title: Lineage_wRNA-p4H1

description:
lineage_profiles_wRNA.txt
p4H1-TARGp4_TTCTACGCCA_S277


title: sciRNA_lib-p3G9

status: Public on May 12 2022

type: SRA

city: Seattle

first: Anna

last: Minkina

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

description:
rna_raw_cell_by_gene_counts.gz
p3G9-RNAp3_CAAGCTTGGC_S177

library_source: transcriptomic single cell

data_processing:
demultiplex using bcl2fastq
adaptor trimming using trim_galore
align to reference genome using STAR
reads deduplicated by UMIs
(All code available at: https://github.com/minkinaa/TheLorax)
sciRNA_lib:
Sequencing was performed as previously described (Cao et al. 2017). Reads were adapter-trimmed using trim_galore and aligned to the reference genome (hg38) using STAR. Non-unique mappers were removed. Reads were then deduplicated using a custom script (190223_sciRNA_remove_duplicates.cpp), taking into account both UMIs and cell indices to call a duplicated read. Only cells with at least 2048 deduplicated non-mitochondrial UMIs were used for subsequent analyses.
A custom script (190704_process_sciRNA_mapped_file.cpp) was used to map reads to genes. Reads which overlapped multiple genes but only fell in an exon in one gene were counted towards that gene.
RNA processing to generate the cell by gene raw counts file is implemented in script 190807_sciRNA_wrapper_ALL.txt, with user-defined UMI cutoff of 2^11.
sciATAC_lib:
For processing sci-ATAC-seq sequencing reads, we first compare observed and expected lists of single cell indices, correcting any indices with a likely off-by-one error. All reads are then adaptor trimmed using trimmomatic (parameters: TRAILING:3 SLIDINGWINDOW:4:10 MINLEN:20), and all reads associated with a single cell are then aligned to the genome using bowtie2 (hg38 genome build). Reads are then deduplicated by UMIs using a custom script (191226_CROPt_process_atac_bedfile.cpp). Both cell by gene and cell by interval counts were generated using a custom script (191226_CROPt_make_cell_by_interval_count_file.cpp).
Lineage_wRNA & Lineage_wATAC:
Processing of raw data to generate the categorical processed data file is described in associated manuscript ("Computational processing and edit calling from lineage target sequencing data") with all associated code at https://github.com/minkinaa/TheLorax.
Cell IDs found in the processed data file are related to raw fastq files as follows:
sciRNA_lib: Each fastq pair file contains information from 25 cells (or less). The cell IDs are a combination of the plate/batch, PCR well index (index #2) during combinatorial indexing (in fastq file name), and index #1, the last 10 bases of the read1 sequence. E.g. the raw data for the cell called "p1A10_ACTAATTGAG", can be found in the raw data file "p1A10-RNA_CCAGGTCTAC_S10", with those sequences with "ACTAATTGAG" as the last 10 bases in the R1 file corresponding to this cell. The first 8 bases of R1 are the UMI.
sciATAC_lib: Cell IDs corresponding to those found in the processed file can be found in the sequence name in the fastq (e.g. "@p2H1_TGAGCTACTT-R1.1" --> cell ID = "p2H1_TGAGCTACTT")
Lineage_wRNA & Lineage_wATAC: Cell IDs are related to fastq file names as described for "sciRNA_lib" except index #1 is located in positions 9-18 in the R1 fastq file. The first 8 bases of R1 are the UMI. Read structure is further describe in manuscript Materials & Methods, and at https://github.com/minkinaa/TheLorax.
A list of index #1's can be found in supplementary file "Index_1_List.txt".
Assembly: hg38
Supplementary files format and content: Tab-separated values, raw cell by gene/tss counts matrices

molecule: total RNA

organism: Homo sapiens

extract_protocol:
sci-RNA-seq: whole cells, methanol fixes; sci-ATAC-seq: nuclei
sci-RNA-seq-2level, sci-ATAC-seq2level, targeted lineage mRNA capture as described

