title: SM-D9EP6_S72_E1-50


title: SM-D9EP6_S71_E1-50

status: Public on Sep 21 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

description:
human_LGN_2021_exon-matrix.csv
human_LGN_2021_intron-matrix.csv

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 HiSeq 2500 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: GRCh38.p2

molecule: polyA RNA

organism: Homo sapiens

source_name: Human - dLGN - PC

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: F

tag: age

value: PC

tag: facs gating

value: NeuN-pos

tag: sequencing batch

tag: cell class

value: Glut

tag: cell cluster

value: MP


title: Cell_0709_E10.5_FACS-Mes_het

city: manchester

first: Muhammmad

middle: Zaki

last: Fadlullah Wilmot

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

data_processing:
Basecall files generated from NextSeq sequencing run were converted to FASTQ format with Illumina’s bcl2fastq. Alignment was performed by STAR 2.4.2a to ensemble reference genome (GRCm38 release 87) with default parameters. Read counts from BAM files were extracted using htseq (version 0.6.1p1) with the following setting --format=bam --stranded=no --type=exon --idattr=gene_id. Count table was loaded into the R environment (R version 3.6.2).
Genome_build: Mus musculus.GRCm38 release 87

organism: Mus musculus

source_name: Aorta gonad mesonephros

extract_protocol:
Single cells were FACS sorted into 384-well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems)

tag: developmental stage

tag: strain

value: ICR

tag: genotype


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source_name: Human - dLGN - MC

value: MC


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value: Non-Neuronal

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title: Cell_0563_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOX_S49_E1-50


title: Cell_0565_E10.5_FACS-Mes_KO


title: SM-D9EOX_S47_E1-50


title: SM-D9EOX_S46_E1-50


title: SM-D9EOX_S52_E1-50


title: Cell_0562_E10.5_FACS-Mes_KO


title: Cell_0572_E10.5_FACS-Mes_KO


title: Cell_0561_E10.5_FACS-Mes_KO


title: Cell_0560_E10.5_FACS-Mes_KO


title: SM-D9EOX_S45_E1-50


title: SM-D9EOX_S44_E1-50


title: Cell_0559_E10.5_FACS-Mes_KO


title: Cell_0557_E10.5_FACS-HE_Runx1_het


title: SM-D9EOX_S43_E1-50


title: SM-D9EOX_S42_E1-50


title: Cell_0556_E10.5_FACS-HE_Runx1_het


title: SM-D9EOX_S38_E1-50


title: SM-D9EOX_S39_E1-50


title: SM-D9EOX_S41_E1-50


title: Cell_0555_E10.5_FACS-HE_Runx1_het


title: Cell_0554_E10.5_FACS-HE_Runx1_het


title: SM-D9EOX_S36_E1-50


title: SM-D9EOX_S37_E1-50


title: Cell_0552_E10.5_FACS-HE_Runx1_het


title: SM-D9EOX_S34_E1-50


title: SM-D9EOX_S33_E1-50


title: SM-D9EOX_S35_E1-50


title: Cell_0558_E10.5_FACS-Mes_KO


title: Cell_0550_E10.5_FACS-Mes_KO


title: Cell_0553_E10.5_FACS-Mes_KO


title: Cell_0548_E10.5_FACS-HE_Runx1_het


title: Cell_0551_E10.5_FACS-HE_Runx1_het


title: SM-D9EOW_S70_E1-50


title: Cell_0549_E10.5_FACS-Mes_KO


title: SM-D9EOW_S69_E1-50


title: Cell_0547_E10.5_FACS-HE_Runx1_het


title: Cell_0546_E10.5_FACS-Mes_het


title: SM-D9EOW_S68_E1-50


title: SM-D9EOW_S66_E1-50


title: Cell_0545_E10.5_FACS-Mes_het


title: Cell_0544_E10.5_FACS-HE_Runx1_het


title: Cell_0543_E10.5_FACS-HE_Runx1_het


title: SM-D9EOW_S63_E1-50


title: SM-D9EOW_S62_E1-50


title: Cell_0542_E10.5_FACS-HE_Runx1_het


title: Cell_0541_E10.5_FACS-Mes_het


title: SM-D9EOW_S58_E1-50


title: SM-D9EOW_S60_E1-50


title: Cell_0539_E10.5_FACS-HE_Runx1_het


title: Cell_0536_E10.5_FACS-Mes_het


title: SM-D9EOW_S61_E1-50


title: SM-D9EOW_S57_E1-50


title: Cell_0538_E10.5_FACS-HE_Runx1_het


title: SM-D9EOW_S56_E1-50


title: Cell_0534_E10.5_FACS-Mes_het


title: Cell_0537_E10.5_FACS-HE_Runx1_het


title: SM-D9EOW_S53_E1-50


title: Cell_0540_E10.5_FACS-Mes_het


title: SM-D9EOW_S52_E1-50


title: SM-D9EOW_S54_E1-50


title: Cell_0532_E10.5_FACS-Mes_het


title: SM-D9EOW_S65_E1-50


title: SM-D9EOW_S51_E1-50


title: SM-D9EOW_S50_E1-50


title: Cell_0533_E10.5_FACS-Mes_het


title: Cell_0531_E10.5_FACS-HE_Runx1_het


title: Cell_0529_E10.5_FACS-HE_Runx1_het


title: SM-D9EOW_S49_E1-50


title: Cell_0528_E10.5_FACS-Mes_het


title: Cell_0530_E10.5_FACS-HE_Runx1_het


title: SM-D9EOW_S46_E1-50


title: SM-D9EOW_S47_E1-50


title: SM-D9EOW_S48_E1-50

value: Micro


title: SM-D9EOW_S55_E1-50

value: F


title: Cell_0527_E10.5_FACS-Mes_het


title: SM-D9EOW_S45_E1-50


title: Cell_0525_E10.5_FACS-HE_Runx1_het


title: SM-D9EOW_S42_E1-50


title: Cell_0524_E10.5_FACS-HE_Runx1_het


title: SM-D9EOW_S39_E1-50


title: SM-D9EOW_S37_E1-50


title: Cell_0520_E10.5_FACS-Mes_het


title: SM-D9EOV_S71_E1-50

value: PC


title: Cell_0522_E10.5_FACS-HE_Runx1_het


title: SM-D9EOV_S69_E1-50

value: NeuN-pos


title: Cell_0519_E10.5_FACS-Mes_het


title: Cell_0518_E10.5_FACS-HE_Runx1_het


title: SM-D9EOW_S33_E1-50

value: Glut


title: SM-D9EOV_S70_E1-50

value: MP


title: Cell_0517_E10.5_FACS-HE_Runx1_het

value: ICR


title: Cell_0521_E10.5_FACS-Mes_het


title: SM-D9EOW_S35_E1-50


title: Cell_0523_E10.5_FACS-Mes_het


title: SM-D9EOV_S67_E1-50


title: Cell_0515_E10.5_FACS-Mes_het


title: Cell_0516_E10.5_FACS-HE_Runx1_het


title: SM-D9EOV_S66_E1-50


title: SM-D9EOV_S62_E1-50


title: Cell_0514_E10.5_FACS-Mes_het


title: SM-D9EOV_S63_E1-50


title: Cell_0513_E10.5_FACS-Mes_het


title: Cell_0526_E10.5_FACS-Mes_het


title: SM-D9EOV_S61_E1-50


title: Cell_0511_E10.5_FACS-HE_Runx1_het


title: Cell_0535_E10.5_FACS-Mes_het


title: SM-D9EOV_S60_E1-50


title: SM-D9EOV_S58_E1-50


title: SM-D9EOV_S68_E1-50


title: SM-D9EOV_S57_E1-50


title: SM-D9EOV_S59_E1-50


title: Cell_0508_E10.5_FACS-Mes_KO


title: SM-D9EOV_S65_E1-50


title: SM-D9EOV_S56_E1-50


title: Cell_0505_E10.5_FACS-Mes_KO


title: Cell_0506_E10.5_FACS-Mes_KO


title: Cell_0507_E10.5_FACS-Mes_KO


title: Cell_0509_E10.5_FACS-Mes_het


title: Cell_0504_E10.5_FACS-HE_Runx1_KO


title: Cell_0512_E10.5_FACS-HE_Runx1_het


title: Cell_0503_E10.5_FACS-HE_Runx1_KO


title: Cell_0510_E10.5_FACS-Mes_het


title: SM-D9EOV_S51_E1-50


title: SM-D9EOV_S53_E1-50


title: Cell_0502_E10.5_FACS-Mes_KO


title: SM-D9EOV_S49_E1-50


title: Cell_0499_E10.5_FACS-Mes_KO


title: Cell_0501_E10.5_FACS-Mes_KO


title: SM-D9EOV_S47_E1-50


title: Cell_0498_E10.5_FACS-Mes_KO


title: SM-D9EOV_S44_E1-50


title: Cell_0497_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOV_S46_E1-50


title: SM-D9EOV_S55_E1-50


title: SM-D9EOV_S45_E1-50


title: SM-D9EOV_S54_E1-50


title: SM-D9EOV_S42_E1-50


title: Cell_0495_E10.5_FACS-HE_Runx1_KO


title: Cell_0496_E10.5_FACS-HE_Runx1_KO


title: Cell_0494_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOV_S50_E1-50


title: Cell_0493_E10.5_FACS-Mes_KO


title: SM-D9EOV_S37_E1-50


title: SM-D9EOV_S38_E1-50


title: Cell_0492_E10.5_FACS-Mes_KO


title: SM-D9EOV_S39_E1-50


title: SM-D9EOV_S41_E1-50


title: Cell_0489_E10.5_FACS-HE_Runx1_KO


title: Cell_0500_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOV_S36_E1-50


title: Cell_0490_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOV_S34_E1-50


title: Cell_0487_E10.5_FACS-Mes_KO


title: SM-D9EOV_S43_E1-50


title: SM-D9EOV_S31_E1-50


title: Cell_0484_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOV_S29_E1-50


title: SM-D9EOV_S35_E1-50


title: Cell_0482_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOV_S27_E1-50


title: Cell_0488_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOV_S30_E1-50


title: Cell_0485_E10.5_FACS-Mes_KO


title: Cell_0486_E10.5_FACS-Mes_KO


title: SM-D9EOV_S33_E1-50


title: Cell_0479_E10.5_FACS-HE_Runx1_het


title: Cell_0491_E10.5_FACS-Mes_KO


title: SM-D9EOV_S28_E1-50


title: SM-D9EOU_S77_E1-50


title: Cell_0475_E10.5_FACS-Mes_KO


title: SM-D9EOV_S25_E1-50


title: SM-D9EOU_S74_E1-50


title: SM-D9EOU_S78_E1-50


title: Cell_0481_E10.5_FACS-HE_Runx1_KO


title: Cell_0478_E10.5_FACS-HE_Runx1_het


title: Cell_0483_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOU_S79_E1-50


