title: Chip91484_r19_c24_Treated

description: Chip91484_r19_c24_Treated_CAGTTATACGA-AAGAGGCA


title: MM_M1_1_sample 2653

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: 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

molecule: genomic DNA

organism: Callithrix jacchus

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: SM-GE8XK_S281_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

library_source: transcriptomic

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: mm10
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: retroseq cells mapped to L2/3,L4,L5 IT 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.

value: F

tag: age

value: 102 days

tag: region

value: SSs

tag: roi

value: GFP-positive/RFP-positive

value: left

value: MOp

tag: batch


title: Chip91484_r19_c11_Treated

city: Rochester

first: Jason

last: Myers

state: NY

address: 601 Elmwood Ave.

institute: University of Rochester

description: Chip91484_r19_c11_Treated_CCAAGTCGTAA-AAGAGGCA

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 cell

molecule: total RNA

organism: Homo sapiens

source_name: 40 year old female

extract_protocol:
Wafergen iCell8 scRNAseq protocol, no offline RNA isolation performed
Wafergen iCell8 scRNAseq library construction protocol

tag: cell line

tag: cell type

value: Invasive Ductal Carcinoma


title: Chip91484_r19_c2_Treated

description: Chip91484_r19_c2_Treated_CCAATAGATCG-AAGAGGCA


title: Chip91484_r19_c27_Treated

description: Chip91484_r19_c27_Treated_CAGCCATCTCT-AAGAGGCA


title: Chip91484_r18_c7_Treated

description: Chip91484_r18_c7_Treated_CATCATTACTG-AAGAGGCA


title: SM-GE8XK_S282_E1-50


title: HS_M1_1_sample 627

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

value: Brain


title: SM-GE8XK_S284_E1-50


title: HS_M1_1_sample 624


title: SM-GE8XK_S283_E1-50


title: MM_M1_1_sample 2652


title: HS_M1_1_sample 626


title: MM_M1_1_sample 2650


title: MM_M1_1_sample 2651


title: SM-GE8XK_S280_E1-50


title: MM_M1_1_sample 2649


title: Chip91484_r18_c64_Untreated

description: Chip91484_r18_c64_Untreated_AGTCGGTCATG-AAGAGGCA


title: MM_M1_1_sample 2655


title: Chip91484_r19_c26_Treated

description: Chip91484_r19_c26_Treated_CATCTTCTTAA-AAGAGGCA


title: SM-GE8XK_S278_E1-50


title: MM_M1_1_sample 2648


title: SM-GE8XK_S287_E1-50


title: Chip91484_r18_c70_Untreated

description: Chip91484_r18_c70_Untreated_AGTCGTCAGGA-AAGAGGCA


title: Chip91484_r18_c53_Treated

description: Chip91484_r18_c53_Treated_CAAGTTCCTGC-AAGAGGCA


title: HS_M1_1_sample 625


title: HS_M1_1_sample 622


title: MM_M1_1_sample 2647


title: HS_M1_1_sample 623


title: Chip91484_r18_c50_Treated

description: Chip91484_r18_c50_Treated_CAGAATCTCGT-AAGAGGCA


title: SM-GE8XK_S277_E1-50


title: MM_M1_1_sample 2645


title: SM-GE8XK_S274_E1-50


title: HS_M1_1_sample 621


title: MM_M1_1_sample 2644


title: SM-GE8XK_S276_E1-50


title: SM-GE8XK_S272_E1-50


title: Chip91484_r18_c3_Treated

description: Chip91484_r18_c3_Treated_CAGCAACTCTT-AAGAGGCA


title: Chip91484_r18_c45_Untreated

description: Chip91484_r18_c45_Untreated_ATTCGCCGATA-AAGAGGCA


title: SM-GE8XK_S275_E1-50


title: HS_M1_1_sample 617


title: HS_M1_1_sample 618


title: HS_M1_1_sample 619


title: MM_M1_1_sample 2643


title: SM-GE8XK_S269_E1-50


title: HS_M1_1_sample 615


title: Chip91484_r18_c24_Treated

description: Chip91484_r18_c24_Treated_CCAAGAGACGG-AAGAGGCA


title: SM-GE8XK_S271_E1-50


title: Chip91484_r18_c41_Untreated

description: Chip91484_r18_c41_Untreated_ATTCTGCTTGA-AAGAGGCA


title: HS_M1_1_sample 620


title: HS_M1_1_sample 616


title: MM_M1_1_sample 2642


title: SM-GE8XK_S267_E1-50


title: MM_M1_1_sample 2641


title: HS_M1_1_sample 613


title: Chip91484_r18_c15_Untreated

description: Chip91484_r18_c15_Untreated_AGTTGACCTGG-AAGAGGCA


title: Chip91484_r17_c57_Treated

description: Chip91484_r17_c57_Treated_CCAACGCAAGC-AAGAGGCA


title: SM-GE8XK_S265_E1-50


title: MM_M1_1_sample 2646


title: Chip91484_r17_c68_Untreated

description: Chip91484_r17_c68_Untreated_ATTATGGCAGC-AAGAGGCA


title: MM_M1_1_sample 2640


title: SM-GE8XK_S192_E1-50

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


title: SM-GE8XK_S268_E1-50


title: MM_M1_1_sample 2637


title: Chip91484_r18_c19_Untreated

description: Chip91484_r18_c19_Untreated_ATAGTTCTCGT-AAGAGGCA


title: MM_M1_1_sample 2639


title: Chip91484_r17_c64_Untreated

description: Chip91484_r17_c64_Untreated_ATGGTCTTCAA-AAGAGGCA


title: MM_M1_1_sample 2638


title: Chip91484_r17_c53_Treated

description: Chip91484_r17_c53_Treated_CCAACGGTTCG-AAGAGGCA


title: Chip91484_r17_c49_Treated

description: Chip91484_r17_c49_Treated_CCAACTATGCG-AAGAGGCA


title: HS_M1_1_sample 611


title: HS_M1_1_sample 612


title: Chip91484_r17_c48_Treated

description: Chip91484_r17_c48_Treated_CCAACGTCTCT-AAGAGGCA


title: SM-GE8XK_S190_E1-50


title: SM-GE8XK_S191_E1-50


title: MM_M1_1_sample 2636


title: MM_M1_1_sample 2635


title: HS_M1_1_sample 614


title: HS_M1_1_sample 610


title: MM_M1_1_sample 2634


title: MM_M1_1_sample 2633


title: Chip91484_r17_c47_Untreated

description: Chip91484_r17_c47_Untreated_AGTCTACCTCT-AAGAGGCA


title: MM_M1_1_sample 2632


title: HS_M1_1_sample 608


title: HS_M1_1_sample 606


title: Chip91484_r17_c44_Untreated

description: Chip91484_r17_c44_Untreated_AGTTACGGCAA-AAGAGGCA


title: MM_M1_1_sample 2631


title: HS_M1_1_sample 607


title: SM-GE8XK_S095_E1-50

value: 99 days

value: SSp

value: VISpl


title: Chip91484_r17_c35_Treated

description: Chip91484_r17_c35_Treated_CAAGCGCGCAG-AAGAGGCA


title: MM_M1_1_sample 2630


title: HS_M1_1_sample 605


title: Chip91484_r17_c34_Treated

description: Chip91484_r17_c34_Treated_CAAGAACGCTA-AAGAGGCA


title: HS_M1_1_sample 604


title: Chip91484_r17_c23_Untreated

description: Chip91484_r17_c23_Untreated_ATTCTCAGCCT-AAGAGGCA


title: SM-GE8XK_S092_E1-50


title: SM-GE8XK_S093_E1-50


title: MM_M1_1_sample 2629


title: Chip91484_r17_c27_Treated

description: Chip91484_r17_c27_Treated_CAAGAACCTGA-AAGAGGCA


title: HS_M1_1_sample 603


title: SM-GE8XK_S090_E1-50


title: SM-GE8XK_S189_E1-50


title: MM_M1_1_sample 2628


title: HS_M1_1_sample 609


title: SM-GE8XK_S096_E1-50


title: MM_M1_1_sample 2626


title: SM-GE8XK_S089_E1-50


title: Chip91484_r17_c13_Untreated

description: Chip91484_r17_c13_Untreated_ATTGAGTATTG-AAGAGGCA


title: Chip91484_r16_c69_Untreated

description: Chip91484_r16_c69_Untreated_AGGTAATGCTT-AAGAGGCA


title: SM-GE8XK_S094_E1-50


title: Chip91484_r16_c61_Untreated

description: Chip91484_r16_c61_Untreated_AGGTTCGTCTC-AAGAGGCA


title: Chip91484_r17_c41_Untreated

description: Chip91484_r17_c41_Untreated_AGTCGTTGCAG-AAGAGGCA


title: SM-GE8XK_S086_E1-50


title: HS_M1_1_sample 599


title: MM_M1_1_sample 2627


title: SM-GE8XK_S085_E1-50


title: HS_M1_1_sample 601


title: Chip91484_r17_c16_Untreated

description: Chip91484_r17_c16_Untreated_ATTCCGGAGGT-AAGAGGCA


title: MM_M1_1_sample 2622


title: HS_M1_1_sample 600


title: MM_M1_1_sample 2625


title: HS_M1_2_sample 267


title: Chip91484_r16_c55_Treated

description: Chip91484_r16_c55_Treated_CAACGAATTAA-AAGAGGCA


title: SM-GE8XK_S091_E1-50

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


title: MM_M1_1_sample 2620


title: Chip91484_r16_c58_Treated

description: Chip91484_r16_c58_Treated_CAACCGCCGAT-AAGAGGCA


title: Chip91484_r16_c52_Treated

description: Chip91484_r16_c52_Treated_CAACCGCCAGC-AAGAGGCA


title: HS_M1_2_sample 269


title: MM_M1_1_sample 2623


title: HS_M1_2_sample 265


title: MM_M1_1_sample 2618


title: Chip91484_r16_c57_Treated

description: Chip91484_r16_c57_Treated_CAACCGATCAA-AAGAGGCA


title: Chip91484_r16_c48_Treated

description: Chip91484_r16_c48_Treated_CAACCGTACCG-AAGAGGCA


title: SM-GE8XK_S088_E1-50


title: MM_M1_1_sample 2617


title: SM-GE8XK_S082_E1-50


title: HS_M1_2_sample 268


title: Chip91484_r16_c37_Untreated

description: Chip91484_r16_c37_Untreated_ATTAGGCGGAG-AAGAGGCA


title: Chip91484_r16_c19_Untreated

description: Chip91484_r16_c19_Untreated_AGTACGAGATA-AAGAGGCA


title: SM-GE8XK_S084_E1-50


title: HS_M1_2_sample 261


title: MM_M1_1_sample 2621


title: MM_M1_1_sample 2624


title: MM_M1_1_sample 2615


title: SM-GE8XK_S079_E1-50


title: SM-GE8XK_S087_E1-50


title: HS_M1_1_sample 602


title: HS_M1_2_sample 266


title: HS_M1_2_sample 263


title: MM_M1_1_sample 2619


title: SM-GE8XK_S083_E1-50


title: Chip91484_r16_c5_Treated

description: Chip91484_r16_c5_Treated_CAACCTAAGCA-AAGAGGCA


title: HS_M1_2_sample 264


title: SM-GE8XK_S081_E1-50


title: SM-GE8XK_S080_E1-50


title: HS_M1_2_sample 259


title: HS_M1_2_sample 260


title: MM_M1_1_sample 2613


title: MM_M1_1_sample 2612


title: SM-GE8XK_S074_E1-50


title: HS_M1_2_sample 258


title: SM-GE8XK_S075_E1-50


title: MM_M1_1_sample 2616


title: MM_M1_1_sample 2609


title: SM-GE8XK_S078_E1-50


title: HS_M1_2_sample 262


title: HS_M1_2_sample 255


title: SQ-80015_S88_E1-50

value: 57 days

value: ALM

value: RFP-positive

value: MOs

value: RV-dGdL-Cre


title: Chip91484_r16_c14_Untreated

description: Chip91484_r16_c14_Untreated_AGTAGGCGCTC-AAGAGGCA


title: HS_M1_2_sample 254

value: brain


title: SQ-80015_S87_E1-50

value: M


title: SM-GE8XK_S077_E1-50


title: MM_M1_1_sample 2608


title: Chip91484_r14_c57_Treated

description: Chip91484_r14_c57_Treated_AGAACGGCTAT-AAGAGGCA


title: HS_M1_2_sample 253

value: F


title: SQ-80015_S86_E1-50


title: Chip91484_r15_c58_Treated

description: Chip91484_r15_c58_Treated_AGCAACCGACG-AAGAGGCA


title: Chip91484_r15_c30_Treated

description: Chip91484_r15_c30_Treated_AGAAGACGGTT-AAGAGGCA


title: MM_M1_1_sample 2614


title: SQ-80015_S85_E1-50


title: Chip91484_r15_c69_Untreated

description: Chip91484_r15_c69_Untreated_ACGATATGAGT-AAGAGGCA


title: HS_M1_2_sample 257


title: Chip91484_r15_c27_Treated

description: Chip91484_r15_c27_Treated_AGAACTTCTAC-AAGAGGCA


title: HS_M1_2_sample 251


title: MM_M1_1_sample 2606


title: MM_M1_1_sample 2605


title: MM_M1_1_sample 2611


title: SM-GE8XK_S073_E1-50


title: Chip91484_r14_c44_Untreated

description: Chip91484_r14_c44_Untreated_ACGAGCTTCGC-AAGAGGCA


title: Chip91484_r15_c21_Untreated

description: Chip91484_r15_c21_Untreated_ACGCAACCGCC-AAGAGGCA


title: Chip91484_r14_c7_Treated

description: Chip91484_r14_c7_Treated_AGAAGACTTAC-AAGAGGCA


title: MM_M1_1_sample 2610


title: HS_M1_2_sample 256


title: MM_M1_1_sample 2604


title: Chip91484_r14_c5_Treated

description: Chip91484_r14_c5_Treated_AGAAGAACTGG-AAGAGGCA


title: SQ-80015_S83_E1-50

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


title: Chip91484_r14_c11_Treated

description: Chip91484_r14_c11_Treated_AGAAGAAGACT-AAGAGGCA


title: SQ-80015_S84_E1-50


title: MM_M1_1_sample 2607


title: HS_M1_2_sample 252


title: MM_M1_1_sample 2603


title: Chip91484_r14_c30_Treated

description: Chip91484_r14_c30_Treated_AGACCAACGGC-AAGAGGCA


title: SM-GE8XK_S076_E1-50


title: HS_M1_2_sample 249


title: HS_M1_2_sample 247


title: Chip91484_r13_c60_Untreated

description: Chip91484_r13_c60_Untreated_ACCTCCGGTCA-AAGAGGCA


title: HS_M1_2_sample 248


title: MM_M1_1_sample 2602


title: SQ-80015_S80_E1-50


title: Chip91484_r14_c27_Treated

