title: COL17_TSA1_S17_ROW31


title: HS_M1_1_sample 399

status: Public on Oct 06 2021

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
M1 regions of human/marmoset brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: tissue

value: Brain

tag: brain region

tag: gender

value: M


title: MM_M1_1_sample 368

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: ASM275486v1
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Callithrix jacchus

value: brain


title: COL17_TSA1_S17_ROW29

city: Rochester

first: Jason

last: Myers

state: NY

address: 601 Elmwood Ave.

institute: University of Rochester

library_source: transcriptomic

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15
Genome Alignment - STAR_2.5.2b, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.5.0p3, featurecounts, -s 2 -t exon -g gene_name
Genome_build: GRCh38 + gencode25
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

molecule: total RNA

source_name: 40 year old female

extract_protocol:
Fluidigm C1 HT scRNAseq protocol, no offline RNA extraction performed
Fluidigm C1 HT scRNAseq library construction protocol

tag: cell line

tag: cell type

value: Invasive Ductal Carcinoma


title: MM_M1_1_sample 372


title: SM-GE67J_S291_E1-50

city: Seattle

first: Hongkui

last: Zeng

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

description:
exon_counts.csv.gz
intron_counts.csv.gz
cpm.csv.gz

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
Supplementary_files_format_and_content: cpm.csv.gz
Supplementary_files_format_and_content: exon_counts.csv.gz
Supplementary_files_format_and_content: intron_counts.csv.gz

molecule: polyA RNA

organism: Mus musculus

source_name: non-retroseq cells mapped to Car3 subclass

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.

extract_protocol:
We isolated single cells as previously described (Hempel et al., 2007; Sugino et al., 2006; Tasic et al., 2016) with modifications. We mostly employed layer-enriching dissections, with focus on a single layer. Broader dissections (no layer enrichment or multiple layers combined) were employed for lines which label small numbers of cells, in order to facilitate isolation of sufficient number of cells. 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.
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/.

treatment_protocol: For retrogradely-labeled samples, we injected AAV2-retro-EF1a-Cre (Tervo et al., 2016), rabies virus RV-dGdL-Cre (Chatterjee et al., 2018), or CAV-Cre (Hnasko et al., 2006) into brains of Ai14 or RCL-Sun1sfGFP mice, RV-dL-FlpO into Ai65F mice, AAV2-retro-EF1a-dTomato into Cux2-CreERT2;Ai140 mice, Gnb4-IRES2-CreERT2;Ai140 mice or Gnb4-IRES2-CreERT2;Ai148 mice, as previously described (Tasic et al., 2016). RFP+ or GFP+ single cells were isolated from various cortical regions, depending on the injection area.