title: Cell_0476_E10.5_FACS-Mes_KO


title: SM-D9EOU_S63_E1-50


title: SM-D9EOU_S73_E1-50


title: SM-D9EOU_S75_E1-50


title: SM-D9EOU_S61_E1-50


title: Cell_0480_E10.5_FACS-Mes_KO


title: Cell_0469_E10.5_FACS-HE_Runx1_het


title: Cell_0474_E10.5_FACS-Mes_KO


title: Cell_0471_E10.5_FACS-HE_Runx1_het


title: SM-D9EOU_S62_E1-50


title: Cell_0473_E10.5_FACS-Mes_KO


title: SM-D9EOU_S76_E1-50


title: Cell_0472_E10.5_FACS-HE_Runx1_het


title: Cell_0470_E10.5_FACS-HE_Runx1_het


title: Cell_0468_E10.5_FACS-Mes_KO


title: SM-D9EOU_S59_E1-50


title: Cell_0477_E10.5_FACS-Mes_KO


title: SM-D9EOU_S58_E1-50


title: SM-D9EOU_S57_E1-50


title: Cell_0467_E10.5_FACS-Mes_KO


title: Cell_0466_E10.5_FACS-Mes_KO


title: Cell_0465_E10.5_FACS-Mes_KO


title: SM-D9EOU_S50_E1-50


title: SM-D9EOU_S55_E1-50


title: SM-D9EOU_S60_E1-50


title: Cell_0460_E10.5_FACS-Mes_het


title: SM-D9EOU_S52_E1-50


title: SM-D9EOU_S56_E1-50


title: SM-D9EOU_S49_E1-50


title: Cell_0463_E10.5_FACS-HE_Runx1_het


title: SM-D9EOU_S54_E1-50


title: SM-D9EOU_S53_E1-50


title: SM-D9EOU_S48_E1-50


title: Cell_0459_E10.5_FACS-Mes_het


title: SM-D9EOU_S51_E1-50


title: Cell_0461_E10.5_FACS-HE_Runx1_het


title: Cell_0462_E10.5_FACS-HE_Runx1_het


title: Cell_0457_E10.5_FACS-Mes_het


title: Cell_0455_E10.5_FACS-Mes_het


title: Cell_0464_E10.5_FACS-HE_Runx1_het


title: SM-D9EOU_S43_E1-50


title: SM-D9EOU_S42_E1-50


title: Cell_0454_E10.5_FACS-Mes_het


title: Cell_0453_E10.5_FACS-Mes_het


title: Cell_0458_E10.5_FACS-Mes_het


title: Cell_0451_E10.5_FACS-HE_Runx1_het


title: SM-D9EOU_S47_E1-50


title: SM-D9EOU_S44_E1-50


title: Cell_0450_E10.5_FACS-HE_Runx1_het


title: Cell_0449_E10.5_FACS-Mes_het


title: Cell_0452_E10.5_FACS-Mes_het


title: SM-D9EOU_S41_E1-50


title: SM-D9EOU_S35_E1-50


title: Cell_0446_E10.5_FACS-HE_Runx1_het


title: SM-D9EOU_S33_E1-50


title: SM-D9EOU_S28_E1-50


title: SM-D9EOU_S25_E1-50


title: SM-D9EOR_S94_E1-50


title: Cell_0442_E10.5_FACS-HE_Runx1_het


title: SM-D9EOR_S95_E1-50


title: Cell_0456_E10.5_FACS-HE_Runx1_het


title: Cell_0441_E10.5_FACS-HE_Runx1_het


title: SM-D9EOU_S36_E1-50


title: Cell_0448_E10.5_FACS-HE_Runx1_het


title: Cell_0438_E10.5_FACS-Mes_het


title: SM-D9EOU_S34_E1-50


title: Cell_0447_E10.5_FACS-HE_Runx1_het


title: Cell_0445_E10.5_FACS-Mes_het


title: SM-D9EOU_S27_E1-50


title: SM-D9EOR_S87_E1-50


title: Cell_0444_E10.5_FACS-Mes_het


title: SM-D9EOR_S89_E1-50


title: SM-D9EOU_S26_E1-50


title: Cell_0443_E10.5_FACS-HE_Runx1_het


title: SM-D9EOU_S39_E1-50


title: GFP n3

city: PARIS

first: nathalie

last: spassky

address: 46 rue d'ULM

country: France

institute: IBENS

data_processing:
Illumina Casava1.7 software used for basecalling.
Using Eoulsan, polyN read tails were trimmed, <= 40 bases reads were removed and reads with a quality score <= 30 were discarded
Using Eoulsan, RNA-Seq reads were aligned with STAR (version 2.5.2b) allowing only uniquely mapping reads and associated to genes annotation with HTSeq-count (version 0.5.3) in unstranded way
Using Eoulsan, differential expression analysis was performed with DESeq2 (version 1.8.1)
Genome_build: mm10 (Ensembl version 91)
Supplementary_files_format_and_content: tab-delimited files with raw counts

molecule: total RNA

source_name: Neural progenitor cells

extract_protocol:
cDNA libraries and RNA sequencing Library preparation and Illumina sequencing were performed at the Ecole normale superieure genomic core facility (Paris, France)
10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech)
Afterwards an average of 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina)
Libraries were multiplexed by 12 on a high-output flow cells
A 75 bp read sequencing was performed on a NextSeq 500 device (Illumina)
A mean of 47 ± 9 million passing Illumina quality filter reads was obtained for each of the 12 samples

treatment_protocol: GFP+ FACS sorted cells from E16.5 mouse forebrains that have been electroporated at E14.5 with either pCAGGS-GemC1- or pCAAGS-Mcidas- and/or H2B-GFP plasmids.

tag: cell sorting

value: GFP+ FACS sorted cells

tag: cell type

value: Neural progenitor cells

tag: electroporated with

tag: timeline

value: 2 days post in utero electroporation


title: SM-D9EOR_S86_E1-50


title: Mcidas n2

value: pCAAGS-Mcidas


title: Cell_0439_E10.5_FACS-Mes_het


title: Cell_0440_E10.5_FACS-Mes_het


title: SM-D9EOU_S37_E1-50

value: MC


title: GemC1 n2


title: SM-D9EOU_S30_E1-50


title: GFP n2


title: SM-D9EOR_S90_E1-50


title: SM-D9EOR_S78_E1-50


title: GFP n1


title: Mcidas n3


title: SM-D9EOR_S93_E1-50


title: SM-D9EOR_S75_E1-50


title: SM-D9EOR_S72_E1-50

value: NeuN-neg

value: Non-Neuronal


title: SM-D9EOR_S85_E1-50

value: KC


title: Mcidas n1


title: SM-D9EOR_S84_E1-50


title: M9_H9_mouse_E3/E3_FAD_microglia

city: Los Angeles

first: Michael

last: Workman

state: CA

address: 8700 Beverly Blvd., AHSP Suite 8405

institute: Cedars-Sinai Medical Center

description:
processed data file: Mouse_Microglia_counts.csv
M9_H9_S29_R1_001

data_processing:
Demultiplexing and conversion of raw sequencing data to FASTQ was performed with Illumina bcl2fastq software
FastQC was used to assess sequence quality and reads were aligned to either human GRCh38.p13 (GENCODE 32) or mouse GRCm38.p6 (GENCODE M23) genome assemblies using Salmon (v1.1.0)
Transcript abundance estimates were quantified with Salmon (v1.1.0) and summarized to gene-level counts with tximport in R
Genome_build: Human GRCh38.p13 (GENCODE 32) or Mouse GRCm38.p6 (GENCODE M23)
Supplementary_files_format_and_content: counts.csv

growth_protocol: Human iPSC-derived microglia were differentiated following the protocol of Douvaras et al., Stem Cell Reports (2017)

extract_protocol:
Total RNA was extracted using a Direct-zol RNA Miniprep kit (#R2051, Zymo Research) with on-column DNAse digestion, according to the manufacturer’s instructions
RNA libraries were generated using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and prepared for sequencing using standard Illumina protocols

treatment_protocol: For metal-treated iMicroglia samples, cells were incubated with 30 uM zinc or 7.5 uM cadmium for 24 h

tag: background

value: FAD transgenic

value: Male

tag: tissue/cell type

value: MACS-sorted CD11b+ cells from brain homogenates

value: Batch 1


title: SM-D9EOR_S83_E1-50

value: F


title: SM-D9EOR_S91_E1-50

value: NeuN-pos


title: GemC1 n3


title: SM-D9EOR_S82_E1-50

value: Glut


title: SM-D9EOR_S81_E1-50

value: MP


title: M94_A10_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M94_A10_S24_R1_001


title: GemC1 n1


title: SM-D9EOR_S67_E1-50

value: PC


title: SM-D9EOR_S65_E1-50


title: SM-D9EOR_S63_E1-50


title: SM-D9EOR_S77_E1-50


title: SM-D9EOR_S73_E1-50


title: SM-D9EOR_S60_E1-50


title: M7_E10_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M7_E10_S23_R1_001


title: M6_B10_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M6_B10_S26_R1_001


title: SM-D9EOR_S74_E1-50


title: M52_G11_mouse_E4/E4_TR_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M52_G11_S17_R1_001

value: Targeted Replacement Control


title: SM-D9EOR_S58_E1-50


title: M17_G10_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M17_G10_S21_R1_001


title: SM-D9EOR_S57_E1-50


title: SM-D9EOR_S71_E1-50


title: SM-D9EOR_S56_E1-50

value: OPC


title: SM-D9EOR_S55_E1-50


title: MA7_F12_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
MA7_F12_S30_R1_001


title: SM-D9EOR_S70_E1-50

value: GABA


title: M10b_D12_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M10b_D12_S7_R1_001


title: SM-D9EOR_S69_E1-50


title: SM-D9EOR_S68_E1-50


title: M8_F10_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M8_F10_S28_R1_001


title: M88_A12_mouse_E4/E4_TR_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M88_A12_S8_R1_001


title: M89_B12_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M89_B12_S14_R1_001


title: SM-D9EOR_S62_E1-50


title: SM-D9EOR_S52_E1-50


title: SM-D9EOR_S51_E1-50


title: FA17_E11_mouse_E4/E4_TR_microglia

description:
processed data file: Mouse_Microglia_counts.csv
FA17_E11_S19_R1_001

value: Female


title: FA66_F11_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
FA66_F11_S18_R1_001


title: F92_A11_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F92_A11_S27_R1_001


title: M16_E12_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M16_E12_S13_R1_001


title: SM-D9EOR_S59_E1-50

value: MC


title: SM-D9EOR_S54_E1-50

value: Oligo


title: SM-D9EOR_S44_E1-50


title: M14_C12_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M14_C12_S15_R1_001


title: M11_D10_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M11_D10_S3_R1_001


title: M10a_C10_mouse_E3/E3_TR_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M10a_C10_S2_R1_001


title: SM-D9EOR_S53_E1-50

description:
human_LGN_2021_exon-matrix.csv
human_LGN_2021_intron-matrix.csv


title: M53_H11_mouse_E4/E4_TR_microglia

description:
processed data file: Mouse_Microglia_counts.csv
M53_H11_S16_R1_001


title: SM-D9EOR_S49_E1-50


title: SM-D9EOR_S42_E1-50


title: SM-D9EOR_S21_E1-50

value: M


title: SM-D9EOR_S45_E1-50


title: SM-D9EOR_S18_E1-50

value: KC


title: F7_C11_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F7_C11_S9_R1_001

value: FAD transgenic


title: F5_E9_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F5_E9_S11_R1_001


title: SM-D9EOR_S41_E1-50


title: F59_D11_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F59_D11_S20_R1_001


title: SM-D9EOR_S23_E1-50

value: Non-Neuronal

value: Astro


title: F4_F9_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F4_F9_S4_R1_001

value: MACS-sorted CD11b+ cells from brain homogenates

value: Batch 1


title: F93_B11_mouse_E4/E4_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F93_B11_S22_R1_001


title: SM-D9EOR_S14_E1-50

value: NeuN-pos


title: SM-D9EOR_S15_E1-50


title: SM-D9EOR_S13_E1-50

value: Glut


title: naive CD4 T cells from CD4 T cell-specific P2Y10 knockout mice, rep3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.7.3a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers. The raw count matrix was batch corrected using CountClust and then normalized with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: library size and batch corrected count table

source_name: MACS-sorted CD4 T cells from peripheral lymph nodes and spleen

growth_protocol: cells were not cultured

extract_protocol:
RNA was isolated from MACS-sorted CD4 T cells using the RNeasy micro kit. (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
500ng total RNA was used as input for VAHTS Universal V6 RNA-seq Library Prep Kit following manufacture’s protocol for stranded mRNA libraries (Vazyme).