tag: cell type

tag: data type

value: sci-RNA-seq


title: Lineage_wRNA-p4H8

description:
lineage_profiles_wRNA.txt
p4H8-TARGp4_CCTATAAGCT_S284

library_source: transcriptomic

value: Targeted lineage amplicon captured alongside sci-RNA-seq


title: sciRNA_lib-p3H11

description:
rna_raw_cell_by_gene_counts.gz
p3H11-RNAp3_AAGATCCAAC_S191


title: sciRNA_lib-p3H7

description:
rna_raw_cell_by_gene_counts.gz
p3H7-RNAp3_AGATCCTATA_S187


title: sciRNA_lib-p3H10

description:
rna_raw_cell_by_gene_counts.gz
p3H10-RNAp3_ATAAGAGGCG_S190


title: sciRNA_lib-p3G8

description:
rna_raw_cell_by_gene_counts.gz
p3G8-RNAp3_TTGGAGTCGG_S176


title: Lineage_wRNA-p4H12

description:
lineage_profiles_wRNA.txt
p4H12-TARGp4_CTGCAATCGC_S288


title: Lineage_wRNA-p4H7

description:
lineage_profiles_wRNA.txt
p4H7-TARGp4_AGATCCTATA_S283


title: Lineage_wRNA-p4H11

description:
lineage_profiles_wRNA.txt
p4H11-TARGp4_AAGATCCAAC_S287


title: Lineage_wRNA-p4H10

description:
lineage_profiles_wRNA.txt
p4H10-TARGp4_ATAAGAGGCG_S286


title: sciRNA_lib-p3G5

description:
rna_raw_cell_by_gene_counts.gz
p3G5-RNAp3_TGATACGAGT_S173


title: sciRNA_lib-p3H4

description:
rna_raw_cell_by_gene_counts.gz
p3H4-RNAp3_TGCCAGATGG_S184


title: sciRNA_lib-p3G6

description:
rna_raw_cell_by_gene_counts.gz
p3G6-RNAp3_CATTATTACC_S174


title: sciRNA_lib-p3G4

description:
rna_raw_cell_by_gene_counts.gz
p3G4-RNAp3_ACGCAACTCC_S172


title: Lineage_wRNA-p4G9

description:
lineage_profiles_wRNA.txt
p4G9-TARGp4_CAAGCTTGGC_S273


title: sciRNA_lib-p3G3

description:
rna_raw_cell_by_gene_counts.gz
p3G3-RNAp3_CAAGATTAAG_S171


title: sciRNA_lib-p3G2

description:
rna_raw_cell_by_gene_counts.gz
p3G2-RNAp3_GTCATTGCGC_S170


title: Lineage_wRNA-p4H3

description:
lineage_profiles_wRNA.txt
p4H3-TARGp4_CCAAGCTGAA_S279


title: Lineage_wRNA-p4G6

description:
lineage_profiles_wRNA.txt
p4G6-TARGp4_CATTATTACC_S270


title: sciRNA_lib-p3G1

description:
rna_raw_cell_by_gene_counts.gz
p3G1-RNAp3_GACCGTAGCA_S169


title: sciRNA_lib-p3G12

description:
rna_raw_cell_by_gene_counts.gz
p3G12-RNAp3_ACTGAATTCC_S180


title: Lineage_wRNA-p4G4

description:
lineage_profiles_wRNA.txt
p4G4-TARGp4_ACGCAACTCC_S268


title: sciRNA_lib-p3G7

description:
rna_raw_cell_by_gene_counts.gz
p3G7-RNAp3_TCTATAAGGA_S175


title: Lineage_wRNA-p4G5

description:
lineage_profiles_wRNA.txt
p4G5-TARGp4_TGATACGAGT_S269


title: Lineage_wRNA-p4G3

description:
lineage_profiles_wRNA.txt
p4G3-TARGp4_CAAGATTAAG_S267


title: Lineage_wRNA-p4G2

description:
lineage_profiles_wRNA.txt
p4G2-TARGp4_GTCATTGCGC_S266


title: sciRNA_lib-p3G10

description:
rna_raw_cell_by_gene_counts.gz
p3G10-RNAp3_ATAGGATATG_S178


title: Lineage_wRNA-p4G1

description:
lineage_profiles_wRNA.txt
p4G1-TARGp4_GACCGTAGCA_S265


title: sciRNA_lib-p3F8

description:
rna_raw_cell_by_gene_counts.gz
p3F8-RNAp3_AGGATTACCA_S164


title: sciRNA_lib-p3G11

description:
rna_raw_cell_by_gene_counts.gz
p3G11-RNAp3_TGGCGTAGGT_S179


title: sciRNA_lib-p3F6

description:
rna_raw_cell_by_gene_counts.gz
p3F6-RNAp3_ACGAGGACCT_S162


title: sciRNA_lib-p3F9

description:
rna_raw_cell_by_gene_counts.gz
p3F9-RNAp3_AACCTAGCTT_S165


title: sciRNA_lib-p3F7

description:
rna_raw_cell_by_gene_counts.gz
p3F7-RNAp3_TATAACTTCC_S163


title: Lineage_wRNA-p4G12

description:
lineage_profiles_wRNA.txt
p4G12-TARGp4_ACTGAATTCC_S276


title: Lineage_wRNA-p4G10

description:
lineage_profiles_wRNA.txt
p4G10-TARGp4_ATAGGATATG_S274


title: Lineage_wRNA-p4G8

description:
lineage_profiles_wRNA.txt
p4G8-TARGp4_TTGGAGTCGG_S272


title: Lineage_wRNA-p4G11

description:
lineage_profiles_wRNA.txt
p4G11-TARGp4_TGGCGTAGGT_S275


title: Lineage_wRNA-p4G7

description:
lineage_profiles_wRNA.txt
p4G7-TARGp4_TCTATAAGGA_S271


title: Lineage_wRNA-p4F8

description:
lineage_profiles_wRNA.txt
p4F8-TARGp4_AGGATTACCA_S260


title: sciRNA_lib-p3F4

description:
rna_raw_cell_by_gene_counts.gz
p3F4-RNAp3_AACGAGGCTA_S160


title: sciRNA_lib-p3F12

description:
rna_raw_cell_by_gene_counts.gz
p3F12-RNAp3_CGAGCTGCCA_S168


title: Lineage_wRNA-p4F6

description:
lineage_profiles_wRNA.txt
p4F6-TARGp4_ACGAGGACCT_S258


title: sciRNA_lib-p3F2

description:
rna_raw_cell_by_gene_counts.gz
p3F2-RNAp3_CGTCCGTCCT_S158


title: sciRNA_lib-p3F11

description:
rna_raw_cell_by_gene_counts.gz
p3F11-RNAp3_ACTATCCGCA_S167


title: Lineage_wRNA-p4F7

description:
lineage_profiles_wRNA.txt
p4F7-TARGp4_TATAACTTCC_S259


title: sciRNA_lib-p3F10

description:
rna_raw_cell_by_gene_counts.gz
p3F10-RNAp3_AGTCCGCGGA_S166


title: Lineage_wRNA-p4F4

description:
lineage_profiles_wRNA.txt
p4F4-TARGp4_AACGAGGCTA_S256


title: Lineage_wRNA-p4F5

description:
lineage_profiles_wRNA.txt
p4F5-TARGp4_ACGTTCAACC_S257


title: sciRNA_lib-p3E9

description:
rna_raw_cell_by_gene_counts.gz
p3E9-RNAp3_TCCGTCGCCA_S153


title: Lineage_wRNA-p4F1

description:
