaka94


title: R8-15101203_S55_E1-50


title: medaka96


title: medaka97


title: SM-GE67U-Q_S066_E1-50


title: SM-GE67U-Q_S075_E1-50


title: R8-15101203_S52_E1-50


title: R8-15101203_S54_E1-50


title: SM-GE67U-Q_S067_E1-50


title: SM-GE67U-Q_S065_E1-50


title: R8-15101203_S51_E1-50

value: Non-Neuronal


title: medaka9


title: R8-15101203_S50_E1-50

value: RFP-positive


title: medaka90


title: medaka84


title: medaka88


title: medaka89


title: SM-GE67S-Q_S192_E1-50


title: SM-GE67S-Q_S191_E1-50


title: medaka82


title: R8-15101203_S48_E1-50


title: medaka78


title: medaka8


title: R8-15101203_S47_E1-50


title: medaka75


title: medaka7


title: R8-15101203_S49_E1-50


title: SM-GE67S-Q_S189_E1-50


title: R8-15101203_S46_E1-50


title: medaka65


title: SM-GE67S-Q_S188_E1-50


title: medaka68


title: medaka67


title: R8-15101203_S43_E1-50

value: GABA


title: SM-GE67S-Q_S186_E1-50


title: SM-GE67S-Q_S187_E1-50


title: R8-15101203_S44_E1-50

value: dLGN - Core


title: SM-GE67S-Q_S190_E1-50

value: 2.3 yrs


title: medaka64


title: medaka76


title: medaka60


title: medaka63


title: SM-GE67S-Q_S185_E1-50


title: R8-15101204_S41_E1-50


title: medaka71


title: medaka6


title: medaka56


title: R8-15101203_S45_E1-50


title: R8-15101203_S32_E1-50


title: medaka52


title: medaka54


title: medaka5


title: SM-GE67S-Q_S183_E1-50

value: MC


title: R8-15101203_S31_E1-50


title: medaka47


title: SM-GE67S-Q_S182_E1-50

value: NeuN-positive


title: R8-15101203_S42_E1-50

value: Glut


title: SM-GE67S-Q_S181_E1-50


title: R8-15101203_S41_E1-50


title: medaka32


title: medaka41


title: medaka4


title: R8-15101203_S30_E1-50


title: SM-GE67S-Q_S180_E1-50


title: SM-GE67S-Q_S179_E1-50


title: medaka3


title: R8-15101203_S29_E1-50


title: medaka29


title: medaka33


title: medaka28


title: medaka27


title: medaka26


title: SM-GE67S-Q_S168_E1-50


title: R8-15101203_S25_E1-50


title: R8-15101203_S28_E1-50


title: R8-15101203_S26_E1-50


title: SM-GE67S-Q_S178_E1-50


title: medaka24


title: SM-GE67S-Q_S167_E1-50


title: SM-GE67S-Q_S166_E1-50


title: medaka18


title: medaka19


title: medaka2


title: medaka22


title: medaka23


title: R8-15101203_S27_E1-50


title: R8-15101203_S23_E1-50


title: medaka14


title: medaka137

value: male


title: medaka140


title: SM-GE67S-Q_S165_E1-50

value: Low Quality


title: R8-15101203_S24_E1-50


title: SM-GE67S-Q_S164_E1-50


title: medaka138


title: R8-15101203_S22_E1-50


title: medaka136


title: R8-15101203_S20_E1-50


title: SM-GE67S-Q_S184_E1-50


title: SM-GE67S-Q_S162_E1-50


title: medaka135


title: R8-15101203_S17_E1-50


title: SM-GE67S-Q_S161_E1-50


title: SM-GE67R-Q_S064_E1-50


title: medaka131


title: medaka130


title: medaka133


title: medaka134


title: SM-GE67S-Q_S163_E1-50


title: R8-15101203_S19_E1-50


title: medaka139


title: medaka132


title: R8-15101203_S21_E1-50


title: medaka127


title: medaka129


title: SM-GE67R-Q_S063_E1-50


title: medaka128


title: R8-15101203_S07_E1-50

value: LP


title: medaka126


title: medaka124


title: R8-15101203_S08_E1-50


title: R8-15101203_S06_E1-50


title: SM-GE67R-Q_S060_E1-50


title: medaka125


title: medaka123


title: SM-GE67R-Q_S062_E1-50


title: SM-GE67R-Q_S061_E1-50


title: medaka122


title: SM-GE67R-Q_S058_E1-50

value: Pulv


title: R8-15101203_S18_E1-50

value: M


title: R8-15101203_S05_E1-50