tag: age

value: 53 days

tag: region

value: AI

tag: roi

value: RFP-positive

value: left

tag: batch

value: Car3 6


title: COL17_TSA1_S17_ROW33


title: MM_M1_1_sample 367


title: HS_M1_1_sample 397


title: COL17_TSA1_S17_ROW28


title: MM_M1_1_sample 366


title: HS_M1_1_sample 401


title: COL17_TSA1_S17_ROW27


title: SM-GE67J_S290_E1-50


title: HS_M1_1_sample 396


title: COL17_TSA1_S17_ROW26


title: MM_M1_1_sample 365


title: SM-GE67J_S288_E1-50

value: F

value: 57 days

value: right


title: HS_M1_1_sample 395


title: SM-GE67J_S283_E1-50


title: SM-GE67J_S292_E1-50


title: COL17_TSA1_S17_ROW25


title: MM_M1_1_sample 364


title: HS_M1_1_sample 394


title: MM_M1_1_sample 363


title: HS_M1_1_sample 393


title: COL17_TSA1_S17_ROW24


title: MM_M1_1_sample 362


title: COL17_TSA1_S17_ROW23


title: HS_M1_1_sample 398


title: SM-GE67J_S276_E1-50

value: Car3 8


title: MM_M1_1_sample 361


title: HS_M1_1_sample 392


title: SM-GE67J_S274_E1-50


title: MM_M1_1_sample 360


title: HS_M1_1_sample 391


title: SM-GE67J_S263_E1-50


title: COL17_TSA1_S17_ROW22


title: SM-GE67J_S265_E1-50

value: Car3 5


title: COL17_TSA1_S17_ROW20


title: MM_M1_1_sample 359


title: COL17_TSA1_S17_ROW21


title: HS_M1_1_sample 389


title: SM-GE67J_S280_E1-50


title: MM_M1_1_sample 358


title: COL17_TSA1_S17_ROW19


title: SM-GE67J_S258_E1-50

value: Car3 7


title: MM_M1_1_sample 357


title: COL17_TSA1_S17_ROW18


title: SM-GE67J_S257_E1-50


title: MM_M1_1_sample 356


title: SM-GE67J_S255_E1-50


title: HS_M1_1_sample 386


title: SM-GE67J_S249_E1-50


title: COL17_TSA1_S17_ROW17


title: HS_M1_1_sample 388


title: MM_M1_1_sample 354


title: COL17_TSA1_S17_ROW16


title: SM-GE67J_S245_E1-50


title: COL17_TSA1_S17_ROW15


title: HS_M1_1_sample 385


title: HS_M1_1_sample 390


title: HS_M1_1_sample 384


title: MM_M1_1_sample 353


title: HS_M1_1_sample 383


title: SM-GE67J_S244_E1-50


title: COL17_TSA1_S17_ROW13


title: COL17_TSA1_S17_ROW14


title: HS_M1_1_sample 382


title: MM_M1_1_sample 352


title: HS_M1_1_sample 387


title: SM-GE67J_S241_E1-50


title: COL17_TSA1_S17_ROW12


title: HS_M1_1_sample 381


title: SM-GE67J_S240_E1-50


title: MM_M1_1_sample 351


title: MM_M1_1_sample 350


title: SM-GE67J_S237_E1-50


title: COL17_TSA1_S17_ROW11


title: MM_M1_1_sample 355


title: SM-GE67J_S222_E1-50


title: MM_M1_1_sample 349


title: SM-GE67J_S214_E1-50


title: COL17_TSA1_S17_ROW10


title: MM_M1_1_sample 348


title: HS_M1_1_sample 380


title: SM-GE67J_S213_E1-50


title: MM_M1_1_sample 347


title: HS_M1_1_sample 378


title: COL17_TSA1_S17_ROW08


title: COL17_TSA1_S17_ROW09


title: MM_M1_1_sample 346


title: SM-GE67J_S211_E1-50


title: HS_M1_1_sample 377


title: COL17_TSA1_S17_ROW07


title: HS_M1_1_sample 376


title: COL17_TSA1_S17_ROW06


title: SM-GE67J_S201_E1-50


title: SM-GE67J_S209_E1-50


title: COL17_TSA1_S17_ROW05


title: HS_M1_1_sample 375


title: HS_M1_1_sample 374


title: MM_M1_1_sample 344


title: COL17_TSA1_S17_ROW04


title: HS_M1_1_sample 373


title: SM-GE67J_S195_E1-50


title: MM_M1_1_sample 343


title: SM-GE67J_S192_E1-50

value: Car3 4


title: MM_M1_1_sample 341


title: COL17_TSA1_S17_ROW03


title: SM-GE67J_S190_E1-50


title: MM_M1_1_sample 342


title: MM_M1_1_sample 340


title: MM_M1_1_sample 339


title: HS_M1_1_sample 372


title: HS_M1_1_sample 370


title: COL17_TSA1_S17_ROW01


title: SM-GE67J_S182_E1-50


title: SM-GE67J_S189_E1-50


title: SM-GE67J_S185_E1-50


title: COL16_TSA2_S38_ROW40


title: MM_M1_1_sample 345


title: SM-GE67J_S181_E1-50


title: MM_M1_1_sample 338


title: MM_M1_1_sample 337


title: COL16_TSA2_S38_ROW39


title: COL16_TSA2_S38_ROW38


title: MM_M1_1_sample 336


title: SM-GE67J_S178_E1-50


title: HS_M1_1_sample 367


title: HS_M1_1_sample 379


title: HS_M1_1_sample 368


title: COL16_TSA2_S38_ROW37


title: HS_M1_1_sample 366


title: SM-GE67J_S177_E1-50


title: COL17_TSA1_S17_ROW02


title: HS_M1_1_sample 371


title: MM_M1_1_sample 335


title: HS_M1_1_sample 369


title: SM-GE67J_S175_E1-50


title: HS_M1_1_sample 364


title: HS_M1_1_sample 365


title: MM_M1_1_sample 334


title: COL16_TSA2_S38_ROW34


title: COL16_TSA2_S38_ROW36


title: MM_M1_1_sample 333


title: COL16_TSA2_S38_ROW35


title: SM-GE67J_S171_E1-50


title: HS_M1_1_sample 363


title: SM-GE67J_S168_E1-50


title: COL16_TSA2_S38_ROW33


title: SM-GE67J_S167_E1-50


title: COL16_TSA2_S38_ROW32


title: MM_M1_1_sample 331


title: MM_M1_1_sample 332


title: HS_M1_1_sample 362


title: MM_M1_1_sample 330


title: SM-GE67J_S164_E1-50


title: MM_M1_1_sample 329


title: HS_M1_1_sample 361


title: HS_M1_1_sample 360


title: SM-GE67J_S161_E1-50


title: COL16_TSA2_S38_ROW30


title: HS_M1_1_sample 359


title: SM-GE67J_S160_E1-50


title: MM_M1_1_sample 328


title: HS_M1_1_sample 358


title: SM-GE67J_S157_E1-50


title: HS_M1_1_sample 357


title: COL16_TSA2_S38_ROW29


title: SM-GE67J_S158_E1-50


title: MM_M1_1_sample 327


title: COL16_TSA2_S38_ROW27


title: MM_M1_1_sample 326


title: COL16_TSA2_S38_ROW28


title: HS_M1_1_sample 356


title: COL16_TSA2_S38_ROW31


title: COL16_TSA2_S38_ROW26


title: HS_M1_1_sample 354


title: SM-GE67J_S155_E1-50


title: COL16_TSA2_S38_ROW25


title: MM_M1_1_sample 324


title: SM-GE67J_S152_E1-50


title: COL16_TSA2_S38_ROW24


title: HS_M1_1_sample 355


title: SM-GE67J_S143_E1-50


title: MM_M1_1_sample 323


title: SM-GE67J_S146_E1-50


title: COL16_TSA2_S38_ROW23


title: MM_M1_1_sample 322


title: MM_M1_1_sample 325


title: SM-GE67J_S139_E1-50


title: HS_M1_1_sample 352


title: HS_M1_1_sample 353


title: MM_M1_1_sample 321


title: COL16_TSA2_S38_ROW22


title: HS_M1_1_sample 351


title: HS_M1_1_sample 350


title: SM-GE67J_S129_E1-50


title: SM-GE67J_S135_E1-50


title: MM_M1_1_sample 320


title: MM_M1_1_sample 319


title: COL16_TSA2_S38_ROW20


title: SM-GE67J_S106_E1-50


title: COL16_TSA2_S38_ROW21


title: MM_M1_1_sample 318


title: MM_M1_1_sample 317


title: SM-GE67J_S098_E1-50


title: HS_M1_1_sample 347


title: HS_M1_1_sample 348


title: MM_M1_1_sample 316


title: COL16_TSA2_S38_ROW16


title: HS_M1_1_sample 349


title: SM-GE67J_S099_E1-50


title: MM_M1_1_sample 314


title: SM-GE67J_S084_E1-50


title: COL16_TSA2_S38_ROW15


title: SM-GE67J_S087_E1-50


title: HS_M1_1_sample 346


title: COL16_TSA2_S38_ROW17


title: COL16_TSA2_S38_ROW14


title: MM_M1_1_sample 313


title: HS_M1_1_sample 344


title: SM-GE67J_S079_E1-50


title: COL16_TSA2_S38_ROW19


title: HS_M1_1_sample 345


title: SM-GE67J_S071_E1-50


title: MM_M1_1_sample 311


title: MM_M1_1_sample 312


title: COL16_TSA2_S38_ROW13


title: COL16_TSA2_S38_ROW18


title: COL16_TSA2_S38_ROW12


title: SM-GE67J_S068_E1-50


title: MM_M1_1_sample 315


title: MM_M1_1_sample 310


title: HS_M1_1_sample 341


title: COL16_TSA2_S38_ROW11


title: HS_M1_1_sample 340


title: SM-GE67J_S066_E1-50


title: HS_M1_1_sample 339


title: SM-GE67J_S063_E1-50


title: COL16_TSA2_S38_ROW10


title: SM-GE67J_S060_E1-50


title: SM-GE67J_S062_E1-50


title: COL16_TSA2_S38_ROW09


title: HS_M1_1_sample 338


title: MM_M1_1_sample 307


title: COL16_TSA2_S38_ROW08


title: HS_M1_1_sample 343


title: HS_M1_1_sample 342


title: MM_M1_1_sample 306


title: HS_M1_1_sample 337


title: SM-GE67J_S058_E1-50


title: COL16_TSA2_S38_ROW07


title: HS_M1_1_sample 335


title: HS_M1_1_sample 336


title: SM-GE67J_S055_E1-50


title: SM-GE67J_S054_E1-50


title: MM_M1_1_sample 305


title: MM_M1_1_sample 309


title: COL16_TSA2_S38_ROW06


title: MM_M1_1_sample 304


title: COL16_TSA2_S38_ROW05


title: SM-GE67J_S049_E1-50


title: MM_M1_1_sample 308


title: COL16_TSA2_S38_ROW04


title: MM_M1_1_sample 303


title: HS_M1_1_sample 334


title: SM-GE67J_S045_E1-50


title: SM-GE67J_S048_E1-50


title: HS_M1_1_sample 332


title: HS_M1_1_sample 333


title: HS_M1_1_sample 331


title: COL16_TSA2_S38_ROW01


title: COL16_TSA2_S38_ROW03


title: COL16_TSA2_S38_ROW02


title: SM-GE67J_S044_E1-50


title: SM-GE67J_S040_E1-50


title: COL16_TSA1_S16_ROW40


title: MM_M1_1_sample 299


title: MM_M1_1_sample 300


title: HS_M1_1_sample 329


title: HS_M1_1_sample 328


title: HS_M1_1_sample 330


title: MM_M1_1_sample 297


title: COL16_TSA1_S16_ROW38


title: MM_M1_1_sample 302


title: COL16_TSA1_S16_ROW39


title: SM-GE67J_S033_E1-50


title: MM_M1_1_sample 296


title: MM_M1_1_sample 301


title: HS_M1_1_sample 327


title: SM-GE67J_S034_E1-50


title: MM_M1_1_sample 295


title: HS_M1_1_sample 325


title: COL16_TSA1_S16_ROW37


title: COL16_TSA1_S16_ROW35


title: SM-GE67J_S027_E1-50


title: MM_M1_1_sample 293


title: HS_M1_1_sample 324


title: MM_M1_1_sample 298


title: COL16_TSA1_S16_ROW34


title: SM-GE67J_S035_E1-50


title: SM-GE67J_S026_E1-50


title: MM_M1_1_sample 292


title: HS_M1_1_sample 326


title: COL16_TSA1_S16_ROW33


title: MM_M1_1_sample 290


title: SM-GE67J_S029_E1-50


title: SM-GE67J_S013_E1-50


title: HS_M1_1_sample 320


title: COL16_TSA1_S16_ROW31


title: SM-GE67J_S030_E1-50


title: MM_M1_1_sample 289


title: MM_M1_1_sample 291


title: HS_M1_1_sample 319


title: SM-GE67J_S012_E1-50


title: COL16_TSA1_S16_ROW36


title: SM-GE67J_S007_E1-50


title: MM_M1_1_sample 294


title: COL16_TSA1_S16_ROW30


title: HS_M1_1_sample 323


title: MM_M1_1_sample 288


title: HS_M1_1_sample 318


title: MM_M1_1_sample 287


title: SM-GE67J_S002_E1-50


title: HS_M1_1_sample 322


title: COL16_TSA1_S16_ROW28


title: SM-GE67I_S384_E1-50


title: COL16_TSA1_S16_ROW32


title: HS_M1_1_sample 317


title: MM_M1_1_sample 286


title: HS_M1_1_sample 316


title: SM-GE67J_S014_E1-50


title: SM-GE67I_S381_E1-50


title: COL16_TSA1_S16_ROW27


title: SM-GE67I_S378_E1-50


title: COL16_TSA1_S16_ROW26


title: COL16_TSA1_S16_ROW25


title: HS_M1_1_sample 314


title: MM_M1_1_sample 285


title: MM_M1_1_sample 284


title: MM_M1_1_sample 283


title: SM-GE67I_S372_E1-50


title: MM_M1_1_sample 282


title: COL16_TSA1_S16_ROW29


title: HS_M1_1_sample 313


title: COL16_TSA1_S16_ROW24


title: COL16_TSA1_S16_ROW23


title: HS_M1_1_sample 312


title: SM-GE67I_S369_E1-50


title: SM-GE67I_S367_E1-50


title: MM_M1_1_sample 280


title: HS_M1_1_sample 310


title: COL16_TSA1_S16_ROW21


title: HS_M1_1_sample 311


title: MM_M1_1_sample 281


title: MM_M1_1_sample 279


title: SM-GE67I_S365_E1-50


title: COL16_TSA1_S16_ROW20


title: SM-GE67I_S374_E1-50


title: COL16_TSA1_S16_ROW19


title: MM_M1_1_sample 278


title: SM-GE67I_S361_E1-50


title: HS_M1_1_sample 308


title: MM_M1_1_sample 277


title: SM-GE67I_S348_E1-50


title: HS_M1_1_sample 321


title: COL16_TSA1_S16_ROW18


title: COL16_TSA1_S16_ROW17


title: SM-GE67I_S342_E1-50


title: HS_M1_1_sample 307


title: COL16_TSA1_S16_ROW22


title: HS_M1_1_sample 306


title: COL16_TSA1_S16_ROW16


title: MM_M1_1_sample 275


title: HS_M1_1_sample 305


title: MM_M1_1_sample 274


title: HS_M1_1_sample 309


title: COL16_TSA1_S16_ROW15


title: MM_M1_1_sample 273


title: SM-GE67I_S341_E1-50


title: HS_M1_1_sample 304


title: HS_M1_1_sample 303


title: COL16_TSA1_S16_ROW14


title: SM-GE67I_S340_E1-50


title: MM_M1_1_sample 272


title: COL16_TSA1_S16_ROW13


title: SM-GE67I_S349_E1-50


title: MM_M1_1_sample 276


title: MM_M1_1_sample 271


title: COL16_TSA1_S16_ROW12


title: HS_M1_1_sample 302


title: SM-GE67I_S322_E1-50


title: SM-GE67I_S329_E1-50


title: SM-GE67I_S337_E1-50


title: MM_M1_1_sample 270


title: COL16_TSA1_S16_ROW11


title: HS_M1_1_sample 301


title: SM-GE67I_S321_E1-50


title: HS_M1_1_sample 299


title: COL16_TSA1_S16_ROW10


title: HS_M1_1_sample 300


title: SM-GE67I_S313_E1-50


title: MM_M1_1_sample 268


title: HS_M1_1_sample 298


title: MM_M1_1_sample 267


title: HS_M1_1_sample 315