treatment_protocol: cells were not treated

value: CD4 T cell

tag: tissue

value: spleen, lymph node

value: CD4 T cell-specific P2Y10 knockout


title: SM-D9EOR_S12_E1-50

tag: donor

value: MP


title: SM-D9EOR_S11_E1-50

tag: Sex


title: naive CD4 T cells from control mice, rep3

value: control


title: naive CD4 T cells from CD4 T cell-specific P2Y10 knockout mice, rep1


title: SM-D9EOR_S09_E1-50

tag: age


title: SM-D9EOR_S47_E1-50

value: F

tag: facs gating


title: F2_D9_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F2_D9_S12_R1_001

value: Female

tag: sequencing batch


title: F26_G9_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F26_G9_S10_R1_001


title: SM-D9EOQ_S87_E1-50

tag: cell class


title: F1_B9_mouse_E3/E3_TR_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F1_B9_S6_R1_001

value: Targeted Replacement Control


title: SM-D9EOQ_S86_E1-50

tag: cell cluster


title: F91_H10_mouse_E4/E4_TR_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F91_H10_S1_R1_001


title: F13_C9_mouse_E3/E3_FAD_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F13_C9_S5_R1_001


title: SM-D9EOQ_S88_E1-50

value: NeuN-neg

value: Oligo


title: F0_A9_mouse_E3/E3_TR_microglia

description:
processed data file: Mouse_Microglia_counts.csv
F0_A9_S25_R1_001


title: SM-D9EOQ_S81_E1-50

value: KC


title: naive CD4 T cells from CD4 T cell-specific P2Y10 knockout mice, rep2


title: Combination treatment of CBL0137 and Panobinostat, Replicate 3

city: Randwick

first: Michelle

last: Haber

state: NSW

address: Lowy Cancer Research Centre, PO BOX 81

country: Australia

institute: Children's Cancer Institute

data_processing:
Illumina paired-end sequencing data was aligned using STAR to the mouse genome assembly mm10
BAM files were sorted and indexed using SAMtools
Gene expression and isoform expression counts were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: txt file that contains TPM counts for each gene in each of the samples

extract_protocol:
RNA was isolated with a Qiagen RNeasy Mini Kit
RNA-seq libraries were generated using Illumina TruSeq Stranded Total RNA with Ribo-Zero prep kit using 1 μg of RNA input

treatment_protocol: Spontaneous tumours were allowed to develop in the homozygous Th-MYCN (tyrosine hydroxylase-MYCN) transgenic mice which phenocopy MYCN-amplified neuroblastoma in patients. When tumours measured around 5 mm by palpation, mice were treated with one dose of the vehicle (IP), CBL0137 (40 mg/kg, intravenously), panobinostat (5 mg/kg, IP), or the combination. Tumours were harvested 16 hours post injection and were flash frozen in liquid nitrogen. RNA was isolated using Qiagen RNeasy spin columns.

tag: treatment

value: Comb


title: Combination treatment of CBL0137 and Panobinostat, Replicate 1


title: SM-D9EOR_S17_E1-50

value: M


title: SM-D9EOQ_S77_E1-50


title: CBLO137 treated, replicate 3

source_name: CBLO137 treated,


title: CBLO137 treated, replicate 2


title: SM-D9EOQ_S75_E1-50


title: SM-D9EOQ_S73_E1-50


title: naive CD4 T cells from control mice, rep1

tag: strain


title: Cell_1288_E10.5_FACS-HE_Runx1_KO

tag: developmental stage

value: ICR

tag: genotype


title: Control replicate 3

source_name: Control

value: Veh


title: SM-D9EOQ_S85_E1-50

value: NeuN-pos


title: Control replicate 2


title: SM-D9EOQ_S84_E1-50

value: Glut


title: SM-D9EOQ_S83_E1-50


title: Control replicate 1


title: SM-D9EOQ_S70_E1-50

value: PC


title: Cell_1285_E10.5_FACS-HE_Runx1_KO


title: naive CD4 T cells from control mice, rep2

tag: cell type

value: CD4 T cell

value: spleen, lymph node


title: Cell_1284_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S68_E1-50


title: SM-D9EOQ_S67_E1-50


title: Cell_1283_E10.5_FACS-HE_Runx1_KO


title: Combination treatment of CBL0137 and Panobinostat, Replicate 2


title: SM-D9EOQ_S66_E1-50


title: SM-D9EOQ_S79_E1-50


title: SM-D9EOQ_S78_E1-50


title: SM-D9EOQ_S76_E1-50

value: Non-Neuronal


title: Panobinostat treated, replicate 3

source_name: Panobinostat treated,

value: Pano


title: Panobinostat treated, replicate 1


title: CBLO137 treated, replicate 1


title: SM-D9EOQ_S74_E1-50

value: F


title: Cell_1286_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S69_E1-50


title: Cell_1277_E10.5_FACS-HE_Runx1_KO


title: Cell_1278_E10.5_FACS-HE_Runx1_KO


title: Cell_1281_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S65_E1-50


title: SM-D9EOQ_S71_E1-50

value: MP


title: Cell_1275_E10.5_FACS-HE_Runx1_KO


title: Cell_1279_E10.5_FACS-HE_Runx1_KO


title: Cell_1287_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S54_E1-50


title: SM-D9EOQ_S53_E1-50


title: SM-D9EOQ_S52_E1-50

value: GABA


title: Cell_1272_E10.5_FACS-HE_Runx1_KO


title: Cell_1280_E10.5_FACS-HE_Runx1_KO


title: Cell_1282_E10.5_FACS-HE_Runx1_KO


title: Cell_1269_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S48_E1-50

value: NeuN-neg


title: SM-D9EOQ_S61_E1-50


title: SM-D9EOQ_S63_E1-50


title: SM-D9EOQ_S58_E1-50


title: SM-D9EOQ_S60_E1-50


title: SM-D9EOQ_S47_E1-50


title: Cell_1268_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S44_E1-50


title: Cell_1266_E10.5_FACS-HE_Runx1_KO


title: Cell_1276_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S51_E1-50


title: Cell_1264_E10.5_FACS-Mes_KO


title: Cell_1274_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S50_E1-50


title: Cell_1262_E10.5_FACS-Mes_KO


title: Cell_1263_E10.5_FACS-Mes_KO


title: Cell_1270_E10.5_FACS-HE_Runx1_KO


title: Cell_1271_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S29_E1-50

value: Astro


title: SM-D9EOQ_S49_E1-50


title: SM-D9EOQ_S28_E1-50

value: KC


title: Cell_1267_E10.5_FACS-HE_Runx1_KO


title: Cell_1265_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S43_E1-50


title: SM-D9EOQ_S42_E1-50


title: Cell_1261_E10.5_FACS-Mes_KO


title: Cell_1260_E10.5_FACS-Mes_KO


title: SM-D9EOQ_S21_E1-50


title: SM-D9EOQ_S17_E1-50


title: SM-D9EOQ_S19_E1-50


title: SM-D9EOQ_S27_E1-50


title: Cell_1257_E10.5_FACS-Mes_KO


title: Cell_1259_E10.5_FACS-Mes_KO


title: Cell_1256_E10.5_FACS-Mes_KO


title: SM-D9EOQ_S15_E1-50


title: SM-D9EOQ_S14_E1-50


title: Cell_1253_E10.5_FACS-Mes_KO


title: SM-D9EOQ_S12_E1-50


title: Cell_1254_E10.5_FACS-Mes_KO


title: SM-D9EOQ_S11_E1-50


title: SM-D9EOQ_S09_E1-50


title: Cell_1251_FE10.5_cs-Endo_Runx1_het


title: SM-D9EOQ_S07_E1-50


title: SM-D9EOQ_S04_E1-50


title: Cell_1258_E10.5_FACS-Mes_KO


title: Cell_1249_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S20_E1-50


title: Cell_1248_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S01_E1-50


title: Cell_1247_E10.5_FACS-HE_Runx1_KO


title: Cell_1246_E10.5_FACS-HE_Runx1_KO


title: Cell_1245_E10.5_FACS-HE_Runx1_KO


title: Cell_1273_E10.5_FACS-HE_Runx1_KO


title: Cell_1255_E10.5_FACS-Mes_KO


title: Cell_1244_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S93_E1-50


title: Cell_1252_FE10.5_cs-Endo_Runx1_het


title: Cell_1243_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S91_E1-50


title: Cell_1250_FE10.5_cs-Endo_Runx1_het


title: Cell_1242_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S06_E1-50


title: Cell_1241_E10.5_FACS-HE_Runx1_KO


title: Cell_1240_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S79_E1-50


title: SM-D9EOP_S77_E1-50


title: SM-D9EOP_S95_E1-50


title: SM-D9EOP_S94_E1-50


title: SM-D9EOP_S92_E1-50


title: Cell_1237_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S76_E1-50


title: Cell_1238_E10.5_FACS-HE_Runx1_KO


title: Cell_1236_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S75_E1-50


title: SM-D9EOP_S74_E1-50

value: Oligo


title: SM-D9EOP_S71_E1-50


title: SM-D9EOP_S90_E1-50


title: Cell_1235_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S73_E1-50


title: Cell_1232_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S70_E1-50


title: SM-D9EOP_S89_E1-50


title: Cell_1233_E10.5_FACS-HE_Runx1_KO


title: Cell_1234_E10.5_FACS-HE_Runx1_KO


title: Cell_1239_E10.5_FACS-HE_Runx1_KO


title: Cell_1231_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S69_E1-50


title: Cell_1229_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S67_E1-50


title: Cell_1230_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S65_E1-50


title: SM-D9EOQ_S62_E1-50


title: Cell_1228_E10.5_FACS-HE_Runx1_KO


title: Cell_1227_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S63_E1-50


title: SM-D9EOP_S62_E1-50


title: SM-D9EOP_S61_E1-50


title: SM-D9EOP_S59_E1-50


title: SM-D9EOP_S60_E1-50


title: Cell_1224_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S68_E1-50


title: Cell_1223_E10.5_FACS-HE_Runx1_KO


title: Cell_1225_E10.5_FACS-HE_Runx1_KO


title: Cell_1221_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S46_E1-50


title: SM-D9EOP_S29_E1-50

value: M


title: Cell_1220_E10.5_FACS-HE_Runx1_KO

value: ICR


title: SM-D9EOP_S30_E1-50


title: Cell_1219_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S66_E1-50


title: SM-D9EOP_S28_E1-50


title: Cell_1217_E10.5_FACS-HE_Runx1_KO


title: Cell_1218_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S26_E1-50


title: Cell_1216_E10.5_FACS-HE_Runx1_KO


title: Cell_1226_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S25_E1-50


title: Cell_1214_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S23_E1-50


title: SM-D9EOP_S21_E1-50


title: SM-D9EOP_S20_E1-50


title: Cell_1213_E10.5_FACS-HE_Runx1_KO


title: Cell_1215_E10.5_FACS-HE_Runx1_KO


title: Cell_1222_E10.5_FACS-HE_Runx1_KO


title: Cell_1212_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S18_E1-50


title: SM-D9EOP_S19_E1-50


title: SM-D9EOP_S15_E1-50


title: SM-D9EOP_S14_E1-50


title: Cell_1209_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S31_E1-50


title: Cell_1210_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S27_E1-50


title: Cell_1207_E10.5_FACS-HE_Runx1_KO


title: Cell_1206_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S11_E1-50


title: SM-D9EOP_S13_E1-50


title: Cell_1208_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S10_E1-50


title: Cell_1205_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S09_E1-50


title: Cell_1203_E10.5_FACS-HE_Runx1_KO


title: Cell_1204_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S07_E1-50


title: Cell_1211_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S05_E1-50


title: Cell_1202_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOQ_S59_E1-50