description: Chip91484_r14_c27_Treated_AGAATCAGATG-AAGAGGCA


title: SQ-80015_S78_E1-50


title: MM_M1_1_sample 2601


title: SQ-80015_S81_E1-50


title: HS_M1_2_sample 246


title: HS_M1_2_sample 250


title: HS_M1_2_sample 244


title: SQ-80015_S79_E1-50


title: Chip91484_r13_c52_Treated

description: Chip91484_r13_c52_Treated_AGAAGTCCTGA-AAGAGGCA


title: MM_M1_1_sample 2600


title: Chip91484_r13_c71_Untreated

description: Chip91484_r13_c71_Untreated_ACCTCCGCCGG-AAGAGGCA


title: SQ-80015_S82_E1-50


title: HS_M1_2_sample 245


title: Chip91484_r13_c43_Untreated

description: Chip91484_r13_c43_Untreated_ACCAACCGTAT-AAGAGGCA


title: Chip91484_r13_c44_Untreated

description: Chip91484_r13_c44_Untreated_ACCAACCTCTT-AAGAGGCA


title: MM_M1_1_sample 2599


title: MM_M1_1_sample 2596


title: Chip91484_r13_c22_Untreated

description: Chip91484_r13_c22_Untreated_ACGAACTGACG-AAGAGGCA


title: MM_M1_1_sample 2595


title: MM_M1_1_sample 2594


title: Chip91484_r12_c63_Untreated

description: Chip91484_r12_c63_Untreated_AAGAGGCATAC-AAGAGGCA


title: SQ-80015_S77_E1-50


title: HS_M1_2_sample 240


title: SQ-80015_S73_E1-50


title: Chip91484_r12_c58_Treated

description: Chip91484_r12_c58_Treated_AGAACCGGAGA-AAGAGGCA


title: HS_M1_2_sample 239


title: MM_M1_1_sample 2593


title: Chip91484_r13_c12_Untreated

description: Chip91484_r13_c12_Untreated_ACGAATTGATA-AAGAGGCA


title: HS_M1_2_sample 238


title: HS_M1_2_sample 243


title: SQ-80015_S76_E1-50


title: HS_M1_2_sample 241


title: HS_M1_2_sample 242


title: MM_M1_1_sample 2597


title: SQ-80015_S71_E1-50

value: 56 days

value: SSs


title: MM_M1_1_sample 2592


title: Chip91484_r13_c40_Untreated

description: Chip91484_r13_c40_Untreated_AATAACCTCGA-AAGAGGCA


title: HS_M1_2_sample 237


title: MM_M1_1_sample 2598


title: SQ-80015_S70_E1-50

value: left


title: SQ-80015_S74_E1-50


title: SQ-80015_S68_E1-50


title: SQ-80015_S72_E1-50


title: SQ-80015_S75_E1-50


title: SQ-80015_S65_E1-50


title: Chip91484_r12_c52_Treated

description: Chip91484_r12_c52_Treated_AGAACCGCTTC-AAGAGGCA


title: HS_M1_2_sample 236


title: MM_M1_1_sample 2589


title: MM_M1_1_sample 2588


title: HS_M1_2_sample 233


title: Chip91484_r12_c36_Untreated

description: Chip91484_r12_c36_Untreated_ACCTAAGAGCG-AAGAGGCA


title: Chip91484_r12_c34_Treated

description: Chip91484_r12_c34_Treated_AGAAGTCAATT-AAGAGGCA


title: MM_M1_1_sample 2590


title: MM_M1_1_sample 2591


title: SQ-80015_S67_E1-50

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


title: Chip91484_r12_c57_Treated

description: Chip91484_r12_c57_Treated_AGAACCGCAAG-AAGAGGCA


title: HS_M1_2_sample 234


title: Infected 12 hours In12h3

city: London

first: Michalis

last: Barkoulas

address: Sir Alexander Fleming Building, Imperial College RD

department: Faculty of Natural Sciences

country: United Kingdom

institute: Imperial College London

description: Infected 12 hours

data_processing:
Fastq.gz files were aligned to the most recent C.elegans transcriptome using Kallisto in a Linux terminal
Kalisto abundance files were converted and analysed using Sleuth in a R pipeline
Standard Sleuth protocols were used to calculate differential expression
Genome_build: WBcel235
Supplementary_files_format_and_content: Tab delimited abundance files for each sample

organism: Caenorhabditis elegans

source_name: whole animal C. elegans at Larval stage 2

growth_protocol: Populations of animals were synchronised by bleaching and grown for until L4 stage, exposed to the pathogen haptoglossa zoospora (Mba01) and post pathogen exposure for either 6 or 12 hours were then harvested and processed for RNA extraction

extract_protocol:
animals were washed using M9 buffer and total RNA was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA) and freeze fracturing. Illumina sequencing was performed by Imperial college London.
RNA libraries were prepared for sequencing using standard Illumina protocols on an Illumina HiSeq 2500  (150 PE reads)

treatment_protocol: Animals at L4 were exposed to infected animals for either 6 or 12 hours

tag: strain

tag: developmental stage

tag: treatment

value: exposed to Haptoglossa zoospora


title: HS_M1_2_sample 235


title: Chip91484_r12_c47_Untreated

description: Chip91484_r12_c47_Untreated_ACCGCATCCAA-AAGAGGCA

value: Invasive Ductal Carcinoma


title: SQ-80015_S64_E1-50


title: HS_M1_2_sample 229


title: Infected 12 hours In12h2

description: Infected 12 hours


title: MM_M1_1_sample 2587


title: HS_M1_2_sample 232


title: MM_M1_1_sample 2586


title: SQ-80015_S66_E1-50


title: HS_M1_2_sample 227


title: HS_M1_2_sample 228


title: Chip91484_r12_c30_Treated

description: Chip91484_r12_c30_Treated_AGAATAAGAGA-AAGAGGCA


title: MM_M1_1_sample 2582


title: SQ-80015_S63_E1-50


title: HS_M1_2_sample 226


title: SQ-80015_S60_E1-50


title: MM_M1_1_sample 2581


title: Infected 6 hours In6h2

description: Infected 6 hours


title: MM_M1_1_sample 2580


title: Control 12 hours C12h3

description: Control 12 hours

value: wild-type


title: SQ-80015_S56_E1-50


title: MM_M1_1_sample 2579


title: SQ-80015_S58_E1-50


title: MM_M1_1_sample 2583


title: SQ-80015_S55_E1-50


title: SQ-80015_S57_E1-50


title: HS_M1_2_sample 225


title: HS_M1_2_sample 231


title: SQ-80015_S62_E1-50


title: Infected 12 hours In12h1

description: Infected 12 hours


title: SQ-80015_S54_E1-50


title: Control 6 hours C6h3

description: Control 6 hours


title: SQ-80015_S59_E1-50


title: MM_M1_1_sample 2585


title: Infected 6 hours In6h1

description: Infected 6 hours


title: Chip91484_r12_c48_Treated

description: Chip91484_r12_c48_Treated_AGAACCTTGCG-AAGAGGCA


title: HS_M1_2_sample 230


title: MM_M1_1_sample 2584


title: HS_M1_2_sample 221


title: Control 12 hours C12h2

description: Control 12 hours


title: MM_M1_1_sample 2575


title: SQ-80015_S53_E1-50


title: MM_M1_1_sample 2578


title: MM_M1_1_sample 2574


title: MM_M1_1_sample 2576


title: HS_M1_2_sample 222


title: HS_M1_2_sample 219


title: Control 6 hours C6h2

description: Control 6 hours


title: MM_M1_1_sample 2571


title: HS_M1_2_sample 224


title: HS_M1_2_sample 223


title: HFMCC_50_MC

city: Dallas

first: Linda

middle: Anne

last: Gilmore

state: TX

address: 4600 HARRY HINES BLVD

department: Clinical Nutrition

institute: UT Southwestern Medical Center

description:
DES_Normalized_counts_mouse.txt
DES_Normalized_counts_human.txt

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, 3.5.2(2018-12-2), Rstudio V1.2.1511 and biomaRt V2.38.0
DESeq2  V1.22.2 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: mouse- GRCm38.84,human
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

organism:
Homo sapiens
Mus musculus

source_name: Tumor

growth_protocol: MDAMB231 (ATCC, Rockville, MD) were maintained per supplier instructions. During study week 9, 14 week old mice were injected  with 2.5×10^6 MDAMB231 cells in 200 μL of 50∶50 Matrigel/Collagen I subcutaneously at the base of the neck. Tumor volume was measured weekly by calipers.

extract_protocol:
Tumors were removed, placed in RNA later and stored at 4° C. Tissues were disrupted and homogenized using the MP FastPrep-24 5G and stored at -80° C. Total RNA was extracted from homogenate supernatant using the Qiagen miRNeasy Mini Kit (Cat#217004).
Lexogen Quant-Seq; indexed and pooled samples, 50bp forward read

treatment_protocol: Mice bearing tumors (>200 mm3) post implantation on the Lean diet were monitored as the diet control group and on the High Fat diet were randomized to one of 4 intervention groups: 1) High Fat diet plus Vehicle (weekly intraperitoneal injection of saline) 2) High Fat diet plus Chemotherapy (weekly intraperitoneal injection of doxorubicin and cyclophosphamide) 3) High Fat Moringa Concentrate diet 4) Hight Fat Moringa Concentrate diet plus Chemotherapy (weekly intraperitoneal injection of doxorubicin and cyclophosphamide).

tag: mouse strain

tag: injected cell line

value: human breast adenocarcinoma derived TNBC cells

tag: intervention/control group

value: High Fat Moringa Concentrate Chemotherapy


title: Infected 6 hours In6h3

description: Infected 6 hours


title: Control 6 hours C6h1

description: Control 6 hours


title: HFMCC_47_MC


title: SQ-80015_S49_E1-50


title: SQ-80015_S48_E1-50


title: HFMCC_52_MC


title: SQ-80015_S61_E1-50


title: MM_M1_1_sample 2573


title: HS_M1_2_sample 220


title: SQ-80015_S50_E1-50


title: SQ-80015_S46_E1-50


title: SQ-80015_S51_E1-50


title: SQ-80015_S47_E1-50


title: HS_M1_2_sample 214


title: HS_M1_2_sample 217


title: HFMCC_25_MC


title: MM_M1_1_sample 2570


title: HFMCC_43_MC


title: HFMCC_05_MC

value: High Fat Moringa Concentrate


title: HS_M1_2_sample 213


title: MM_M1_1_sample 2572


title: HFMC_48_MC


title: MM_M1_1_sample 2569


title: HS_M1_2_sample 218


title: SQ-80015_S45_E1-50


title: HS_M1_2_sample 212


title: HS_M1_2_sample 215


title: HFMC_42_MC

description:
Extract Protocol Modification:
Rneasy RNA cleanup (cat#74104)
DES_Normalized_counts_mouse.txt
DES_Normalized_counts_human.txt


title: HS_M1_2_sample 211


title: MM_M1_1_sample 2568


title: HFMC_59_MC


title: MM_M1_1_sample 2567


title: HS_M1_2_sample 216


title: SQ-80015_S44_E1-50


title: MM_M1_1_sample 2566


title: SQ-80015_S43_E1-50


title: MM_M1_1_sample 2564


title: HFMC_41_MC


title: SQ-80015_S40_E1-50


title: MM_M1_1_sample 2565


title: HFMC_06_MC


title: SQ-80015_S42_E1-50


title: HS_M1_2_sample 209


title: HS_M1_2_sample 210


title: HFC_67_MC

value: High Fat Chemotherapy


title: SQ-80015_S39_E1-50

value: ALM


title: MM_M1_1_sample 2561


title: MM_M1_1_sample 2563


title: HS_M1_2_sample 208


title: HS_M1_2_sample 207


title: MM_M1_1_sample 2560


title: MM_M1_1_sample 2562


title: HFC_34_MC


title: SQ-80015_S38_E1-50

value: RFP-positive


title: HFC_33_MC


title: SQ-80015_S35_E1-50


title: MM_M1_1_sample 2558


title: SQ-80015_S37_E1-50


title: HS_M1_2_sample 206


title: SQ-80015_S34_E1-50


title: MM_M1_1_sample 2557


title: HS_M1_2_sample 205


title: HFC_19_MC


title: HFC_30_MC


title: SQ-80015_S36_E1-50


title: HFV_70_MC

value: High Fat Vehicle


title: SQ-80015_S33_E1-50

value: RV-dGdL-Cre


title: MM_M1_1_sample 2559

value: brain


title: HS_M1_2_sample 203


title: MM_M1_1_sample 2556

value: M


title: HS_M1_2_sample 204

value: F


title: HFV_44_MC


title: HFV_31_MC


title: MM_M1_1_sample 2554


title: HS_M1_2_sample 201


title: SQ-80015_S32_E1-50

value: 56 days


title: SQ-80015_S31_E1-50

value: SSs


title: HS_M1_2_sample 199


title: MM_M1_1_sample 2553


title: SQ-80015_S30_E1-50

value: left


title: HS_M1_2_sample 198


title: L_54_MC

value: Lean


title: SQ-80015_S29_E1-50


title: L_21_MC


title: SQ-80015_S28_E1-50


title: HS_M1_2_sample 197


title: HS_M1_2_sample 202


title: MM_M1_1_sample 2555


title: HFV_17_MC


title: HS_M1_2_sample 196


title: L_03_MC


title: NC3

city: Guangzhou

first: Yu

last: Kuang

state: Guangdong

address: 58 Zhongshan 2nd Road, Yuexiu District

department: Rheumatology and Immunology

country: China

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

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: rheumatoid fibroblast-like synoviocytes