title: COL16_TSA1_S16_ROW09


title: COL16_TSA1_S16_ROW08


title: SM-GE67I_S291_E1-50


title: MM_M1_1_sample 266


title: HS_M1_1_sample 296


title: SM-GE67I_S283_E1-50


title: SM-GE67I_S310_E1-50


title: HS_M1_1_sample 297


title: HS_M1_1_sample 295


title: MM_M1_1_sample 265


title: SM-GE67I_S277_E1-50


title: SM-GE67I_S272_E1-50


title: COL16_TSA1_S16_ROW07


title: HS_M1_1_sample 294


title: COL16_TSA1_S16_ROW05


title: MM_M1_1_sample 264


title: SM-GE67I_S271_E1-50


title: HS_M1_1_sample 293


title: MM_M1_1_sample 263


title: HS_M1_1_sample 292


title: MM_M1_1_sample 262


title: COL16_TSA1_S16_ROW04


title: COL16_TSA1_S16_ROW06


title: SM-GE67I_S270_E1-50


title: HS_M1_1_sample 291


title: SM-GE67I_S268_E1-50


title: COL16_TSA1_S16_ROW02


title: HS_M1_1_sample 290


title: SM-GE67I_S264_E1-50


title: MM_M1_1_sample 259


title: MM_M1_1_sample 269


title: SM-GE67I_S256_E1-50


title: COL16_TSA1_S16_ROW03


title: COL15_TSA2_S37_ROW40


title: MM_M1_1_sample 258


title: COL15_TSA2_S37_ROW38


title: HS_M1_1_sample 289


title: SM-GE67I_S250_E1-50


title: MM_M1_1_sample 257


title: HS_M1_1_sample 288


title: HS_M1_1_sample 287


title: SM-GE67I_S245_E1-50


title: MM_M1_1_sample 255


title: SM-GE67I_S244_E1-50


title: MM_M1_1_sample 256


title: COL15_TSA2_S37_ROW36


title: COL16_TSA1_S16_ROW01


title: COL15_TSA2_S37_ROW39


title: MM_M1_1_sample 261


title: MM_M1_1_sample 260


title: COL15_TSA2_S37_ROW37


title: HS_M1_1_sample 286


title: MM_M1_1_sample 254


title: HS_M1_1_sample 285


title: COL15_TSA2_S37_ROW35


title: SM-GE67I_S239_E1-50


title: HS_M1_1_sample 284


title: SM-GE67I_S242_E1-50


title: COL15_TSA2_S37_ROW34


title: MM_M1_1_sample 253


title: SM-GE67I_S236_E1-50


title: MM_M1_1_sample 252


title: MM_M1_1_sample 251


title: SM-GE67I_S238_E1-50


title: HS_M1_1_sample 282


title: COL15_TSA2_S37_ROW32


title: COL15_TSA2_S37_ROW31


title: HS_M1_1_sample 281


title: HS_M1_1_sample 283


title: COL15_TSA2_S37_ROW29


title: SM-GE67I_S232_E1-50


title: SM-GE67I_S224_E1-50


title: COL15_TSA2_S37_ROW30


title: MM_M1_1_sample 249


title: HS_M1_1_sample 280


title: MM_M1_1_sample 250


title: HS_M1_1_sample 278


title: MM_M1_1_sample 248


title: HS_M1_1_sample 277


title: HS_M1_1_sample 279


title: MM_M1_1_sample 246


title: MM_M1_1_sample 247


title: SM-GE67I_S223_E1-50


title: SM-GE67I_S234_E1-50


title: COL15_TSA2_S37_ROW27


title: SM-GE67I_S218_E1-50


title: COL15_TSA2_S37_ROW28


title: SM-GE67I_S206_E1-50


title: COL15_TSA2_S37_ROW33


title: HS_M1_1_sample 276


title: SM-GE67I_S168_E1-50


title: HS_M1_1_sample 275


title: COL15_TSA2_S37_ROW26


title: MM_M1_1_sample 244


title: COL15_TSA2_S37_ROW25


title: MM_M1_1_sample 243


title: HS_M1_1_sample 274


title: COL15_TSA2_S37_ROW23


title: COL15_TSA2_S37_ROW24


title: SM-GE67I_S166_E1-50


title: HS_M1_1_sample 273


title: SM-GE67I_S164_E1-50

value: Car3 1


title: SM-GE67I_S165_E1-50


title: MM_M1_1_sample 241


title: COL15_TSA2_S37_ROW22


title: MM_M1_1_sample 242


title: COL15_TSA2_S37_ROW21


title: MM_M1_1_sample 240


title: SM-GE67I_S162_E1-50


title: MM_M1_1_sample 239


title: HS_M1_1_sample 270

value: Brain


title: HS_M1_1_sample 269

value: M


title: HS_M1_1_sample 271


title: COL15_TSA2_S37_ROW20


title: MM_M1_1_sample 238

value: brain


title: COL15_TSA2_S37_ROW19

value: Invasive Ductal Carcinoma


title: SM-GE67I_S080_E1-50

value: 53 days


title: MM_M1_1_sample 245


title: HS_M1_1_sample 268


title: HS_M1_1_sample 267


title: COL15_TSA2_S37_ROW18


title: SM-GE67I_S079_E1-50

value: AI


title: MM_M1_1_sample 236


title: MM_M1_1_sample 237


title: HS_M1_1_sample 266


title: MM_M1_1_sample 234


title: SM-GE67I_S038_E1-50

value: RFP-positive


title: SM-GE67I_S051_E1-50

value: left


title: MM_M1_1_sample 235


title: SM-GE67T_S371_E1-50

value: Car3 6


title: HS_M1_1_sample 272


title: COL15_TSA2_S37_ROW14


title: HS_M1_1_sample 265


title: COL15_TSA2_S37_ROW16


title: COL15_TSA2_S37_ROW15


title: MM_M1_1_sample 233


title: SM-GE67I_S002_E1-50


title: SM-GE67I_S142_E1-50


title: HS_M1_1_sample 264


title: HS_M1_1_sample 263


title: SM-GE8ZG_S099_E1-50

value: F

value: ORB


title: SM-GE67I_S155_E1-50


title: MM_M1_1_sample 232


title: HS_M1_1_sample 262


title: MM_M1_1_sample 231


title: COL15_TSA2_S37_ROW12


title: HS_M1_1_sample 261


title: COL15_TSA2_S37_ROW17


title: COL15_TSA2_S37_ROW11


title: COL15_TSA2_S37_ROW10


title: COL15_TSA2_S37_ROW13


title: SM-GE8ZE_S094_E1-50

value: 65 days

value: SSs

value: GFP-positive


title: SM-GE8ZE_S093_E1-50


title: MM_M1_1_sample 229


title: MM_M1_1_sample 228


title: HS_M1_1_sample 259


title: COL15_TSA2_S37_ROW09


title: SM-GE8ZE_S091_E1-50


title: MM_M1_1_sample 226


title: HS_M1_1_sample 256


title: MM_M1_1_sample 227


title: SM-GE8ZE_S092_E1-50


title: COL15_TSA2_S37_ROW08


title: HS_M1_1_sample 257


title: MM_M1_1_sample 225


title: HS_M1_1_sample 255


title: SM-GE8ZE_S090_E1-50


title: COL15_TSA2_S37_ROW06


title: COL15_TSA2_S37_ROW07


title: SM-GE8ZE_S089_E1-50


title: SM-GE8ZF_S107_E1-50

value: 57 days


title: MM_M1_1_sample 230


title: HS_M1_1_sample 260


title: COL15_TSA2_S37_ROW05


title: MM_M1_1_sample 224


title: SM-GE8ZE_S088_E1-50

value: 100 days

value: CTXsp


title: MM_M1_1_sample 223


title: HS_M1_1_sample 254

value: Brain


title: COL15_TSA2_S37_ROW04


title: SM-GE8ZE_S087_E1-50


title: HS_M1_1_sample 258

value: M


title: COL15_TSA2_S37_ROW03


title: HS_M1_1_sample 252


title: MM_M1_1_sample 221

value: brain


title: MM_M1_1_sample 222


title: HS_M1_1_sample 253


title: HS_M1_1_sample 251


title: COL15_TSA2_S37_ROW01

value: Invasive Ductal Carcinoma


title: SM-GE8ZE_S084_E1-50


title: SM-GE8ZE_S086_E1-50


title: COL15_TSA2_S37_ROW02


title: HS_M1_1_sample 250


title: COL15_TSA1_S15_ROW40


title: MM_M1_1_sample 220


title: SM-GE8ZE_S083_E1-50


title: MM_M1_1_sample 218


title: MM_M1_1_sample 219


title: HS_M1_1_sample 248


title: COL15_TSA1_S15_ROW38


title: COL15_TSA1_S15_ROW39


title: MM_M1_1_sample 217


title: SM-GE8ZE_S082_E1-50


title: HS_M1_1_sample 249


title: MM_M1_1_sample 216


title: SM-GE8ZE_S081_E1-50


title: COL15_TSA1_S15_ROW37


title: HS_M1_1_sample 246


title: SM-GE66X_S136_E1-50

value: right


title: SM-GE8ZE_S085_E1-50


title: MM_M1_1_sample 215


title: COL15_TSA1_S15_ROW36


title: SM-GE66X_S135_E1-50


title: MM_M1_1_sample 214


title: COL15_TSA1_S15_ROW35


title: MM_M1_1_sample 213


title: HS_M1_1_sample 243


title: HS_M1_1_sample 244


title: MM_M1_1_sample 212


title: SM-GE66X_S133_E1-50


title: COL15_TSA1_S15_ROW33


title: MM_M1_1_sample 211


title: HS_M1_1_sample 242


title: SM-GE66X_S132_E1-50


title: HS_M1_1_sample 247


title: SM-GE66X_S131_E1-50


title: COL15_TSA1_S15_ROW32


title: MM_M1_1_sample 210


title: COL15_TSA1_S15_ROW31


title: SM-GE66X_S130_E1-50


title: MM_M1_1_sample 209


title: HS_M1_1_sample 245


title: SM-GE66X_S129_E1-50


title: SM-GE66X_S134_E1-50

value: Car3 1


title: COL15_TSA1_S15_ROW29


title: HS_M1_1_sample 239


title: MM_M1_1_sample 208


title: COL15_TSA1_S15_ROW34


title: HS_M1_1_sample 238


title: COL15_TSA1_S15_ROW28


title: SM-GE66X_S128_E1-50


title: MM_M1_1_sample 206


title: SM-GE66X_S127_E1-50


title: HS_M1_1_sample 241


title: HS_M1_1_sample 235


title: SM-GE66X_S126_E1-50


title: SM-GE66X_S125_E1-50


title: MM_M1_1_sample 204


title: COL15_TSA1_S15_ROW25


title: SM-GE66X_S124_E1-50


title: HS_M1_1_sample 234


title: HS_M1_1_sample 240


title: COL15_TSA1_S15_ROW30


title: COL15_TSA1_S15_ROW24


title: MM_M1_1_sample 203


title: HS_M1_1_sample 233


title: MM_M1_1_sample 202


title: MM_M1_1_sample 207


title: SM-GE66X_S123_E1-50


title: HS_M1_1_sample 232


title: COL15_TSA1_S15_ROW23


title: COL15_TSA1_S15_ROW22


title: HS_M1_1_sample 237


title: SM-GE66X_S122_E1-50


title: MM_M1_1_sample 201


title: HS_M1_1_sample 231


title: HS_M1_1_sample 236


title: MM_M1_1_sample 205


title: SM-GE66X_S121_E1-50


title: COL15_TSA1_S15_ROW26


title: COL15_TSA1_S15_ROW27


title: SM-GE66X_S120_E1-50


title: COL15_TSA1_S15_ROW21


title: HS_M1_1_sample 230


title: COL15_TSA1_S15_ROW20


title: MM_M1_1_sample 199


title: HS_M1_1_sample 229


title: SM-GE66X_S119_E1-50


title: COL15_TSA1_S15_ROW19


title: MM_M1_1_sample 198


title: HS_M1_1_sample 228


title: SM-GE66X_S118_E1-50


title: MM_M1_1_sample 197


title: COL15_TSA1_S15_ROW18


title: HS_M1_1_sample 227


title: COL15_TSA1_S15_ROW17


title: SM-GE66X_S117_E1-50


title: MM_M1_1_sample 196


title: SM-GE66X_S116_E1-50


title: COL15_TSA1_S15_ROW16


title: MM_M1_1_sample 195


title: SM-GE66X_S115_E1-50


title: HS_M1_1_sample 226


title: MM_M1_1_sample 194


title: HS_M1_1_sample 225


title: COL15_TSA1_S15_ROW15


title: HS_M1_1_sample 224


title: MM_M1_1_sample 193


title: COL15_TSA1_S15_ROW14


title: MM_M1_1_sample 200


title: MM_M1_1_sample 192


title: HS_M1_1_sample 223


title: MM_M1_1_sample 191


title: HS_M1_1_sample 221


title: SM-GE66X_S112_E1-50


title: SM-GE66X_S113_E1-50


title: COL15_TSA1_S15_ROW11


title: COL15_TSA1_S15_ROW13


title: HS_M1_1_sample 219


title: COL15_TSA1_S15_ROW12


title: MM_M1_1_sample 187


title: HS_M1_1_sample 218


title: HS_M1_1_sample 217


title: SM-GE66X_S111_E1-50


title: MM_M1_1_sample 186


title: COL15_TSA1_S15_ROW07


title: HS_M1_1_sample 216


title: MM_M1_1_sample 190


title: HS_M1_1_sample 220


title: MM_M1_1_sample 184


title: COL15_TSA1_S15_ROW10


title: SM-GE66X_S110_E1-50


title: MM_M1_1_sample 189


title: SM-GE66X_S109_E1-50


title: SM-GE66X_S056_E1-50


title: MM_M1_1_sample 188


title: COL15_TSA1_S15_ROW09


title: HS_M1_1_sample 213


title: SM-GE66X_S108_E1-50


title: SM-GE66X_S114_E1-50


title: COL15_TSA1_S15_ROW03


title: COL15_TSA1_S15_ROW08


title: SM-GE66X_S107_E1-50


title: HS_M1_1_sample 212


title: SM-GE66X_S054_E1-50


title: HS_M1_1_sample 222


title: SM-GE66X_S106_E1-50


title: MM_M1_1_sample 185


title: MM_M1_1_sample 181


title: COL15_TSA1_S15_ROW06


title: HS_M1_1_sample 215


title: COL15_TSA1_S15_ROW02


title: SM-GE66X_S053_E1-50


title: SM-GE66X_S105_E1-50


title: COL15_TSA1_S15_ROW05


title: HS_M1_1_sample 214


title: SM-GE66X_S052_E1-50


title: MM_M1_1_sample 183


title: COL15_TSA1_S15_ROW04


title: SM-GE66X_S055_E1-50


title: HS_M1_1_sample 208


title: COL14_TSA2_S36_ROW39


title: MM_M1_1_sample 182


title: COL14_TSA2_S36_ROW38


title: MM_M1_1_sample 177


title: HS_M1_1_sample 207


title: MM_M1_1_sample 180


title: MM_M1_1_sample 179


title: HS_M1_1_sample 210


title: HS_M1_1_sample 206


title: SM-GE66X_S048_E1-50


title: HS_M1_1_sample 209


title: COL15_TSA1_S15_ROW01


title: COL14_TSA2_S36_ROW36


title: MM_M1_1_sample 178


title: HS_M1_1_sample 205


title: MM_M1_1_sample 175


title: MM_M1_1_sample 174


title: SM-GE66X_S047_E1-50


title: SM-GE66X_S050_E1-50


title: SM-GE66X_S051_E1-50


title: SM-GE66X_S049_E1-50


title: MM_M1_1_sample 176


title: COL14_TSA2_S36_ROW37


title: HS_M1_1_sample 211


title: HS_M1_1_sample 203


title: HS_M1_1_sample 202


title: COL14_TSA2_S36_ROW32


title: COL14_TSA2_S36_ROW33


title: SM-GE66X_S044_E1-50


title: HS_M1_1_sample 200


title: HS_M1_1_sample 201


title: COL14_TSA2_S36_ROW40


title: COL14_TSA2_S36_ROW35


title: COL14_TSA2_S36_ROW30


title: HS_M1_1_sample 199


title: HS_M1_1_sample 204


title: COL14_TSA2_S36_ROW29


title: MM_M1_1_sample 167


title: SM-GE66X_S039_E1-50


title: MM_M1_1_sample 166


title: COL14_TSA2_S36_ROW27


title: SM-GE66X_S046_E1-50


title: MM_M1_1_sample 165


title: MM_M1_1_sample 164


title: HS_M1_1_sample 195


title: COL14_TSA2_S36_ROW25