title: Cell_1199_E10.5_FACS-HE_Runx1_KO


title: Cell_1200_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S06_E1-50


title: SM-D9EOP_S03_E1-50


title: SM-D9EOP_S02_E1-50


title: Cell_1201_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOP_S01_E1-50


title: Cell_1197_E10.5_FACS-HE_Runx1_KO


title: Cell_1196_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S95_E1-50


title: Cell_1194_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S92_E1-50


title: SM-D9EOO_S94_E1-50


title: SM-D9EOO_S93_E1-50


title: Cell_1198_E10.5_FACS-HE_Runx1_KO


title: Cell_1195_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S90_E1-50


title: Cell_1192_E10.5_FACS-HE_Runx1_KO


title: Cell_1193_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S89_E1-50


title: SM-D9EOO_S86_E1-50


title: Cell_1189_E10.5_FACS-HE_Runx1_KO


title: Cell_1190_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S84_E1-50


title: Cell_1188_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S83_E1-50


title: SM-D9EOO_S82_E1-50


title: SM-D9EOO_S96_E1-50

value: OPC


title: Cell_1186_E10.5_FACS-HE_Runx1_KO


title: Cell_1184_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S81_E1-50

value: NeuN-pos


title: Cell_1191_E10.5_FACS-HE_Runx1_KO


title: Cell_1185_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S71_E1-50

value: Glut


title: SM-D9EOO_S87_E1-50

value: PC


title: SM-D9EOO_S69_E1-50


title: SM-D9EOO_S63_E1-50


title: SM-D9EOO_S66_E1-50


title: SM-D9EOO_S65_E1-50


title: SM-D9EOO_S67_E1-50


title: Cell_1182_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S68_E1-50


title: Cell_1180_E10.5_FACS-HE_Runx1_KO


title: Cell_1178_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S62_E1-50


title: Cell_1179_E10.5_FACS-HE_Runx1_KO


title: Cell_1187_E10.5_FACS-HE_Runx1_KO


title: Cell_1177_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S61_E1-50


title: Cell_1175_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S60_E1-50


title: Cell_1174_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S59_E1-50


title: SM-D9EOO_S58_E1-50


title: Cell_1183_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S57_E1-50


title: Cell_1173_E10.5_FACS-HE_Runx1_KO


title: Cell_1172_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S32_E1-50


title: Cell_1181_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S31_E1-50


title: SM-D9EOO_S30_E1-50


title: Cell_1171_E10.5_FACS-HE_Runx1_KO


title: Cell_1170_E10.5_FACS-HE_Runx1_KO


title: Cell_1169_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S28_E1-50


title: Cell_1167_E10.5_FACS-HE_Runx1_KO


title: Cell_1168_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S26_E1-50


title: Cell_1165_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S25_E1-50


title: Cell_1164_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S23_E1-50


title: SM-D9EOO_S21_E1-50


title: SM-D9EOO_S22_E1-50


title: Cell_1163_E10.5_FACS-HE_Runx1_KO


title: Cell_1162_E10.5_FACS-HE_Runx1_KO


title: Cell_1161_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S19_E1-50


title: SM-D9EOO_S20_E1-50


title: Cell_1160_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S17_E1-50


title: Cell_1159_E10.5_FACS-HE_Runx1_KO


title: Cell_1158_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S14_E1-50


title: Cell_1166_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S12_E1-50


title: Cell_1156_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S13_E1-50


title: SM-D9EOO_S07_E1-50


title: SM-D9EOO_S09_E1-50


title: SM-D9EOO_S05_E1-50


title: Cell_1153_E10.5_FACS-HE_Runx1_KO


title: Cell_1157_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S04_E1-50


title: Cell_1155_E10.5_FACS-HE_Runx1_KO


title: Cell_1150_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S02_E1-50


title: Cell_1154_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S01_E1-50


title: Cell_1151_E10.5_FACS-HE_Runx1_KO


title: Cell_1149_E10.5_FACS-HE_Runx1_KO


title: SM-D9D8B_S08_E1-50

value: MC


title: SM-D9D8B_S07_E1-50


title: Cell_1148_E10.5_FACS-HE_Runx1_KO


title: SM-D9D8B_S05_E1-50


title: Cell_1147_E10.5_FACS-HE_Runx1_KO


title: Cell_1146_E10.5_FACS-HE_Runx1_KO


title: SM-D9EOO_S10_E1-50


title: Cell_1145_E10.5_FACS-HE_Runx1_KO


title: SM-D9D8B_S03_E1-50


title: Cell_1144_E10.5_FACS-Mes_KO


title: SM-D9EOO_S03_E1-50


title: SM-D9D8B_S02_E1-50


title: SM-D9D8A_S08_E1-50


title: SM-D9D8B_S01_E1-50


title: Cell_1143_E10.5_FACS-Mes_KO


title: Cell_1141_E10.5_FACS-Mes_KO


title: SM-D9D89_S14_E1-50


title: SM-D9D89_S15_E1-50


title: Cell_1142_E10.5_FACS-Mes_KO


title: Cell_1140_E10.5_FACS-Mes_KO


title: Cell_1138_E10.5_FACS-Mes_KO


title: SM-D9D89_S13_E1-50


title: SM-D9D89_S12_E1-50


title: SM-D9D89_S07_E1-50


title: SM-D9D89_S09_E1-50


title: Cell_1139_E10.5_FACS-Mes_KO


title: Cell_1137_E10.5_FACS-Mes_KO


title: Cell_1136_E10.5_FACS-Mes_KO


title: SM-D9D89_S06_E1-50


title: SM-D9D89_S05_E1-50


title: Cell_1135_E10.5_FACS-Mes_KO


title: Cell_1134_E10.5_FACS-Mes_KO


title: SM-D9D89_S03_E1-50


title: Cell_1133_E10.5_FACS-Mes_KO


title: SM-D9D89_S02_E1-50


title: Cell_1132_E10.5_FACS-HE_Runx1_KO


title: Cell_1152_E10.5_FACS-HE_Runx1_KO


title: Cell_1129_E10.5_FACS-HE_Runx1_KO


title: SM-D9D88_S11_E1-50


title: SM-D9D88_S10_E1-50


title: SM-D9D88_S16_E1-50

value: Micro


title: Cell_1127_E10.5_FACS-HE_Runx1_KO


title: Cell_1128_E10.5_FACS-HE_Runx1_KO


title: Cell_1130_E10.5_FACS-HE_Runx1_KO


title: SM-D9D88_S08_E1-50

value: Non-Neuronal


title: SM-D9D88_S06_E1-50


title: SM-D9D88_S12_E1-50


title: Cell_1131_E10.5_FACS-HE_Runx1_KO


title: SM-D9D88_S04_E1-50


title: Cell_1125_E10.5_FACS-HE_Runx1_KO


title: SM-D9D83_S22_E1-50


title: SM-D9D88_S02_E1-50


title: Cell_1126_E10.5_FACS-HE_Runx1_KO


title: SM-D9D83_S24_E1-50


title: SM-D9D83_S20_E1-50


title: Cell_1122_E10.5_FACS-HE_Runx1_KO


title: Cell_1120_E10.5_FACS-HE_Runx1_KO


title: SM-D9D83_S19_E1-50


title: Cell_1121_E10.5_FACS-HE_Runx1_KO


title: Cell_0437_E10.5_FACS-Mes_het


title: SM-D9D83_S08_E1-50


title: Cell_0436_E10.5_FACS-Mes_het


title: Cell_0435_E10.5_FACS-HE_Runx1_het


title: Cell_1123_E10.5_FACS-HE_Runx1_KO


title: SM-D9D82_S22_E1-50


title: Cell_0433_E10.5_FACS-HE_Runx1_het


title: Cell_1124_E10.5_FACS-HE_Runx1_KO


title: Cell_0434_E10.5_FACS-HE_Runx1_het


title: SM-D9D83_S06_E1-50


title: SM-D9D82_S20_E1-50


title: Cell_0431_E10.5_FACS-Mes_het


title: SM-D9D83_S01_E1-50


title: Cell_0432_E10.5_FACS-HE_Runx1_het


title: SM-D9D82_S17_E1-50


title: Cell_0429_E10.5_FACS-Mes_het


title: SM-D9D82_S19_E1-50


title: Cell_0428_E10.5_FACS-HE_Runx1_het


title: SM-D9D82_S15_E1-50


title: Cell_0430_E10.5_FACS-Mes_het


title: SM-D9D83_S17_E1-50


title: SM-D9D82_S16_E1-50


title: SM-D9D82_S13_E1-50


title: Cell_0427_E10.5_FACS-HE_Runx1_het


title: SM-D9D82_S18_E1-50


title: SM-D9D82_S14_E1-50


title: Cell_0426_E10.5_FACS-HE_Runx1_het


title: Cell_0425_E10.5_FACS-Mes_het


title: SM-D9D82_S12_E1-50


title: SM-D9D82_S11_E1-50


title: Cell_0420_E10.5_FACS-HE_Runx1_het


title: Cell_0421_E10.5_FACS-HE_Runx1_het


title: Cell_0423_E10.5_FACS-HE_Runx1_het


title: Cell_0422_E10.5_FACS-HE_Runx1_het


title: SM-D9D81_S09_E1-50


title: SM-D9D81_S11_E1-50


title: SM-D9D82_S09_E1-50


title: Cell_0418_E10.5_FACS-Mes_het


title: SM-D9D81_S04_E1-50


title: SM-D9D81_S02_E1-50


title: SM-D9D81_S05_E1-50


title: Cell_0424_E10.5_FACS-Mes_het


title: SM-D9D81_S07_E1-50


title: Cell_0417_E10.5_FACS-Mes_het


title: Cell_0414_E10.5_FACS-HE_Runx1_het


title: Cell_0413_E10.5_FACS-HE_Runx1_het


title: SM-D9D7Z_S12_E1-50


title: SM-D9D7Z_S09_E1-50


title: SM-D9D7Z_S15_E1-50


title: Cell_0416_E10.5_FACS-HE_Runx1_het


title: Cell_0415_E10.5_FACS-HE_Runx1_het


title: Cell_0419_E10.5_FACS-Mes_het


title: SM-D9D7Z_S07_E1-50


title: Cell_0412_E11.5_FACS-HE_Gfi1_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Cell_0411_E11.5_FACS-HE_Gfi1_het


title: Cell_1176_E10.5_FACS-HE_Runx1_KO


title: SM-D9D81_S16_E1-50


title: SM-D9D7Z_S06_E1-50


title: Cell_0404_E11.5_FACS-HE_Gfi1_het


title: Cell_0407_E11.5_FACS-HE_Gfi1_het


title: SM-D9D7Z_S03_E1-50


title: SM-D9D7U_S16_E1-50


title: SM-D9D7Z_S01_E1-50


title: SM-D9D7U_S13_E1-50


title: Cell_0402_E10.5_FACS-HE_Gfi1_1b_KO

value: Gfi1:Tomato/Tomato Gfi1b:GFP/GFP


title: SM-D9D7U_S10_E1-50


title: Cell_0405_E11.5_FACS-HE_Gfi1_het


title: SM-D9D7U_S11_E1-50


title: SM-D9D7Z_S13_E1-50


title: Cell_0399_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9D7U_S07_E1-50