lineage_profiles_wRNA.txt
p4F1-TARGp4_AACTACCGAC_S253


title: Lineage_wRNA-p4F2

description:
lineage_profiles_wRNA.txt
p4F2-TARGp4_CGTCCGTCCT_S254


title: Lineage_wRNA-p4F3

description:
lineage_profiles_wRNA.txt
p4F3-TARGp4_GGTCCAGGAG_S255


title: sciRNA_lib-p3E8

description:
rna_raw_cell_by_gene_counts.gz
p3E8-RNAp3_ACCGTTACGA_S152


title: Lineage_wRNA-p4F9

description:
lineage_profiles_wRNA.txt
p4F9-TARGp4_AACCTAGCTT_S261


title: sciRNA_lib-p3E7

description:
rna_raw_cell_by_gene_counts.gz
p3E7-RNAp3_TCCGGTAATC_S151


title: sciRNA_lib-p3F3

description:
rna_raw_cell_by_gene_counts.gz
p3F3-RNAp3_GGTCCAGGAG_S159


title: sciRNA_lib-p3F5

description:
rna_raw_cell_by_gene_counts.gz
p3F5-RNAp3_ACGTTCAACC_S161


title: Lineage_wRNA-p4F10

description:
lineage_profiles_wRNA.txt
p4F10-TARGp4_AGTCCGCGGA_S262


title: Lineage_wRNA-p4E9

description:
lineage_profiles_wRNA.txt
p4E9-TARGp4_TCCGTCGCCA_S249


title: Lineage_wRNA-p4F11

description:
lineage_profiles_wRNA.txt
p4F11-TARGp4_ACTATCCGCA_S263


title: sciRNA_lib-p3E4

description:
rna_raw_cell_by_gene_counts.gz
p3E4-RNAp3_AAGCCGGCTG_S148


title: sciRNA_lib-p3E6

description:
rna_raw_cell_by_gene_counts.gz
p3E6-RNAp3_CATGCATCTC_S150


title: Lineage_wRNA-p4E8

description:
lineage_profiles_wRNA.txt
p4E8-TARGp4_ACCGTTACGA_S248


title: sciRNA_lib-p3F1

description:
rna_raw_cell_by_gene_counts.gz
p3F1-RNAp3_AACTACCGAC_S157


title: Lineage_wRNA-p4E7

description:
lineage_profiles_wRNA.txt
p4E7-TARGp4_TCCGGTAATC_S247


title: Lineage_wRNA-p4E6

description:
lineage_profiles_wRNA.txt
p4E6-TARGp4_CATGCATCTC_S246


title: sciRNA_lib-p3E5

description:
rna_raw_cell_by_gene_counts.gz
p3E5-RNAp3_CTCCGGTTCT_S149


title: sciRNA_lib-p3E2

description:
rna_raw_cell_by_gene_counts.gz
p3E2-RNAp3_ACTATCTTGA_S146


title: Lineage_wRNA-p4E5

description:
lineage_profiles_wRNA.txt
p4E5-TARGp4_CTCCGGTTCT_S245


title: sciRNA_lib-p3E1

description:
rna_raw_cell_by_gene_counts.gz
p3E1-RNAp3_GCTCTCGCCT_S145


title: sciRNA_lib-p3E12

description:
rna_raw_cell_by_gene_counts.gz
p3E12-RNAp3_ACTTCCGAAT_S156


title: Lineage_wRNA-p4E4

description:
lineage_profiles_wRNA.txt
p4E4-TARGp4_AAGCCGGCTG_S244


title: Lineage_wRNA-p4F12

description:
lineage_profiles_wRNA.txt
p4F12-TARGp4_CGAGCTGCCA_S264


title: Lineage_wRNA-p4E3

description:
lineage_profiles_wRNA.txt
p4E3-TARGp4_AGGTCAATTA_S243


title: sciRNA_lib-p3E10

description:
rna_raw_cell_by_gene_counts.gz
p3E10-RNAp3_GGCTATGACT_S154


title: sciRNA_lib-p3E11

description:
rna_raw_cell_by_gene_counts.gz
p3E11-RNAp3_TGGACTTGAC_S155


title: Lineage_wRNA-p4E1

description:
lineage_profiles_wRNA.txt
p4E1-TARGp4_GCTCTCGCCT_S241


title: sciRNA_lib-p3D7

description:
rna_raw_cell_by_gene_counts.gz
p3D7-RNAp3_ACCAAGATCT_S139


title: sciRNA_lib-p3D9

description:
rna_raw_cell_by_gene_counts.gz
p3D9-RNAp3_GACCTCTCTG_S141


title: Lineage_wRNA-p4E2

description:
lineage_profiles_wRNA.txt
p4E2-TARGp4_ACTATCTTGA_S242


title: sciRNA_lib-p3E3

description:
rna_raw_cell_by_gene_counts.gz
p3E3-RNAp3_AGGTCAATTA_S147


title: Lineage_wRNA-p4E10

description:
lineage_profiles_wRNA.txt
p4E10-TARGp4_GGCTATGACT_S250


title: sciRNA_lib-p3D8

description:
rna_raw_cell_by_gene_counts.gz
p3D8-RNAp3_CGATCATTAC_S140


title: sciRNA_lib-p3D6

description:
rna_raw_cell_by_gene_counts.gz
p3D6-RNAp3_CTAACTCCAA_S138


title: sciRNA_lib-p3D5

description:
rna_raw_cell_by_gene_counts.gz
p3D5-RNAp3_TCTAGAACTA_S137


title: Lineage_wRNA-p4D9

description:
lineage_profiles_wRNA.txt
p4D9-TARGp4_GACCTCTCTG_S237


title: sciRNA_lib-p3D4

description:
rna_raw_cell_by_gene_counts.gz
p3D4-RNAp3_GACCTCCGCC_S136


title: Lineage_wRNA-p4D8

description:
lineage_profiles_wRNA.txt
p4D8-TARGp4_CGATCATTAC_S236


title: Lineage_wRNA-p4E11

description:
lineage_profiles_wRNA.txt
p4E11-TARGp4_TGGACTTGAC_S251


title: sciRNA_lib-p3D3

description:
rna_raw_cell_by_gene_counts.gz
p3D3-RNAp3_CGGCGAGACC_S135


title: sciRNA_lib-p3D1

description:
rna_raw_cell_by_gene_counts.gz
p3D1-RNAp3_CGCCGCCTCC_S133


title: Lineage_wRNA-p4D7

description:
lineage_profiles_wRNA.txt
p4D7-TARGp4_ACCAAGATCT_S235


title: sciRNA_lib-p3D2

description:
rna_raw_cell_by_gene_counts.gz
p3D2-RNAp3_CAAGTACTGG_S134


title: Lineage_wRNA-p4D4

description:
lineage_profiles_wRNA.txt
p4D4-TARGp4_GACCTCCGCC_S232


title: Lineage_wRNA-p4D6

description:
lineage_profiles_wRNA.txt
p4D6-TARGp4_CTAACTCCAA_S234


title: sciRNA_lib-p3D10

description:
rna_raw_cell_by_gene_counts.gz
p3D10-RNAp3_GGCTAATTAA_S142


title: Lineage_wRNA-p4D5

description:
lineage_profiles_wRNA.txt
p4D5-TARGp4_TCTAGAACTA_S233


title: Lineage_wRNA-p4D2

description:
lineage_profiles_wRNA.txt
p4D2-TARGp4_CAAGTACTGG_S230


title: Lineage_wRNA-p4D3

description:
lineage_profiles_wRNA.txt
p4D3-TARGp4_CGGCGAGACC_S231


title: Lineage_wRNA-p4E12

description:
lineage_profiles_wRNA.txt