title: HS_M1_1_sample 194


title: MM_M1_1_sample 173


title: COL14_TSA2_S36_ROW34


title: SM-GE66X_S045_E1-50


title: MM_M1_1_sample 172


title: MM_M1_1_sample 163


title: HS_M1_1_sample 193


title: MM_M1_1_sample 171


title: SM-GE66X_S034_E1-50


title: SM-GE66X_S043_E1-50


title: COL14_TSA2_S36_ROW31


title: MM_M1_1_sample 170


title: SM-GE66X_S041_E1-50


title: HS_M1_1_sample 198


title: MM_M1_1_sample 168


title: SM-GE66X_S042_E1-50


title: COL14_TSA2_S36_ROW23


title: SM-GE66X_S040_E1-50


title: SM-GE66X_S033_E1-50


title: COL14_TSA2_S36_ROW28


title: COL14_TSA2_S36_ROW22


title: HS_M1_1_sample 191


title: HS_M1_1_sample 197


title: MM_M1_1_sample 169


title: SM-GE66X_S038_E1-50


title: HS_M1_1_sample 196


title: COL14_TSA2_S36_ROW26


title: HS_M1_1_sample 190


title: SM-GE66W_S168_E1-50


title: MM_M1_1_sample 159


title: COL14_TSA2_S36_ROW20


title: SM-GE66X_S037_E1-50


title: SM-GE66W_S166_E1-50


title: MM_M1_1_sample 158


title: SM-GE66X_S036_E1-50


title: SM-GE66W_S165_E1-50


title: COL14_TSA2_S36_ROW17


title: COL14_TSA2_S36_ROW18


title: COL14_TSA2_S36_ROW24


title: SM-GE66W_S164_E1-50


title: HS_M1_1_sample 185


title: MM_M1_1_sample 162


title: MM_M1_1_sample 154


title: HS_M1_1_sample 192


title: MM_M1_1_sample 161


title: HS_M1_1_sample 184


title: SM-GE66W_S162_E1-50


title: MM_M1_1_sample 153


title: SM-GE66W_S190_E1-50

value: 67 days

value: VISp

value: Car3 5


title: HS_M1_1_sample 183


title: SM-GE66W_S161_E1-50

value: F

value: Car3 6


title: MM_M1_1_sample 160


title: COL14_TSA2_S36_ROW21


title: MM_M1_1_sample 152


title: HS_M1_1_sample 189


title: COL14_TSA2_S36_ROW19


title: SM-GE66W_S167_E1-50

value: 65 days


title: HS_M1_1_sample 181


title: HS_M1_1_sample 182


title: COL14_TSA2_S36_ROW14


title: HS_M1_1_sample 180


title: MM_M1_1_sample 157


title: HS_M1_1_sample 187


title: HS_M1_1_sample 188


title: MM_M1_1_sample 149


title: COL14_TSA2_S36_ROW13


title: MM_M1_1_sample 156


title: COL14_TSA2_S36_ROW10


title: HS_M1_1_sample 186


title: HS_M1_1_sample 179


title: COL14_TSA2_S36_ROW16


title: MM_M1_1_sample 155


title: SM-GE66W_S163_E1-50

value: Car3 4


title: HS_M1_1_sample 178


title: COL14_TSA2_S36_ROW11


title: SM-GE66W_S155_E1-50

value: GFP-positive


title: MM_M1_1_sample 147


title: SM-GE66W_S154_E1-50


title: SM-GE66W_S159_E1-50


title: MM_M1_1_sample 146


title: COL14_TSA2_S36_ROW15


title: COL14_TSA2_S36_ROW07


title: MM_M1_1_sample 151


title: MM_M1_1_sample 150


title: MM_M1_1_sample 145


title: SM-GE66W_S158_E1-50


title: COL14_TSA2_S36_ROW06


title: HS_M1_1_sample 175


title: MM_M1_1_sample 144


title: COL14_TSA2_S36_ROW05


title: SM-GE66W_S157_E1-50


title: SM-GE66W_S156_E1-50


title: MM_M1_1_sample 148


title: HS_M1_1_sample 177


title: COL14_TSA2_S36_ROW09


title: SM-GE66W_S151_E1-50

value: left


title: HS_M1_1_sample 173


title: COL14_TSA2_S36_ROW04


title: COL14_TSA2_S36_ROW12


title: COL14_TSA2_S36_ROW08


title: MM_M1_1_sample 140


title: MM_M1_1_sample 139


title: SM-GE66W_S153_E1-50


title: SM-GE66W_S150_E1-50


title: MM_M1_1_sample 143


title: HS_M1_1_sample 174


title: SM-GE66W_S152_E1-50


title: HS_M1_1_sample 176


title: MM_M1_1_sample 142


title: COL14_TSA1_S14_ROW38


title: MM_M1_1_sample 138


title: COL14_TSA1_S14_ROW39


title: COL14_TSA2_S36_ROW02


title: HS_M1_1_sample 167


title: COL14_TSA2_S36_ROW03


title: HS_M1_1_sample 171


title: HS_M1_1_sample 172


title: SM-GE66W_S149_E1-50


title: COL14_TSA2_S36_ROW01


title: SM-GE66W_S148_E1-50


title: MM_M1_1_sample 141


title: MM_M1_1_sample 136


title: HS_M1_1_sample 166


title: SM-GE66W_S147_E1-50


title: HS_M1_1_sample 170


title: HS_M1_1_sample 165


title: HS_M1_1_sample 168


title: COL14_TSA1_S14_ROW40


title: MM_M1_1_sample 137


title: HS_M1_1_sample 169


title: SM-GE66W_S146_E1-50


title: SM-GE66W_S142_E1-50


title: COL14_TSA1_S14_ROW37


title: SM-GE66W_S144_E1-50


title: SM-GE66W_S145_E1-50


title: COL14_TSA1_S14_ROW34


title: MM_M1_1_sample 133


title: COL14_TSA1_S14_ROW35


title: COL14_TSA1_S14_ROW36


title: SM-GE66W_S143_E1-50


title: SM-GE66W_S140_E1-50


title: MM_M1_1_sample 131


title: SM-GE66W_S139_E1-50


title: COL14_TSA1_S14_ROW32


title: SM-GE66W_S138_E1-50


title: HS_M1_1_sample 163


title: SM-GE66W_S141_E1-50


title: HS_M1_1_sample 161


title: MM_M1_1_sample 130


title: HS_M1_1_sample 164


title: MM_M1_1_sample 134


title: SM-GE66W_S137_E1-50


title: COL14_TSA1_S14_ROW33


title: MM_M1_1_sample 135


title: MM_M1_1_sample 132


title: HS_M1_1_sample 162


title: HS_M1_1_sample 159


title: HS_M1_1_sample 160


title: HS_M1_1_sample 157


title: SM-GE66W_S136_E1-50


title: COL14_TSA1_S14_ROW30


title: MM_M1_1_sample 129


title: COL14_TSA1_S14_ROW27


title: COL14_TSA1_S14_ROW31


title: COL14_TSA1_S14_ROW29


title: HS_M1_1_sample 155


title: SM-GE66W_S135_E1-50


title: MM_M1_1_sample 127


title: MM_M1_1_sample 128


title: SM-GE66W_S134_E1-50


title: COL14_TSA1_S14_ROW28


title: MM_M1_1_sample 126


title: COL14_TSA1_S14_ROW26


title: MM_M1_1_sample 123


title: HS_M1_1_sample 153


title: COL14_TSA1_S14_ROW23


title: HS_M1_1_sample 156


title: MM_M1_1_sample 121


title: COL14_TSA1_S14_ROW22


title: HS_M1_1_sample 150


title: COL14_TSA1_S14_ROW21


title: MM_M1_1_sample 118


title: SM-GE66W_S124_E1-50


title: MM_M1_1_sample 117


title: COL14_TSA1_S14_ROW20


title: SM-GE66W_S123_E1-50


title: COL14_TSA1_S14_ROW19


title: MM_M1_1_sample 116


title: COL14_TSA1_S14_ROW17


title: COL14_TSA1_S14_ROW16


title: MM_M1_1_sample 115


title: SM-GE66W_S131_E1-50


title: COL14_TSA1_S14_ROW25


title: MM_M1_1_sample 124


title: MM_M1_1_sample 125


title: SM-GE66W_S130_E1-50


title: HS_M1_1_sample 158


title: COL14_TSA1_S14_ROW24


title: SM-GE66W_S128_E1-50


title: SM-GE66W_S132_E1-50


title: MM_M1_1_sample 122


title: SM-GE66W_S127_E1-50


title: HS_M1_1_sample 154


title: MM_M1_1_sample 113


title: COL14_TSA1_S14_ROW14


title: HS_M1_1_sample 151


title: MM_M1_1_sample 112


title: SM-GE66W_S126_E1-50


title: SM-GE66W_S129_E1-50


title: MM_M1_1_sample 119


title: HS_M1_1_sample 149


title: HS_M1_1_sample 152


title: SM-GE66W_S125_E1-50


title: HS_M1_1_sample 148


title: HS_M1_1_sample 147


title: COL14_TSA1_S14_ROW18


title: MM_M1_1_sample 120


title: HS_M1_1_sample 143


title: HS_M1_1_sample 141


title: HS_M1_1_sample 146


title: COL14_TSA1_S14_ROW11


title: SM-GE66W_S122_E1-50


title: HS_M1_1_sample 140


title: SM-GE66W_S121_E1-50


title: HS_M1_1_sample 145


title: MM_M1_1_sample 114


title: COL14_TSA1_S14_ROW15


title: SM-GE66W_S067_E1-50


title: HS_M1_1_sample 139


title: MM_M1_1_sample 108


title: HS_M1_1_sample 138


title: SM-GE66W_S072_E1-50


title: HS_M1_1_sample 137


title: HS_M1_1_sample 144


title: SM-GE66W_S071_E1-50


title: SM-GE66W_S065_E1-50


title: COL14_TSA1_S14_ROW13


title: MM_M1_1_sample 106


title: HS_M1_1_sample 142


title: MM_M1_1_sample 107


title: COL14_TSA1_S14_ROW07


title: SM-GE66W_S070_E1-50


title: HS_M1_1_sample 136


title: COL14_TSA1_S14_ROW12


title: MM_M1_1_sample 111


title: SM-GE66W_S064_E1-50


title: HS_M1_1_sample 135


title: SM-GE66W_S063_E1-50


title: MM_M1_1_sample 110


title: COL14_TSA1_S14_ROW05


title: SM-GE66W_S068_E1-50


title: MM_M1_1_sample 109


title: COL14_TSA1_S14_ROW10


title: COL14_TSA1_S14_ROW09


title: SM-GE66W_S066_E1-50


title: SM-GE66W_S069_E1-50


title: COL14_TSA1_S14_ROW08


title: COL14_TSA1_S14_ROW03


title: COL14_TSA1_S14_ROW06


title: MM_M1_1_sample 105


title: HS_M1_1_sample 132


title: SM-GE66W_S059_E1-50


title: HS_M1_1_sample 134


title: MM_M1_1_sample 104


title: HS_M1_1_sample 133


title: COL14_TSA1_S14_ROW04


title: MM_M1_1_sample 103


title: SM-GE66W_S061_E1-50


title: MM_M1_1_sample 99


title: MM_M1_1_sample 102


title: SM-GE66W_S062_E1-50


title: HS_M1_1_sample 129


title: MM_M1_1_sample 98


title: SM-GE66W_S060_E1-50


title: COL14_TSA1_S14_ROW02


title: SM-GE66W_S057_E1-50


title: COL13_TSA2_S35_ROW39


title: HS_M1_1_sample 131


title: COL14_TSA1_S14_ROW01


title: HS_M1_1_sample 130


title: SM-GE66W_S058_E1-50


title: SM-GE66W_S055_E1-50

value: SSs


title: SM-GE66W_S056_E1-50


title: COL13_TSA2_S35_ROW40


title: MM_M1_1_sample 97


title: MM_M1_1_sample 101


title: MM_M1_1_sample 100


title: HS_M1_1_sample 126


title: COL13_TSA2_S35_ROW38


title: MM_M1_1_sample 96


title: HS_M1_1_sample 127


title: HS_M1_1_sample 125


title: COL13_TSA2_S35_ROW37


title: COL13_TSA2_S35_ROW34


title: MM_M1_1_sample 92


title: MM_M1_1_sample 94


title: SM-GE66W_S053_E1-50


title: HS_M1_1_sample 122


title: COL13_TSA2_S35_ROW35


title: HS_M1_1_sample 124


title: SM-GE66W_S050_E1-50


title: SM-GE66W_S052_E1-50


title: COL13_TSA2_S35_ROW36


title: HS_M1_1_sample 128


title: MM_M1_1_sample 90


title: SM-GE66W_S048_E1-50

value: CTXsp


title: COL13_TSA2_S35_ROW32


title: HS_M1_1_sample 120

value: Brain


title: COL13_TSA2_S35_ROW31


title: HS_M1_1_sample 123

value: M


title: MM_M1_1_sample 93

value: brain


title: COL13_TSA2_S35_ROW30

value: Invasive Ductal Carcinoma


title: SM-GE66W_S051_E1-50

value: right


title: COL13_TSA2_S35_ROW33


title: COL13_TSA2_S35_ROW29


title: SM-GE66W_S054_E1-50


title: MM_M1_1_sample 91


title: HS_M1_1_sample 121


title: HS_M1_1_sample 118


title: SM-GE66W_S046_E1-50


title: COL13_TSA2_S35_ROW28


title: SM-GE66W_S045_E1-50


title: HS_M1_1_sample 117


title: COL13_TSA2_S35_ROW27


title: MM_M1_1_sample 95


title: MM_M1_1_sample 89


title: HS_M1_1_sample 119


title: SM-GE66W_S047_E1-50


title: MM_M1_1_sample 88


title: HS_M1_1_sample 115


title: COL13_TSA2_S35_ROW26


title: MM_M1_1_sample 87


title: HS_M1_1_sample 114


title: SM-GE66W_S049_E1-50


title: SM-GE66W_S044_E1-50


title: HS_M1_1_sample 116


title: MM_M1_1_sample 86


title: COL13_TSA2_S35_ROW24


title: MM_M1_1_sample 82


title: HS_M1_1_sample 113


title: SM-GE66W_S043_E1-50


title: MM_M1_1_sample 85


title: SM-GE66W_S040_E1-50


title: COL13_TSA2_S35_ROW23


title: HS_M1_1_sample 111


title: MM_M1_1_sample 84


title: COL13_TSA2_S35_ROW25


title: SM-GE66W_S042_E1-50


title: SM-GE66W_S041_E1-50


title: MM_M1_1_sample 83


title: MM_M1_1_sample 80


title: COL13_TSA2_S35_ROW19


title: MM_M1_1_sample 79


title: COL13_TSA2_S35_ROW22


title: SM-GE66W_S037_E1-50


title: HS_M1_1_sample 108


title: MM_M1_1_sample 81


title: SM-GE66W_S038_E1-50


title: MM_M1_1_sample 77


title: SM-GE66W_S036_E1-50


title: SM-GE66W_S039_E1-50


title: COL13_TSA2_S35_ROW21


title: SM-GE66W_S035_E1-50


title: HS_M1_1_sample 107


title: COL13_TSA2_S35_ROW20


title: COL13_TSA2_S35_ROW17


title: SM-GE66W_S034_E1-50


title: MM_M1_1_sample 78


title: MM_M1_1_sample 75


title: SM-GE66W_S033_E1-50


title: HS_M1_1_sample 109


title: COL13_TSA2_S35_ROW18


title: MM_M1_1_sample 76


title: HS_M1_1_sample 112


title: COL13_TSA2_S35_ROW16


title: COL13_TSA2_S35_ROW15


title: HS_M1_1_sample 110


title: COL13_TSA2_S35_ROW14


title: SM-GE66W_S032_E1-50


title: HS_M1_1_sample 105


title: HS_M1_1_sample 103


title: MM_M1_1_sample 73


title: MM_M1_1_sample 72


title: COL13_TSA2_S35_ROW13


title: HS_M1_1_sample 102


title: HS_M1_1_sample 106


title: SM-GE66W_S031_E1-50


title: MM_M1_1_sample 70


title: MM_M1_1_sample 69


title: SM-GE66W_S029_E1-50


title: HS_M1_1_sample 100


title: COL13_TSA2_S35_ROW11


title: HS_M1_1_sample 104


title: MM_M1_1_sample 74


title: MM_M1_1_sample 71


title: SM-GE66W_S030_E1-50


title: HS_M1_1_sample 101


title: SM-GE66W_S027_E1-50


title: HS_M1_1_sample 99


title: SM-GE66W_S028_E1-50


title: MM_M1_1_sample 68


title: SM-GE66W_S026_E1-50