title: SM-GE67R-Q_S059_E1-50


title: medaka120


title: medaka121


title: R8-15101203_S03_E1-50

value: LGd


title: R8-15101203_S04_E1-50


title: medaka119

value: d-rR lhb:GFP


title: medaka115

value: female


title: medaka117

value: not determined


title: SM-GE67R-Q_S057_E1-50


title: medaka116


title: medaka110


title: medaka118


title: SM-GE67L_S192_E1-50

value: PC

value: P


title: medaka114


title: R8-15101203_S02_E1-50

value: RFP-positive


title: R8-15101203_S01_E1-50

value: dLGN - Core


title: medaka108


title: SM-GE67L_S191_E1-50

value: 2.3 yrs


title: medaka111


title: medaka112


title: SM-GE67L_S190_E1-50


title: medaka109


title: R8-15101202_S79_E1-50

value: GABA


title: R8-15101202_S78_E1-50


title: SM-GE67L_S189_E1-50

value: NeuN-positive


title: SM-GE67L_S187_E1-50

value: Glut


title: medaka106


title: R8-15101202_S76_E1-50


title: medaka103


title: SM-GE67L_S188_E1-50


title: R8-15101202_S77_E1-50


title: medaka104


title: SM-GE67L_S186_E1-50


title: medaka100


title: medaka101


title: R8-15101202_S75_E1-50


title: R8-15101202_S74_E1-50


title: IBP5（control group）

city: Dalian

first: Shuo

last: Wu

address: Linggong Road No.2

institute: Dalian university of technology

data_processing:
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Illumina Casava1.7 software used for basecalling.
Quality control.Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Quantification of gene expression level.HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis.Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways. For the SNP analysis, Picard-tools (v1.96) and samtools (v 0.1.18) were used to sort, mark duplicated reads and reorder the bam alignment results of each sample. GATK2 software was used to perform SNP calling.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

organism: Pseudoalteromonas sp. GCY

source_name: Marine Sediment

extract_protocol:
strain GCY were centrifuged and collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Marine bacteria

value: untreated


title: IBP6（control group）


title: medaka10


title: medaka1


title: R8-15101202_S73_E1-50


title: SM-GE67L_S185_E1-50


title: IBP4（control group）


title: IBP3（Treat group）

value: IBP treated for 27h


title: SM-GE67L_S184_E1-50


title: R8-15101202_S72_E1-50


title: R8-15101202_S71_E1-50


title: IBP1（Treat group）


title: SM-GE67L_S183_E1-50

value: Low Quality


title: SM-GE67L_S182_E1-50

value: M


title: IBP2（Treat group）


title: Isolated_3

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

department: Research center

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

description: Experimental group that were separated from their parents 8 hours daily from postnatal day 2

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to (analyze) fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12).
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test .
The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes FPKM values for each Sample

growth_protocol: Mice were subjected to parental isolation for 8 hours a day (9am~5pm) from postnatal day 2. Specifically, mice were divided in 2 group: Father-only, control group that stay with their fathers. Isolated: experimental group that were separated from their parents. On postnatal day 7, mice were sacrificed to isolate astrocyte by ITGP5 immunopanning.