p4E12-TARGp4_ACTTCCGAAT_S252


title: sciRNA_lib-p3C9

description:
rna_raw_cell_by_gene_counts.gz
p3C9-RNAp3_GCAACTGGCA_S129


title: Lineage_wRNA-p4D1

description:
lineage_profiles_wRNA.txt
p4D1-TARGp4_CGCCGCCTCC_S229


title: sciRNA_lib-p3C8

description:
rna_raw_cell_by_gene_counts.gz
p3C8-RNAp3_AATTGCCTAC_S128


title: sciRNA_lib-p3C7

description:
rna_raw_cell_by_gene_counts.gz
p3C7-RNAp3_TCGTAGGCTT_S127


title: sciRNA_lib-p3C4

description:
rna_raw_cell_by_gene_counts.gz
p3C4-RNAp3_CTGCTTCGAC_S124


title: Lineage_wRNA-p4D11

description:
lineage_profiles_wRNA.txt
p4D11-TARGp4_CGAGTTAGAG_S239


title: sciRNA_lib-p3C6

description:
rna_raw_cell_by_gene_counts.gz
p3C6-RNAp3_AGTTGCATCT_S126


title: Lineage_wRNA-p4C8

description:
lineage_profiles_wRNA.txt
p4C8-TARGp4_AATTGCCTAC_S224


title: Lineage_wRNA-p4C9

description:
lineage_profiles_wRNA.txt
p4C9-TARGp4_GCAACTGGCA_S225


title: sciRNA_lib-p3C5

description:
rna_raw_cell_by_gene_counts.gz
p3C5-RNAp3_CCTAGCGCCT_S125


title: sciRNA_lib-p3C3

description:
rna_raw_cell_by_gene_counts.gz
p3C3-RNAp3_GACTAGTCTA_S123


title: sciRNA_lib-p3D12

description:
rna_raw_cell_by_gene_counts.gz
p3D12-RNAp3_GATGATCGTA_S144


title: Lineage_wRNA-p4D10

description:
lineage_profiles_wRNA.txt
p4D10-TARGp4_GGCTAATTAA_S238


title: sciRNA_lib-p3C12

description:
rna_raw_cell_by_gene_counts.gz
p3C12-RNAp3_CTCGGTCAAT_S132


title: sciRNA_lib-p3C2

description:
rna_raw_cell_by_gene_counts.gz
p3C2-RNAp3_TCATCTCGAT_S122


title: Lineage_wRNA-p4C4

description:
lineage_profiles_wRNA.txt
p4C4-TARGp4_CTGCTTCGAC_S220


title: Lineage_wRNA-p4C7

description:
lineage_profiles_wRNA.txt
p4C7-TARGp4_TCGTAGGCTT_S223


title: sciRNA_lib-p3C11

description:
rna_raw_cell_by_gene_counts.gz
p3C11-RNAp3_GGTAGGTCTC_S131


title: Lineage_wRNA-p4C6

description:
lineage_profiles_wRNA.txt
p4C6-TARGp4_AGTTGCATCT_S222


title: sciRNA_lib-p3C1

description:
rna_raw_cell_by_gene_counts.gz
p3C1-RNAp3_GTTCCGACGA_S121


title: Lineage_wRNA-p4C3

description:
lineage_profiles_wRNA.txt
p4C3-TARGp4_GACTAGTCTA_S219


title: Lineage_wRNA-p4C5

description:
lineage_profiles_wRNA.txt
p4C5-TARGp4_CCTAGCGCCT_S221


title: sciRNA_lib-p3D11

description:
rna_raw_cell_by_gene_counts.gz
p3D11-RNAp3_CGAGTTAGAG_S143


title: sciRNA_lib-p3C10

description:
rna_raw_cell_by_gene_counts.gz
p3C10-RNAp3_GATACCTAAG_S130


title: Lineage_wRNA-p4C2

description:
lineage_profiles_wRNA.txt
p4C2-TARGp4_TCATCTCGAT_S218


title: Lineage_wRNA-p4C1

description:
lineage_profiles_wRNA.txt
p4C1-TARGp4_GTTCCGACGA_S217


title: Lineage_wRNA-p4D12

description:
lineage_profiles_wRNA.txt
p4D12-TARGp4_GATGATCGTA_S240


title: Lineage_wRNA-p4C12

description:
lineage_profiles_wRNA.txt
p4C12-TARGp4_CTCGGTCAAT_S228


title: sciRNA_lib-p3B9

description:
rna_raw_cell_by_gene_counts.gz
p3B9-RNAp3_AGCGTCAATG_S117


title: Lineage_wRNA-p4C11

description:
lineage_profiles_wRNA.txt
p4C11-TARGp4_GGTAGGTCTC_S227


title: Lineage_wRNA-p4B9

description:
lineage_profiles_wRNA.txt
p4B9-TARGp4_AGCGTCAATG_S213


title: Lineage_wRNA-p4B6

description:
lineage_profiles_wRNA.txt
p4B6-TARGp4_GTCGCTCAGT_S210


title: Lineage_wRNA-p4B8

description:
lineage_profiles_wRNA.txt
p4B8-TARGp4_CCGTCGGAGG_S212


title: sciRNA_lib-p3B8

description:
rna_raw_cell_by_gene_counts.gz
p3B8-RNAp3_CCGTCGGAGG_S116


title: sciRNA_lib-p3B7

description:
rna_raw_cell_by_gene_counts.gz
p3B7-RNAp3_TGATTCCTCA_S115


title: Lineage_wRNA-p4B7

description:
lineage_profiles_wRNA.txt
p4B7-TARGp4_TGATTCCTCA_S211


title: Lineage_wRNA-p4B3

description:
lineage_profiles_wRNA.txt
p4B3-TARGp4_GAACTGCATC_S207


title: sciRNA_lib-p3B5

description:
rna_raw_cell_by_gene_counts.gz
p3B5-RNAp3_ACTCTCTCAA_S113


title: Lineage_wRNA-p4B2

description:
lineage_profiles_wRNA.txt
p4B2-TARGp4_GGACTCATTG_S206


title: Lineage_wRNA-p4B5

description:
lineage_profiles_wRNA.txt
p4B5-TARGp4_ACTCTCTCAA_S209


title: Lineage_wRNA-p4B1

description:
lineage_profiles_wRNA.txt
p4B1-TARGp4_TTAACGTACC_S205


title: CL1-5_Stably expressing V5-tagged MTAP gene_MTAP-2

type: RNA

city: Taipei

first: Wen-Hsin

last: Chang

address: 7F, No.2, Syu-jhou Road

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CL1-5 stably expressing V5-tagged MTAP gene

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The expression data were analyzed by GeneSpring GX 13.0 (Silicon Genetics, Redwood City, CA). The Affymetrix CEL files were transformed by GC-RMA algorithm, and each probe set was summarized using the median of the corresponding probes.

label: biotin

source_name: Lung cancer cell CL1-5, stably expressing V5-tagged MTAP gene

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: The human lung cancer cell line, CL1-5, was grown in DMEM media supplemented with 10% FBS. All cell lines were incubated at 37°C in a humidified 20% O2/5% CO2 environment.