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes

value: treated with NC for 24 hours


title: HS_M1_2_sample 195


title: L_24_MC

value: human breast adenocarcinoma derived TNBC cells


title: SQ-80014_S96_E1-50

value: 57 days

value: MOs


title: MM_M1_1_sample 2551


title: MM_M1_1_sample 2548


title: NC2


title: HS_M1_2_sample 200


title: SQ-80015_S27_E1-50

value: ALM


title: MM_M1_1_sample 2550


title: NC1


title: MM_M1_1_sample 2549


title: HS_M1_2_sample 193


title: SQ-80014_S94_E1-50

value: RFP-positive


title: SQ-80015_S25_E1-50


title: SQ-80014_S93_E1-50


title: DMSO3

value: untreated


title: MM_M1_1_sample 2546


title: SQ-80014_S92_E1-50

value: RV-dGdL-Cre


title: MM_M1_1_sample 2544

value: brain


title: DMSO1


title: HS_M1_2_sample 191


title: HS_M1_2_sample 190


title: HS_M1_2_sample 194


title: MM_M1_1_sample 2543

value: M


title: SQ-80014_S95_E1-50


title: HS_M1_2_sample 192

value: F


title: SQ-80014_S90_E1-50

value: 56 days


title: Post_3

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Pre-processed ATAC-Seq reads were mapped against reference genome (GRCh38) with a pipeline that used bowtie as aligner, Piccard to mark duplicate alignments, and samtools to eliminate duplicates.
Bigwig files for visualizing were created with Deeptools and Wiggletools. Tracks were represented in IGV browser. Final aggregated figures were represented with custom python scripts available under request.
Supplementary_files_format_and_content: BW files of mapped fragments
Genome_build: GRCh38

source_name: Monocytes isolated from blood

extract_protocol:
50,000 monocytes from HC, acute and post-COVID-19 patients were isolated and cryopreserved in 10% DMSO + 90% SF (n = 3 for each condition). After rapidly unfrozen, cells were counted, lysed (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% TritonX-100 for 5 min at 4ºC and centrifuged at 800 x g. Supernatant was discarded and nuclei were resuspended in transposase reaction buffer with transposase5 (1 µl Tn5 / 10.000 cells) and incubated for 30 min at 37 ºC. Later, SDS at a final concentration of 0.1% was added to stop the reaction (30 min, 40°C) and DNA was isolated with KAPA Pure beads (SPRI beads). Briefly, lysates were incubated with SPRI beads (2x), placed on the magnet, washed twice with 70% ethanol, and air-dried. DNA was eluted with elution buffer (EB) and its concentration measured with Qubit kit (Invitrogen). For DNA library generation, qPCR with i5 and i7 primers (NEXTERA barcoding) was performed (98ºC 2´, 98ºC 20¨, 63ºC 30¨, 72 ºC 1´, 4ºC ∞; 14 cycles). Then, a size cut off was conducted. First, amplified DNA was incubated with 0.5x concentration of SPRI beads. Then, beads were discarded and supernatant was incubated with 1.8x concentration of SPRI beads. Beads were washed twice with 70% ethanol, eluted with EB, and measured with Qubit. Finally, Agilent HS Bionalyzer was performed to assess peak sizes and percentages.
Libraries were applied to an Illumina flow cell for cluster generation (PE Cluster Kit cBot) and sequence-by-synthesis paired reads of 50 and 91 base length using the SBS Kit (Illumina) were generated on the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. ATAC-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

tag: tissue/cell type

value: Monocytes isolated from blood

tag: infection

value: Post Infection


title: HS_M1_2_sample 189

tag: tissue


title: SQ-80014_S91_E1-50

value: left

value: SSs


title: MM_M1_1_sample 2545

tag: brain region


title: MM_M1_1_sample 2547

tag: gender


title: HS_M1_2_sample 188


title: SQ-80014_S89_E1-50

tag: age


title: DMSO2

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes


title: Post_1


title: Post_2


title: HS_M1_2_sample 187


title: HS_M1_2_sample 185


title: MM_M1_1_sample 2539


title: MM_M1_1_sample 2541


title: MM_M1_1_sample 2540


title: Control_2

value: Healthy


title: Control_3


title: MM_M1_1_sample 2552


title: MM_M1_1_sample 2542


title: MM_M1_1_sample 2537


title: Control_1


title: SQ-80014_S79_E1-50

value: 57 days

tag: region


title: Acute_3

value: Acute


title: MM_M1_1_sample 2538


title: SQ-80014_S80_E1-50

value: ALM

tag: roi

value: MOs


title: HS_M1_2_sample 184


title: MM_M1_1_sample 2535


title: HS_M1_2_sample 186


title: SQ-80014_S78_E1-50

value: RFP-positive

tag: batch


title: SQ-80014_S77_E1-50

value: RV-dGdL-Cre


title: SQ-80014_S76_E1-50


title: MM_M1_1_sample 2536

value: brain


title: Acute_2


title: HS_M1_2_sample 183


title: SQ-80014_S75_E1-50

value: M


title: MM_M1_1_sample 2534


title: Acute_1


title: OC_071

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

data_processing:
Trimmomatic was used for adapter trimming using TruSeq3-SE.fa  reference file. Reads were alligned to Hg19 reference genome using STAR. Picard tools were used for adding a read group.
SAMtools were used for .sam-to-.bam file conversion and data sorting per read name and chromosome.
A custom filterBamCigar.pl script [PMID: 30894694] was used for intron-spanning read selection, and finally HTSeq for read summarization.
Gencode GRCh37.p13 was used for annotation
Data normalization was performed using DESeq-2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2-normalized expression

source_name: Tumor educated platelets from blood

extract_protocol:
Blood collected in Gdańsk was processed within 48 hours upon collection, strictly according to thromboSeq protocol [PMID: 30894694]. Briefly, tubes were centrifuged to obtain platelet rich plasma (20 minutes, 120g), pelleted (20 minutes 360g) and carefully resuspended in RNAlater (Thermo Scientific). After overnight incubation at 4°C, platelets were stored at -80°C. Blood collected in Gdańsk was shipped to Cancer Center Amsterdam, VU University Medical Center for further processing. RNA was extracted with mirVana miRNA isolation kit (Ambion, Thermo Scientific). For RNA quality verification the RNA 6000 Picochip (Bioanalyzer 2100, Agilent) was used. Subsequently, SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech) was used for cDNA amplification. Next, cDNA was subjected to nucleic acid shearing by sonication (Covaris Inc) and then labeled with single index barcodes for Illumina sequencing using the Truseq Nano DNA Sample Prep Kit (Illumina). Labeled platelet cDNA library was measured with the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High quality samples were pooled and submitted for 100 bp Single-Read sequencing on the Illumina HiSeq 2500 and HiSeq 4000 platform.
100 bp single-end reads. Standard Illumina protocol