title: Cell_0409_E11.5_FACS-HE_Gfi1_het


title: SM-D9D7U_S09_E1-50


title: Cell_0410_E11.5_FACS-HE_Gfi1_het


title: SM-D9D7U_S08_E1-50


title: Cell_0406_E11.5_FACS-HE_Gfi1_het


title: Cell_0396_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0400_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0403_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0401_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9D7U_S06_E1-50


title: Cell_0408_E11.5_FACS-HE_Gfi1_het


title: Cell_0398_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9D7U_S12_E1-50


title: SM-D9D7U_S05_E1-50


title: Cell_0395_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9D7U_S01_E1-50

value: MP


title: SM-D9D7U_S02_E1-50


title: SM-D9D7U_S03_E1-50


title: SM-D9CXN_S94_E1-50


title: SM-D9CXN_S96_E1-50


title: Cell_0394_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0393_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0392_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S95_E1-50

value: GABA


title: Cell_0390_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0389_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S93_E1-50


title: Cell_0397_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0387_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S92_E1-50


title: SM-D9CXN_S89_E1-50


title: SM-D9CXN_S85_E1-50


title: SM-D9CXN_S91_E1-50


title: SM-D9CXN_S83_E1-50


title: Cell_0386_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0384_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0385_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S81_E1-50


title: SM-D9CXN_S78_E1-50


title: Cell_0382_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S80_E1-50

value: NeuN-neg


title: Cell_0391_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S77_E1-50


title: SM-D9CXN_S72_E1-50

value: Astro


title: Cell_0381_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0380_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0379_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S76_E1-50


title: SM-D9CXN_S65_E1-50


title: Cell_0378_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0377_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0388_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S64_E1-50


title: SM-D9CXN_S60_E1-50


title: SM-D9CXN_S57_E1-50


title: Cell_0383_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S58_E1-50


title: SM-D9CXM_S95_E1-50


title: Cell_0373_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0371_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0375_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0372_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXN_S74_E1-50


title: Cell_0370_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXM_S94_E1-50


title: SM-D9CXM_S92_E1-50


title: SM-D9CXM_S91_E1-50


title: Cell_0368_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0367_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0369_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXM_S86_E1-50


title: SM-D9CXM_S89_E1-50


title: Cell_0366_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0374_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0376_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0364_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0363_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXM_S85_E1-50


title: SM-D9CXM_S84_E1-50


title: Cell_0365_E10.5_FACS-HE_Gfi1_1b_KO


title: SM-D9CXM_S83_E1-50


title: SM-D9CXM_S76_E1-50


title: SM-D9CXM_S77_E1-50


title: Cell_0358_E10.5_FACS-IAHC_het


title: Cell_0361_E10.5_FACS-IAHC_het


title: SM-D9CXN_S59_E1-50


title: Cell_0362_E10.5_FACS-HE_Gfi1_1b_KO


title: Cell_0359_E10.5_FACS-IAHC_het


title: SM-D9CXM_S73_E1-50


title: Cell_0360_E10.5_FACS-IAHC_het


title: SM-D9CXM_S75_E1-50


title: SM-D9CXM_S72_E1-50


title: SM-D9CXM_S74_E1-50


title: Cell_0357_E10.5_FACS-IAHC_het


title: SM-D9CXM_S70_E1-50


title: SM-D9CXL_S96_E1-50


title: Cell_0356_E10.5_FACS-IAHC_het


title: Cell_0355_E10.5_FACS-IAHC_het


title: Cell_0354_E10.5_FACS-IAHC_het


title: Cell_0352_E10.5_FACS-IAHC_het


title: Cell_0353_E10.5_FACS-IAHC_het


title: rrmd_ts2

city: Lausanne

first: Franziska

last: Gruhl

address: University of Lausanne, Quartier Sorge

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

data_processing:
Read quality assessment and mapping: Basecalling was performed with the Illumina Casava software (v 1.9) and read quality assessed with FastQC (v 0.10.1). The ensembl annotations for opossum (monDom5), mouse (mm10), rat (rn5), rhesus macaque (rheMac2) and human (hg38) were used to build transcriptome indexes for mapping with TopHat2 (v 2.0.11). TopHat2 was run with default settings and the --mate-inner-dist and --mate-std-dev options set to 50 and 200 respectively. The mate-inner-distance parameter was estimated based on the fragment analyzer report.
CircRNA annotation: We developed a custom pipeline to detect circRNAs, which performs the following steps: Unmapped reads with a phred quality value of at least 25 are used to generate 20 bp anchor pairs from the terminal 3' and 5'-ends of the read. Anchors are remapped with bowtie2 (v 2.1.0) on the reference genome. Mapped anchor pairs are filtered for 1) being on the same chromosome, 2) being on the same strand and 3) for having a genomic mapping distance to each other of a maximum of 100 kb. Next, anchors are extended upstream and downstream of their mapping locus. They are kept if pairs are extendable to the full read length. During this procedure a maximum of two mismatches is allowed. Next, all unpaired reads are selected from the accepted_hits.bam file generated by TopHat2 (singletons) and assessed for whether the mate read (second read of a paired-end sequencing read) of the anchor pair mapped between the backsplice coordinates. All anchor pairs for which 1) the mate did not map between the genomic backsplice coordinates, 2) the mate mapped to another backsplice junction or 3) the extension procedure could not reveal a clear breakpoint are removed. Based on the remaining candidates, a backsplice index is built with bowtie2 and all reads are remapped on this index to increase the read coverage by detecting reads that cover the BSJ with less than 20 bp, but at least 8 bp. Candidate reads that were used to build the backsplice index and now mapped to another backsplice junction are removed. Upon this procedure, the pipeline provides a first list of backsplice junctions. The set of scripts, which performs the identification of putative BSJs, as well as a short description of how to run the pipeline are reposited on GitHub (https://github.com/Frenzchen/ncSplice_circRNAdetection).
CircRNA expression levels: CPM (counts per million) values for backsplice junctions were calculated for each tissue as follows: counts = mean(counts_rep1, counts_rep2, counts_rep3); totalMappedReads =mean(mappedReads_rep1, mappedReads_rep2, mappedReads_rep3); CPM= counts*10^6/totalMappedReads  To distinguish putative backsplice junctions from the technical and biological noise background, the enrichment of the previously defined junctions in RNase R treated samples was calculated. The enrichment was defined as CPM increase in RNase R treated versus untreated samples: enrichment = CPM_RNase R/CPM_untreated  Candidates with a log2-enrichment of smaller 1.5 were removed. Expression levels for all circRNAs can be found in the files mdCircRNA_cpms.txt (opossum), mmCircRNA_cpms.txt (mouse), rnCircRNA_cpms.txt (rat), rmCircRNA_cpms.txt (rhesus macaque) and hsCircRNA_cpms.txt (human).
CircRNA transcript reconstruction: To reconstruct the exon structure of circRNA transcripts in each tissue, we made use of the junction enrichment in RNase R treated samples. To normalize junction reads across libraries, the size factors ( size factor = median(x/geometric mean) ) based on the geometric mean ( geometric mean = product(x)^(1/length(x)) ) of common junctions in untreated and treated samples was calculat, with x being a vector containing the number of reads per junction. We then compared read coverage for junctions outside and inside the BSJ for each gene and used the log2-change of junctions outside the backsplice junction to construct the expected background distribution of change in junction coverage upon RNase R treatment. The observed coverage change of junctions inside the backsplice was then compared to the expected change in the background distribution and junctions with a log2-change outside the 90% confidence interval were assigned as circRNA junction. A loose cut-off was chosen here, because involved junctions can show a decrease in coverage if their linear isoform was present at high levels before (degradation levels of linear isoforms do not correlate with the enrichment levels of circRNAs). Next, we reconstructed a splicing graph for each circRNA candidate, in which network nodes are exons connected by splice junctions (edges). Connections between nodes are weighted by the coverage in the RNase R treated samples. The resulting network graph is directed (because of the known circRNA start and stop coordinates), acyclic (because splicing always proceeds in one direction), weighted and relatively small. We used a simple breadth-first-search algorithm to traverse the graph and to define the strength for each possible isoform by its mean coverage. For further analyses, only the strongest isoform was considered.  A gtf-file with the circRNA annotation for each species has been deposited (mdCircRNAs.gtf, mmCircRNA.gtf, rnCircRNAs.gtf, rmCircRNAs.gtf, hsCircRNAs.gtf).
Genome_build: opossum: monDom5 (ensembl release 75, feb 2014); mouse: mm10 (ensembl release 75, feb 2014); rat: rn5 (ensembl release 75, feb 2014); rhesus macaque: rheMac2 (ensembl release 77, oct 2014); human: hg38 (ensembl release 77, oct 2014)
Supplementary_files_format_and_content: tab-delimited text files include CPM values for all circRNAs.
Supplementary_files_format_and_content: gtf-files contain the circRNA annotation (genes, transcripts and exons) for each species.

organism: Monodelphis domestica

source_name: Testis

extract_protocol:
Tissue was dissected at indicated ages (see section ”Samples” in GEO metadata). RNA for mouse, rat, rhesus and human was extracted using the RNeasy protocol from QIAGEN; for opossum, a TRIzol/chloroform-based protocol was used. Tissues were stored at -80 C until library preparation.
We used 5µg of RNA per tissue as starting material for library preparation, which were treated with RNase R for 1 h at 37 ̊C to degrade linear RNAs, followed by RNA purification with RNA Clean & Concentrator-5 kit (Zymo Research) according to the manufacturer’s protocol. Libraries were prepared from the purified RNA with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold according to the protocol with the following modifications to select larger fragments: 1). Instead of the recommended 8 min at 68 ̊C for fragmentation, we incubated samples for only 4 min at 68 ̊C to increase the fragment size; 2). In the final PCR clean-up after enrichment of the DNA fragments, we changed the 1:1 ratio of DNA to AMPure XP Beads to a 0.7:1 ratio to select for binding of larger fragments. Libraries were analyzed on the fragment analyzer for their quality and sequenced with the Illumina HiSeq 2500 platform.

value: Testis

value: wild type

value: 13 months

value: RNase R-treated


title: SM-D9CXL_S92_E1-50

value: M

value: Oligo


title: rrmd_ts3

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

value: 15.5 months


title: SM-D9CXL_S89_E1-50

value: NeuN-pos


title: rrmd_ts1

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

value: 21 months


title: comd_ts3

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

value: untreated


title: SM-D9CXL_S88_E1-50

value: PC

value: Non-Neuronal


title: Cell_0351_E10.5_FACS-IAHC_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: SM-D9CXL_S86_E1-50

value: GABA


title: SM-D9CXL_S87_E1-50


title: SM-D9CXL_S84_E1-50


title: comd_ts2

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt


title: Cell_0348_E10.5_FACS-IAHC_het


title: rrmd_ce3

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

source_name: Cerebellum

value: Cerebellum


title: comd_ts1

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt


title: Cell_0349_E10.5_FACS-IAHC_het


title: SM-D9CXL_S83_E1-50


title: SM-D9CXL_S95_E1-50

value: MC


title: rrmd_ce2

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

value: 19.5 months


title: rrmd_ce1

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

value: wild type


title: comd_ce3

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt


title: comd_ce2

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt


title: comd_ce1

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt


title: Cell_0347_E10.5_FACS-IAHC_het


title: Cell_0346_E10.5_FACS-IAHC_het


title: SM-D9CXL_S81_E1-50

value: Glut

value: MP


title: rrmd_lv2

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

source_name: Liver

value: Liver

value: RNase R-treated


title: Cell_0350_E10.5_FACS-IAHC_het


title: rrmd_lv3

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

value: 13 months


title: SM-D9CXL_S78_E1-50

value: M

value: NeuN-pos

value: Astro


title: SM-D9CXL_S80_E1-50

value: PC

value: NeuN-neg

value: OPC


title: Cell_0344_E10.5_FACS-IAHC_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: comd_lv2