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

treatment_protocol: CL1-5 cells were transfected with pcDNA3.1 vector or pcDNA3.1-MTAP, respectively. The stable cell lines were maintained in complete media with G418 (Geneticin).

tag: cell line

tag: tumor type

value: lung adenocacinoma

tag: ethnicity

value: Asian

tag: age

value: 64 years

tag: gender

value: male


title: Lineage_wRNA-p4B12

description:
lineage_profiles_wRNA.txt
p4B12-TARGp4_TGAGGTAGAA_S216


title: Lineage_wRNA-p4B4

description:
lineage_profiles_wRNA.txt
p4B4-TARGp4_GGAACGATGG_S208


title: CL1-5_Stably expressing V5-tagged MTAP gene_MTAP-3


title: sciRNA_lib-p3B6

description:
rna_raw_cell_by_gene_counts.gz
p3B6-RNAp3_GTCGCTCAGT_S114


title: 1B_EB40

city: Hangzhou

first: Xiaowen

last: Shi

state: Zhejiang

address: 866 Yuhangtang Road NongshenghuanA443

department: College of Agriculture and Biotechnology

country: China

institute: Zhejiang University

description:
also uploaded in GSE127500 as EB40
rpm_miRNA.txt
results_counts_miRNA.txt

data_processing:
1. the 3' end of the reads was trimmed for Illumina adapters, for ambiguous nucleotides (N's), and for artificial poly-G using cutadapt version 1.16.
2. Low quality reads were removed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, fastq_quality_filter -Q33 -q20 -p80).
3. Reads mapped to known structural RNAs (rRNAs, tRNAs, sn-RNAs, and sno-RNAs) from Rfam 14.0 using bowtie 2 were removed.
4. Reads of 18-30 nt without poly(A) tails were aligned to the maize reference genome W22v2, the maize chloroplast, and mitochondrial genomes.
5. Read counts were normarlized with RPM and differential gene expression analysis were performed via edgeR.
Supplementary_files_format_and_content: Tab-delimited text files include raw count table of mapped miRNA generated by ShortStack and RPM normalized counts.

organism: Zea mays

source_name: Leaf tissue

growth_protocol: 45-day grown in the greenhouse

extract_protocol:
Extracted by mirVana™ miRNA Isolation Kit
sRNA libraries were prepared for sequencing using standard Illumina protocols

tag: diploid aneuploids, disomy, whole-ploidy, or b chromosome

value: B chromosome comparison


title: sciRNA_lib-p3B4

description:
rna_raw_cell_by_gene_counts.gz
p3B4-RNAp3_GGAACGATGG_S112


title: 1B_EB23

description:
also uploaded in GSE127500 as EB23
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p3B3

description:
rna_raw_cell_by_gene_counts.gz
p3B3-RNAp3_GAACTGCATC_S111


title: sciRNA_lib-p3B2

description:
rna_raw_cell_by_gene_counts.gz
p3B2-RNAp3_GGACTCATTG_S110


title: Lineage_wRNA-p4B10

description:
lineage_profiles_wRNA.txt
p4B10-TARGp4_CGAAGGACGA_S214


title: CL1-5_Stably expressing V5-tagged MTAP gene_MTAP-1


title: 1B_EB37

description:
also uploaded in GSE127500 as EB37
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p4C10

description:
lineage_profiles_wRNA.txt
p4C10-TARGp4_GATACCTAAG_S226


title: Lineage_wRNA-p4A8

description:
lineage_profiles_wRNA.txt
p4A8-TARGp4_GATCAGTCAT_S200


title: Lineage_wRNA-p4A7

description:
lineage_profiles_wRNA.txt
p4A7-TARGp4_TTAGATTCCG_S199


title: CL1-5_Stably expressing control vector_Mock-2

description: Gene expression data from CL1-5 stably expressing control vector

source_name: Lung cancer cell CL1-5, stably expressing control vector


title: Lineage_wRNA-p4A9

description:
lineage_profiles_wRNA.txt
p4A9-TARGp4_TCGATATTGA_S201


title: CL1-5_Stably expressing control vector_Mock-3


title: sciRNA_lib-p3B1

description:
rna_raw_cell_by_gene_counts.gz
p3B1-RNAp3_TTAACGTACC_S109


title: 1B_EB2

description:
also uploaded in GSE127500 as EB2
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p4B11

description:
lineage_profiles_wRNA.txt
p4B11-TARGp4_TTGAGTATCA_S215


title: sciRNA_lib-p3B12

description:
rna_raw_cell_by_gene_counts.gz
p3B12-RNAp3_TGAGGTAGAA_S120


title: CL1-5_Stably expressing control vector_Mock-1


title: sciRNA_lib-p3B11

description:
rna_raw_cell_by_gene_counts.gz
p3B11-RNAp3_TTGAGTATCA_S119


title: Lineage_wRNA-p4A5

description:
lineage_profiles_wRNA.txt
p4A5-TARGp4_GCTCTAACGA_S197


title: 0B_D3

description:
also uploaded in GSE127500 as D3
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p4A4

description:
lineage_profiles_wRNA.txt
p4A4-TARGp4_CTCGTCTAGG_S196


title: 0B_D4

description:
also uploaded in GSE127500 as D4
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p4A6

description:
lineage_profiles_wRNA.txt
p4A6-TARGp4_TGATAGAACG_S198


title: sciRNA_lib-p3B10

description:
rna_raw_cell_by_gene_counts.gz
p3B10-RNAp3_CGAAGGACGA_S118


title: Lineage_wRNA-p4A2

description:
lineage_profiles_wRNA.txt
p4A2-TARGp4_CGACTACCAA_S194


title: 0B_D2

description:
also uploaded in GSE127500 as D2
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p4A11

description:
lineage_profiles_wRNA.txt
p4A11-TARGp4_TTGGTCATAA_S203


title: Lineage_wRNA-p4A1

description:
lineage_profiles_wRNA.txt
p4A1-TARGp4_CTCGATGGAG_S193


title: Lineage_wRNA-p4A10

description:
lineage_profiles_wRNA.txt
p4A10-TARGp4_CCAGGTCTAC_S202


title: sciRNA_lib-p3A8

description:
rna_raw_cell_by_gene_counts.gz
p3A8-RNAp3_GATCAGTCAT_S104


title: sciRNA_lib-p3A9

description:
rna_raw_cell_by_gene_counts.gz
p3A9-RNAp3_TCGATATTGA_S105


title: sciRNA_lib-p3A7

description:
rna_raw_cell_by_gene_counts.gz
p3A7-RNAp3_TTAGATTCCG_S103


title: 7Lb_9Lc_10L19_h1D_Hh73

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-7Lb, 9Lc, 10L19)


title: Lineage_wRNA-p3H9

description:
lineage_profiles_wRNA.txt
p3H9-TARGp3_GATTGCAGAC_S189


title: Lineage_wRNA-p3H8

description:
lineage_profiles_wRNA.txt
p3H8-TARGp3_CCTATAAGCT_S188


title: 7Lb_9Lc_10L19_h1D_Hh74

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p4A12

description:
lineage_profiles_wRNA.txt
p4A12-TARGp4_AACGGACCAA_S204


title: Lineage_wRNA-p3H7

description:
lineage_profiles_wRNA.txt
p3H7-TARGp3_AGATCCTATA_S187


title: sciRNA_lib-p3A6

description:
rna_raw_cell_by_gene_counts.gz
p3A6-RNAp3_TGATAGAACG_S102


title: Lineage_wRNA-p4A3

description:
lineage_profiles_wRNA.txt
p4A3-TARGp4_GTTGACGGCC_S195


title: Lineage_wRNA-p3H5

description:
lineage_profiles_wRNA.txt
p3H5-TARGp3_AACTTATAAG_S185


title: 7Lb_9Lc_10L19_h1D_Hh72

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3H6

description:
lineage_profiles_wRNA.txt
p3H6-TARGp3_TCATCTAATC_S186


title: 0B_D1

description:
also uploaded in GSE127500 as D1
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3H1