title: COL13_TSA2_S35_ROW10


title: COL13_TSA2_S35_ROW08


title: COL13_TSA2_S35_ROW09


title: SM-GE66W_S025_E1-50


title: MM_M1_1_sample 67


title: HS_M1_1_sample 97


title: HS_M1_1_sample 98


title: MM_M1_1_sample 64


title: COL13_TSA2_S35_ROW12


title: COL13_TSA2_S35_ROW06


title: COL13_TSA2_S35_ROW07


title: HS_M1_1_sample 96


title: HS_M1_1_sample 95


title: SM-GE66V_S152_E1-50

value: 100 days


title: SM-GE66V_S151_E1-50


title: MM_M1_1_sample 63


title: HS_M1_1_sample 94


title: COL13_TSA2_S35_ROW05


title: SM-GE66V_S150_E1-50


title: MM_M1_1_sample 62


title: COL13_TSA2_S35_ROW04


title: SM-GE66V_S148_E1-50


title: MM_M1_1_sample 60


title: MM_M1_1_sample 59


title: SM-GE66V_S149_E1-50


title: SM-GE66V_S146_E1-50


title: HS_M1_1_sample 93


title: HS_M1_1_sample 90


title: MM_M1_1_sample 61


title: COL13_TSA2_S35_ROW02


title: COL13_TSA1_S13_ROW40


title: COL13_TSA2_S35_ROW03


title: MM_M1_1_sample 66


title: MM_M1_1_sample 57


title: HS_M1_1_sample 92


title: HS_M1_1_sample 88


title: SM-GE66V_S145_E1-50


title: COL13_TSA1_S13_ROW39


title: COL13_TSA1_S13_ROW38


title: MM_M1_1_sample 55


title: SM-GE66V_S147_E1-50


title: MM_M1_1_sample 58


title: COL13_TSA2_S35_ROW01


title: HS_M1_1_sample 89


title: SM-GE66V_S136_E1-50


title: SM-GE66V_S134_E1-50


title: MM_M1_1_sample 56


title: MM_M1_1_sample 54


title: HS_M1_1_sample 87


title: SM-GE66V_S135_E1-50


title: HS_M1_1_sample 86


title: COL13_TSA1_S13_ROW36


title: COL13_TSA1_S13_ROW37


title: HS_M1_1_sample 91


title: SM-GE66V_S132_E1-50


title: HS_M1_1_sample 84


title: COL13_TSA1_S13_ROW34


title: MM_M1_1_sample 51


title: SM-GE66V_S131_E1-50


title: SM-GE66V_S130_E1-50


title: HS_M1_1_sample 82


title: HS_M1_1_sample 85


title: SM-GE66V_S133_E1-50


title: COL13_TSA1_S13_ROW35


title: MM_M1_1_sample 49


title: SM-GE66V_S129_E1-50


title: COL13_TSA1_S13_ROW31


title: MM_M1_1_sample 52


title: MM_M1_1_sample 53


title: HS_M1_1_sample 81


title: SM-GE66V_S127_E1-50


title: HS_M1_1_sample 83


title: MM_M1_1_sample 47


title: HS_M1_1_sample 78


title: COL13_TSA1_S13_ROW33


title: MM_M1_1_sample 50


title: COL13_TSA1_S13_ROW32


title: HS_M1_1_sample 76


title: SM-GE66V_S128_E1-50


title: COL13_TSA1_S13_ROW27


title: HS_M1_1_sample 80


title: MM_M1_1_sample 48


title: COL13_TSA1_S13_ROW26


title: COL13_TSA1_S13_ROW30


title: MM_M1_1_sample 44


title: HS_M1_1_sample 79


title: HS_M1_1_sample 74


title: COL13_TSA1_S13_ROW25


title: HS_M1_1_sample 77


title: SM-GE66V_S126_E1-50


title: HS_M1_1_sample 73


title: MM_M1_1_sample 46


title: COL13_TSA1_S13_ROW28


title: COL13_TSA1_S13_ROW29


title: MM_M1_1_sample 45


title: SM-GE66V_S125_E1-50


title: COL13_TSA1_S13_ROW23


title: MM_M1_1_sample 41


title: SM-GE66V_S124_E1-50


title: COL13_TSA1_S13_ROW22


title: HS_M1_1_sample 75


title: SM-GE66V_S123_E1-50


title: MM_M1_1_sample 43


title: SM-GE66V_S122_E1-50


title: COL13_TSA1_S13_ROW24


title: HS_M1_1_sample 72


title: MM_M1_1_sample 38


title: MM_M1_1_sample 42


title: COL13_TSA1_S13_ROW20


title: SM-GE66V_S121_E1-50


title: SM-GE66V_S118_E1-50


title: MM_M1_1_sample 39


title: COL13_TSA1_S13_ROW21


title: SM-GE66V_S120_E1-50


title: SM-GE66V_S116_E1-50


title: HS_M1_1_sample 70


title: HS_M1_1_sample 69


title: MM_M1_1_sample 40


title: COL13_TSA1_S13_ROW19


title: SM-GE66V_S117_E1-50


title: HS_M1_1_sample 67


title: SM-GE66V_S119_E1-50


title: HS_M1_1_sample 71


title: MM_M1_1_sample 36


title: MM_M1_1_sample 37


title: SM-GE66V_S115_E1-50


title: COL13_TSA1_S13_ROW18


title: SM-GE66V_S114_E1-50


title: COL13_TSA1_S13_ROW16


title: COL13_TSA1_S13_ROW17


title: HS_M1_1_sample 66


title: MM_M1_1_sample 33


title: MM_M1_1_sample 34


title: MM_M1_1_sample 32


title: HS_M1_1_sample 64


title: COL13_TSA1_S13_ROW15


title: SM-GE66V_S112_E1-50


title: COL13_TSA1_S13_ROW14


title: HS_M1_1_sample 65


title: HS_M1_1_sample 68


title: SM-GE66V_S111_E1-50


title: MM_M1_1_sample 31


title: HS_M1_1_sample 63


title: HS_M1_1_sample 62


title: MM_M1_1_sample 35


title: COL13_TSA1_S13_ROW13


title: COL13_TSA1_S13_ROW11


title: HS_M1_1_sample 60


title: COL13_TSA1_S13_ROW12


title: MM_M1_1_sample 29


title: SM-GE66V_S108_E1-50


title: SM-GE66V_S110_E1-50


title: MM_M1_1_sample 28


title: SM-GE66V_S109_E1-50


title: HS_M1_1_sample 61


title: SM-GE66V_S113_E1-50


title: COL13_TSA1_S13_ROW10


title: SM-GE66V_S107_E1-50


title: HS_M1_1_sample 59


title: COL13_TSA1_S13_ROW09


title: HS_M1_1_sample 58


title: COL13_TSA1_S13_ROW08


title: SM-GE66V_S105_E1-50


title: MM_M1_1_sample 26


title: MM_M1_1_sample 25


title: MM_M1_1_sample 30


title: SM-GE66V_S104_E1-50


title: SM-GE66V_S103_E1-50


title: HS_M1_1_sample 57


title: MM_M1_1_sample 23


title: HS_M1_1_sample 55


title: COL13_TSA1_S13_ROW07


title: MM_M1_1_sample 24


title: COL13_TSA1_S13_ROW05


title: MM_M1_1_sample 22


title: SM-GE66V_S101_E1-50


title: COL13_TSA1_S13_ROW06


title: SM-GE66V_S100_E1-50


title: MM_M1_1_sample 27


title: COL13_TSA1_S13_ROW04


title: MM_M1_1_sample 21


title: SM-GE66V_S106_E1-50


title: HS_M1_1_sample 53


title: SM-GE66V_S099_E1-50


title: HS_M1_1_sample 56


title: HS_M1_1_sample 52


title: COL13_TSA1_S13_ROW02


title: HS_M1_1_sample 54


title: SM-GE66V_S098_E1-50


title: COL13_TSA1_S13_ROW03


title: MM_M1_1_sample 18


title: HS_M1_1_sample 50


title: HS_M1_1_sample 51


title: COL12_TSA2_S34_ROW40


title: MM_M1_1_sample 19


title: COL13_TSA1_S13_ROW01


title: COL12_TSA2_S34_ROW39


title: HS_M1_1_sample 49


title: LS-15556_S26_E1-50

source_name: retroseq cells mapped to L2/3,L4,L5 IT subclass

value: 55 days

value: ALM

value: RFP-positive


title: LS-15556_S25_E1-50


title: LS-15556_S23_E1-50


title: MM_M1_1_sample 20


title: MM_M1_1_sample 17


title: HS_M1_1_sample 47


title: LS-15556_S24_E1-50


title: MM_M1_1_sample 15


title: COL12_TSA2_S34_ROW38


title: COL12_TSA2_S34_ROW37


title: MM_M1_1_sample 14


title: LS-15556_S22_E1-50


title: HS_M1_1_sample 46


title: HS_M1_1_sample 45


title: COL12_TSA2_S34_ROW36


title: COL12_TSA2_S34_ROW35


title: MM_M1_1_sample 13


title: HS_M1_1_sample 44


title: LS-15556_S20_E1-50


title: MM_M1_1_sample 12


title: COL12_TSA2_S34_ROW34


title: HS_M1_1_sample 48


title: HS_M1_1_sample 43


title: MM_M1_1_sample 16


title: MM_M1_1_sample 11


title: LS-15556_S18_E1-50


title: MM_M1_1_sample 9


title: HS_M1_1_sample 41


title: HS_M1_1_sample 42


title: COL12_TSA2_S34_ROW31


title: MM_M1_1_sample 10


title: LS-15556_S17_E1-50


title: COL12_TSA2_S34_ROW32


title: LS-15556_S21_E1-50


title: LS-15556_S16_E1-50


title: COL12_TSA2_S34_ROW30


title: MM_M1_1_sample 8


title: HS_M1_1_sample 39


title: LS-15556_S15_E1-50


title: LS-15556_S14_E1-50


title: COL12_TSA2_S34_ROW29


title: LS-15556_S19_E1-50


title: MM_M1_1_sample 7


title: COL12_TSA2_S34_ROW33


title: COL12_TSA2_S34_ROW28


title: MM_M1_1_sample 6


title: HS_M1_1_sample 37


title: MM_M1_1_sample 5


title: COL12_TSA2_S34_ROW27


title: MM_M1_1_sample 4


title: LS-15556_S13_E1-50


title: HS_M1_1_sample 40


title: LS-15556_S12_E1-50


title: HS_M1_1_sample 36


title: MM_M1_1_sample 3


title: HS_M1_1_sample 35


title: COL12_TSA2_S34_ROW24


title: LS-15556_S10_E1-50


title: HS_M1_1_sample 34


title: COL12_TSA2_S34_ROW25


title: HS_M1_1_sample 38


title: LS-15556_S09_E1-50


title: MM_M1_1_sample 2


title: HS_M1_1_sample 33


title: LS-15556_S08_E1-50


title: MM_M1_1_sample 0


title: HS_M1_1_sample 32


title: HS_M1_1_sample 31


title: LS-15556_S07_E1-50


title: COL12_TSA2_S34_ROW22


title: MM_M1_1_sample 1


title: LS-15556_S06_E1-50


title: HS_M1_1_sample 30


title: COL12_TSA2_S34_ROW26


title: COL12_TSA2_S34_ROW21


title: COL12_TSA2_S34_ROW19


title: FH_Embryo_FH3

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

data_processing:
Sample demultiplexing, barcode processing, and gene counting were performed with  Cell Ranger Single-Cell Software v.3.10 (https://support.10xgenomics.com/single-cell-gene-expression/software)
Data filter. Doublets were identified by using Seurat’s standard pipeline  (https://satijalab.org/seurat/v3.2/pbmc3k_tutorial.html), and barcodes were removed if they had  fewer than 500 UMIs, more than 30000 UMIs, or >5% mitochondrial UMIs. Cells were removed  if they had <200 detected genes or if >25% of the transcripts were from mitochondrial genes.
Mitochondrial genes and other transcript identifiers were removed without mapping to the official gene symbols from later analyses
Data were normalized as directed in the online Seurat tutorial (https://satijalab.org/seurat/v3.2/pbmc3k_tutorial.html); total expression was multiplied by a factor of 10,000 and then log-transformed.
Genome_build: Sscrofa11.1 premRNA
Supplementary_files_format_and_content: The process data is in file Cardiomyocyte_Seurat.Robj. This file contains both the metadata and processed expression. The file can be directly opened by R, with Seurat package installed.

organism: Sus scrofa

growth_protocol: All experimental protocols were approved by The Institutional Animal Care and Use Committee 5  (IACUC) at the University of Alabama at Birmingham and performed in accordance with the  National Institutes of Health Guide for the Care and Use of Laboratory Animals (NIH publication No 85-23). Prestage farm pigs at various ages were purchase from Prestage Farm Inc. (West Point, MS).  All pigs younger than P14 were housed in an incubator at a temperature of ~850F and room air.  Piglets were fed with bovine colostrum every 4 hours for the first 2 days of life, 1:1  colostrum/sow’s milk at day 3 of life, and sow’s milk thereafter. Animals were given  supplemental iron at day 7.

extract_protocol:
Tissues were cut while submerged in cold phosphate-buffered saline (PBS) or UW  solution and washed to remove blood; then, the solution was replaced with 1 mL lysis buffer (10  mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet™ P40 Substitute, and 50 U/mL RNase  inhibitor in DEPC-treated water). Tissues were cut into even smaller pieces and aspirated with  the lysis buffer into a 50 mL tube; then, 10 mL of lysis buffer was added, the tissues were  ground for 20-30 s, and more lysis buffer was added. The mixture was placed on ice for ten minutes, filtered with 100-μm and 70-μm strainers, and centrifuged for 5 min at 700 rcf and 4°C; then, the supernatant was removed, and the pellet was resuspended in 10 mL nuclei wash and resuspension buffer (1X PBS, 1.0% bovine serum albumin [BSA], and 50 U/mL RNase  inhibitor). The suspension was passed through a 40-μm strainer and the nuclei were centrifuged again for 5 min at 700 rcf and 4°C. The supernatant was removed and the pellet was resuspended in 1 mL nuclei wash and resuspension buffer; then, the nuclei were centrifuged again for 5 min at 700 rcf and 4 °C, the supernatant was removed, and the pellet was resuspended in 5 mL sucrose cushion buffer I (2.7 mL Nuclei PURE 2M Sucrose Cushion  Solution and 300 μL Nuclei PURE Sucrose Cushion Buffer) and mixed with 10 mL sucrose  buffer. The mixture was layered over 5 mL of sucrose cushion buffer in a second Eppendorf  tube and then centrifuged for 60 min at 13000 g and 4 °C. All but 100 μL of the supernatant was removed, and nuclei wash and resuspension buffer was added. The nuclei were resuspended, and the solution was passed through a 40-μm strainer; then, the nuclei concentration was determined with a cell counter or hemocytometer and adjusted to 1000 nuclei/μL.
The nuclei  were placed on ice, stained with propidium iodide for 5 min, and then immediately processed via the 10× Genomics® Single-Cell Protocol.