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

value: 21 months

value: untreated


title: SM-D9CXL_S77_E1-50

value: Non-Neuronal


title: rrmd_lv1

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt

value: wild type

value: 15.5 months


title: Cell_0343_E10.5_FACS-IAHC_het


title: comd_lv3

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt


title: comd_lv1

description:
mdCircRNAs.gtf
mdCircRNA_cpms.txt


title: Cell_0342_E10.5_FACS-IAHC_het


title: rrrn_ts3

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt

organism: Rattus norvegicus

value: Testis

value: 16 weeks


title: SM-D9CXL_S76_E1-50

value: GABA


title: rrrn_ts2

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt

value: RNase R-treated


title: rrrn_ts1

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: SM-D9CXL_S75_E1-50

value: M


title: Cell_0345_E10.5_FACS-IAHC_het


title: corn_ts3

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: Cell_0341_E10.5_FACS-IAHC_het


title: SM-D9CXL_S74_E1-50

value: NeuN-pos

value: Glut

value: MP


title: corn_ts1

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: rrrn_ce2

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt

value: Cerebellum


title: SM-D9CXL_S71_E1-50

value: PC

value: Astro


title: Cell_0339_E10.5_FACS-IAHC_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Cell_0340_E10.5_FACS-IAHC_het


title: Cell_0338_E10.5_FACS-IAHC_het


title: corn_ts2

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt

value: untreated


title: corn_ce1

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: rrrn_lv3

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt

value: Liver


title: SM-D9CXL_S73_E1-50

value: Non-Neuronal


title: rrrn_lv2

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt

value: wild type


title: rrrn_ce3

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: SM-D9CXL_S70_E1-50


title: corn_ce3

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: corn_ce2

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: rrrn_ce1

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: SM-D9CXL_S69_E1-50

value: Oligo


title: corn_lv3

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt

value: 16 weeks


title: corn_lv2

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: corn_lv1

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt


title: Cell_0336_E10.5_FACS-IAHC_het


title: Cell_0333_E10.5_FACS-IAHC_het


title: MDAMB468_EV_T3_R2

city: Burlington

first: Frances

last: Carr

state: Vermont

address: 149 Beaumont Ave, HSRF 340

institute: University of Vermont

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Fastq Quality Trimmer
Ribosomal reads were removed with BBDuk
STAR 2.7 was used to align fastq files to hg38
Htseq 0.10 was used to count aligned reads
SARTools/DESeq2 was used for differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files with raw counts values for each sample
Supplementary_files_format_and_content: matrix table with normalized counts; DESeq2 output

source_name: basal-like breast cancer cell line, with control vector, with T3 treatment

growth_protocol: cells were hormone starved in phenol-red free culture media with charcoal stripped FBS for 24 hours, followed by the addition of  10nM T3 or vehicle (NaOH) treatment for 24 hours

extract_protocol:
cells were lysed in Trizol reagent, RNA was extracted, followed by BioAnalyzer analysis and all RIN values were  >7
NEBNext Ultra II RNA Kit was used for library construction, 1ug of RNA was used per sample per manufacturers instructions.

treatment_protocol: cells were treated with 10nM T3 or vehicle (NaOH) treatment for 24 hours

tag: vector

value: pCDH-EV

value: 10nM T3

tag: cell line

tag: treatment time

value: 24 hours


title: MDAMB468_EV_T3_R3


title: SM-D9CXL_S68_E1-50

value: M

value: NeuN-pos


title: Cell_0332_E10.5_FACS-IAHC_het


title: Cell_0335_E10.5_FACS-IAHC_het


title: MDAMB468_EV_T3_R1


title: SM-D9CXL_S66_E1-50

value: GABA


title: MDAMB468_EV_Vehicle_R3

source_name: basal-like breast cancer cell line, with control vector, without T3 treatment

value: vehicle (NaOH)


title: MDAMB468_EV_Vehicle_R2


title: Cell_0331_E10.5_FACS-IAHC_het


title: SM-D9CXK_S81_E1-50

value: MC


title: MDAMB468_EV_Vehicle_R1


title: Cell_0334_E10.5_FACS-IAHC_het


title: rrrn_lv1

description:
rnCircRNAs.gtf
rnCircRNA_cpms.txt

value: RNase R-treated


title: SM-D9CXK_S83_E1-50


title: SM-D9CXK_S87_E1-50


title: Cell_0330_E10.5_FACS-IAHC_het

value: ICR


title: Cell_0337_E10.5_FACS-IAHC_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: MDAMB468_TRB_T3_R2

source_name: basal-like breast cancer cell line, with stable TRB expression, with T3 treatment

value: pCDH-TRB


title: MDAMB468_TRB_Vehicle_R3

source_name: basal-like breast cancer cell line, with stable TRB expression, without T3 treatment


title: Cell_0329_E10.5_FACS-IAHC_het


title: SM-D9CXK_S74_E1-50

value: PC


title: SM-D9CXK_S79_E1-50

value: Glut

value: MP


title: MDAMB468_TRB_Vehicle_R2


title: MDAMB468_TRB_T3_R1


title: SM-D9CXK_S80_E1-50

value: NeuN-neg

value: Non-Neuronal

value: Astro


title: Cell_0327_E10.5_FACS-IAHC_het


title: MDAMB468_TRB_Vehicle_R1


title: SM-D9CXK_S72_E1-50

value: Micro


title: Cell_0328_E10.5_FACS-IAHC_het


title: Cell_0326_E10.5_FACS-IAHC_het


title: SM-D9CXK_S71_E1-50


title: SM-D9CXK_S69_E1-50

value: Oligo


title: MDAMB468_TRB_T3_R3

value: 10nM T3

value: 24 hours


title: Cell_0324_E10.5_FACS-IAHC_het


title: ubc9-6 (rep 2)

city: Toronto

first: Emanuel

last: Rosonina

state: ON

address: 4700 Keele Street

department: Biology

country: Canada

institute: York University

data_processing:
Genome alignments were performed with HISAT2 (2.1.0) with the sacCer3 reference genome
Gene assignments were performed with featureCounts from the Subread package (2.0.0)
Differential expression analysis was performed with edgeR (3.32.1)
Genome_build: sacCer3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Differential expression analysis for W303a vs ubc9-6 strains
Supplementary_files_format_and_content: Differential expression analysis for Tfg1-HA vs Tfg1-K60,61R-HA strains

organism: Saccharomyces cerevisiae

source_name: ubc9-6 (rep 2)

growth_protocol: Strains were grown in SC medium at 30°C to mid-log phase.

extract_protocol:
Cell pellets were mixed in a phenol-containing solution,then underwent two freeze-heat-mix cycles. RNA was then extracted with phenol-chloroform, followed by ethanol precipitation and further purified with the RNeasy kit (Qiagen).
NEB Ultra II directional mRNA library prep (PolyA enrichment)


title: Tfg1-K60,61R-HA (rep 2)


title: Cell_0325_E10.5_FACS-IAHC_het


title: Tfg1-HA (rep 2)

source_name: Tfg1-HA (rep 2)


title: SM-D9CXK_S68_E1-50

source_name: Human - dLGN - PC

value: M

value: NeuN-pos


title: SM-D9CXK_S66_E1-50


title: Cell_0321_E10.5_FACS-IAHC_het

source_name: Aorta gonad mesonephros


title: SM-D9CXK_S65_E1-50


title: Tfg1-K60,61R-HA (rep 1)


title: Tfg1-HA (rep 1)

source_name: Tfg1-HA (rep 1)


title: Cell_0323_E10.5_FACS-IAHC_het


title: Cell_0322_E10.5_FACS-IAHC_het


title: SM-D9CXK_S64_E1-50


title: SM-D9CXK_S67_E1-50


title: RNAPII IP  Tfg1-HA (rep 2)

library_source: genomic

data_processing:
Genome alignment performed with Bowtie2 (2.3.5.1) with the sacCer3 reference genome
Peak calling performed with MACS (2.2.7.1)
Genome_build: sacCer3
Supplementary_files_format_and_content: broadPeak files generated with MACS2.

molecule: genomic DNA

source_name: RNAPII IP  Tfg1-HA (rep 2)

extract_protocol:
Cross-linked samples were lysed, sonicated, clarified, and RNAPII-bound chromatin fragments were isolated by immunoprecipitation with the 8WG16 RNAPII antibody.
Libraries were synthesized using the NEBNext Ultra II DNA library prep kit (New England Biolabs)

tag: chip antibody


title: ubc9-6 (rep 1)

source_name: ubc9-6 (rep 1)


title: W303a (rep 1)

value: WT


title: Cell_0320_E10.5_FACS-IAHC_het


title: metastasis (rep3)

type: RNA

city: Ramat Gan,

first: Maya

middle: Ramot

last: Goshen

address: Derech Sheba 2,

department: Clinical Microbiology and Immunology

country: Israel

institute: Tel Aviv University

description:
test
WM266_2

data_processing: CEL files were processed using Affymetrix Expression Console Software into log2 RMA values using Affymetrix default analysis settings. When combining the 3 replicates together, in order to remove batch effect the first component in the principal component analysis was subtracted. The normalized data for all 3 replicates together can be found in the file "normalized_data_with_gene_name.txt" on the series record.

label: biotin

source_name: skin melanoma

label_protocol: Biotinylated cRNA were prepared  using WT expression kit according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

growth_protocol: cell lines WM115 and WM266-4 were obtained from the ATCC and were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1%NaP, 1%L-glu, 1%pen/strep and 1%non-essential amino acids all purchased from Biological-Industries, Israel

extract_protocol: For the first repeat, the total RNA was extracted using the miRNeasy micro kit (Qiagen) and RNA was loaded on Affymetrix Human Gene 1.0 ST Array Strip. In the following 2 biological repeats, total RNA was extracted using GeneAll Hybrid-R miRNA kit and RNA was loaded on Affymetrix Human Gene 2.1 ST Array Strip.

tag: tumor stage

value: skin metastasis


title: Input  Tfg1-HA (rep 2)

source_name: Input  Tfg1-HA (rep 2)


title: primary (rep2)

description:
control
WM115_1

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: skin primary tumor


title: primary (rep3)

description:
control
WM115_2

scan_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)


title: RNAPII IP  Tfg1-K60,61R-HA (rep 2)

source_name: RNAPII IP  Tfg1-K60,61R-HA (rep 2)


title: metastasis (rep2)

description:
test
WM266_1


title: RNAPII IP  Tfg1-K60,61R-HA (rep 1)

source_name: RNAPII IP  Tfg1-K60,61R-HA (rep 1)


title: W303a (rep 2)


title: Input  Tfg1-HA (rep 1)

source_name: Input  Tfg1-HA (rep 1)


title: SM-D9CXK_S62_E1-50

tag: donor


title: Cell_0319_E10.5_FACS-EHT_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Input  Tfg1-K60,61R-HA (rep 1)

source_name: Input  Tfg1-K60,61R-HA (rep 1)


title: Cell_0318_E10.5_FACS-EHT_het


title: RNAPII IP  Tfg1-HA (rep 1)

source_name: RNAPII IP  Tfg1-HA (rep 1)


title: Input  Tfg1-K60,61R-HA (rep 2)

source_name: Input  Tfg1-K60,61R-HA (rep 2)


title: Input from W303a_for_SUMO_IP, heat-shock (rep 2)

data_processing:
Genome alignment performed with Bowtie2 (2.3.5) with the sacCer3 reference genome
Peak calling performed with MACS2 (2.1.1.20160309)
Differential binding analysis performed with DiffBind (2.10.0)
Genome_build: sacCer3
Supplementary_files_format_and_content: narrowPeak files generated with MACS2

source_name: Input from W303a, heat-shock (rep 2)

extract_protocol:
Cross-linked samples were lysed, sonicated, clarified, and SUMO-bound chromatin fragments were isolated by immunoprecipitation with an Smt3 (yeast SUMO) antibody.
Libraries were synthesized using the NEBNext Ultra II DNA library prep kit (New England Biolabs)

treatment_protocol: Heat-shocked samples were transferred to 37°C for 12 min prior to processing.