tag: group

value: Other

value: F

tag: Stage

value: IA

tag: description

value: borderline tumor

tag: libsize


title: SQ-80014_S73_E1-50

value: left


title: MM_M1_1_sample 2533


title: HS_M1_2_sample 181


title: SQ-80014_S74_E1-50


title: HS_M1_2_sample 179


title: HS_M1_2_sample 182


title: MM_M1_1_sample 2531


title: SQ-80014_S71_E1-50

value: 56 days

value: SSs


title: SQ-80014_S72_E1-50


title: SQ-80014_S70_E1-50


title: HS_M1_2_sample 177


title: OC_055


title: OC_092

value: After resection, before chemotherapy


title: HS_M1_2_sample 176


title: HS_M1_2_sample 178


title: SQ-80014_S69_E1-50


title: MM_M1_1_sample 2529


title: HS_M1_2_sample 180


title: SQ-80014_S68_E1-50


title: MM_M1_1_sample 2532


title: MM_M1_1_sample 2530


title: MM_M1_1_sample 2528


title: OC_003


title: HS_M1_2_sample 175


title: OC_026


title: SQ-80014_S66_E1-50


title: HS_M1_2_sample 173


title: SQ-80014_S67_E1-50


title: MM_M1_1_sample 2526


title: OC_043

value: Relapse

value: Ovarian cancer relapse


title: HS_M1_2_sample 174


title: OC_072


title: OC_062


title: SQ-80014_S64_E1-50


title: OC_009

value: OC

value: No data

value: serous adenocarcinoma


title: SQ-80014_S65_E1-50

value: ALM

value: RFP-positive


title: MM_M1_1_sample 2525

value: brain


title: HS_M1_2_sample 172


title: MM_M1_1_sample 2527

value: M


title: MM_M1_1_sample 2524


title: MM_M1_1_sample 2523


title: HS_M1_2_sample 170


title: HS_M1_2_sample 171


title: SQ-80014_S63_E1-50

value: RV-dGdL-Cre


title: HS_M1_2_sample 169

value: F


title: OC_122

value: Other


title: OC_104

value: Serrous ovarian cancer


title: OC_074

value: serous carcinoma


title: SQ-80014_S61_E1-50

value: 56 days

value: left


title: OC_070

value: IVB


title: HS_M1_2_sample 168


title: MM_M1_1_sample 2522


title: SQ-80014_S60_E1-50

value: SSs


title: EC_057


title: HS_M1_2_sample 166


title: OC_136

value: IIIC


title: SQ-80014_S59_E1-50


title: SQ-80014_S56_E1-50


title: MM_M1_1_sample 2520


title: SQ-80014_S57_E1-50


title: HS_M1_2_sample 167


title: OC_035

value: OC


title: MM_M1_1_sample 2518


title: HS_M1_2_sample 164


title: SQ-80014_S58_E1-50


title: MM_M1_1_sample 2521


title: MM_M1_1_sample 2517


title: HS_M1_2_sample 163


title: HS_M1_2_sample 162


title: OC_102


title: MM_M1_1_sample 2519


title: HS_M1_2_sample 161


title: HS_M1_2_sample 165


title: OC_018


title: MM_M1_1_sample 2512


title: HS_M1_2_sample 160


title: HS_M1_2_sample 158


title: HS_M1_2_sample 159


title: OC_002


title: SQ-80014_S50_E1-50


title: OC_015

value: serous cystadenocarcinoma


title: MM_M1_1_sample 2516


title: HS_M1_2_sample 157


title: OC_132

value: IIIB

value: serous adenocarcinoma


title: HS_M1_2_sample 156


title: SQ-80014_S48_E1-50

value: ALM

value: RFP-positive


title: HS_M1_2_sample 155

value: brain


title: OC_138

value: IIIA


title: OC_105

value: F


title: SQ-80014_S47_E1-50

value: M

value: RV-dGdL-Cre


title: MM_M1_1_sample 2515


title: OC_039


title: HS_M1_2_sample 154


title: SQ-80014_S46_E1-50


title: SQ-80014_S55_E1-50


title: SQ-80014_S54_E1-50


title: OC_052


title: SQ-80014_S52_E1-50


title: MM_M1_1_sample 2507


title: SQ-80014_S51_E1-50


title: SQ-80014_S45_E1-50


title: HS_M1_2_sample 153


title: SQ-80014_S53_E1-50


title: EC_011

value: IIC


title: MM_M1_1_sample 2509


title: SQ-80014_S43_E1-50

value: 56 days


title: MM_M1_1_sample 2513


title: HS_M1_2_sample 149


title: OC_016


title: OC_137


title: MM_M1_1_sample 2502


title: SQ-80014_S42_E1-50

value: left


title: OC_040

value: IIA


title: SQ-80014_S49_E1-50

value: SSs


title: MM_M1_1_sample 2514


title: MM_M1_1_sample 2504


title: MM_M1_1_sample 2511


title: OC_051

value: seromucinous adenocarcinoma


title: HS_M1_2_sample 150


title: MM_M1_1_sample 2508


title: SQ-80014_S41_E1-50


title: MM_M1_1_sample 2510


title: HS_M1_2_sample 151


title: HS_M1_2_sample 147


title: OC_131

value: OC

value: IC


title: OC_130


title: SQ-80014_S44_E1-50


title: SQ-80014_S39_E1-50


title: HS_M1_2_sample 152


title: MM_M1_1_sample 2503


title: OC_139

value: IIB


title: OC_113

value: clear cell adenocarcinoma


title: SQ-80014_S37_E1-50

value: ALM


title: MM_M1_1_sample 2498


title: OC_061

value: IA


title: OC_025


title: SQ-80014_S40_E1-50

value: RFP-positive


title: MM_M1_1_sample 2505

value: brain


title: HS_M1_2_sample 148

value: F


title: MM_M1_1_sample 2497

value: M


title: HS_M1_2_sample 144


title: MM_M1_1_sample 2506


title: MM_M1_1_sample 2501


title: SQ-80014_S35_E1-50

value: RV-dGdL-Cre


title: MM_M1_1_sample 2499


title: SQ-80014_S34_E1-50


title: OC_004

value: endometrioid adenocarcinoma


title: MM_M1_1_sample 2500


title: HS_M1_2_sample 145


title: SQ-80014_S36_E1-50

value: 56 days


title: SQ-80014_S33_E1-50

value: left


title: OC_047

value: CTRL

value: cyst


title: OC_028


title: HS_M1_2_sample 141


title: SQ-80014_S38_E1-50

value: SSs


title: OC_058


title: OC_010


title: MM_M1_1_sample 2496


title: HS_M1_2_sample 140


title: HS_M1_2_sample 143


title: HS_M1_2_sample 146


title: MM_M1_1_sample 2495


title: HS_M1_2_sample 139


title: HS_M1_2_sample 142


title: SQ-80012_S80_E1-50

value: 54 days


title: MM_M1_1_sample 2494


title: MM_M1_1_sample 2492


title: MM_M1_1_sample 2493


title: OC_036

value: myoma uteri


title: SQ-80012_S78_E1-50


title: SQ-80012_S79_E1-50


title: HS_M1_2_sample 138


title: OC_045


title: SQ-80012_S77_E1-50


title: HS_M1_2_sample 137


title: MM_M1_1_sample 2490


title: OC_021


title: SQ-80012_S75_E1-50


title: HS_M1_2_sample 134


title: HS_M1_2_sample 136


title: MM_M1_1_sample 2487


title: MM_M1_1_sample 2488


title: OC_049

value: Brenner tumor


title: MM_M1_1_sample 2489


title: OC_031


title: SQ-80012_S74_E1-50


title: SQ-80012_S76_E1-50


title: MM_M1_1_sample 2491


title: OC_014


title: HS_M1_2_sample 132


title: MM_M1_1_sample 2486


title: SQ-80012_S64_E1-50


title: MM_M1_1_sample 2485


title: OC_048


title: SQ-80012_S63_E1-50


title: HS_M1_2_sample 135


title: SQ-80012_S73_E1-50


title: HS_M1_2_sample 133


title: SQ-80012_S62_E1-50


title: OC_022


title: HS_M1_2_sample 131


title: OC_023


title: OC_020


title: HS_M1_2_sample 128


title: SQ-80012_S60_E1-50


title: OC_060


title: OC_144

value: pseudomyxoma peritonei


title: MM_M1_1_sample 2484


title: MM_M1_1_sample 2481


title: MM_M1_1_sample 2483


title: HS_M1_2_sample 127


title: MM_M1_1_sample 2482


title: HS_M1_2_sample 130


title: MM_M1_1_sample 2480


title: SQ-80012_S61_E1-50

value: ALM


title: OC_124

value: Endometriosis


title: HS_M1_2_sample 129


title: SQ-80012_S58_E1-50

value: RFP-positive


title: HS_M1_2_sample 126

value: brain


title: SQ-80012_S57_E1-50


title: MM_M1_1_sample 2477


title: OC_046

value: F

value: mature teratoma


title: EC_125

value: complex atypical endometrial hyperplasia


title: HS_M1_2_sample 123


title: HS_M1_2_sample 125


title: MM_M1_1_sample 2479

value: M


title: SQ-80012_S56_E1-50

value: RV-dGdL-Cre


title: OC_108

value: normal tissue


title: EC_107

value: CTRL

value: endometrial hyperplastic polyp


title: HS_M1_2_sample 124


title: MM_M1_1_sample 2478


title: MM_M1_1_sample 2474


title: MM_M1_1_sample 2476


title: OC_101


title: SQ-80012_S51_E1-50

value: left

value: SSs


title: SQ-80012_S54_E1-50

value: 54 days


title: MM_M1_1_sample 2475


title: SQ-80012_S55_E1-50


title: OC_098


title: SQ-80012_S52_E1-50


title: OC_094


title: MM_M1_1_sample 2473


title: HS_M1_2_sample 122


title: SQ-80012_S53_E1-50


title: MM_M1_1_sample 2472


title: SQ-80012_S49_E1-50


title: HS_M1_2_sample 118


title: OC_096

value: myoma uteri


title: OC_093


title: MM_M1_1_sample 2471


title: EC_067

value: adenomyosis


title: SQ-80012_S48_E1-50

value: ALM


title: HS_M1_2_sample 117


title: HS_M1_2_sample 121


title: MM_M1_1_sample 2470


title: HS_M1_2_sample 120


title: SQ-80012_S47_E1-50


title: HS_M1_2_sample 116


title: EC_068


title: EC_069


title: EC_076


title: SQ-80012_S46_E1-50


title: HS_M1_2_sample 119


title: HS_M1_2_sample 115


title: MM_M1_1_sample 2468


title: MM_M1_1_sample 2467


title: HS_M1_2_sample 114


title: SQ-80012_S50_E1-50


title: SQ-80012_S44_E1-50


title: OC_073

value: polypus adenoleiomyomatosus


title: HS_M1_2_sample 112


title: HS_M1_2_sample 113


title: MM_M1_1_sample 2465


title: SQ-80012_S43_E1-50

value: RFP-positive


title: SQ-80012_S42_E1-50


title: HS_M1_2_sample 111

value: brain


title: MM_M1_1_sample 2469


title: HS_M1_2_sample 110

value: F


title: MM_M1_1_sample 2463


title: SQ-80012_S41_E1-50


title: Rep_2__SUM149PT__TSA__5000_Cells

data_processing:
CellRanger v1.3.1 was used to demultiplex and prcoess to gene counts per cell using default settings
Genome_build: GRCh38
Supplementary_files_format_and_content: 3 filtered_gene_bs_matricies files per sample

extract_protocol:
Qiagen Rneasy PLUS Micro
10X Genomics recommended library construction protocol

tag: cell line

tag: cell type

value: Invasive Ductal Carcinoma


title: MM_M1_1_sample 2462


title: SQ-80012_S45_E1-50


title: Rep_2__SUM149PT__TSA__2000_Cells


title: MM_M1_1_sample 2461


title: Rep_2__SUM149PT__TSA__10000_Cells


title: Rep_2__SUM149PT__DMSO__2000_Cells


title: HS_M1_2_sample 109


title: MM_M1_1_sample 2466


title: Rep_2__SUM149PT__TSA__1000_Cells


title: Rep_2__SUM149PT__DMSO__5000_Cells


title: EC_064


title: HS_M1_2_sample 107


title: MM_M1_1_sample 2460


title: SQ-80010_S47_E1-50


title: SQ-80010_S46_E1-50


title: SQ-80010_S45_E1-50


title: Rep_2__SUM149PT__DMSO__10000_Cells


title: MM_M1_1_sample 2464


title: HS_M1_2_sample 105


title: SQ-80010_S44_E1-50


title: MM_M1_1_sample 2458


title: MM_M1_1_sample 2459


title: SQ-80010_S48_E1-50


title: HS_M1_2_sample 104


title: Rep_2__SUM149PT__DMSO__1000_Cells


title: MM_M1_1_sample 2457


title: Rep_1__SUM149PT__TSA__5000_Cells


title: HS_M1_2_sample 108


title: SQ-80010_S43_E1-50


title: HS_M1_2_sample 103


title: HS_M1_2_sample 106


title: SQ-80010_S42_E1-50


title: Rep_1__SUM149PT__TSA__2000_Cells


title: MM_M1_1_sample 2456


title: Rep_1__SUM149PT__TSA__10000_Cells


title: SQ-80010_S40_E1-50


title: HS_M1_2_sample 102


title: MM_M1_1_sample 2455


title: MM_M1_1_sample 2454


title: HS_M1_2_sample 101


title: MM_M1_1_sample 2453


title: Rep_1__SUM149PT__TSA__1000_Cells


title: HS_M1_2_sample 100


title: SQ-80010_S36_E1-50


title: HS_M1_2_sample 98


title: SQ-80010_S37_E1-50


title: HS_M1_2_sample 99


title: SQ-80010_S39_E1-50


title: Rep_1__SUM149PT__DMSO__5000_Cells


title: SQ-80010_S38_E1-50


title: MM_M1_1_sample 2451


title: HS_M1_2_sample 97


title: MM_M1_1_sample 2452


title: SQ-80010_S35_E1-50


title: MM_M1_1_sample 2450


title: Rep_1__SUM149PT__DMSO__10000_Cells


title: Rep_1__SUM149PT__DMSO__1000_Cells


title: HS_M1_2_sample 96


title: SQ-80010_S34_E1-50


title: MM_M1_1_sample 2449


title: HS_M1_2_sample 95


title: MM_M1_1_sample 2448


title: HS_M1_2_sample 94


title: MIL3

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

country: South Korea

institute: KAIST

data_processing:
Sample libraries were sequenced by HiSeq 4000 with paired end reads
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 using STAR 2.7.9a
Read count extraction and nomalization were performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: CSV file including normalized read counts for each samples

source_name: Mouse lung

growth_protocol: Control group was uninfected and MCMV-infected group was infected with MCMV 1x10^6 pfu i.p. 30 days after infection, 0.5 million TC-1 cells diluted in 100ul of PBS were injected through mouse tail vein. After 7 days of injection, 2ug of IL-15 were injected to intra-peritoneal twice with interval of 2 days. At day 21, mouse lung was harvested and dissociated into single cells with mechanical and enzymatic digestion. CD45- cells were seperated from those single cells by MACS cell sorter with CD45 negative isolation.

extract_protocol:
RNA was extracted from cells with TRIzol RNA isolation reagents.
Poly(A) RNA Selection + TruSeq Stranded mRNA Library Prep assay

treatment_protocol: 1 x 10^6 PFU of MCMV / 2ug of IL-15 (twice)

tag: cell line origin

value: Mouse lung CD45- cells

tag: treatment


title: SQ-80010_S32_E1-50

value: M


title: MIL4


title: MM_M1_1_sample 2447


title: Rep_1__SUM149PT__DMSO__2000_Cells


title: MIL2


title: SQ-80010_S31_E1-50

value: RV-dGdL-Cre


title: HS_M1_2_sample 93


title: SQ-80010_S30_E1-50


title: MM_M1_1_sample 2446


title: MIL1


title: HS_M1_2_sample 92


title: SQ-80010_S29_E1-50


title: CIL3


title: HS_M1_2_sample 91


title: MM_M1_1_sample 2444


title: SQ-80010_S28_E1-50


title: CIL2


title: HS_M1_2_sample 90


title: SQ-80010_S33_E1-50


title: MM_M1_1_sample 2443


title: CIL1


title: HS_M1_2_sample 89


title: SQ-80010_S27_E1-50


title: MM_M1_1_sample 2442


title: MP4

value: MCMV-infected/PBS-treated


title: HS_M1_2_sample 88


title: SQ-80010_S26_E1-50


title: HS_M1_2_sample 87


title: MP3


title: SQ-80010_S25_E1-50


title: HS_M1_2_sample 86


title: MP2


title: MM_M1_1_sample 2445


title: MM_M1_1_sample 2441


title: MM_M1_1_sample 2440


title: SQ-80010_S24_E1-50


title: MM_M1_1_sample 2439


title: HS_M1_2_sample 85


title: MM_M1_1_sample 2438


title: MP1


title: CP3

value: Uninfected/PBS-treated


title: CP1


title: SQ-80010_S22_E1-50


title: CP2


title: HS_M1_2_sample 84


title: MM_M1_1_sample 2436


title: SQ-80010_S23_E1-50


title: HS_M1_2_sample 82


title: SQ-80010_S21_E1-50


title: RAW_WT_4

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were trimmed using Trimmomatic version 0.36.
Read alignment done by Hisat2 version 2.3.4.3
Count data were generated by means of the HTSeq method.
Genome_build: GRCm3
Supplementary_files_format_and_content: counts

source_name: macrophages

growth_protocol: RAW264.7 cells (TIB-71; ATCC) were cultured in IMDM medium supplemented with 10% FCS, 2 mM  L-glutamine, 100 units/mL penicillin and 500 μg/mL streptomycin. Cells were maintained in a humidified incubator at 37 °C, 5% CO2 and 95% air.

extract_protocol:
Total RNA was isolated using the Nucleospin RNA Isolation kit. RNA quality was assessed by bioanalysis (Agilent); samples with RNA integrity number > 7 were included for RNA sequencing.
Libraries were prepared from 100-200 ng total RNA using KAPA RNA Hyperprep with RiboErase (Roche) kits.

treatment_protocol: Cells were used without any stimulation.

tag: donorid

tag: experiment

tag: genotype

value: CEBPD wild type


title: MM_M1_1_sample 2435

tag: tissue

tag: brain region


title: SQ-80010_S20_E1-50

tag: gender

tag: age

value: left


title: SQ-80010_S19_E1-50

tag: region

tag: roi

value: SSs


title: HS_M1_2_sample 81


title: HS_M1_2_sample 83


title: RAW_WT_2


title: HS_M1_2_sample 79


title: MM_M1_1_sample 2433


title: MM_M1_1_sample 2434


title: MM_M1_1_sample 2432


title: RAW_TAD_2

value: CEBPD TAD mutant


title: SQ-80010_S18_E1-50

value: 54 days

tag: batch


title: MM_M1_1_sample 2437


title: HS_M1_2_sample 77


title: RAW_WT_1


title: RAW_TAD_1


title: SQ-80006_S93_E1-50

value: 59 days

value: PERI


title: SQ-80010_S17_E1-50

value: ALM


title: HS_M1_2_sample 75


title: MM_M1_1_sample 2428


title: HS_M1_2_sample 73


title: MM_M1_1_sample 2427


title: HS_M1_2_sample 72


title: RAW_KO_5

value: CEBPD KO


title: HS_M1_2_sample 80

value: brain


title: SQ-80008_S89_E1-50

value: 55 days

value: RFP-positive


title: HS_M1_2_sample 78

value: F


title: SQ-80006_S94_E1-50


title: SQ-80006_S89_E1-50


title: SQ-80006_S90_E1-50


title: SQ-80006_S92_E1-50


title: Vehicle-treated knockout 3

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type and knock-out mouse pups in one cage.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Memantine hydrochloride (Sigma, M9292; 20 mg/kg) was orally administered to mice with a pipette, and 0.1% saccharin without memantine was used as vehicle. The treatment was given twice-a-day for two weeks (P7–21).