treatment_protocol: Briefly, pigs were anesthetized with isoflurane and placed in a dorsal recumbent position on a  heating pad, and a median sternotomy was performed to expose the heart. Then, the sternum  was re-approximated, the chest was closed in layers, and the air was evacuated from the  mediastinum. After surgery, the animals were maintained in a temperature-controlled incubator  until old enough to maintain their body temperature. On P28, animals came back to the  operating room, and the left anterior descending coronary artery distal to the second diagonal  was ligated by a ligature. The chest was closed in layers, and animals were allowed to recover.

value: Heart

tag: arp1 (yes/no)

value: no

tag: mip28 (yes/no)

tag: harvest postnatal day (p)

value: Fetal


title: LS-15556_S04_E1-50


title: FH_Embryo_FH2


title: HS_M1_1_sample 28


title: COL12_TSA2_S34_ROW23


title: LS-15556_S05_E1-50


title: LS-15556_S03_E1-50


title: CTL-P56_8052_RZ


title: COL12_TSA2_S34_ROW17


title: FH_Embryo_FH1


title: LS-15556_S01_E1-50


title: LS-15556_S02_E1-50


title: COL12_TSA2_S34_ROW18


title: HS_M1_1_sample 27


title: CTL-P56_8052_AZ


title: LS-15555_S71_E1-50

value: 56 days

value: MOs


title: HS_M1_1_sample 29


title: COL12_TSA2_S34_ROW15


title: COL12_TSA2_S34_ROW20


title: HS_M1_1_sample 25


title: LS-15555_S72_E1-50

value: left


title: HS_M1_1_sample 26


title: CTL-P28_8046_BZ


title: CTL-P28_8046_RZ


title: HS_M1_1_sample 24


title: LS-15555_S70_E1-50


title: HS_M1_1_sample 23


title: COL12_TSA2_S34_ROW14


title: CTL-P1_8095


title: LS-15555_S69_E1-50


title: HS_M1_1_sample 22


title: COL12_TSA2_S34_ROW12


title: COL12_TSA2_S34_ROW13


title: LS-15555_S68_E1-50


title: HS_M1_1_sample 21


title: CTL-P1_8094


title: MI28_P56_8086RZ

value: yes

tag: heart zone

value: Remote zone


title: COL12_TSA2_S34_ROW11


title: HS_M1_1_sample 20

value: Brain


title: HS_M1_1_sample 19

value: M


title: MI28_P56_8086BZ

value: Border zone


title: LS-15555_S67_E1-50


title: COL12_TSA2_S34_ROW10

value: Invasive Ductal Carcinoma


title: COL12_TSA2_S34_ROW16


title: CTL-P1_8026_p1


title: MI28_P56_8085RZ


title: LS-15555_S66_E1-50


title: HS_M1_1_sample 16


title: LS-15555_S64_E1-50


title: LS-15555_S63_E1-50


title: HS_M1_1_sample 15


title: MI28_P56_8085BZ


title: COL12_TSA2_S34_ROW05


title: COL12_TSA2_S34_ROW09


title: AR1_P56_8097CZ


title: LS-15555_S65_E1-50


title: HS_M1_1_sample 17


title: COL12_TSA2_S34_ROW08


title: HS_M1_1_sample 18


title: HS_M1_1_sample 13


title: AR1_P56_8097RZ


title: LS-15555_S62_E1-50


title: LS-15555_S60_E1-50


title: AR1_P56_8096RZ


title: HS_M1_1_sample 14


title: AR1_P28_8030_RZ


title: COL12_TSA2_S34_ROW03


title: COL12_TSA2_S34_ROW06


title: LS-15555_S61_E1-50


title: AR1_P56_8096CZ


title: COL12_TSA2_S34_ROW04


title: COL12_TSA2_S34_ROW07


title: COL12_TSA2_S34_ROW01


title: HS_M1_1_sample 10


title: COL12_TSA2_S34_ROW02


title: HS_M1_1_sample 12


title: LS-15555_S59_E1-50


title: COL12_TSA1_S12_ROW40


title: HS_M1_1_sample 11


title: AR1_P28_ 8030_CZ


title: HS_M1_1_sample 9


title: HS_M1_1_sample 8


title: LS-15555_S57_E1-50


title: AR1_P28_8014RZ


title: AR1_P28_8014BZ


title: LS-15555_S48_E1-50

value: SSs


title: COL12_TSA1_S12_ROW39


title: AR1_MI28_P56_8060IZ


title: AR1_MI28_P56_8060RZ


title: LS-15555_S47_E1-50


title: COL12_TSA1_S12_ROW37


title: HS_M1_1_sample 7


title: LS-15555_S46_E1-50


title: HS_M1_1_sample 5


title: COL12_TSA1_S12_ROW36


title: LS-15555_S45_E1-50


title: AR1_MI28_P56_8060AZ


title: HS_M1_1_sample 6


title: AR1_MI28_P56_7995_RZ


title: LS-15555_S58_E1-50


title: AR1_MI28_P56_7995_BZ


title: COL12_TSA1_S12_ROW35


title: HS_M1_1_sample 4


title: LS-15555_S44_E1-50


title: LS-15555_S43_E1-50


title: COL12_TSA1_S12_ROW34


title: AR1_MI28_P42_8094RZ


title: COL12_TSA1_S12_ROW38


title: HS_M1_1_sample 3


title: AR1_MI28_P42_8094AZ


title: HS_M1_1_sample 1


title: HS_M1_1_sample 0


title: COL12_TSA1_S12_ROW33


title: LS-15555_S39_E1-50


title: LS-15555_S42_E1-50


title: AR1_MI28_P35_8095RZ


title: COL12_TSA1_S12_ROW32


title: LS-15555_S41_E1-50


title: LS-15555_S40_E1-50


title: COL12_TSA1_S12_ROW31


title: AR1_MI28_P35_8095AZ


title: COL12_TSA1_S12_ROW30


title: AR1_MI28_P35_8065RZ


title: COL12_TSA1_S12_ROW28


title: HS_M1_1_sample 2


title: AR1_MI28_P35_8095BZ


title: LS-15555_S38_E1-50


title: T26683_WT3

city: Freiburg

first: Connor

middle: Patrick

last: O'Meara

address: Stuebeweg

country: Germany

institute: MPI

description:
Processed data files generated from multiple samples
processed data file:
log2.RAG1.tabular.txt
n.counts.RAG1.tabular.txt

data_processing:
Reads were aligned to the reference genome with STAR 2.5.2b-1 (Dobin A. et al. Bioinformatics 2013) and the reference annotation from Ensembl (Zv10.85, http://www.ensembl.org/info/data/ftp/index.html)
Resulting alignments were quantified at the gene level with featureCounts version 1.6.0.1 (Liao Y, Smyth G.K., and Shi W., Bioinformatics 2014) and differential expression performed using DESeq2 version 2.11.40.1 (Love M.I., Huber W. and Anders S. Genome Biol 2014). All tools were used with default parameters unless otherwise stated.
Genome_build: z10.85
Supplementary_files_format_and_content: DESeq2 tables of differential gene expression analysis are provided (log2 fold-change and normalized counts)

organism: Danio rerio

source_name: ENU mutagenesis forward genetic screen

growth_protocol: zebrafish embryos (5 d.p.f)

extract_protocol:
Individual zebrafish embryos (5 d.p.f) from an incross of heterozygous carriers were homogenized in 100 μL of Tri Reagent (Sigma, Cat#93289) and transferred to 2 mL deep 96 well plates containing an additional 400μL of Tri Reagent. The RNA-containing aqueous phase was stored at -80°C until genotyping was completed. DNA was extracted from the interphase and organic phase by phenol-chloroform according to the manufacturer’s instructions. Following genotyping, RNA was extracted from embryos homozygous mutants and sibling homozygous wt. DNA was removed from RNA extraction using TURBO DNA-free kit (Invitrogen, Cat#AM1907). RNA was quantified using Qubit RNA HS Assay Kit (ThermoScientific, Cat#Q32852) and the Qubit 4 Fluoromter (ThermoScientific, Q33226). RNA quality was checked by 18S/28S rRNA ratio using the Fragment Analyzer RNA Kit (ThermoScientific, Cat#DNF-471-0500) and the 5200 Fragment Analyzer System (ThermoScientific, Cat#M5310AA).
cDNA libraries were prepared from 1μg of mRNA following poly-A selection using TruSeq stranded mRNA Library Prep (Illumina, Cat#20020595) according to manufacturer’s instuctions. RNA-Seq was performed using mutant and wt sibling from each zebrafish line (n = 2 – 6). The libraries were sequenced in paired-end 75 bp mode at a depth of 25 million reads on an Illumina HiSeq 2500/3000 instrument.

tag: genotype

value: WT

tag: strain background

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

tag: population

value: whole embryo

tag: surface phenotype

value: normal lymphoid development in thymus


title: T26683_WT2


title: LS-15555_S35_E1-50

value: ALM

value: RFP-positive


title: LS-15555_S37_E1-50


title: AR1_MI28_P35_8065CZ

tag: tissue

value: Heart


title: LS-15555_S36_E1-50

value: 56 days


title: T26683_WT1


title: AR1_MI28_P35_8065AZ


title: T26683_MUT2

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: T26683_MUT4


title: AR1_MI28_P30_8064AZ

value: yes


title: AR1_MI28_P30_8064RZ

value: Remote zone


title: T26683_MUT1


title: COL12_TSA1_S12_ROW26


title: COL12_TSA1_S12_ROW27


title: AR1_MI28_P30_8064CZ


title: COL12_TSA1_S12_ROW29


title: LS-15555_S31_E1-50

value: 55 days

value: left


title: COL12_TSA1_S12_ROW25


title: LS-15555_S32_E1-50

value: M


title: LS-15555_S33_E1-50


title: COL12_TSA1_S12_ROW24

value: Invasive Ductal Carcinoma


title: NASH_65

city: Frederiksberg C.

first: Josephine

last: Skat-Rørdam

address: Ridebanevej 9

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: Københavns Universitet

description:
N65
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt

data_processing:
Base calling was performed on NextSeq500 (Illumina) using RTA 2.0, and the resulting BCL files were converted to fastq files using the bcl2fastq software (Illumina).
Fastq files were trimmed for adaptor sequences and any reads below 50 nt. were discarded using the Trimmomatic 0.38.0 software with the input HEADCROP: 9, MINLEN: 50
The trimmed reads were mapped using the HISAT2 2.1.0 mapper. The Cavia Porcellus genome and annotation (CavPor.3.0.98) was acquired from Ensembl, and used as reference genome.
Initial transcript assembly was performed by StringTie 1.3.6 using the guinea pig annotation file (CavPor.3.0.98) as a guide. StringTie merge 1.3.6 was run on Stringtie output from all samples with the guinea pig annotation file as a guide, and default parameters. For quantification StringTie was run on the StringTie merge file separately for each sample by using the guinea pig annotation file as a guide, setting the -e parameter was set to "yes" and the output type to deseq2.
Raw counts for each StringTie file was assembled into a collected file and to obtain translatability and more annotation, BioMart was used to find human orthologs for each transcript. To diminish background noise genes with raw counts below 200 across all samples were discarded. Finally Deseq2 was used for differential expression.
Genome_build: CavPor3 (Cavpor3.0)
Supplementary_files_format_and_content: raw_counts_GP.txt: Matrix file with raw counts for each Cavia Porcellus gene ID and each sample.
Supplementary_files_format_and_content: GP_rlogs.txt: Normalized and transformed values (normalized according to DESeqs' size factor, and rlog transformed) for each sample, and each gene (gene names are obtained by finding human orthologs).

organism: Cavia porcellus

source_name: Liver

extract_protocol:
Liver sections from the left lateral lobe were snap frozen in liquid nitrogen. 12-24 mg of liver from each sample was sent to Qiagen for purification.
500 ng of total RNA was enriched for mRNA by using oligodT bead system. Library preparation was performed by Qiagen using the TruSeq mRNA sample preparation kit (Illumina Inc.), and standard Illumina protocols.

treatment_protocol: Animals were given either a chow, or high fat diet for 25 weeks.