value: none (input)

value: heat shock


title: Input from W303a_for_SUMO_IP, untreated (rep 2)

source_name: Input from W303a, untreated (rep 2)

value: untreated


title: Cell_0317_E10.5_FACS-EHT_het


title: SM-D9CXK_S60_E1-50

tag: Sex

value: PC

value: GABA


title: Cell_0316_E10.5_FACS-EHT_het


title: Input from ubc9-6_for_SUMO_IP, untreated (rep 2)

source_name: Input from ubc9-6, untreated (rep 2)


title: SM-D9CXK_S58_E1-50

tag: age

value: Glut

value: MP


title: SM-D9CXK_S57_E1-50

tag: facs gating

value: Non-Neuronal

value: Astro


title: SUMO IP in ubc9-6, untreated (rep 2)

source_name: SUMO IP in ubc9-6, untreated (rep 2)

value: Smt3 (y-84; Santa Cruz, sc-28649


title: Cell_0315_E10.5_FACS-EHT_het


title: Input from W303a_for_SUMO_IP, heat-shock (rep 1)

source_name: Input from W303a, heat-shock (rep 1)


title: SM-D9CXJ_S96_E1-50

source_name: Human - dLGN - PC

value: M

value: NeuN-neg

tag: sequencing batch


title: Cell_0314_E10.5_FACS-EHT_het

source_name: Aorta gonad mesonephros


title: Input from ubc9-6_for_SUMO_IP, untreated (rep 1)

source_name: Input from ubc9-6, untreated (rep 1)


title: SM-D9CXJ_S92_E1-50

value: NeuN-pos

tag: cell class


title: Input from W303a_for_SUMO_IP, untreated (rep 1)

source_name: Input from W303a, untreated (rep 1)

value: WT


title: SUMO IP in W303a, heat-shock (rep 1)

source_name: SUMO IP in W303a, heat-shock (rep 1)


title: SUMO IP in ubc9-6, untreated (rep 1)

source_name: SUMO IP in ubc9-6, untreated (rep 1)


title: Cell_0313_E10.5_FACS-EHT_het


title: SM-D9CXJ_S91_E1-50

tag: cell cluster


title: SM-D9CXK_S59_E1-50

value: OPC


title: SM-D9CXJ_S90_E1-50


title: Input from W303a, heat-shock (rep 2)

data_processing:
Genome alignments were performed with Bowtie2 (2.3.5) with the sacCer3 reference genome
Peak calling was performed with MACS2 (2.1.1.20160309)
Genome_build: sacCer3
Supplementary_files_format_and_content: broadPeak files generated with MACS2

tag: treatment


title: Cell_0312_E10.5_FACS-EHT_het

tag: strain

value: ICR


title: SUMO IP in W303a, untreated (rep 1)

source_name: SUMO IP in W303a, untreated (rep 1)


title: Input in ubc9-6, heat-shock (rep 2)

source_name: Input in ubc9-6, heat-shock (rep 2)


title: SM-D9CXJ_S89_E1-50


title: Cell_0311_E10.5_FACS-EHT_het

tag: developmental stage

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: SUMO IP in W303a, heat-shock (rep 2)

source_name: SUMO IP in W303a, heat-shock (rep 2)

tag: genotype


title: RNAPII IP in ubc9-6, heat-shock (rep 2)

source_name: RNAPII IP in ubc9-6, heat-shock (rep 2)


title: Input from ubc9-6, untreated (rep 2)

value: none (input)


title: Cell_0310_E10.5_FACS-EHT_het


title: Input from W303a, untreated (rep 2)


title: SM-D9CXJ_S80_E1-50

value: Oligo


title: Cell_0309_E10.5_FACS-EHT_het


title: SUMO IP in W303a, untreated (rep 2)

source_name: SUMO IP in W303a, untreated (rep 2)

value: untreated


title: SM-D9CXJ_S77_E1-50

value: PC


title: RNAPII IP in ubc9-6, untreated (rep 2)

source_name: RNAPII IP in ubc9-6, untreated (rep 2)


title: Input in ubc9-6, heat-shock (rep 1)

source_name: Input in ubc9-6, heat-shock (rep 1)

value: heat shock


title: SM-D9CXJ_S75_E1-50

value: GABA


title: Cell_0308_E10.5_FACS-EHT_het


title: Input from W303a, untreated (rep 1)


title: Input from ubc9-6, untreated (rep 1)


title: RNAPII IP in W303a, untreated (rep 2)

source_name: RNAPII IP in W303a, untreated (rep 2)


title: RNAPII IP in W303a, heat-shock (rep 2)

source_name: RNAPII IP in W303a, heat-shock (rep 2)


title: Cell_0305_E10.5_FACS-EHT_het


title: RNAPII IP in ubc9-6, heat-shock (rep 1)

source_name: RNAPII IP in ubc9-6, heat-shock (rep 1)


title: RNAPII IP in W303a, heat-shock (rep 1)

source_name: RNAPII IP in W303a, heat-shock (rep 1)


title: Cell_0306_E10.5_FACS-EHT_het


title: Input from W303a, heat-shock (rep 1)

source_name: Input from W303a, heat-shock (rep 1)


title: Cell_0307_E10.5_FACS-EHT_het

source_name: Aorta gonad mesonephros


title: SM-D9CXJ_S74_E1-50

source_name: Human - dLGN - PC

value: Glut

value: MP


title: RNAPII IP in ubc9-6, untreated (rep 1)

source_name: RNAPII IP in ubc9-6, untreated (rep 1)


title: Cell_0304_E10.5_FACS-EHT_het


title: RNAPII IP in W303a, untreated (rep 1)

source_name: RNAPII IP in W303a, untreated (rep 1)


title: Cell_0303_E10.5_FACS-EHT_het


title: Cell_0302_E10.5_FACS-EHT_het


title: SM-D9CXJ_S70_E1-50

value: Non-Neuronal


title: SM-D9CXJ_S73_E1-50


title: SM-D9CXJ_S68_E1-50


title: SM-D9CXJ_S72_E1-50

value: Astro


title: SM-D9CXJ_S67_E1-50

value: M


title: SM-D9CXJ_S66_E1-50


title: Cell_0301_E10.5_FACS-EHT_het


title: SM-D9CXJ_S65_E1-50


title: SM-D9CXJ_S64_E1-50

source_name: Human - dLGN - MC

value: MC

value: NeuN-neg


title: Cell_0299_E10.5_FACS-EHT_het


title: Cell_0300_E10.5_FACS-EHT_het


title: Cell_0298_E10.5_FACS-EHT_het


title: Cell_0297_E10.5_FACS-EHT_het


title: Cell_0295_E10.5_FACS-EHT_het


title: Cell_0296_E10.5_FACS-EHT_het


title: Cell_0294_E10.5_FACS-EHT_het


title: SM-D9CXJ_S62_E1-50

value: NeuN-pos


title: SM-D9CXJ_S61_E1-50


title: Cell_0293_E10.5_FACS-EHT_het


title: SM-D9CXJ_S60_E1-50


title: SM-D9CXJ_S56_E1-50


title: SM-D9CXJ_S45_E1-50


title: SM-D9CXJ_S48_E1-50

value: Micro


title: Cell_0292_E10.5_FACS-EHT_het

value: ICR


title: SM-D9CXJ_S40_E1-50


title: SM-D9CXJ_S39_E1-50


title: Cell_0290_E10.5_FACS-EHT_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Cell_0291_E10.5_FACS-EHT_het


title: SM-D9CXJ_S38_E1-50


title: MEL7

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using the minfi package running on RStudio version 1.3.1093 based on the statistical language R version 3.5.1

label: Cy5 and Cy3

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

tag: type

value: Normal melanocytes

tag: exact anatomic site

value: Melanocytes


title: Cell_0289_E10.5_FACS-EHT_het


title: MEL5


title: NC9

value: Mucosal melanoma

value: Nasal


title: MEL8


title: UV10

value: Uveal melanoma

value: Uvea


title: SM-D9CXJ_S37_E1-50

value: Oligo


title: MEL2


title: Cell_0288_E10.5_FACS-EHT_het


title: CO1

value: Conjunctival melanoma

value: Conjunctiva


title: SM-D9CXJ_S35_E1-50

value: Non-Neuronal


title: GE15

value: Genital


title: MEL4


title: NC14


title: Cell_0287_E10.5_FACS-EHT_het


title: SK13

value: Cutaneous melanoma

value: Skin


title: MEL1


title: SM-D9CXJ_S33_E1-50

value: M

value: MC

value: NeuN-pos

value: Glut

value: MP


title: NC11


title: SK7


title: MEL3

value: Normal melanocytes

value: Melanocytes


title: MEL6


title: CO9


title: PS2

value: Mucosal melanoma

value: Sinus


title: PS1


title: Cell_0286_E10.5_FACS-EHT_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: MO3

value: Mouth


title: NC6

value: Nasal


title: SK10


title: SM-D9CXJ_S31_E1-50

value: GABA


title: SK24


title: NC5


title: SK23


title: Cell_0284_E10.5_FACS-EHT_het


title: SM-D9CXJ_S26_E1-50

value: Non-Neuronal

value: Oligo


title: Cell_0285_E10.5_FACS-EHT_het


title: Cell_0282_E10.5_FACS-EHT_het


title: SM-D9CXJ_S24_E1-50

value: PC

value: NeuN-neg

value: Micro


title: SM-D9CXJ_S21_E1-50

value: M

value: NeuN-pos


title: Cell_0283_E10.5_FACS-EHT_het


title: SK5

value: Cutaneous melanoma

value: Skin


title: Cell_0281_E10.5_FACS-EHT_het


title: SM-D9CXJ_S20_E1-50

value: Astro


title: MO5

value: Mucosal melanoma


title: SM-D9CXJ_S19_E1-50


title: Cell_0280_E10.5_FACS-EHT_het


title: Cell_0278_E11.5_FACS-EHT_het


title: SM-D9CXJ_S17_E1-50


title: SM-D9CXJ_S18_E1-50


title: NC1


title: SM-D9CXJ_S16_E1-50


title: Cell_0279_E10.5_FACS-EHT_het


title: SM-D9CXJ_S14_E1-50


title: Cell_0276_E11.5_FACS-EHT_het


title: Cell_0277_E11.5_FACS-EHT_het


title: CO8

value: Conjunctival melanoma

value: Conjunctiva


title: NC15


title: PS3

value: Sinus


title: SK17


title: SK6


title: AN13

value: Anorectal


title: SM-D9CXJ_S13_E1-50


title: PS4


title: Cell_0275_E11.5_FACS-EHT_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: SM-D9CXJ_S12_E1-50

value: Non-Neuronal


title: Cell_0274_E11.5_FACS-EHT_het


title: SK11


title: CO2


title: Cell_0273_E11.5_FACS-EHT_het


title: GE10

value: Genital


title: SM-D9CXJ_S10_E1-50

value: PC

value: Glut

value: MP


title: UV9

value: Uveal melanoma

value: Uvea


title: SM-D9CXJ_S09_E1-50

value: M

value: NeuN-pos

value: GABA


title: GE7

value: Mucosal melanoma


title: Cell_0272_E11.5_FACS-EHT_het


title: MO2

value: Mouth


title: SK20

value: Cutaneous melanoma

value: Skin


title: SM-D9CXJ_S08_E1-50

value: NeuN-neg

value: Oligo


title: SK16


title: UV5


title: Cell_0271_E11.5_FACS-EHT_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: SM-D9CXJ_S07_E1-50