tag: strain

value: whole brain

tag: Sex

value: male


title: Vehicle-treated knockout 2


title: SQ-80006_S91_E1-50


title: HS_M1_2_sample 70


title: RAW_TAD_5


title: MM_M1_1_sample 2430

value: M


title: RAW_KO_1


title: MM_M1_1_sample 2423


title: RAW_KO_2


title: SQ-80006_S85_E1-50

value: RV-dGdL-Cre


title: MM_M1_1_sample 2426


title: SQ-80006_S88_E1-50


title: MM_M1_1_sample 2422


title: MM_M1_1_sample 2431


title: HS_M1_2_sample 67


title: MM_M1_1_sample 2420


title: Vehicle-treated wildtype 1


title: HS_M1_2_sample 66


title: SQ-80006_S83_E1-50


title: Memantine-treated knockout 3


title: HS_M1_2_sample 65


title: HS_M1_2_sample 76


title: MM_M1_1_sample 2425


title: MM_M1_1_sample 2429


title: SQ-80006_S82_E1-50


title: HS_M1_2_sample 69


title: SQ-80006_S87_E1-50


title: SQ-80006_S81_E1-50


title: Vehicle-treated wildtype 2


title: MM_M1_1_sample 2424


title: Memantine-treated knockout 2


title: HS_M1_2_sample 61


title: Memantine-treated wildtype 1


title: Memantine-treated wildtype 3


title: HS_M1_2_sample 63


title: MM_M1_1_sample 2415


title: HS_M1_2_sample 62


title: SQ-80006_S78_E1-50


title: SQ-80006_S77_E1-50


title: SQ-80006_S76_E1-50


title: HS_M1_2_sample 59


title: Memantine-treated wildtype 2


title: MM_M1_1_sample 2413


title: SQ-80006_S80_E1-50


title: TB-2

city: Clermont-Ferrand

first: David

middle: H

last: VOLLE

address: 28 place Henri Dunant

country: France

institute: INSERM

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto the mm10 assembly of the mouse genome using TopHat v2.0.1027 and the BoWtie2 v2.1.0 aligner28. Only uniquely aligned reads were retained for further analysis. Quantification of gene expression was performed using HTSeq v0.5.4p329 using gene annotations from Ensembl release 77.
Read counts were normalized across libraries with the method proposed by Anders and Huber30. Comparison between groups was performed using the method proposed by 31 implemented in the DESeq2 Bioconductor library (DESeq2 v1.0.19). Resulting p values were adjusted for multiple testing using the method of Benjamini and Hochberg32
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized counts

source_name: GC1spg siTGR5 Busulfan

extract_protocol:
RNA were extracted from GC1 cells using Nucleospin RNA L (Macherey Nagel)
RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: GC1spg cell line

tag: genotype/variation

tag: agent

value: Busulfan


title: HS_M1_2_sample 60


title: MM_M1_1_sample 2414


title: TD-1

source_name: GC1spg siTGR5 DMSO

tag: cell line

value: DMSO


title: HS_M1_2_sample 58


title: SQ-80006_S74_E1-50

value: left

value: SSs


title: SQ-80006_S75_E1-50


title: TB-1


title: HS_M1_2_sample 57


title: TD-3


title: HS_M1_2_sample 55


title: MM_M1_1_sample 2410


title: SQ-80006_S73_E1-50


title: HS_M1_2_sample 56


title: TD-2


title: MM_M1_1_sample 2416


title: MM_M1_1_sample 2409


title: SQ-80006_S72_E1-50

value: 58 days

value: MOp


title: GB-3

source_name: GC1spg sigfp busulfan

value: sigfp


title: HS_M1_2_sample 54


title: SQ-80006_S71_E1-50

value: ALM


title: HS_M1_2_sample 53

value: brain


title: MM_M1_1_sample 2408


title: SQ-80006_S70_E1-50


title: MM_M1_1_sample 2407


title: GB-2


title: HS_M1_2_sample 68


title: HS_M1_2_sample 52


title: HS_M1_2_sample 71


title: SQ-80006_S69_E1-50


title: MM_M1_1_sample 2406


title: SQ-80006_S84_E1-50

value: 55 days


title: GD-3

source_name: GC1spg sigfp DMSO


title: Memantine-treated knockout 1


title: SQ-80006_S68_E1-50

value: RFP-positive


title: HS_M1_2_sample 51

value: F


title: SQ-80006_S67_E1-50


title: MM_M1_1_sample 2405


title: SQ-80006_S66_E1-50


title: SQ-80006_S65_E1-50


title: MM_M1_1_sample 2402


title: TD-4


title: TB-3


title: SQ-80006_S64_E1-50


title: MM_M1_1_sample 2404


title: MM_M1_1_sample 2401


title: HS_M1_2_sample 50


title: HS_M1_2_sample 46


title: HS_M1_2_sample 49


title: MM_M1_1_sample 2403


title: TD-5


title: MM_M1_1_sample 2421


title: HS_M1_2_sample 48


title: HS_M1_2_sample 47


title: TB-4


title: SQ-80006_S61_E1-50


title: GB-4


title: SQ-80006_S60_E1-50


title: GB-1


title: SQ-80006_S62_E1-50


title: MM_M1_1_sample 2400


title: SQ-80006_S79_E1-50


title: MM_M1_1_sample 2397


title: HS_M1_2_sample 45


title: HS_M1_2_sample 42


title: SQ-80006_S56_E1-50


title: SQ-80006_S57_E1-50


title: GD-5


title: HS_M1_2_sample 44


title: HS_M1_2_sample 41


title: MM_M1_1_sample 2396


title: SQ-80006_S53_E1-50


title: MM_M1_1_sample 2398


title: HS_M1_2_sample 40


title: Control (Emx-Cre) rep3

city: Durham

first: Wei

last: Yang

state: NC

address: 303 Research Drive

department: Anesthesiology

institute: Duke University Medical Center

data_processing:
TrimGalore toolkit which employed Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads . Only reads that were 20 nt or longer after trimming were reserved for further analysis.
STAR RNA-Seq for alignment. Reads were reserved for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool. Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression were performed using the DESeq2 Bioconductor package with the R statistical programming environment .
Genome_build: GRCm38v68 version of the mouse genome
Supplementary_files_format_and_content: Excel file with normalized expression values.

source_name: hippocampus

extract_protocol:
Hippocampus were removed and snap frozen in liquid nitrogen. RNA was prepared using Trizol reagent (Invitrogen), treated with DNase, and purified with RNA Cleanup kit (Qiagen). The KAPA Stranded mRNA-Seq Kit (KapaBioSystems) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

value: 2-month old


title: MM_M1_1_sample 2394

value: M


title: HS_M1_2_sample 43


title: SQ-80006_S58_E1-50


title: GD-1


title: MM_M1_1_sample 2399


title: GD-2


title: HS_M1_2_sample 38


title: SQ-80006_S52_E1-50


title: MM_M1_1_sample 2419


title: sATF6-KI rep3


title: SQ-80006_S51_E1-50


title: HS_M1_2_sample 37


title: Vehicle-treated wildtype 3

value: whole brain

value: male


title: MM_M1_1_sample 2391


title: sATF6-KI rep2


title: MM_M1_1_sample 2395


title: sATF6-KI rep1


title: SQ-80006_S54_E1-50


title: HS_M1_2_sample 35


title: MM_M1_1_sample 2389


title: HS_M1_2_sample 39


title: HS_M1_2_sample 34


title: HS_M1_2_sample 33


title: MM_M1_1_sample 2393


title: MM_M1_1_sample 2392


title: Vehicle-treated knockout 1


title: Control (Emx-Cre) rep2


title: MM_M1_1_sample 2412


title: SQ-80006_S46_E1-50


title: Control (Emx-Cre) rep1


title: HS_M1_2_sample 36


title: MH-Ctrl-2

type: RNA

city: kunming

first: shubai

last: Liu

state: yunnan

address: 132 lanhei road,

institute: kunming institute of botany, chinese academic of science

description: The whole transcriptome Gene expression profile data

hyb_protocol: GeneChips were scanned using the  Affymetrix GeneAtlas hyberzation station according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the  Affymetrix GeneAtlas Fluidic station according to the manufacturer's instructions.

data_processing: The data were analyzed with Affymetrix Expression Console  using Robust Mutichip Average (RMA) preprocessing followed by “per chip” normalization across all samples. All Affymetrix control genes were removed from the expression data and the remaining Affymetrix probe clusters were imported into the Affymetrix Power Tools software (APT package).

label: biotin

source_name: Control

label_protocol: The quality and quantity of the RNA were tested using Bioanalyzer (Agilent Technologies, Santa Clara, CA). 4.5 μg of RNA from each sample was used for target labeling by a two-round amplification protocol (Expression Analysis Technical Manual, 20012, Affymetrix).

growth_protocol: The human macrophages derived by PMA induced were cultured as descripted in the manuscipt.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: the cell lines  were treated with control and HMEOs  as descripted in the manuscript.