extract_protocol:
Total RNA was extracted from the tissues using Trizol(Invitrogen, Carlsbad, CA, USA) accordingto manual instruction
RNA libraries were prepared for sequencing using standard BGI protocols

value: postnatal day 7

value: separated from parents

value: Astrocyte


title: Isolated_2

source_name: Experimental group that were separated from their parents 8 hours daily from postnatal day 2


title: SM-GE67L_S181_E1-50


title: R8-15101202_S70_E1-50


title: Father-only_3

description: Control group that stay with their fathers 8 hours daily from postnatal day 2

value: with fathers


title: R8-15101202_S69_E1-50


title: Father-only_2

source_name: Control group that stay with their fathers 8 hours daily from postnatal day 2


title: Isolated_1


title: R8-15101202_S68_E1-50


title: SM-GE67L_S179_E1-50

value: PC


title: SM-GE67L_S180_E1-50

value: P


title: R8-15101202_S66_E1-50

value: RFP-positive


title: C2C12_myotube_rep2

city: La Jolla

first: Ukrae

last: Cho

state: CA

address: 10010 N Torrey Pines Rd

department: Molecular and Cell Biology

institute: Salk Institute for Biological Studies

data_processing:
HISAT2
SAMtools
StringTie
DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: csv and tabular files

growth_protocol: C2C12 cells were differentiated in DMEM supplemented with 2% horse serum and penicillin-streptomycin.

extract_protocol:
1-2 million C2C12 cells were lysed in 1 ml TRIzol. 0.4 ml chloroform was added and vigorously shaken for RNA extraction. The aqueous phase was transferred to a fresh tube, and one volume of 70% ethanol was added dropwise while vortexing at the lowest speed at room temperature. The mixture was purified using RNeasy Mini kit (Qiagen) to yield several hundred ng/uL total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: myotube


title: C2C12_reserve_rep1

value: reserve cell


title: C2C12_D5RC_neg_IgG

data_processing:
Library strategy: CUT&RUN-sequencing
TrimGalore
Bowtie2
SAMtools
MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and csv files

extract_protocol:
Cell Signaling Technology CUT&RUN assay kit
Sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina and NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7645 and E7600).

tag: cell line


title: C2C12_myotube_rep1

tag: cell type


title: R8-15101202_S67_E1-50

value: dLGN - Core

value: GABA


title: SM-GE67L_S168_E1-50

value: 2.3 yrs

value: NeuN-positive

value: Glut


title: SM-GE67L_S178_E1-50


title: SM-GE67L_S177_E1-50


title: C2C12_myoblast_rep2

value: myoblast


title: R8-15101202_S39_E1-50


title: Father-only_1

tag: strain


title: C2C12_reserve_rep2


title: R8-15101202_S38_E1-50


title: SM-GE67L_S166_E1-50

value: Low Quality


title: R8-15101202_S65_E1-50

value: M


title: SM-GE67L_S165_E1-50


title: C2C12_myoblast_rep1


title: C2C12_D0_neg_IgG


title: C2C12_D0_H3K4Me3


title: R8-15101202_S36_E1-50


title: SM-GE67L_S167_E1-50


title: C2C12_D5RC_H3K4Me3


title: C2C12_D5MT_neg_IgG


title: C2C12_D0_MBD2


title: R8-15101202_S40_E1-50


title: C2C12_D5RC_MBD2


title: C2C12_D5MT_MBD2


title: C2C12_D5MT_H3K4Me3


title: Control_1

city: Guangzhou

first: Ying-chun

last: Guo

address: NO.17, Shougouling Rd.

institute: Sixth Affiliated Hospital of Sun Yat-sen University

data_processing:
FastQC filtering
HISAT2 aligment
edgeR transcript abundance estimation
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...

source_name: Granulosa cells

extract_protocol:
Total RNA of each sample was extracted and purified using TRIzol reagent
Sequencing data were generated on Illumina Novaseq™ 6000

value: Kunming

tag: tissue

value: ovary

value: Granulosa cells

value: derived from follicles grown in vitro for 6 days


title: NT4_1

value: derived from follicles grown in vitro with NT-4 for 6 days


title: C_6d_2

data_processing:
FastQC filtering
HISAT2 aligment
edgeR transcript abundance estimation
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample ...