value: Non-Neuronal


title: SK21


title: SK12


title: UV8


title: Cell_0270_E11.5_FACS-EHT_het


title: SK2


title: UV4


title: UV3


title: NC4

value: Nasal


title: NC2


title: SM-D9CXJ_S05_E1-50

value: PC


title: SM-D9CXJ_S06_E1-50


title: Cell_0269_E11.5_FACS-EHT_het


title: Cell_0268_E11.5_FACS-EHT_het


title: Cell_0267_E11.5_FACS-EHT_het


title: SM-D9CXJ_S04_E1-50


title: CO6

value: Conjunctival melanoma

value: Conjunctiva


title: Cell_0266_E11.5_FACS-EHT_het


title: SM-D9CXJ_S01_E1-50

value: OPC


title: Cell_0265_E11.5_FACS-EHT_het


title: LS-15932_S94_E1-50

source_name: Human - dLGN - KC

value: M

value: KC


title: Cell_0264_E11.5_FACS-EHT_het


title: SK9


title: CO7


title: GE2

value: Genital


title: LS-15932_S93_E1-50

value: NeuN-pos

value: Glut

value: MP


title: Cell_0263_E11.5_FACS-EHT_het


title: SM-D9CXJ_S03_E1-50


title: GE12

value: Mucosal melanoma


title: UV6

value: Uveal melanoma

value: Uvea


title: LS-15932_S91_E1-50


title: Cell_0262_E11.5_FACS-EHT_het

value: ICR


title: LS-15932_S90_E1-50


title: UV7


title: Cell_0261_E11.5_FACS-EHT_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: SK4

value: Cutaneous melanoma

value: Skin


title: SK25


title: LS-15932_S89_E1-50

value: Non-Neuronal

value: Oligo


title: SK14


title: Cell_0260_E11.5_FACS-EHT_het


title: SK8


title: SK18


title: PS9

value: Sinus


title: SK15


title: LS-15932_S87_E1-50


title: UV1


title: Cell_0258_E11.5_FACS-EHT_het


title: Cell_0259_E11.5_FACS-EHT_het


title: LS-15932_S86_E1-50


title: CO4

value: Conjunctival melanoma

value: Conjunctiva


title: MO4

value: Mouth


title: CO5


title: MO9


title: LS-15932_S85_E1-50

value: M

value: KC


title: mice_WT_RNA-seq.rep2

city: Irvine

first: Yumei

last: Li

address: 825 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California, Irvine

data_processing:
Raw RNA-seq reads were filtered to remove low-quality reads.
The reads were aligned to mouse genome (mm10) using HISAT2 (V2.2.1)
Read count for genes were calculated using featureCount.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files; scores represent read count for each gene

source_name: wild type lung

extract_protocol:
Total RNA was extracted from wild type lungs, Kras and mNSD2;Kras lung tumors, and primary cells derived from mNSD2;Kras tumors (sgControl or sgNSD2) using Trizol reagent (Invitrogen).
RNA-seq libraries were constructed and sequenced in BGI.

tag: tissue

value: lung

value: wild type


title: SK3


title: Cell_0257_E11.5_FACS-EHT_het


title: LS-15932_S84_E1-50

value: NeuN-pos

value: Glut

value: MP


title: AN4

value: Mucosal melanoma

value: Anorectal


title: PS5


title: LS-15932_S83_E1-50


title: mice_WT_RNA-seq.rep1


title: Cell_0256_E11.5_FACS-EHT_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: Cell_0255_E11.5_FACS-EHT_het


title: LS-15932_S82_E1-50


title: mice_RAS_RNA-seq.rep2

source_name: Kras lung tumor

value: lung tumor

value: Kras


title: Cell_0254_E11.5_FACS-EHT_het


title: CO3


title: SK1

value: Cutaneous melanoma

value: Skin


title: mice_RAS_RNA-seq.rep1


title: Cell_0253_E11.5_FACS-EHT_het


title: AN7


title: NC3

value: Nasal


title: AN5


title: Cell_0252_E11.5_FACS-EHT_het


title: LS-15932_S80_E1-50

value: PC

value: NeuN-neg

value: Non-Neuronal

value: Oligo


title: LS-15932_S79_E1-50

value: M

value: GABA


title: Cell_0251_E11.5_FACS-EHT_het


title: PS7

value: Sinus


title: LS-15932_S76_E1-50

value: NeuN-pos

value: Glut

value: MP


title: mice_NSD2_KD_RNA-seq.rep2

source_name: primary cells from mNSD2;Kras tumor (sgNSD2)

value: NSD2 knockdown


title: UV2

value: Uveal melanoma

value: Uvea


title: Cell_0250_E11.5_FACS-EHT_het

value: ICR

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: mice_RAS_NSD2_RNA-seq.rep2

source_name: mNSD2;Kras lung tumor

value: lung tumor


title: mice_RAS_NSD2_RNA-seq.rep1


title: MO1

value: Mucosal melanoma

value: Mouth


title: Cell_0249_E11.5_FACS-EHT_het


title: LS-15932_S81_E1-50

value: KC


title: LS-15932_S75_E1-50

value: PC


title: MO7


title: mice_NSD2_KD_RNA-seq.rep1


title: LS-15932_S74_E1-50


title: Cell_0248_E11.5_FACS-EHT_het


title: mice_NSD2EK2_Ctrl_RNA-seq.rep2

source_name: primary cells from mNSD2;Kras tumor (sgControl)

value: control


title: AN12

value: Anorectal


title: SK22

value: Cutaneous melanoma

value: Skin


title: mice_NSD2EK1_Ctrl_RNA-seq.rep1


title: Cell_0246_E11.5_FACS-EHT_het


title: GE9

value: Mucosal

value: Genital


title: LS-15932_S70_E1-50

value: M

value: NeuN-pos

value: Non-Neuronal

value: Oligo


title: LS-15932_S69_E1-50


title: Cell_0245_E11.5_FACS-EHT_het

value: ICR


title: SK19


title: GE6


title: NSD2_Control_CUT-RUN

data_processing:
Library strategy: CUT&RUN
The raw sequencing reads were trimmed to remove sequencing adapters and low-quality bases in read ends using trim_galore (Version 0.6.5)
Then the reads were mapped to both mouse (mm10) and drosophila (dm6) genome using Bowtie2 (Version 2.2.7, --mm --no-unal --no-mixed --no-discordant -X 1000)
Mapped reads were filtered to only keep proper-paired and high mapping quality reads.
The PCR duplicates were removed using Picard MarkDuplicates tool
Genome_build: mm10 for mouse; dm6 for drosophila
Supplementary_files_format_and_content: bigWig files; scores represent mouse read intensity normalized to the number of drosophila reads

extract_protocol:
This assay was performed as described previously with some modifications. Buffer exchange was performed by centrifugation at 4 °C, 600g for 5 minutes. After the addition of concanavalin A beads, the buffer exchange was performed with a magnetic stand, allowing at least 5 minutes for the beads to completely bind to the magnet. Cells were harvested into a single cell suspension, counted, washed once with ice-cold PBS (Corning) and resuspended with ice-cold Nuclear Extraction (NE) buffer to a final concentration of 10x106 cells/mL. After 10 minutes on ice, cells were washed with Wash Buffer (WB) and resuspended in WB at a final concentration of 5x106 cells/mL. Efficient nuclear extraction was confirmed by Trypan Blue staining. In case of presence of nuclear aggregates, suspension was filtered through a 40um strainer before proceeding to next step. Concanavalin A beads were equilibrated in ice-cold binding buffer and mixed with the isolated nuclei (10ul bead slurry per 5x105 cells). The nuclei-beads mixture was incubated for 10 minutes rotating at 4°C. Successful nuclei-bead binding was confirmed with Trypan Blue staining. Beads-coated nuclei were resuspended in WB at a final concentration of 5x106 cells/mL and 100 μL were aliquoted into each sample tube. While gently vortexing, 100 μL of 2x primary antibody mix was added to the corresponding sample tube. Tube samples were mixed and incubated in rotation overnight at 4°C. Next day, nuclei were washed twice with 1 mL of ice-cold WB and resuspended in 25 μL of ice-cold WB. While gently vortexing, 25 μL of 2x pAG-MNase mix was added to each tube and samples were incubated for 1 hour at 4°C. Nuclei were washed twice with WB and resuspended in 150 μL of ice-cold WB. While gently vortexing, 3 μL of pre-chilled 100 μM CaCl2 were added and after briefly flicking to mix, tubes were incubated for 30 minutes in a 0 °C water bath. After 30 minutes, the MNase was inactivated by adding 150 μL of 2x STOP buffer. To isolate the digested DNA though diffusion, samples were incubated 20 minutes at 37 °C with no shaking. Samples were centrifuged at 16,000g for 5 minutes at 4°C and the resulting supernatant was treated with 3 μL of 10% SDS and 2.5 μL of 20 mg/mL proteinase K at 65 °C for 1 hour to overnight without shaking. DNA was purified with Qiagen MinElute PCR purification kit.
Sequencing libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645L) following the manufacturer’s manual.


title: Cell_0247_E11.5_FACS-EHT_het

value: Gfi1:Tomato/WT Gfi1b:GFP/WT


title: GE1


title: GE8


title: LS-15932_S68_E1-50

value: GABA


title: MO10

value: Mucosal melanoma


title: H3K36me2_NSD2KD_CUT-RUN

value: lung tumor

value: NSD2 knockdown


title: Cell_0244_E11.5_FACS-EHT_het


title: LS-15932_S73_E1-50

value: PC

value: Glut

value: MP


title: NSD2_NSD2KD_CUT-RUN


title: Cell_0243_E11.5_FACS-EHT_het


title: H3K36me2_Control_CUT-RUN

value: control


title: LS-15932_S66_E1-50


title: H3K27me3_NSD2KD_CUT-RUN


title: LS-15932_S65_E1-50


title: Cell_0242_E11.5_FACS-EHT_het


title: LS-15932_S64_E1-50

value: NeuN-neg

value: Astro


title: H3K27me3_Control_CUT-RUN


title: AN9

value: Anorectal


title: Cell_0241_E11.5_FACS-EHT_het


title: NC16

value: Nasal


title: NC12


title: LS-15932_S63_E1-50

value: M

value: NeuN-pos


title: AN6


title: R1-tassel

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

data_processing:
Library strategy: degradome-seq
Illumina’s Genome Analyzer Sequencing Control Software and Pipeline Analysis Software
The raw sequences were filtered to remove low quality reads and the ones that passed the quality filter were trimmed to remove the adaptor sequences.
CleaveLand4.pl was used to processed the data
Supplementary_files_format_and_content: txt file, the result of CleaveLand4, degradome density file

organism: Zea mays

source_name: RNA from Tassel

growth_protocol: Maize (Zea mays ssp. mays) ‘B73’ plants were cultivated in a phytotron at 25°C with 65% relative humidity under a 14-h/10-h light/dark cycle.

extract_protocol:
Total RNA was extracted from the maize tissues using TRIzol reagent (Molecular Research Center) according to the manufacturer’s instructions. Agilent Bioanalyzer 2100 system was used to check the quality of the extracted RNA, and only RNA of high integrity was used for the analysis.
The degradome-seq library was constructed based on a previously described method (Zhai et al., 2014). Degradome-seq was performed on the Illumina HiSeq 2500 platform (Berry Genomics) to produce 50-bp single- end reads.

tag: cultivar


title: Cell_0240_E11.5_FACS-EHT_het