tag: strain

value: Dunkin Hartley

tag: diet

value: High fat diet

tag: time on diet

value: 25 weeks

tag: disease state

value: NASH

value: Liver


title: KW059_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.SNAPC3.tabular.txt
n.counts.SNAPC3.tabular.txt

value: WT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo

value: normal lymphoid development in thymus


title: COL12_TSA1_S12_ROW23

tag: cell line

tag: cell type


title: Negative_ctrl2


title: LS-15555_S30_E1-50

tag: gender

tag: age

tag: region

value: ALM

tag: roi

value: RFP-positive

value: SSs


title: KW059_WT3


title: NASH_11

description:
N11
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt


title: LS-15555_S29_E1-50

tag: batch


title: LS-15555_S28_E1-50


title: COL12_TSA1_S12_ROW19


title: NASH_41

description:
N41
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt


title: COL12_TSA1_S12_ROW20


title: NASH_9

description:
N9
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt


title: T26683_MUT3

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: COL12_TSA1_S12_ROW22


title: LS-15555_S34_E1-50

value: 56 days

value: left


title: COL12_TSA1_S12_ROW21

value: Invasive Ductal Carcinoma


title: KW059_WT2


title: LS-15555_S26_E1-50

value: M

value: 55 days


title: COL12_TSA1_S12_ROW17


title: KW059_WT1


title: COL12_TSA1_S12_ROW16


title: COL12_TSA1_S12_ROW15


title: NASH_2

description:
N2
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt

value: Dunkin Hartley

value: High fat diet

value: 25 weeks


title: COL12_TSA1_S12_ROW18


title: LS-15555_S27_E1-50


title: LS-15555_S22_E1-50


title: KW059_MUT4


title: Control_10

description:
C10
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt

value: Chow

value: Healthy

value: Liver


title: COL12_TSA1_S12_ROW13


title: KW059_MUT1

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo


title: Control_56

description:
C56
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt


title: LS-15555_S21_E1-50

value: ALM

value: RFP-positive


title: NASH_20

description:
N20
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt

value: NASH


title: Control_45

description:
C45
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt


title: LS-15555_S25_E1-50

value: SSs


title: Control_32

description:
C32
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt


title: Control_5

description:
C5
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt


title: LS-15555_S24_E1-50


title: Control_31

description:
C31
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt


title: LS-15555_S23_E1-50


title: KW059_MUT3

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: donor #3 SIRPa low macrophage

city: Atlanta

first: Lei

last: Shi

state: GA

address: 100 Piedmont Avenue SE

department: Department of Biology

institute: Center for Diagnostics & Therapeutics

data_processing:
Basecalls performed using Zebracall process version 0.5.0.13875
In order to decrease noise of sequencing data, data filtering was done firstly, which included: (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio is more than 50%; (3) Removing reads whose unknown base ('N' base) ratio is more than 10%. Then, all clean readswere  mapped to mm9 whole genome.
The fragment counts of each gene were normalized by fragments per kb per million (FPKM).
RNA-seq data were analyzed using R version 3.3.3 and the R package DeSeq2 for differential gene expression, graphical representation, and statistical analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Text files include FPKM values and GO information for each sample

source_name: macrophage

growth_protocol: Macrophages were derived from human PBMC with human macrophage colony stimulating factor (M-CSF)-conditioned RPMI-1640 medium for 5 days.

extract_protocol:
After treatment,  RNA samples from 3 SIRPα-low or 3 SIRPα-normal macrophages were harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Human PBMC derived macrophage  produced from matched donors were treated with Phago-Act for 2d

value: Human PBMC derived macrophage

tag: treatment

value: Phago-Act for 2d


title: COL12_TSA1_S12_ROW14

value: Invasive Ductal Carcinoma


title: KL069_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.GEMIN5.tabular.txt
n.counts.GEMIN5.tabular.txt

tag: genotype

value: WT

value: normal lymphoid development in thymus


title: KL069_WT3

tag: strain background


title: COL12_TSA1_S12_ROW10


title: KL069_MUT4

tag: population


title: COL12_TSA1_S12_ROW08


title: COL12_TSA1_S12_ROW12


title: donor #1 SIRPa low macrophage


title: LS-15555_S16_E1-50

value: M

value: 55 days

value: left


title: KL069_WT2

tag: surface phenotype


title: LS-15555_S20_E1-50


title: donor #3 SIRPa normal macrophage

value: untreated


title: 5Y_ecircCUX1_3

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of ecircCUX1

data_processing:
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. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: SH-SY5Y stably transfected with ecircCUX1 replicate 3

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Oligo(dT)-attached magnetic beads were used to purified mRNA.
Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library.

treatment_protocol: The ecircCUX1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of neomycin.

tag: tissue

value: neuroblastoma

tag: passages


title: KW059_MUT2

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo


title: LS-15555_S14_E1-50

description:
exon_counts.csv.gz
intron_counts.csv.gz
cpm.csv.gz

value: ALM

value: RFP-positive


title: COL12_TSA1_S12_ROW11


title: 5Y_ecircCUX1_2

source_name: SH-SY5Y stably transfected with ecircCUX1 replicate 2


title: LS-15555_S13_E1-50

value: SSs


title: COL12_TSA1_S12_ROW04


title: KL069_WT1


title: LS-15555_S19_E1-50


title: LS-15555_S12_E1-50


title: donor #2 SIRPa low macrophage


title: 5Y_ecircCUX1_1

source_name: SH-SY5Y stably transfected with ecircCUX1 replicate 1


title: KH025_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.EIF5.tabular.txt
n.counts.EIF5.tabular.txt


title: LS-15555_S18_E1-50


title: COL12_TSA1_S12_ROW09


title: KL069_MUT3

value: MUT


title: COL12_TSA1_S12_ROW05


title: LS-15555_S17_E1-50


title: KL069_MUT2

value: lymphoid development, defect in rag1 expression in thymus


title: donor #2 SIRPa normal macrophage

value: Human PBMC derived macrophage


title: COL12_TSA1_S12_ROW02


title: COL12_TSA1_S12_ROW07


title: KL069_MUT1


title: LS-15555_S15_E1-50


title: COL12_TSA1_S12_ROW06


title: KH025_WT3


title: COL12_TSA1_S12_ROW01


title: donor #1 SIRPa normal macrophage


title: 5Y_mock empty vector_3

description: Gene expression after stable transfection of empty vector

source_name: SH-SY5Y stably transfected with empty vector replicate 3


title: LS-15555_S11_E1-50


title: KH025_MUT3


title: LS-15555_S09_E1-50


title: KH025_WT2


title: SC1810_CPF-resistance_rep3

city: Yucheng

first: Bowen

last: Zheng

address: Rm.22,Area 3,Sichuan agricultural University,No.46 Xinkang Road,Yucheng District,Ya'an City,Sichuan

department: Sichuan Agricultural University

institute: Sichuan

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using Novaseq 6000 PE Cluster Kit (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150bp paired-end reads were generated.
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. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
The index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.1.1. Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq R package (v1.42.0), which provides statistical routines for determining differential expression in digital gene expression data using a model based on a negative binomial distribution.
The resulting P-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR, q-value).
Genome_build: SUB9215048
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Actinobacillus pleuropneumoniae

source_name: bacterial

growth_protocol: cultured in TSB medium (with 0.01% NAD and 5% bovine serum) for 8 h at 37 °C

extract_protocol:
RNA was harvested using the Total RNA Isolation System (Promega, Madison, WI, USA) according to the manufacturer’s instructions. RNA degradation and contamination were monitored on 1% agarose gels, and RNA purity (OD260/280) was detected using a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration and integrity were assessed using a Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technology, CA, USA) and RNA Nano 6000 Assay Kit of Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mutant


title: KH025_WT1


title: SC1810_CPF-resistance_rep2


title: KH025_MUT2


title: KH025_MUT4


title: COL11_TSA2_S33_ROW38

value: Invasive Ductal Carcinoma


title: LS-15555_S10_E1-50


title: JZ061_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.FLI1A.tabular.txt
n.counts.FLI1A.tabular.txt

value: WT


title: 5Y_mock empty vector_2

source_name: SH-SY5Y stably transfected with empty vector replicate 2


title: KH025_MUT1


title: COL12_TSA1_S12_ROW03


title: LS-15555_S08_E1-50


title: COL11_TSA2_S33_ROW39


title: JZ061_WT3

value: normal lymphoid development in thymus


title: SC1810_rep3

value: wild type


title: LS-15555_S07_E1-50

value: M

value: 55 days


title: LS-15555_S05_E1-50

value: left


title: COL11_TSA2_S33_ROW40


title: SC1810_CPF-resistance_rep1


title: COL11_TSA2_S33_ROW37


title: LS-15555_S04_E1-50


title: COL11_TSA2_S33_ROW36


title: JZ061_MUT4


title: 5Y_mock empty vector_1

source_name: SH-SY5Y stably transfected with empty vector replicate 1

value: neuroblastoma


title: LS-15555_S06_E1-50


title: JZ061_MUT3

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen


title: LS-15555_S01_E1-50


title: Schizont/T5_InputDNA

city: Singapore

first: Mark

middle: Stephen

last: Featherstone

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Paired-end reads from ChIP-Seq were run through FastQC (Version 0.11.4) to generate quality reports, followed by quality and length trimming using trim_galore (Version 0.4.1).
Reads from ChIP and input DNA samples were mapped to PlasmoDbv9.0 using Bowtie2 (Version 2.2.6).
Alignments with a MAPQ of 10 and properly paired were extracted using Samtools (Version 1.3).
Heatmap and profile plots were generated by deepTools (Version 2.3.4)
Peak calling was done using MACS2 (Version 2.1.1) with p = 0.05. Peak to gene annotation was done with bespoke scripts based on Bedtools (Version 2.25.0) suite
Genome_build: PlasmoDbv9.0

organism: Plasmodium falciparum

source_name: Asexual stages

growth_protocol: P. falicparum was culture in RPMI at 2% haematocrit and sorbitol synchronized

extract_protocol: Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA library prep kit from Illumina

treatment_protocol: P. falciparum was formaldehyde cross-linked and 5x108 schizonts,1x109 trophozoites or 2x109 ring stage parasites were harvested for Chromatin immunoprecipitation.

tag: developmental stage

value: Schizont stage

tag: strain

tag: chip antibody


title: SC1810_rep2


title: LS-15555_S03_E1-50

value: ALM


title: COL11_TSA2_S33_ROW35

tag: cell line


title: JZ061_WT1

value: whole embryo


title: LS-15553_S07_E1-50

value: RFP-positive

value: MOs

value: RV-dGdL-Cre


title: COL11_TSA2_S33_ROW34

tag: cell type


title: SC1810_rep1


title: LS-15555_S02_E1-50

tag: gender

value: SSs


title: COL11_TSA2_S33_ROW33


title: Schizont/T5_Ser2/5-P_ChIP-Seq

value: Anti-Ser2/5-P (Rai et al., 2014)


title: COL11_TSA2_S33_ROW32

value: Invasive Ductal Carcinoma


title: JZ061_WT2

value: WT


title: LS-15553_S08_E1-50

tag: age


title: COL11_TSA2_S33_ROW31


title: Trophozoite_Ser2/5-P_ChIP-Seq

value: Trophozoite stage


title: JZ061_MUT2

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: COL11_TSA2_S33_ROW28


title: S16_grn HSD rep4

city: Helsinki

first: Krista

last: Kokki

address: Viikinkaari 9, Biocenter 1, Institute of Biotechnology P.O.Box. 56

department: Department of Biosciences (Genetics)

country: Finland

institute: University of Helsinki

data_processing:
Sequenced reads were trimmed with Trimmomatic with parameters ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36
Sequences were mapped using TopHat (v2.1.0) to dmel R6.10 with parameter -p 4 and quantified with HTSeq (v2.7.6) with parameters -m HTSeq.scripts.count -m union -s reverse -a 10 -t exon -i Parent
Differentially expressed genes were calculated with R package limma with Benjamini-Hochberg correction, with genes with low counts (cpm<1 in more than one replicate) filtered
Genome_build: Flybase Drosophila melanogaster R6.10
Supplementary_files_format_and_content: grn_all_comparisons.txt file includes read counts for expressed genes for all samples and their statistics

organism: Drosophila melanogaster

source_name: grn HSD_whole larvae

growth_protocol: 1st instar larvae were collected 24 hours after egg laying to plates with LSD (low sugar diet, 10% yeast) at a controlled density. Early 2nd instar larvae were transferred at 48 hours after egg laying to plates containing either LSD or HSD (high sugar diet, 10% yeast supplemented with 15% sugar). After 8 hours of diet exposure, 20 larvae per sample were collected and snap-frozen in liquid nitrogen.

extract_protocol:
The larvae were homogenised and total RNA was extracted with the Nucleospin RNA II kit (Macherey-Nagel) according to the manufacturer’s instruction.
Libraries were prepared with the TruSeq Stranded mRNA kit (Illumina), and RNA-sequencing was performed to an average depth of 20 million reads per sample with Illumina NextSeq500 technology using the 75bp cycle kit (Illumina).

value: erk7 mutant

value: 3rd instar larvae

value: whole larvae


title: JM087_WT2

description:
Processed data files generated from multiple samples
processed data file:
log2.ANAPC1.tabular.txt
n.counts.ANAPC1.tabular.txt