tag: cell type

value: macrophages

value: control


title: SQ-80006_S50_E1-50

value: left


title: MM_M1_1_sample 2390


title: MH-HMEO2

source_name: HMEO treated

tag: treatment

value: human milk exosomes extracted oligosaccharides


title: MM_M1_1_sample 2386


title: MM_M1_1_sample 2385


title: MM_M1_1_sample 2388


title: SQ-80006_S47_E1-50

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

value: 58 days


title: HS_M1_2_sample 29


title: MM_M1_1_sample 2383


title: Chip91484_r12_c23_Untreated

description: Chip91484_r12_c23_Untreated_AAGCAACGAGT-AAGAGGCA

source_name: 40 year old female

value: Invasive Ductal Carcinoma


title: MH-Ctrl-1


title: MM_M1_1_sample 2387


title: HS_M1_2_sample 28


title: MM_M1_1_sample 2418


title: Chip91484_r12_c22_Untreated

description: Chip91484_r12_c22_Untreated_AAGATAACCGT-AAGAGGCA


title: Chip91484_r12_c28_Treated

description: Chip91484_r12_c28_Treated_AGAAGTATGAC-AAGAGGCA


title: MM_M1_1_sample 2417


title: SQ-80006_S49_E1-50

value: MOp


title: HS_M1_2_sample 31


title: HS_M1_2_sample 32


title: MM_M1_1_sample 2381


title: Chip91484_r12_c1_Treated

description: Chip91484_r12_c1_Treated_AGAACGCCATC-AAGAGGCA


title: Chip91484_r12_c19_Untreated

description: Chip91484_r12_c19_Untreated_AAGTAACCTCT-AAGAGGCA


title: SQ-80006_S39_E1-50

value: ALM

value: MOs


title: Chip91484_r12_c27_Treated

description: Chip91484_r12_c27_Treated_AGAAGTAACTG-AAGAGGCA


title: MH-HMEO1


title: HS_M1_2_sample 25

value: brain


title: MM_M1_1_sample 2382


title: HS_M1_2_sample 30


title: HS_M1_2_sample 24


title: HS_M1_2_sample 64


title: SQ-80006_S38_E1-50

value: 55 days

value: RFP-positive


title: Chip91484_r12_c25_Treated

description: Chip91484_r12_c25_Treated_AGAATACGACC-AAGAGGCA


title: MM_M1_1_sample 2378


title: MM_M1_1_sample 2380


title: SQ-80006_S44_E1-50


title: SQ-80006_S42_E1-50


title: SQ-80006_S43_E1-50


title: SQ-80006_S45_E1-50


title: MM_M1_1_sample 2384


title: SQ-80006_S37_E1-50


title: HS_M1_2_sample 27

value: F


title: Chip91484_r11_c52_Treated

description: Chip91484_r11_c52_Treated_AGAAGATCGAG-AAGAGGCA


title: HS_M1_2_sample 22


title: HS_M1_2_sample 26


title: SQ-80006_S40_E1-50


title: HS_M1_2_sample 21


title: SQ-80004_S94_E1-50


title: MM_M1_1_sample 2379


title: Chip91484_r11_c58_Treated

description: Chip91484_r11_c58_Treated_AGAAGATGAGG-AAGAGGCA


title: SQ-80006_S41_E1-50

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


title: Chip91484_r11_c44_Untreated

description: Chip91484_r11_c44_Untreated_AAGAGCTTACG-AAGAGGCA


title: SQ-80006_S48_E1-50


title: MM_M1_1_sample 2411


title: SQ-80004_S91_E1-50


title: MM_M1_1_sample 2373


title: HS_M1_2_sample 23


title: SQ-80004_S96_E1-50


title: MM_M1_1_sample 2377


title: MM_M1_1_sample 2371


title: Chip91484_r11_c57_Treated

description: Chip91484_r11_c57_Treated_AGAAGATAATC-AAGAGGCA


title: Chip91484_r11_c50_Treated

description: Chip91484_r11_c50_Treated_AGAAGGAGAGC-AAGAGGCA


title: SQ-80004_S93_E1-50


title: Chip91484_r11_c51_Treated

description: Chip91484_r11_c51_Treated_AGAAGATAGCA-AAGAGGCA


title: MM_M1_1_sample 2376


title: MM_M1_1_sample 2374


title: MM_M1_1_sample 2375


title: HS_M1_2_sample 18


title: MM_M1_1_sample 2369


title: SQ-80004_S92_E1-50


title: Chip91484_r10_c71_Untreated

description: Chip91484_r10_c71_Untreated_AACTAGTTCTC-AAGAGGCA


title: HS_M1_2_sample 19


title: SQ-80004_S87_E1-50


title: MM_M1_1_sample 2367


title: HS_M1_2_sample 13


title: GD-4

value: GC1spg cell line

value: sigfp

value: DMSO


title: Chip91484_r11_c22_Untreated

description: Chip91484_r11_c22_Untreated_ACCAGAACCGC-AAGAGGCA


title: MM_M1_1_sample 2366

value: M


title: Chip91484_r11_c32_Treated

description: Chip91484_r11_c32_Treated_AGAACCGACGT-AAGAGGCA


title: MM_M1_1_sample 2368


title: Chip91484_r11_c35_Treated

description: Chip91484_r11_c35_Treated_AGAACCAACCG-AAGAGGCA


title: HS_M1_2_sample 20


title: SQ-80004_S89_E1-50


title: SQ-80004_S83_E1-50


title: SQ-80004_S90_E1-50


title: HS_M1_2_sample 10


title: MM_M1_1_sample 2365


title: SQ-80004_S81_E1-50


title: HS_M1_2_sample 16


title: MM_M1_1_sample 2370


title: HS_M1_2_sample 17


title: HS_M1_2_sample 8


title: HS_M1_2_sample 15


title: MM_M1_1_sample 2372


title: HS_M1_2_sample 14


title: Chip91484_r11_c18_Untreated

description: Chip91484_r11_c18_Untreated_ACCATAATACT-AAGAGGCA


title: SQ-80004_S88_E1-50


title: Chip91484_r11_c14_Untreated

description: Chip91484_r11_c14_Untreated_ACCATGATTCG-AAGAGGCA


title: Chip91484_r10_c45_Untreated

description: Chip91484_r10_c45_Untreated_AACTGATCGTA-AAGAGGCA


title: HS_M1_2_sample 7


title: Chip91484_r10_c58_Treated

description: Chip91484_r10_c58_Treated_AAGAAGGAACC-AAGAGGCA


title: Chip91484_r10_c59_Treated

description: Chip91484_r10_c59_Treated_AAGAAGTAGCA-AAGAGGCA


title: HS_M1_2_sample 12


title: SQ-80004_S86_E1-50


title: Chip91484_r10_c42_Untreated

description: Chip91484_r10_c42_Untreated_AACTGCTCTAA-AAGAGGCA


title: HS_M1_2_sample 11


title: HS_M1_2_sample 9


title: Chip91484_r10_c55_Treated

description: Chip91484_r10_c55_Treated_AAGAATAGGAA-AAGAGGCA


title: HS_M1_2_sample 5


title: MM_M1_1_sample 2364


title: MM_M1_1_sample 2363


title: SQ-80004_S85_E1-50


title: SQ-80004_S80_E1-50


title: MM_M1_1_sample 2359


title: Chip91484_r10_c68_Untreated

description: Chip91484_r10_c68_Untreated_AACTATCTGGA-AAGAGGCA


title: MM_M1_1_sample 2358


title: HS_M1_2_sample 4


title: MM_M1_1_sample 2362


title: Chip91484_r10_c44_Untreated

description: Chip91484_r10_c44_Untreated_AACTGGCAGGT-AAGAGGCA


title: SQ-80004_S79_E1-50

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


title: Chip91484_r10_c46_Untreated

description: Chip91484_r10_c46_Untreated_AACTGCATCCG-AAGAGGCA


title: SQ-80004_S77_E1-50


title: HS_M1_2_sample 6


title: SQ-80004_S73_E1-50


title: HS_M1_2_sample 2


title: MM_M1_1_sample 2361


title: SQ-80004_S74_E1-50


title: Chip91484_r10_c32_Treated

description: Chip91484_r10_c32_Treated_AAGAGATAAGT-AAGAGGCA


title: Chip91484_r10_c4_Treated

description: Chip91484_r10_c4_Treated_ACTCGTCTTGC-AAGAGGCA


title: SQ-80004_S78_E1-50


title: SQ-80004_S71_E1-50


title: MM_M1_1_sample 2360


title: SQ-80004_S75_E1-50


title: Chip91484_r10_c26_Treated

description: Chip91484_r10_c26_Treated_AAGAGATACCA-AAGAGGCA


title: HS_M1_2_sample 0


title: MM_M1_1_sample 2357


title: MM_M1_1_sample 2353


title: HS_M1_1_sample 3059

value: Brain


title: Chip91484_r10_c21_Untreated

description: Chip91484_r10_c21_Untreated_AAGAGATAGTC-AAGAGGCA


title: SQ-80004_S72_E1-50


title: HS_M1_2_sample 3


title: Chip91484_r10_c20_Untreated

description: Chip91484_r10_c20_Untreated_AAGAGCGTAAT-AAGAGGCA


title: MM_M1_1_sample 2352


title: HS_M1_1_sample 3058


title: HS_M1_2_sample 1


title: MM_M1_1_sample 2351


title: HS_M1_1_sample 3057


title: SQ-80004_S67_E1-50


title: Chip91484_r10_c17_Untreated

description: Chip91484_r10_c17_Untreated_AAGAGCATCGG-AAGAGGCA


title: Chip91484_r10_c38_Untreated

description: Chip91484_r10_c38_Untreated_AACTGGCCGTC-AAGAGGCA


title: MM_M1_1_sample 2350


title: SQ-80004_S66_E1-50


title: HS_M1_1_sample 3056


title: MM_M1_1_sample 2356


title: MM_M1_1_sample 2349


title: MM_M1_1_sample 2354


title: HS_M1_1_sample 3055


title: Chip91484_r10_c23_Untreated

description: Chip91484_r10_c23_Untreated_AAGAGCATGAC-AAGAGGCA


title: Chip91484_r1_c65_Untreated

description: Chip91484_r1_c65_Untreated_AACCGCCTGCT-AAGAGGCA


title: Chip91484_r10_c29_Treated

description: Chip91484_r10_c29_Treated_AAGAGACGGAA-AAGAGGCA


title: SQ-80004_S70_E1-50


title: SQ-80004_S62_E1-50


title: HS_M1_1_sample 3060


title: Chip91484_r1_c43_Untreated

description: Chip91484_r1_c43_Untreated_AACCAGCCATC-AAGAGGCA


title: SQ-80004_S69_E1-50


title: Chip91484_r1_c26_Treated

description: Chip91484_r1_c26_Treated_AACGACTACGG-AAGAGGCA


title: MM_M1_1_sample 2346


title: HS_M1_1_sample 3052


title: SQ-80004_S61_E1-50


title: MM_M1_1_sample 2345


title: Chip91484_r10_c14_Untreated

description: Chip91484_r10_c14_Untreated_AAGAGCTCCTA-AAGAGGCA


title: SQ-80004_S58_E1-50


title: HS_M1_1_sample 3051


title: MM_M1_1_sample 2344


title: SQ-80004_S68_E1-50


title: HS_M1_1_sample 3054


title: HS_M1_1_sample 3050


title: Chip91484_r1_c22_Untreated

description: Chip91484_r1_c22_Untreated_AACCGGATATG-AAGAGGCA


title: SQ-80004_S64_E1-50


title: MM_M1_1_sample 2355


title: Chip91484_r1_c52_Treated

description: Chip91484_r1_c52_Treated_AACGCATTGAC-AAGAGGCA


title: SQ-80004_S57_E1-50

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


title: SQ-80004_S55_E1-50


title: MM_M1_1_sample 2342


title: MM_M1_1_sample 2348


title: SQ-80004_S65_E1-50


title: HS_M1_1_sample 3048


title: Chip91484_r0_c65_Untreated

description: Chip91484_r0_c65_Untreated_AACCAACTGAC-AAGAGGCA


title: SQ-80004_S54_E1-50


title: Chip91484_r1_c36_Untreated

description: Chip91484_r1_c36_Untreated_AACCAGAGACG-AAGAGGCA


title: SQ-80004_S59_E1-50


title: MM_M1_1_sample 2347


title: Chip91484_r1_c23_Untreated

description: Chip91484_r1_c23_Untreated_AACCGGTACGT-AAGAGGCA


title: MM_M1_1_sample 2340


title: MM_M1_1_sample 2343


title: Chip91484_r1_c14_Untreated

description: Chip91484_r1_c14_Untreated_AACCGTTAACT-AAGAGGCA


title: HS_M1_1_sample 3053


title: MM_M1_1_sample 2341


title: SQ-80004_S53_E1-50


title: HS_M1_1_sample 3047


title: HS_M1_1_sample 3049


title: MM_M1_1_sample 2339


title: Chip91484_r0_c42_Untreated

description: Chip91484_r0_c42_Untreated_AACCGCCTCGG-AAGAGGCA


title: Chip91484_r0_c62_Untreated

description: Chip91484_r0_c62_Untreated_AACCAATAAGC-AAGAGGCA


title: HS_M1_1_sample 3046


title: Chip91484_r0_c4_Treated

description: Chip91484_r0_c4_Treated_AACCTTCCTTA-AAGAGGCA


title: MM_M1_1_sample 2338


title: SQ-80004_S51_E1-50


title: HS_M1_1_sample 3045


title: HS_M1_1_sample 3044


title: MM_M1_1_sample 2337


title: SQ-80001_S96_E1-50

value: 57 days

value: SSs


title: SQ-80004_S52_E1-50

value: left


title: HS_M1_1_sample 3043


title: MM_M1_1_sample 2336


title: SQ-80001_S95_E1-50


title: SQ-80004_S49_E1-50

value: 58 days


title: Chip91481_r9_c54_Treated

description: Chip91481_r9_c54_Treated_AAGACTCGAAC-AGGCAGAA

value: Invasive Ductal Carcinoma


title: SQ-80001_S93_E1-50


title: SQ-80004_S50_E1-50

value: MOp


title: HS_M1_1_sample 3038


title: Chip91484_r0_c34_Treated

description: Chip91484_r0_c34_Treated_AACGCATATGG-AAGAGGCA


title: MM_M1_1_sample 2333


title: SQ-80001_S92_E1-50

value: ALM


title: SQ-80001_S91_E1-50


title: MM_M1_1_sample 2335


title: MM_M1_1_sample 2331


title: MM_M1_1_sample 2330


title: Chip91484_r0_c29_Treated

description: Chip91484_r0_c29_Treated_AACGCCAAGAC-AAGAGGCA


title: HS_M1_1_sample 3042


title: HS_M1_1_sample 3036


title: Chip91481_r9_c25_Treated

description: Chip91481_r9_c25_Treated_AAGAATAACGA-AGGCAGAA


title: MM_M1_1_sample 2327


title: Chip91481_r9_c31_Treated

description: Chip91481_r9_c31_Treated_AAGAATAAGTC-AGGCAGAA


title: Chip91484_r0_c12_Untreated

description: Chip91484_r0_c12_Untreated_AACCAAGCCTG-AAGAGGCA


title: Chip91484_r0_c35_Treated

description: Chip91484_r0_c35_Treated_AACGCCAGAGC-AAGAGGCA


title: Chip91481_r9_c18_Untreated