source_name: oocyte

extract_protocol:
Each sample containing 6 oocytes were collected in lysate buffer. Whole oocyte total RNA was ampliﬁed using the SMARTSeq2 protocol. Paired-end sequencing was performed with an Illumina Novaseq™ 6000.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: R8-15101202_S31_E1-50

tag: donor


title: C2C12_D1_neg_IgG


title: R8-15101202_S37_E1-50

tag: Sex


title: C2C12_D1_H3K4Me3


title: C2C12_D1_MBD2


title: SM-GE67L_S164_E1-50

value: PC

value: P


title: R8-15101202_S35_E1-50

tag: genotype

value: RFP-positive


title: C_6d_1


title: SM-GE67L_S163_E1-50

tag: facs gating


title: R8-15101202_S30_E1-50

tag: sequencing batch


title: SM-GE67L_S162_E1-50

tag: cell class


title: R8-15101202_S29_E1-50

tag: cell cluster


title: NT_6d_1


title: SM-GE67L_S158_E1-50


title: R8-15101202_S34_E1-50


title: SM-GE67L_S161_E1-50


title: R8-15101202_S27_E1-50


title: NT_10d_2

value: derived from follicles grown in vitro with NT-4 for 10 days


title: R8-15101202_S32_E1-50

value: dLGN - Core


title: SM-GE67L_S160_E1-50


title: C_6d_3


title: NT4_2


title: NT_6d_3


title: Control_2


title: NT_10d_3


title: SM-GE67L_S157_E1-50


title: NT_10d_1


title: R8-15101202_S25_E1-50

value: GABA


title: R8-15101202_S24_E1-50


title: SM-GE67L_S156_E1-50

value: 2.3 yrs


title: C_10d_2

value: derived from follicles grown in vitro for 10 days


title: R8-15101202_S26_E1-50


title: SM-GE67L_S159_E1-50

value: NeuN-positive

value: Glut


title: SM-GE67L_S155_E1-50


title: NT_6d_2


title: Invivo_4

value: derived from in-vivo-grown follicles


title: Invivo_3


title: SM-GE67L_S154_E1-50

value: M


title: SM-GE67L_S150_E1-50


title: C_10d_1

value: Kunming


title: Invivo_2

value: ovary


title: R8-15101202_S23_E1-50


title: SM-GE67L_S153_E1-50


title: SM-GE67L_S152_E1-50


title: R8-15101202_S22_E1-50


title: ZT10_GR_WT

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
6299_S39
Sample_6299

data_processing:
RNA-seq and ChIP-seq sequencing data was aligned to mm10 or rn5 using STAR
RNAseq data was quantified by HOMER and normalised using DESeq2
GR ChIPseq peaks and bedgraph files were generated using HOMER
Genome_build: mm10 or rn5
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text files with DESeq2 normalised RNAseq data

source_name: Liver

growth_protocol: Mice were housed at 12 hour light/dark cycles and trained to night restricted feeding. Primary hepatocytes were isolated from Male Sprague Dawley rats and seeded on collagen coated plates in Gibo Medium 199 + GlutaMAX (Gibco life technologies, cat: 41150-020) supplemented with 100 nM.  Decadron (dex), 1 % P/S, 4 % FCS and 1 nM human insulin. 2-3 hours after isolation, the medium was changed to Gibo Medium 199 + GlutaMAX supplemented with 1 % P/S, 0.1 % FCS, 1 nM human Insulin and kept overnight.

extract_protocol:
RNA_seq: Primary hepatocytes: Cells were lysed in TRIzol-RNA lysis reagent  (ThermoFisher). Liver tissue: Approximately 5 mg of liver tissues were homogenized using Ultra-Thorax in TRIzol-RNA lysis reagent. RNA was purified using  EconoSpin columns (Epoc Life) according to manufacturer’s instructions.
ChIP-seq: Chromatin was prepared from 100-150mg formaldehyde crosslinked liver tissu. Crosslinked sonicated chromatin was IP'ed antibody and protein A/G agarose beads. DNA was extracted by phenol/choloroform.
Libraries from ChIP'ed DNA were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions. Total RNA (1000 ng) was prepared for sequencing using ribosome depletion followed by random primed cDNA synthesis or polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina.