description:
lineage_profiles_wRNA.txt
p3H1-TARGp3_TTCTACGCCA_S181


title: sciRNA_lib-p3A5

description:
rna_raw_cell_by_gene_counts.gz
p3A5-RNAp3_GCTCTAACGA_S101


title: Lineage_wRNA-p3H2

description:
lineage_profiles_wRNA.txt
p3H2-TARGp3_TGGCCGCAAT_S182


title: Lineage_wRNA-p3H3

description:
lineage_profiles_wRNA.txt
p3H3-TARGp3_CCAAGCTGAA_S183


title: Lineage_wRNA-p3H4

description:
lineage_profiles_wRNA.txt
p3H4-TARGp3_TGCCAGATGG_S184


title: 7Lb_9Lc_10L19_h1D_Hh70

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3H11

description:
lineage_profiles_wRNA.txt
p3H11-TARGp3_AAGATCCAAC_S191


title: Lineage_wRNA-p3H12

description:
lineage_profiles_wRNA.txt
p3H12-TARGp3_CTGCAATCGC_S192


title: 3Sb_4Lb_6Lc_h1D_Hh68

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-3Sb, 4Lb, 6Lc)


title: 3Sb_4Lb_6Lc_h1D_Hh69

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p3A3

description:
rna_raw_cell_by_gene_counts.gz
p3A3-RNAp3_GTTGACGGCC_S99


title: Lineage_wRNA-p3G9

description:
lineage_profiles_wRNA.txt
p3G9-TARGp3_CAAGCTTGGC_S177


title: Lineage_wRNA-p3H10

description:
lineage_profiles_wRNA.txt
p3H10-TARGp3_ATAAGAGGCG_S190


title: Lineage_wRNA-p3G7

description:
lineage_profiles_wRNA.txt
p3G7-TARGp3_TCTATAAGGA_S175


title: sciRNA_lib-p3A4

description:
rna_raw_cell_by_gene_counts.gz
p3A4-RNAp3_CTCGTCTAGG_S100


title: sciRNA_lib-p3A2

description:
rna_raw_cell_by_gene_counts.gz
p3A2-RNAp3_CGACTACCAA_S98


title: sciRNA_lib-p3A1

description:
rna_raw_cell_by_gene_counts.gz
p3A1-RNAp3_CTCGATGGAG_S97


title: 3Sb_4Lb_6Lc_h1D_Hh66

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 3La_7Sc_h1D_Hh60

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-3La, 7Sc)


title: Lineage_wRNA-p3G6

description:
lineage_profiles_wRNA.txt
p3G6-TARGp3_CATTATTACC_S174


title: Lineage_wRNA-p3G4

description:
lineage_profiles_wRNA.txt
p3G4-TARGp3_ACGCAACTCC_S172


title: Lineage_wRNA-p3G8

description:
lineage_profiles_wRNA.txt
p3G8-TARGp3_TTGGAGTCGG_S176


title: 7Lb_9Lc_10L19_h1D_Hh71

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p3A11

description:
rna_raw_cell_by_gene_counts.gz
p3A11-RNAp3_TTGGTCATAA_S107


title: 3La_7Sc_h1D_Hh58

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p3A12

description:
rna_raw_cell_by_gene_counts.gz
p3A12-RNAp3_AACGGACCAA_S108


title: Lineage_wRNA-p3G5

description:
lineage_profiles_wRNA.txt
p3G5-TARGp3_TGATACGAGT_S173


title: Lineage_wRNA-p3G3

description:
lineage_profiles_wRNA.txt
p3G3-TARGp3_CAAGATTAAG_S171


title: 3La_7Sc_h1D_Hh57

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p3A10

description:
rna_raw_cell_by_gene_counts.gz
p3A10-RNAp3_CCAGGTCTAC_S106


title: Lineage_wRNA-p3G1

description:
lineage_profiles_wRNA.txt
p3G1-TARGp3_GACCGTAGCA_S169


title: sciRNA_lib-p2H9

description:
rna_raw_cell_by_gene_counts.gz
p2H9-RNAp2_GATTGCAGAC_S93


title: Lineage_wRNA-p3G2

description:
lineage_profiles_wRNA.txt
p3G2-TARGp3_GTCATTGCGC_S170


title: Lineage_wRNA-p3G12

description:
lineage_profiles_wRNA.txt
p3G12-TARGp3_ACTGAATTCC_S180


title: Lineage_wRNA-p3G11

description:
lineage_profiles_wRNA.txt
p3G11-TARGp3_TGGCGTAGGT_S179


title: Lineage_wRNA-p3F9

description:
lineage_profiles_wRNA.txt
p3F9-TARGp3_AACCTAGCTT_S165


title: 1Sb_h1D_Hh47

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-1Sb)


title: 1Sb_h1D_Hh50

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2H8

description:
rna_raw_cell_by_gene_counts.gz
p2H8-RNAp2_CCTATAAGCT_S92


title: Lineage_wRNA-p3G10

description:
lineage_profiles_wRNA.txt
p3G10-TARGp3_ATAGGATATG_S178


title: 1Sb_h1D_Hh48

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2H7

description:
rna_raw_cell_by_gene_counts.gz
p2H7-RNAp2_AGATCCTATA_S91


title: 1Sb_h1D_Hh46

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3F7

description:
lineage_profiles_wRNA.txt
p3F7-TARGp3_TATAACTTCC_S163


title: sciRNA_lib-p2H6

description:
rna_raw_cell_by_gene_counts.gz
p2H6-RNAp2_TCATCTAATC_S90


title: Lineage_wRNA-p3F8

description:
lineage_profiles_wRNA.txt
p3F8-TARGp3_AGGATTACCA_S164


title: 2Sanormal_2Sadeletion_h1D_Hh45

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-2Sa, 2Sa_deletion)