description: Chip91481_r9_c18_Untreated_AACTGCGATCT-AGGCAGAA


title: MM_M1_1_sample 2334


title: SQ-80001_S87_E1-50


title: SQ-80001_S94_E1-50


title: HS_M1_1_sample 3040


title: MM_M1_1_sample 2332


title: HS_M1_1_sample 3039


title: HS_M1_1_sample 3041


title: HS_M1_1_sample 3032


title: MM_M1_1_sample 2325


title: MM_M1_1_sample 2328


title: Chip91481_r9_c2_Treated

description: Chip91481_r9_c2_Treated_AAGAGAGGTAC-AGGCAGAA


title: Chip91481_r9_c30_Treated

description: Chip91481_r9_c30_Treated_AAGAAGGTTCG-AGGCAGAA


title: HS_M1_1_sample 3035


title: SQ-80001_S88_E1-50

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


title: SQ-80001_S89_E1-50


title: Chip91481_r9_c27_Treated

description: Chip91481_r9_c27_Treated_AAGAAGCAATA-AGGCAGAA


title: Chip91481_r9_c17_Untreated

description: Chip91481_r9_c17_Untreated_AACTGCCGCTC-AGGCAGAA


title: HS_M1_1_sample 3034


title: MM_M1_1_sample 2326


title: SQ-80001_S90_E1-50


title: HS_M1_1_sample 3033


title: SQ-80001_S86_E1-50


title: HS_M1_1_sample 3037


title: Chip91481_r8_c54_Treated

description: Chip91481_r8_c54_Treated_AAGAACTGCGC-AGGCAGAA


title: MM_M1_1_sample 2329


title: HS_M1_1_sample 3030


title: SQ-80001_S84_E1-50


title: Chip91481_r8_c9_Treated

description: Chip91481_r8_c9_Treated_AAGAACGGATG-AGGCAGAA


title: Chip91481_r8_c43_Untreated

description: Chip91481_r8_c43_Untreated_AACTGAAGGAC-AGGCAGAA


title: SQ-80001_S83_E1-50


title: HS_M1_1_sample 3031


title: HS_M1_1_sample 3027


title: MM_M1_1_sample 2323


title: Chip91481_r8_c40_Untreated

description: Chip91481_r8_c40_Untreated_AACTCTAACCT-AGGCAGAA


title: MM_M1_1_sample 2322


title: HS_M1_1_sample 3026


title: Chip91481_r8_c37_Untreated

description: Chip91481_r8_c37_Untreated_AACTGAACTAT-AGGCAGAA


title: HS_M1_1_sample 3025


title: HS_M1_1_sample 3024


title: SQ-80001_S82_E1-50


title: Chip91481_r8_c2_Treated

description: Chip91481_r8_c2_Treated_AAGAAGATCTC-AGGCAGAA


title: SQ-80001_S80_E1-50


title: SQ-80001_S81_E1-50


title: MM_M1_1_sample 2317


title: HS_M1_1_sample 3029


title: MM_M1_1_sample 2318


title: Chip91481_r8_c25_Treated

description: Chip91481_r8_c25_Treated_AAGACTCTCTC-AGGCAGAA


title: SQ-80001_S85_E1-50


title: Chip91481_r8_c16_Untreated

description: Chip91481_r8_c16_Untreated_AACTACCGCGA-AGGCAGAA


title: Chip91481_r8_c19_Untreated

description: Chip91481_r8_c19_Untreated_AACTACTTAGC-AGGCAGAA


title: MM_M1_1_sample 2321


title: HS_M1_1_sample 3028


title: MM_M1_1_sample 2320


title: SQ-80001_S79_E1-50


title: MM_M1_1_sample 2316


title: MM_M1_1_sample 2324


title: SQ-80001_S78_E1-50


title: SQ-80001_S77_E1-50


title: MM_M1_1_sample 2319


title: HS_M1_1_sample 3021


title: SQ-80001_S75_E1-50


title: Chip91481_r71_c39_Treated

description: Chip91481_r71_c39_Untreated_TTGCAGTCTAC-AGGCAGAA


title: MM_M1_1_sample 2312


title: SQ-80001_S73_E1-50


title: MM_M1_1_sample 2311


title: SQ-80001_S76_E1-50


title: SQ-80001_S74_E1-50


title: MM_M1_1_sample 2315


title: MM_M1_1_sample 2310


title: SQ-80001_S71_E1-50


title: HS_M1_1_sample 3016


title: Chip91481_r70_c60_Treated

description: Chip91481_r70_c60_Untreated_TTCTTAAGATG-AGGCAGAA


title: Chip91481_r70_c67_Treated

description: Chip91481_r70_c67_Untreated_TTCTTCTATTC-AGGCAGAA


title: MM_M1_1_sample 2313


title: Chip91481_r70_c9_Treated

description: Chip91481_r70_c9_Treated_TTGAGATGAAC-AGGCAGAA


title: Chip91481_r71_c44_Treated

description: Chip91481_r71_c44_Untreated_TTGCCTCCAGG-AGGCAGAA


title: Chip91481_r70_c61_Treated

description: Chip91481_r70_c61_Untreated_TTCTTCTACGG-AGGCAGAA


title: Chip91481_r8_c14_Untreated

description: Chip91481_r8_c14_Untreated_AACTAGAGCCT-AGGCAGAA


title: MM_M1_1_sample 2314


title: HS_M1_1_sample 3023


title: MM_M1_1_sample 2309


title: SQ-80001_S72_E1-50

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


title: Chip91481_r70_c59_Treated

description: Chip91481_r70_c59_Treated_TTCTTAGCGAG-AGGCAGAA


title: SQ-80001_S70_E1-50


title: HS_M1_1_sample 3019


title: HS_M1_1_sample 3017


title: HS_M1_1_sample 3015


title: HS_M1_1_sample 3022


title: HS_M1_1_sample 3020


title: SQ-80001_S69_E1-50


title: HS_M1_1_sample 3018


title: MM_M1_1_sample 2308


title: HS_M1_1_sample 3014


title: Chip91481_r70_c57_Treated

description: Chip91481_r70_c57_Treated_TTCTGCCATAA-AGGCAGAA


title: MM_M1_1_sample 2304


title: SQ-80001_S64_E1-50

value: MOs


title: MM_M1_1_sample 2303

value: brain


title: Chip91481_r70_c54_Treated

description: Chip91481_r70_c54_Treated_TTCTTCCGAAT-AGGCAGAA


title: HS_M1_1_sample 3009


title: MM_M1_1_sample 2302


title: SQ-80001_S62_E1-50


title: SQ-80001_S61_E1-50


title: MM_M1_1_sample 2300


title: Chip91481_r70_c17_Treated

description: Chip91481_r70_c17_Untreated_TTGAGCTGACT-AGGCAGAA


title: Chip91481_r70_c39_Treated

description: Chip91481_r70_c39_Untreated_TTGAAGCTAGG-AGGCAGAA


title: HS_M1_1_sample 3010


title: MM_M1_1_sample 2306


title: SQ-80001_S65_E1-50


title: HS_M1_1_sample 3007


title: MM_M1_1_sample 2307


title: Chip91481_r70_c36_Treated

description: Chip91481_r70_c36_Untreated_TTGACCGGCCG-AGGCAGAA


title: Chip91481_r70_c45_Treated

description: Chip91481_r70_c45_Untreated_TTGAAGCCGGA-AGGCAGAA


title: SQ-80001_S66_E1-50


title: HS_M1_1_sample 3006


title: SQ-80001_S63_E1-50


title: HS_M1_1_sample 3012


title: HS_M1_1_sample 3005


title: HS_M1_1_sample 3011


title: HS_M1_1_sample 3013


title: SQ-80001_S60_E1-50


title: Chip91481_r70_c31_Treated

description: Chip91481_r70_c31_Treated_TTGAGAACGTT-AGGCAGAA


title: MM_M1_1_sample 2305


title: HS_M1_1_sample 3008


title: HS_M1_1_sample 3004


title: Chip91481_r70_c53_Treated

description: Chip91481_r70_c53_Treated_TTCTTACTTGC-AGGCAGAA


title: SQ-80001_S67_E1-50


title: SQ-80001_S57_E1-50


title: MM_M1_1_sample 2299


title: Chip91481_r7_c58_Treated

description: Chip91481_r7_c58_Treated_AAGACCGTAGG-AGGCAGAA


title: Chip91481_r7_c59_Treated

description: Chip91481_r7_c59_Treated_AAGACGAACTT-AGGCAGAA


title: MM_M1_1_sample 2295


title: SQ-80001_S56_E1-50


title: SQ-80001_S59_E1-50


title: SQ-80001_S58_E1-50


title: Chip91481_r7_c62_Untreated

description: Chip91481_r7_c62_Untreated_AACTCGCTCGA-AGGCAGAA


title: Chip91481_r70_c11_Treated

description: Chip91481_r70_c11_Treated_TTGAGGAGCTT-AGGCAGAA


title: MM_M1_1_sample 2298


title: HS_M1_1_sample 3003


title: MM_M1_1_sample 2297


title: SQ-80001_S55_E1-50


title: SQ-80001_S53_E1-50


title: Chip91481_r7_c3_Treated

description: Chip91481_r7_c3_Treated_AAGACCTACTG-AGGCAGAA


title: HS_M1_1_sample 3000


title: Chip91481_r7_c28_Treated

description: Chip91481_r7_c28_Treated_AACTTGAGCAG-AGGCAGAA


title: MM_M1_1_sample 2296


title: Chip91481_r7_c21_Untreated

description: Chip91481_r7_c21_Untreated_AACTCCGGCCT-AGGCAGAA


title: Chip91481_r7_c27_Treated

description: Chip91481_r7_c27_Treated_AACTTGACTCT-AGGCAGAA


title: SQ-80001_S52_E1-50

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


title: HS_M1_1_sample 2999


title: HS_M1_1_sample 3001


title: MM_M1_1_sample 2293


title: HS_M1_1_sample 3002


title: MM_M1_1_sample 2292


title: SQ-80001_S54_E1-50


title: MM_M1_1_sample 2289


title: Chip91481_r69_c63_Treated

description: Chip91481_r69_c63_Untreated_TGGTCGATCTC-AGGCAGAA


title: Chip91481_r7_c13_Untreated

description: Chip91481_r7_c13_Untreated_AACTCGGAACT-AGGCAGAA


title: MM_M1_1_sample 2291


title: MM_M1_1_sample 2294


title: HS_M1_1_sample 2998


title: MM_M1_1_sample 2290


title: SQ-80001_S51_E1-50


title: HS_M1_1_sample 2997


title: Chip91481_r69_c9_Treated

description: Chip91481_r69_c9_Treated_TTCGTTCGCGG-AGGCAGAA


title: SQ-80001_S50_E1-50


title: HS_M1_1_sample 2996


title: Chip91481_r69_c56_Treated

description: Chip91481_r69_c56_Treated_TTCGCCTAACG-AGGCAGAA


title: Chip91481_r69_c48_Treated

description: Chip91481_r69_c48_Treated_TTCGACGTACC-AGGCAGAA


title: HS_M1_1_sample 2995


title: Chip91481_r69_c50_Treated

description: Chip91481_r69_c50_Treated_TTCGCCTCCGA-AGGCAGAA


title: LS-15561_S96_E1-50

value: 55 days


title: MM_M1_1_sample 2288


title: LS-15561_S94_E1-50

value: RFP-positive


title: HS_M1_1_sample 2993


title: LS-15561_S95_E1-50


title: Chip91481_r69_c45_Treated

description: Chip91481_r69_c45_Untreated_TTCGCGCGTCA-AGGCAGAA


title: SQ-80001_S49_E1-50

value: F


title: MM_M1_1_sample 2285


title: MM_M1_1_sample 2286


title: LS-15561_S93_E1-50


title: HS_M1_1_sample 2991


title: MM_M1_1_sample 2284


title: MM_M1_1_sample 2287


title: Chip91481_r69_c43_Treated

description: Chip91481_r69_c43_Untreated_TTCGGTCGCCA-AGGCAGAA


title: MM_M1_1_sample 2282


title: MM_M1_1_sample 2283


title: Chip91481_r69_c37_Treated

description: Chip91481_r69_c37_Untreated_TTCGGTCATAT-AGGCAGAA


title: Chip91481_r69_c42_Treated

description: Chip91481_r69_c42_Untreated_TTCGGATAATG-AGGCAGAA


title: LS-15561_S91_E1-50


title: HS_M1_1_sample 2989


title: HS_M1_1_sample 2994


title: LS-15561_S90_E1-50


title: Chip91481_r69_c32_Treated

description: Chip91481_r69_c32_Treated_TTCGTATTGCC-AGGCAGAA


title: HS_M1_1_sample 2992


title: MM_M1_1_sample 2281


title: MM_M1_1_sample 2280


title: LS-15561_S92_E1-50


title: LS-15561_S89_E1-50


title: Chip91481_r69_c24_Treated

description: Chip91481_r69_c24_Treated_TTCGGCTTGGA-AGGCAGAA


title: MM_M1_1_sample 2279


title: Chip91481_r69_c28_Treated

description: Chip91481_r69_c28_Treated_TTCGCTGATTA-AGGCAGAA


title: HS_M1_1_sample 2990


title: LS-15561_S88_E1-50


title: MM_M1_1_sample 2278


title: LS-15561_S87_E1-50


title: Chip91481_r69_c14_Treated

description: Chip91481_r69_c14_Untreated_TTCTCGCATAG-AGGCAGAA


title: Chip91481_r69_c11_Treated

description: Chip91481_r69_c11_Treated_TTCTATACGAC-AGGCAGAA


title: HS_M1_1_sample 2987


title: HS_M1_1_sample 2986


title: HS_M1_1_sample 2985


title: MM_M1_1_sample 2277


title: LS-15561_S86_E1-50


title: MM_M1_1_sample 2276


title: LS-15561_S85_E1-50


title: Chip91481_r69_c10_Treated

description: Chip91481_r69_c10_Treated_TTCTACCAATT-AGGCAGAA


title: HS_M1_1_sample 2988


title: HS_M1_1_sample 2983


title: LS-15561_S84_E1-50

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


title: MM_M1_1_sample 2275


title: Chip91481_r68_c7_Treated

description: Chip91481_r68_c7_Treated_TTATAAGCTGA-AGGCAGAA


title: MM_M1_1_sample 2274


title: LS-15561_S83_E1-50


title: HS_M1_1_sample 2980


title: MM_M1_1_sample 2273


title: Chip91481_r68_c65_Treated

description: Chip91481_r68_c65_Untreated_TGGCCTTCATG-AGGCAGAA


title: MM_M1_1_sample 2271


title: Chip91481_r68_c50_Treated

description: Chip91481_r68_c50_Treated_TTATAACTTAC-AGGCAGAA


title: LS-15561_S82_E1-50


title: MM_M1_1_sample 2272


title: LS-15561_S81_E1-50


title: HS_M1_1_sample 2977


title: HS_M1_1_sample 2984


title: HS_M1_1_sample 2979


title: HS_M1_1_sample 2982


title: HS_M1_1_sample 2978


title: MM_M1_1_sample 2269


title: MM_M1_1_sample 2270


title: HS_M1_1_sample 2976


title: LS-15558_S96_E1-50

value: 56 days


title: LS-15558_S95_E1-50


title: LS-15558_S94_E1-50


title: HS_M1_1_sample 2981


title: MM_M1_1_sample 2268


title: Chip91481_r68_c42_Treated

description: Chip91481_r68_c42_Untreated_TGGTCTAGCGG-AGGCAGAA


title: Chip91481_r68_c52_Treated