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: normal lymphoid development in thymus


title: JM087_WT4


title: JZ061_MUT1


title: Trophozoite_InputDNA


title: LS-15553_S04_E1-50

value: M

value: 55 days

tag: region

value: ALM

value: left


title: COL11_TSA2_S33_ROW30


title: LS-15553_S01_E1-50

tag: roi

value: RFP-positive

value: MOs

value: RV-dGdL-Cre


title: COL11_TSA2_S33_ROW29

value: Invasive Ductal Carcinoma


title: Ring/T2_Ser2/5-P_ChIP-Seq

value: Ring stage

value: Anti-Ser2/5-P (Rai et al., 2014)


title: JM087_MUT4

value: MUT

value: whole embryo


title: COL11_TSA2_S33_ROW26


title: JM087_WT3

value: WT


title: LS-15553_S03_E1-50

tag: batch


title: Ring/T2_inputDNA


title: JM087_MUT3

value: lymphoid development, defect in rag1 expression in thymus


title: COL11_TSA2_S33_ROW24


title: S15_grn HSD rep3

value: erk7 mutant

value: 3rd instar larvae

tag: treatment

value: HSD (high sugar diet, 10% yeast supplemented with 15% sugar)

value: whole larvae


title: COL11_TSA2_S33_ROW27


title: LS-15552_S24_E1-50

value: M

value: 55 days


title: COL11_TSA2_S33_ROW23


title: S14_grn HSD rep2

tag: genotype


title: LS-15553_S02_E1-50

value: ALM

value: left


title: JM087_WT1

tag: strain background

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: normal lymphoid development in thymus


title: LS-15552_S22_E1-50

value: RFP-positive

value: MOs

value: RV-dGdL-Cre


title: S13_grn HSD rep1


title: LS-15552_S23_E1-50


title: S12_grn LSD rep4

source_name: grn LSD_whole larvae

value: wild type

value: LSD (low sugar diet, 10% yeast)


title: LS-15552_S21_E1-50


title: JI073_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.NAA50.tabular.txt
n.counts.NAA50.tabular.txt

value: WT

tag: population

value: whole embryo


title: S9_grn LSD rep1


title: COL11_TSA2_S33_ROW21

value: Invasive Ductal Carcinoma


title: JM087_MUT1

value: MUT

tag: surface phenotype

value: lymphoid development, defect in rag1 expression in thymus


title: LS-15552_S19_E1-50


title: JI073_WT2


title: LS-15552_S18_E1-50


title: S11_grn LSD rep3

value: 3rd instar larvae

tag: tissue

value: whole larvae


title: LS-15552_S20_E1-50

value: M

value: 55 days


title: COL11_TSA2_S33_ROW22


title: S10_grn LSD rep2


title: S7_control HSD rep3

source_name: control HSD_whole larvae

value: erk7 mutant

value: HSD (high sugar diet, 10% yeast supplemented with 15% sugar)


title: COL11_TSA2_S33_ROW18

source_name: 40 year old female


title: COL11_TSA2_S33_ROW25


title: LS-15552_S17_E1-50

value: ALM

value: left


title: COL11_TSA2_S33_ROW20


title: S8_control HSD rep4


title: JI073_WT1

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: normal lymphoid development in thymus


title: COL11_TSA2_S33_ROW17


title: S5_control HSD rep1


title: LS-15552_S15_E1-50

value: RFP-positive

value: MOs

value: RV-dGdL-Cre


title: JI073_MUT4

value: whole embryo


title: LS-15552_S16_E1-50


title: S6_control HSD rep2


title: COL11_TSA2_S33_ROW19

value: Invasive Ductal Carcinoma


title: JI073_MUT2

value: MUT


title: LS-15552_S14_E1-50


title: S4_control LSD rep4

source_name: control LSD_whole larvae

value: wild type

value: LSD (low sugar diet, 10% yeast)


title: JI073_MUT3

value: lymphoid development, defect in rag1 expression in thymus


title: JI073_WT3

value: WT


title: COL11_TSA2_S33_ROW15


title: JI073_MUT1


title: S3_control LSD rep3

value: 3rd instar larvae

value: whole larvae


title: JH051_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.CCT5.tabular.txt
n.counts.CCT5.tabular.txt


title: COL11_TSA2_S33_ROW13


title: LS-15552_S13_E1-50

source_name: retroseq cells mapped to L2/3,L4,L5 IT subclass

value: M

value: 55 days


title: S2_control LSD rep2


title: LS-15552_S12_E1-50

value: ALM

value: left


title: COL11_TSA2_S33_ROW14


title: S1_control LSD rep1


title: COL11_TSA2_S33_ROW16


title: LS-15552_S11_E1-50


title: COL11_TSA2_S33_ROW12


title: COL11_TSA2_S33_ROW11


title: JH051_WT2

source_name: ENU mutagenesis forward genetic screen

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: normal lymphoid development in thymus


title: JH051_WT1


title: Testis-anti-PD-L1 treated_rep3

city: Qingdao

first: Luoyang

last: Wang

state: Shandong

address: 308 Ningxia Road

institute: Qingdao University

data_processing:
Illumina Casava 1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sicklewith default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: testis

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

treatment_protocol: Testes were colloceted 7 days later post-treatment with anti-PD-L1 or control IgG

value: testis

value: twice intraperitoneal (IP) injection of 200 μg anti-PD-L1

value: 8 weeks


title: Testis-anti-PD-L1 treated_rep2


title: COL11_TSA2_S33_ROW10

value: Invasive Ductal Carcinoma


title: LS-15552_S09_E1-50

value: RFP-positive

value: MOs

value: RV-dGdL-Cre


title: Testis-anti-PD-L1 treated_rep4


title: JH051_MUT4

value: MUT

value: whole embryo

value: lymphoid development, defect in rag1 expression in thymus


title: Testis-anti-PD-L1 treated_rep1


title: LS-15552_S10_E1-50


title: JH051_MUT3


title: LS-15552_S07_E1-50


title: COL11_TSA2_S33_ROW08


title: JH051_MUT2


title: LS-15552_S06_E1-50


title: Testis-IgG isotype CTR_rep4

value: twice intraperitoneal (IP) injection of 200 μg  IgG2b isotype


title: JH051_MUT1


title: COL11_TSA2_S33_ROW06


title: COL11_TSA2_S33_ROW07


title: IY071_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.DNMT1.tabular.txt
n.counts.DNMT1.tabular.txt

value: WT


title: COL11_TSA2_S33_ROW05


title: LS-15552_S05_E1-50

value: M

value: 55 days


title: JH051_WT3


title: Testis-IgG isotype CTR_rep3


title: LS-15552_S08_E1-50

value: ALM

value: left


title: Testis-IgG isotype CTR_rep2


title: LS-15552_S04_E1-50


title: COL11_TSA2_S33_ROW09


title: COL11_TSA2_S33_ROW04


title: IY071_WT3

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: normal lymphoid development in thymus


title: Testis-IgG isotype CTR_rep1

value: testis


title: LS-15552_S02_E1-50


title: COL11_TSA2_S33_ROW03


title: IY071_Mut4_2

description:
Processed data files generated from multiple samples
processed data file:
log2.DNMT1_2.tabular.txt
n.counts.DNMT1_2.tabular.txt


title: IY071_WT1


title: LS-15546_S96_E1-50

value: 54 days

value: SSs


title: IY071_Mut3_2


title: COL11_TSA2_S33_ROW02

value: Invasive Ductal Carcinoma


title: LS-15546_S95_E1-50

value: RFP-positive


title: COL11_TSA2_S33_ROW01


title: LS-15546_S94_E1-50

value: RV-dGdL-Cre


title: COL11_TSA1_S11_ROW40


title: LS-15552_S03_E1-50

value: MOs


title: IY071_WT2

value: whole embryo


title: JM087_MUT2

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: COL11_TSA1_S11_ROW38


title: COL11_TSA1_S11_ROW39


title: IY071_Mut1_2


title: IY071_MUT4


title: IY071_Mut2_2


title: COL11_TSA1_S11_ROW37


title: IY071_MUT3


title: LS-15546_S80_E1-50


title: COL11_TSA1_S11_ROW36


title: LS-15546_S79_E1-50


title: IY071_MUT2


title: LS-15546_S78_E1-50


title: LS-15546_S92_E1-50


title: LS-15546_S77_E1-50


title: IY071_MUT1


title: COL11_TSA1_S11_ROW34


title: IU191_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.CSTF3.tabular.txt
n.counts.CSTF3.tabular.txt

value: WT


title: COL11_TSA1_S11_ROW35


title: LS-15546_S75_E1-50

value: M


title: COL11_TSA1_S11_ROW33


title: LS-15546_S76_E1-50


title: IU191_WT3


title: LS-15546_S74_E1-50


title: IU191_WT2


title: COL11_TSA1_S11_ROW32


title: COL11_TSA1_S11_ROW31


title: IU191_WT1


title: LS-15546_S73_E1-50


title: LS-15546_S72_E1-50


title: IU191_Mut4


title: COL11_TSA1_S11_ROW30


title: COL11_TSA1_S11_ROW29


title: LS-15546_S71_E1-50


title: IU191_Mut3


title: COL11_TSA1_S11_ROW28


title: LS-15546_S69_E1-50


title: IU191_Mut2


title: 39.4 week Baby abdomen Male skin biopsy sample [GSS2656_92]

type: RNA

city: MASON

first: Jay

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

description:
GSS2656_92
Gene expression data from infant skin biopsy.

hyb_protocol: Biotinylated cRNA was fragmented by limited alkaline hydrolysis and then hybridized overnight to Affymetrix GeneTitan U219 array plates using the Affymetrix GeneTitan instrument and protocol.

scan_protocol: Affymetrix GeneTitan U219 array plates were scanned using the Affymetrix GeneTitan instrument and protocol.

data_processing: Chip images were converted to numeric data with the probe logarithmic intensity error algorithm as executed in the Affymetrix GeneChip Expression Console.

label: biotin

label_protocol: Purified RNA was converted to biotin-labeled complementary RNA copies with the Affymetrix HT 3’ IVT Plus kit per protocol provided at a Beckman Biomek FXP Laboratory Automation Workstation.

extract_protocol: Total RNA was extracted from biopsies by homogenizing in Trizol Reagent using protocol provided by supplier. Extracted RNA was further purified using Qiagen RNeasy Micro columns and protocol provided by supplier.

value: Male

value: 39.4 week

value: Skin

tag: biopsy site

value: abdomen

tag: subjectid

tag: sampleID


title: 63 year Adult Buttocks Female skin biopsy sample [GSS2656_91]

description:
GSS2656_91
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Female

value: 63 year

value: Buttocks


title: LS-15546_S68_E1-50

value: 54 days

value: ALM

value: left

value: SSs


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_86]

description:
GSS2656_86
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 24 year


title: 37.2 week Baby head Female skin biopsy sample [GSS2656_83]

description:
GSS2656_83
Gene expression data from infant skin biopsy.

value: 37.2 week

value: head


title: 42.1 week Baby chest Female skin biopsy sample [GSS2656_89]

description:
GSS2656_89
Gene expression data from infant skin biopsy.

value: 42.1 week

value: chest


title: 60 year Adult Buttocks Female skin biopsy sample [GSS2656_90]

description:
GSS2656_90
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 60 year


title: IU191_Mut1

value: MUT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo

value: lymphoid development, defect in rag1 expression in thymus


title: 23 year Adult Buttocks Female skin biopsy sample [GSS2656_85]

description:
GSS2656_85
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Female

value: 23 year

value: Skin


title: 40.8 week Baby chest Female skin biopsy sample [GSS2656_79]

description:
GSS2656_79
Gene expression data from infant skin biopsy.

value: 40.8 week


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_87]

description:
GSS2656_87
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Buttocks


title: 37.5 week Baby back Female skin biopsy sample [GSS2656_81]

description:
GSS2656_81
Gene expression data from infant skin biopsy.

value: 37.5 week

value: back


title: 22 year Adult Buttocks Female skin biopsy sample [GSS2656_78]

description:
GSS2656_78
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 22 year


title: 61 year Adult Buttocks Female skin biopsy sample [GSS2656_82]

description:
GSS2656_82
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 61 year


title: 42.3 week Baby abdomen Male skin biopsy sample [GSS2656_80]

description:
GSS2656_80
Gene expression data from infant skin biopsy.

value: Male

value: 42.3 week

value: abdomen


title: COL11_TSA1_S11_ROW27

value: Invasive Ductal Carcinoma


title: IT429_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.NEK7.tabular.txt
n.counts.NEK7.tabular.txt

value: WT

value: normal lymphoid development in thymus


title: 61 year Adult Buttocks Female skin biopsy sample [GSS2656_77]

description:
GSS2656_77
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.


title: 30.7 week Baby back Male skin biopsy sample [GSS2656_75]

description:
GSS2656_75
Gene expression data from infant skin biopsy.

value: 30.7 week


title: IT429_WT3

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo


title: LS-15546_S67_E1-50

description:
exon_counts.csv.gz
intron_counts.csv.gz
cpm.csv.gz

value: M

value: 54 days

value: ALM

value: RFP-positive

value: left

value: SSs

value: RV-dGdL-Cre


title: IT429_WT2


title: LS-15546_S63_E1-50


title: COL11_TSA1_S11_ROW26


title: LS-15546_S62_E1-50


title: LS-15546_S66_E1-50


title: COL11_TSA1_S11_ROW23


title: IT429_WT1


title: COL11_TSA1_S11_ROW22


title: 64 year Adult Buttocks Female skin biopsy sample [GSS2656_84]

description:
GSS2656_84
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Female

value: 64 year

value: Skin

value: Buttocks


title: COL11_TSA1_S11_ROW21

value: Invasive Ductal Carcinoma


title: LS-15546_S61_E1-50


title: LS-15546_S59_E1-50


title: LS-15546_S60_E1-50


title: COL11_TSA1_S11_ROW20


title: IT429_MUT3

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: IT429_MUT2


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_74]

description:
GSS2656_74
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 24 year


title: LS-15546_S56_E1-50


title: COL11_TSA1_S11_ROW19


title: LS-15546_S55_E1-50


title: IT429_MUT1

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen


title: 34.3 week Baby abdomen Male skin biopsy sample [GSS2656_73]

description:
GSS2656_73
Gene expression data from infant skin biopsy.

value: Male

value: 34.3 week

value: abdomen