title: sciRNA_lib-p2H5

description:
rna_raw_cell_by_gene_counts.gz
p2H5-RNAp2_AACTTATAAG_S89


title: Lineage_wRNA-p3F5

description:
lineage_profiles_wRNA.txt
p3F5-TARGp3_ACGTTCAACC_S161


title: 2Sanormal_2Sadeletion_h1D_Hh44

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3F6

description:
lineage_profiles_wRNA.txt
p3F6-TARGp3_ACGAGGACCT_S162


title: Lineage_wRNA-p3F1

description:
lineage_profiles_wRNA.txt
p3F1-TARGp3_AACTACCGAC_S157


title: Lineage_wRNA-p3F12

description:
lineage_profiles_wRNA.txt
p3F12-TARGp3_CGAGCTGCCA_S168


title: Lineage_wRNA-p3F4

description:
lineage_profiles_wRNA.txt
p3F4-TARGp3_AACGAGGCTA_S160


title: 2Sanormal_2Sadeletion_h1D_Hh43

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3F11

description:
lineage_profiles_wRNA.txt
p3F11-TARGp3_ACTATCCGCA_S167


title: sciRNA_lib-p2H3

description:
rna_raw_cell_by_gene_counts.gz
p2H3-RNAp2_CCAAGCTGAA_S87


title: sciRNA_lib-p2H2

description:
rna_raw_cell_by_gene_counts.gz
p2H2-RNAp2_TGGCCGCAAT_S86


title: Lineage_wRNA-p3F10

description:
lineage_profiles_wRNA.txt
p3F10-TARGp3_AGTCCGCGGA_S166


title: Lineage_wRNA-p3E8

description:
lineage_profiles_wRNA.txt
p3E8-TARGp3_ACCGTTACGA_S152


title: 2Sanormal_2Sadeletion_h1D_Hh39

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 1La_5Lb_8Lc_h1D_Hh26

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-1La, 5Lb, 8Lc)


title: Lineage_wRNA-p3E7

description:
lineage_profiles_wRNA.txt
p3E7-TARGp3_TCCGGTAATC_S151


title: Lineage_wRNA-p3E5

description:
lineage_profiles_wRNA.txt
p3E5-TARGp3_CTCCGGTTCT_S149


title: sciRNA_lib-p2H12

description:
rna_raw_cell_by_gene_counts.gz
p2H12-RNAp2_CTGCAATCGC_S96


title: Lineage_wRNA-p3E6

description:
lineage_profiles_wRNA.txt
p3E6-TARGp3_CATGCATCTC_S150


title: Lineage_wRNA-p3F3

description:
lineage_profiles_wRNA.txt
p3F3-TARGp3_GGTCCAGGAG_S159


title: Lineage_wRNA-p3F2

description:
lineage_profiles_wRNA.txt
p3F2-TARGp3_CGTCCGTCCT_S158


title: sciRNA_lib-p2H4

description:
rna_raw_cell_by_gene_counts.gz
p2H4-RNAp2_TGCCAGATGG_S88


title: Lineage_wRNA-p3E4

description:
lineage_profiles_wRNA.txt
p3E4-TARGp3_AAGCCGGCTG_S148


title: 1La_5Lb_8Lc_h1D_Hh24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 1La_5Lb_8Lc_h1D_Hh23

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3E1

description:
lineage_profiles_wRNA.txt
p3E1-TARGp3_GCTCTCGCCT_S145


title: sciRNA_lib-p2H10

description:
rna_raw_cell_by_gene_counts.gz
p2H10-RNAp2_ATAAGAGGCG_S94


title: 4Sa_9Sd_h1D_Hh20

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-4Sa, 9Sd)


title: sciRNA_lib-p2H11

description:
rna_raw_cell_by_gene_counts.gz
p2H11-RNAp2_AAGATCCAAC_S95


title: Lineage_wRNA-p3E3

description:
lineage_profiles_wRNA.txt
p3E3-TARGp3_AGGTCAATTA_S147


title: Lineage_wRNA-p3E12

description:
lineage_profiles_wRNA.txt
p3E12-TARGp3_ACTTCCGAAT_S156


title: Lineage_wRNA-p3E2

description:
lineage_profiles_wRNA.txt
p3E2-TARGp3_ACTATCTTGA_S146


title: sciRNA_lib-p2G9

description:
rna_raw_cell_by_gene_counts.gz
p2G9-RNAp2_CAAGCTTGGC_S81


title: Lineage_wRNA-p3E11

description:
lineage_profiles_wRNA.txt
p3E11-TARGp3_TGGACTTGAC_S155


title: Lineage_wRNA-p3E9

description:
lineage_profiles_wRNA.txt
p3E9-TARGp3_TCCGTCGCCA_S153


title: Lineage_wRNA-p3E10

description:
lineage_profiles_wRNA.txt
p3E10-TARGp3_GGCTATGACT_S154


title: sciRNA_lib-p2H1

description:
rna_raw_cell_by_gene_counts.gz
p2H1-RNAp2_TTCTACGCCA_S85


title: sciRNA_lib-p2G8

description:
rna_raw_cell_by_gene_counts.gz
p2G8-RNAp2_TTGGAGTCGG_S80


title: Lineage_wRNA-p3D9

description:
lineage_profiles_wRNA.txt
p3D9-TARGp3_GACCTCTCTG_S141


title: sciRNA_lib-p2G7

description:
rna_raw_cell_by_gene_counts.gz
p2G7-RNAp2_TCTATAAGGA_S79


title: Lineage_wRNA-p3D8

description:
lineage_profiles_wRNA.txt
p3D8-TARGp3_CGATCATTAC_S140


title: 4Sa_9Sd_h1D_Hh18

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 4Sa_9Sd_h1D_Hh19

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 1La_5Lb_8Lc_h1D_Hh27

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 4Sa_9Sd_h1D_Hh17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3D6

description:
lineage_profiles_wRNA.txt
p3D6-TARGp3_CTAACTCCAA_S138


title: Lineage_wRNA-p3D4

description:
lineage_profiles_wRNA.txt
p3D4-TARGp3_GACCTCCGCC_S136


title: 9Sd_h2D_9Sdh9

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-9Sd)


title: sciRNA_lib-p2G5

description:
rna_raw_cell_by_gene_counts.gz
p2G5-RNAp2_TGATACGAGT_S77


title: sciRNA_lib-p2G4

description:
rna_raw_cell_by_gene_counts.gz
p2G4-RNAp2_ACGCAACTCC_S76


title: Lineage_wRNA-p3D5

description:
lineage_profiles_wRNA.txt
p3D5-TARGp3_TCTAGAACTA_S137


title: Lineage_wRNA-p3D2

description:
lineage_profiles_wRNA.txt
p3D2-TARGp3_CAAGTACTGG_S134


title: Lineage_wRNA-p3D12

description:
lineage_profiles_wRNA.txt
p3D12-TARGp3_GATGATCGTA_S144


title: Lineage_wRNA-p3D1

description:
lineage_profiles_wRNA.txt
p3D1-TARGp3_CGCCGCCTCC_S133


title: 9Sd_h2D_9Sdh12

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3D10

description:
lineage_profiles_wRNA.txt
p3D10-TARGp3_GGCTAATTAA_S142


title: 9Sd_h2D_9Sdh11

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3D3

description:
lineage_profiles_wRNA.txt
p3D3-TARGp3_CGGCGAGACC_S135


title: sciRNA_lib-p2G2

description:
rna_raw_cell_by_gene_counts.gz
p2G2-RNAp2_GTCATTGCGC_S74


title: 9Sd_h2D_9Sdh13

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3C9

description:
lineage_profiles_wRNA.txt
p3C9-TARGp3_GCAACTGGCA_S129


title: 9Lc_h2D_9Lch43

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-9Lc)