description: Chip91481_r68_c52_Treated_TTAGGTAGAAC-AGGCAGAA


title: Chip91481_r68_c37_Treated

description: Chip91481_r68_c37_Untreated_TGGTTACCTAC-AGGCAGAA


title: Chip91481_r68_c17_Treated

description: Chip91481_r68_c17_Untreated_TGGCGAGAGAC-AGGCAGAA


title: LS-15558_S93_E1-50


title: HS_M1_1_sample 2975


title: HS_M1_1_sample 2973


title: MM_M1_1_sample 2267


title: MM_M1_1_sample 2266


title: LS-15558_S91_E1-50


title: HS_M1_1_sample 2972


title: LS-15558_S90_E1-50


title: MM_M1_1_sample 2264


title: HS_M1_1_sample 2974


title: MM_M1_1_sample 2262


title: Chip91481_r68_c3_Treated

description: Chip91481_r68_c3_Treated_TTAGGTTAGGC-AGGCAGAA


title: LS-15558_S87_E1-50


title: HS_M1_1_sample 2970


title: MM_M1_1_sample 2265


title: Chip91481_r68_c13_Treated

description: Chip91481_r68_c13_Untreated_TGGCGCATAGG-AGGCAGAA


title: Chip91481_r67_c65_Treated

description: Chip91481_r67_c65_Untreated_TGGTATAAGTA-AGGCAGAA


title: Chip91481_r67_c62_Neg

description: Chip91481_r67_c62_Neg_Ctrl_TGGTCATTCTA-AGGCAGAA


title: Chip91481_r67_c71_Treated

description: Chip91481_r67_c71_Untreated_TGGTATCAGAT-AGGCAGAA


title: MM_M1_1_sample 2263


title: HS_M1_1_sample 2969


title: Chip91481_r68_c39_Treated

description: Chip91481_r68_c39_Untreated_TGGTCCTATTG-AGGCAGAA


title: HS_M1_1_sample 2971


title: LS-15558_S86_E1-50


title: Chip91481_r68_c11_Treated

description: Chip91481_r68_c11_Treated_TTAGTCTTCAG-AGGCAGAA


title: LS-15558_S89_E1-50


title: Chip91481_r67_c53_Treated

description: Chip91481_r67_c53_Treated_TTCCAATAGAT-AGGCAGAA


title: HS_M1_1_sample 2968


title: MM_M1_1_sample 2260


title: Chip91481_r67_c49_Treated

description: Chip91481_r67_c49_Treated_TTCCGTCGGCC-AGGCAGAA


title: LS-15558_S85_E1-50

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


title: LS-15558_S92_E1-50


title: HS_M1_1_sample 2967


title: LS-15558_S84_E1-50


title: MM_M1_1_sample 2259


title: LS-15558_S72_E1-50


title: HS_M1_1_sample 2966


title: LS-15558_S82_E1-50


title: Chip91481_r67_c27_Treated

description: Chip91481_r67_c27_Treated_TTAGATTGAAG-AGGCAGAA


title: HS_M1_1_sample 2963


title: MM_M1_1_sample 2257


title: Chip91481_r67_c46_Treated

description: Chip91481_r67_c46_Untreated_TGGATTGCCAA-AGGCAGAA


title: MM_M1_1_sample 2254


title: LS-15558_S71_E1-50


title: LS-15558_S83_E1-50


title: Chip91481_r67_c38_Neg

description: Chip91481_r67_c38_Neg_Ctrl_TGGCCAGCAGT-AGGCAGAA


title: MM_M1_1_sample 2258


title: MM_M1_1_sample 2261


title: Chip91481_r67_c37_Treated

description: Chip91481_r67_c37_Untreated_TGGCATGGAGT-AGGCAGAA


title: HS_M1_1_sample 2965


title: HS_M1_1_sample 2964


title: MM_M1_1_sample 2256


title: HS_M1_1_sample 2962


title: LS-15558_S88_E1-50


title: Chip91481_r66_c69_Treated

description: Chip91481_r66_c69_Untreated_TGGAGTTATAA-AGGCAGAA


title: LS-15558_S70_E1-50


title: MM_M1_1_sample 2255


title: Chip91481_r66_c9_Treated

description: Chip91481_r66_c9_Treated_TTAGATCAACG-AGGCAGAA


title: HS_M1_1_sample 2961


title: LS-15558_S81_E1-50


title: LS-15558_S69_E1-50


title: Chip91481_r66_c49_Treated

description: Chip91481_r66_c49_Treated_TTACTTGGTCG-AGGCAGAA


title: LS-15558_S68_E1-50


title: Chip91481_r66_c32_Treated

description: Chip91481_r66_c32_Treated_TTCAGGAGGCA-AGGCAGAA


title: HS_M1_1_sample 2959


title: MM_M1_1_sample 2252


title: HS_M1_1_sample 2960


title: Chip91481_r66_c11_Treated

description: Chip91481_r66_c11_Treated_TTAGCCTGGCA-AGGCAGAA


title: MM_M1_1_sample 2253


title: LS-15558_S65_E1-50


title: MM_M1_1_sample 2248


title: LS-15558_S67_E1-50


title: HS_M1_1_sample 2956


title: LS-15558_S66_E1-50


title: HS_M1_1_sample 2954


title: MM_M1_1_sample 2250


title: LS-15558_S63_E1-50


title: MM_M1_1_sample 2246


title: Chip91481_r66_c21_Treated

description: Chip91481_r66_c21_Untreated_TGGATGCGAGG-AGGCAGAA


title: MM_M1_1_sample 2251


title: HS_M1_1_sample 2955


title: MM_M1_1_sample 2247


title: Chip91481_r66_c47_Treated

description: Chip91481_r66_c47_Untreated_TGGTAAGTATC-AGGCAGAA


title: Chip91481_r65_c69_Treated

description: Chip91481_r65_c69_Untreated_TGGCGGCGATA-AGGCAGAA


title: HS_M1_1_sample 2952


title: HS_M1_1_sample 2957


title: HS_M1_1_sample 2951


title: Chip91481_r65_c58_Treated

description: Chip91481_r65_c58_Treated_TTATATCTTCG-AGGCAGAA


title: Chip91481_r65_c68_Treated

description: Chip91481_r65_c68_Untreated_TGGCTCGACGT-AGGCAGAA


title: Chip91481_r65_c64_Treated

description: Chip91481_r65_c64_Untreated_TGGCGTACTGC-AGGCAGAA


title: LS-15558_S64_E1-50


title: LS-15558_S59_E1-50


title: HS_M1_1_sample 2958


title: HS_M1_1_sample 2949


title: LS-15558_S58_E1-50


title: Chip91481_r65_c66_Treated

description: Chip91481_r65_c66_Untreated_TGGCTATGCCG-AGGCAGAA


title: MM_M1_1_sample 2249


title: HS_M1_1_sample 2948


title: MM_M1_1_sample 2245


title: MM_M1_1_sample 2241


title: Chip91481_r65_c53_Treated

description: Chip91481_r65_c53_Treated_TTATCCTTGGT-AGGCAGAA


title: MM_M1_1_sample 2242


title: Chip91481_r65_c50_Treated

description: Chip91481_r65_c50_Treated_TTATGCTCAAC-AGGCAGAA


title: LS-15558_S60_E1-50

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


title: MM_M1_1_sample 2239


title: Chip91481_r65_c55_Treated

description: Chip91481_r65_c55_Treated_TTATGCCGCTA-AGGCAGAA


title: HS_M1_1_sample 2946


title: LS-15558_S62_E1-50


title: LS-15558_S57_E1-50


title: MM_M1_1_sample 2238


title: MM_M1_1_sample 2244


title: Chip91481_r65_c56_Treated

description: Chip91481_r65_c56_Treated_TTATGCGACTC-AGGCAGAA


title: MM_M1_1_sample 2237


title: LS-15558_S61_E1-50


title: MM_M1_1_sample 2236


title: Chip91481_r65_c5_Treated

description: Chip91481_r65_c5_Treated_TTATTCTCTGA-AGGCAGAA


title: LS-15558_S51_E1-50


title: MM_M1_1_sample 2235


title: Chip91481_r65_c11_Treated

description: Chip91481_r65_c11_Treated_TTATTCTGGCT-AGGCAGAA


title: HS_M1_1_sample 2944


title: MM_M1_1_sample 2243


title: MM_M1_1_sample 2240


title: LS-15558_S55_E1-50


title: Chip91481_r64_c70_Treated

description: Chip91481_r64_c70_Untreated_TGGACTATACC-AGGCAGAA


title: LS-15558_S50_E1-50


title: LS-15558_S56_E1-50


title: HS_M1_1_sample 2950


title: HS_M1_1_sample 2947


title: HS_M1_1_sample 2940


title: Chip91481_r65_c49_Treated

description: Chip91481_r65_c49_Treated_TTATGAGTCTT-AGGCAGAA


title: HS_M1_1_sample 2953


title: HS_M1_1_sample 2942


title: Chip91481_r65_c27_Treated

description: Chip91481_r65_c27_Treated_TTACCAGTCGG-AGGCAGAA


title: HS_M1_1_sample 2945


title: HS_M1_1_sample 2943


title: Chip91481_r65_c34_Treated

description: Chip91481_r65_c34_Treated_TTACCTTCTAA-AGGCAGAA


title: Chip91481_r64_c62_Treated

description: Chip91481_r64_c62_Untreated_TGGAGCTGGAG-AGGCAGAA


title: LS-15558_S48_E1-50


title: MM_M1_1_sample 2231


title: HS_M1_1_sample 2941


title: HS_M1_1_sample 2938


title: LS-15558_S46_E1-50


title: LS-15558_S53_E1-50


title: Chip91481_r64_c53_Treated

description: Chip91481_r64_c53_Treated_TGGTTCTGCTT-AGGCAGAA


title: LS-15558_S52_E1-50


title: HS_M1_1_sample 2936


title: MM_M1_1_sample 2234


title: LS-15558_S45_E1-50


title: MM_M1_1_sample 2233


title: MM_M1_1_sample 2232


title: LS-15558_S54_E1-50


title: Chip91481_r64_c57_Treated

description: Chip91481_r64_c57_Treated_TGGTTCAGCAA-AGGCAGAA


title: HS_M1_1_sample 2937


title: Chip91481_r64_c64_Treated

description: Chip91481_r64_c64_Untreated_TGGACTAATCA-AGGCAGAA


title: MM_M1_1_sample 2227


title: LS-15558_S44_E1-50


title: HS_M1_1_sample 2939


title: LS-15558_S49_E1-50


title: HS_M1_1_sample 2934


title: MM_M1_1_sample 2230


title: HS_M1_1_sample 2935


title: Chip91481_r64_c51_Treated

description: Chip91481_r64_c51_Treated_TGGTTCATACG-AGGCAGAA


title: MM_M1_1_sample 2229


title: MM_M1_1_sample 2228


title: LS-15558_S47_E1-50


title: Chip91481_r64_c43_Treated

description: Chip91481_r64_c43_Untreated_TGGCTCAGAAT-AGGCAGAA


title: Chip91481_r64_c36_Treated

description: Chip91481_r64_c36_Untreated_TGGCGTTATCT-AGGCAGAA


title: Chip91481_r64_c42_Treated

description: Chip91481_r64_c42_Untreated_TGGCGTTCCAG-AGGCAGAA


title: Chip91481_r64_c34_Treated

description: Chip91481_r64_c34_Treated_TTATAGTTCTC-AGGCAGAA


title: LS-15558_S41_E1-50

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


title: MM_M1_1_sample 2224


title: Chip91481_r64_c26_Treated

description: Chip91481_r64_c26_Treated_TTATGACTATG-AGGCAGAA


title: HS_M1_1_sample 2933


title: HS_M1_1_sample 2932


title: LS-15558_S42_E1-50


title: MM_M1_1_sample 2225


title: LS-15558_S40_E1-50


title: Chip91481_r64_c24_Treated

description: Chip91481_r64_c24_Treated_TTATCATATAA-AGGCAGAA


title: LS-15558_S39_E1-50


title: HS_M1_1_sample 2930


title: LS-15558_S43_E1-50


title: MM_M1_1_sample 2222


title: Chip91481_r64_c23_Treated

description: Chip91481_r64_c23_Untreated_TGGAGACTACC-AGGCAGAA


title: HS_M1_1_sample 2929


title: HS_M1_1_sample 2928


title: MM_M1_1_sample 2221


title: MM_M1_1_sample 2226


title: HS_M1_1_sample 2927


title: Chip91481_r64_c21_Treated

description: Chip91481_r64_c21_Untreated_TGGACTCTTGG-AGGCAGAA


title: LS-15558_S38_E1-50


title: LS-15558_S35_E1-50


title: HS_M1_1_sample 2931


title: MM_M1_1_sample 2223


title: Chip91481_r63_c59_Treated

description: Chip91481_r63_c59_Treated_TGGAAGGCGGC-AGGCAGAA


title: MM_M1_1_sample 2219


title: LS-15558_S36_E1-50


title: LS-15558_S33_E1-50


title: HS_M1_1_sample 2923


title: MM_M1_1_sample 2215


title: LS-15558_S31_E1-50


title: MM_M1_1_sample 2220


title: MM_M1_1_sample 2214


title: HS_M1_1_sample 2921


title: Chip91481_r63_c45_Treated

description: Chip91481_r63_c45_Untreated_TCGTTGCGTAC-AGGCAGAA


title: LS-15558_S29_E1-50


title: LS-15558_S34_E1-50


title: HS_M1_1_sample 2925


title: HS_M1_1_sample 2920


title: MM_M1_1_sample 2216


title: LS-15558_S32_E1-50


title: Chip91481_r63_c61_Treated

description: Chip91481_r63_c61_Untreated_TTGGTCTCCAT-AGGCAGAA


title: Chip91481_r63_c58_Treated

description: Chip91481_r63_c58_Treated_TGCTTGGTATG-AGGCAGAA


title: Chip91481_r63_c49_Treated

description: Chip91481_r63_c49_Treated_TGGAATTGAGA-AGGCAGAA


title: MM_M1_1_sample 2217


title: MM_M1_1_sample 2213


title: MM_M1_1_sample 2218


title: Chip91481_r63_c4_Treated

description: Chip91481_r63_c4_Treated_TGGAAGATATC-AGGCAGAA


title: LS-15558_S27_E1-50


title: HS_M1_1_sample 2926


title: MM_M1_1_sample 2211


title: Chip91481_r63_c25_Treated

description: Chip91481_r63_c25_Treated_TGCATGCCGAT-AGGCAGAA


title: LS-15558_S26_E1-50


title: LS-15558_S30_E1-50


title: MM_M1_1_sample 2209


title: Chip91481_r63_c47_Treated

description: Chip91481_r63_c47_Untreated_TCTAGCATGGC-AGGCAGAA


title: Chip91481_r63_c43_Treated

description: Chip91481_r63_c43_Untreated_TCTATGAATTG-AGGCAGAA


title: HS_M1_1_sample 2922


title: HS_M1_1_sample 2918


title: HS_M1_1_sample 2924


title: Chip91481_r63_c14_Treated

description: Chip91481_r63_c14_Untreated_TTGGTTGGCCT-AGGCAGAA


title: HS_M1_1_sample 2915


title: HS_M1_1_sample 2916


title: Chip91481_r63_c39_Treated

description: Chip91481_r63_c39_Untreated_TCGTTGGTCCG-AGGCAGAA


title: Chip91481_r63_c18_Treated

description: Chip91481_r63_c18_Untreated_TTGGTCTATGC-AGGCAGAA


title: Chip91481_r62_c71_Treated

description: Chip91481_r62_c71_Untreated_TCGTCTGAATG-AGGCAGAA