treatment_protocol: Nr3c1fl/fl mice were injected with AAV-tbg-GFP or AAV-tbg-CRE ten days before sacrifice. The primary hepatocytes were serum depleted in Gibo Medium 199 + GlutaMAX supplemented with 1 % P/S and 0.1 % HAS for 4 hours before cells were stimulated with 500 nM dex for 2.5 hours, human insulin for 2 hours or in a combination and RNA was harvested.

tag: aav injection

value: AAV-tbg-GFP

value: unfed

tag: circadian timepoint

tag: tissue/cell type

value: Liver

tag: chip antibody

value: Cocktail:PA1-511A (Invitrogen), MA1-510 (Invitrogen), sc-1004 (Santa-Cruz)


title: C2C12_200_3

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

data_processing:
trim_galore
Hisat2
Stringtie
Genome_build: GRCm38
Supplementary_files_format_and_content: matrix table and raw fastq sequencing data

extract_protocol:
Total RNA samples were extracted using the Total RNA Isolation Reagent (Biosharp).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse myoblast

tag: Stage

value: myoblast differentiation day 4


title: C2C12_200_2


title: C2C12_200_1


title: R8-15101202_S19_E1-50

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: mm10, Mmul_10

extract_protocol:
We isolated single cells and nuclei as previously described (Tasic et al., 2016, Bakken et al., 2018) with modifications. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C. For nuclei isolation, dissected regions of interest were transferred to microcentrifuge tubes, snap frozen in a slurry of dry ice and ethanol, and stored at -80°C until the time of use. To isolate nuclei, frozen tissues were placed into a homogenization buffer that consisted of 10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNasin Plus RNase inhibitor (Promega), 1X protease inhibitor (Promega), and 0.1mM DTT. Tissues were placed into a 1ml dounce homogenizer (Wheaton) and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30μm cell strainer (Miltenyi Biotech) and centrifuged at 900xg for 10 minutes to pellet nuclei. Nuclei were then resuspended in staining buffer containing 1X PBS supplemented with 0.8% nuclease-free BSA and 0.5% RNasin Plus RNase inhibitor.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

value: RFP-positive


title: C2C12_5_3


title: C2C12_5_2


title: R8-15101202_S21_E1-50

value: dLGN - Core


title: ZT22fed_r3

description:
SM4491_S33
Sample_4491
processed data file: RNAseq_RAW_CT_FED_FAST.txt

value: non treated

tag: treatment

value: fed


title: C2C12_5_1

tag: cell line


title: C_10d_3

value: derived from follicles grown in vitro for 10 days


title: R8-15101202_S18_E1-50

value: GABA


title: ZT22unfed_r3

description:
SM4488_S30
Sample_4488
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: R8-15101202_S17_E1-50


title: R8-15101202_S20_E1-50


title: ZT10_GR_LGRKO

description:
6300_S40
Sample_6300

value: AAV-tbg-CRE


title: SM-GE67L_S149_E1-50

tag: age

value: 2.3 yrs

value: PC

value: NeuN-positive

value: Glut

value: P


title: ZT22fed_r2

description:
SM4490_S32
Sample_4490
processed data file: RNAseq_RAW_CT_FED_FAST.txt

tag: strain


title: SM-GE67L_S151_E1-50

value: M

value: Low Quality


title: SM-GE67L_S148_E1-50


title: ZT22fed_r1

description:
SM4489_S31
Sample_4489
processed data file: RNAseq_RAW_CT_FED_FAST.txt

value: Liver


title: SM-GE67L_S147_E1-50


title: ZT22unfed_r2

description:
SM4487_S29
Sample_4487
processed data file: RNAseq_RAW_CT_FED_FAST.txt

value: unfed


title: SM-GE67L_S145_E1-50


title: SM-GE67L_S146_E1-50


title: ZT18unfed_r3

description:
SM4482_S24
Sample_4482
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: ZT22unfed_r1

description:
SM4486_S28
Sample_4486
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: R8-15101202_S14_E1-50


title: ZT18fed_r3

description:
SM4485_S27
Sample_4485
processed data file: RNAseq_RAW_CT_FED_FAST.txt


title: ZT18unfed_r1

description:
SM4480_S22
Sample_4480
processed data file: RNAseq_RAW_CT_FED_FAST.txt