title: Lineage_wRNA-p3C7

description:
lineage_profiles_wRNA.txt
p3C7-TARGp3_TCGTAGGCTT_S127


title: sciRNA_lib-p2G1

description:
rna_raw_cell_by_gene_counts.gz
p2G1-RNAp2_GACCGTAGCA_S73


title: Lineage_wRNA-p3D7

description:
lineage_profiles_wRNA.txt
p3D7-TARGp3_ACCAAGATCT_S139


title: Lineage_wRNA-p3C6

description:
lineage_profiles_wRNA.txt
p3C6-TARGp3_AGTTGCATCT_S126


title: Lineage_wRNA-p3C4

description:
lineage_profiles_wRNA.txt
p3C4-TARGp3_CTGCTTCGAC_S124


title: sciRNA_lib-p2G3

description:
rna_raw_cell_by_gene_counts.gz
p2G3-RNAp2_CAAGATTAAG_S75


title: 9Lc_h2D_9Lch38

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3D11

description:
lineage_profiles_wRNA.txt
p3D11-TARGp3_CGAGTTAGAG_S143


title: sciRNA_lib-p2G10

description:
rna_raw_cell_by_gene_counts.gz
p2G10-RNAp2_ATAGGATATG_S82


title: 9Lc_h2D_9Lch34

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3C11

description:
lineage_profiles_wRNA.txt
p3C11-TARGp3_GGTAGGTCTC_S131


title: Lineage_wRNA-p3C10

description:
lineage_profiles_wRNA.txt
p3C10-TARGp3_GATACCTAAG_S130


title: 9Lc_h2D_9Lch44

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3B9

description:
lineage_profiles_wRNA.txt
p3B9-TARGp3_AGCGTCAATG_S117


title: Lineage_wRNA-p3C12

description:
lineage_profiles_wRNA.txt
p3C12-TARGp3_CTCGGTCAAT_S132


title: Lineage_wRNA-p3C5

description:
lineage_profiles_wRNA.txt
p3C5-TARGp3_CCTAGCGCCT_S125


title: sciRNA_lib-p2G6

description:
rna_raw_cell_by_gene_counts.gz
p2G6-RNAp2_CATTATTACC_S78


title: sciRNA_lib-p2G12

description:
rna_raw_cell_by_gene_counts.gz
p2G12-RNAp2_ACTGAATTCC_S84


title: Lineage_wRNA-p3B7

description:
lineage_profiles_wRNA.txt
p3B7-TARGp3_TGATTCCTCA_S115


title: Lineage_wRNA-p3B6

description:
lineage_profiles_wRNA.txt
p3B6-TARGp3_GTCGCTCAGT_S114


title: Lineage_wRNA-p3C8

description:
lineage_profiles_wRNA.txt
p3C8-TARGp3_AATTGCCTAC_S128


title: Lineage_wRNA-p3C3

description:
lineage_profiles_wRNA.txt
p3C3-TARGp3_GACTAGTCTA_S123


title: Lineage_wRNA-p3B4

description:
lineage_profiles_wRNA.txt
p3B4-TARGp3_GGAACGATGG_S112


title: sciRNA_lib-p2G11

description:
rna_raw_cell_by_gene_counts.gz
p2G11-RNAp2_TGGCGTAGGT_S83


title: Lineage_wRNA-p3C2

description:
lineage_profiles_wRNA.txt
p3C2-TARGp3_TCATCTCGAT_S122


title: Lineage_wRNA-p3C1

description:
lineage_profiles_wRNA.txt
p3C1-TARGp3_GTTCCGACGA_S121


title: Lineage_wRNA-p3B3

description:
lineage_profiles_wRNA.txt
p3B3-TARGp3_GAACTGCATC_S111


title: 8Lc_h2D_8Lch20

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-8Lc)


title: sciRNA_lib-p2F9

description:
rna_raw_cell_by_gene_counts.gz
p2F9-RNAp2_AACCTAGCTT_S69

value: sci-RNA-seq


title: Lineage_wRNA-p3B2

description:
lineage_profiles_wRNA.txt
p3B2-TARGp3_GGACTCATTG_S110

value: Targeted lineage amplicon captured alongside sci-RNA-seq


title: sciRNA_lib-p2F8

description:
rna_raw_cell_by_gene_counts.gz
p2F8-RNAp2_AGGATTACCA_S68


title: Lineage_wRNA-p3B12

description:
lineage_profiles_wRNA.txt
p3B12-TARGp3_TGAGGTAGAA_S120


title: 8Lc_h2D_8Lch16

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3B1

description:
lineage_profiles_wRNA.txt
p3B1-TARGp3_TTAACGTACC_S109


title: sciRNA_lib-p2F7

description:
rna_raw_cell_by_gene_counts.gz
p2F7-RNAp2_TATAACTTCC_S67


title: 8Lc_h2D_8Lch13

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 7Sc_h2D_7Sch35

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-7Sc)


title: Lineage_wRNA-p3B10

description:
lineage_profiles_wRNA.txt
p3B10-TARGp3_CGAAGGACGA_S118


title: sciRNA_lib-p2F5

description:
rna_raw_cell_by_gene_counts.gz
p2F5-RNAp2_ACGTTCAACC_S65


title: sciRNA_lib-p2F2

description:
rna_raw_cell_by_gene_counts.gz
p2F2-RNAp2_CGTCCGTCCT_S62


title: Lineage_wRNA-p3A9

description:
lineage_profiles_wRNA.txt
p3A9-TARGp3_TCGATATTGA_S105


title: Lineage_wRNA-p3A8

description:
lineage_profiles_wRNA.txt
p3A8-TARGp3_GATCAGTCAT_S104


title: Lineage_wRNA-p3B5

description:
lineage_profiles_wRNA.txt
p3B5-TARGp3_ACTCTCTCAA_S113


title: Lineage_wRNA-p3B8

description:
lineage_profiles_wRNA.txt
p3B8-TARGp3_CCGTCGGAGG_S116


title: Lineage_wRNA-p3A7

description:
lineage_profiles_wRNA.txt
p3A7-TARGp3_TTAGATTCCG_S103


title: 7Lb_h2D_7Lbh47

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-7Lb)


title: 9Lc_h2D_9Lch35

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2F4

description:
rna_raw_cell_by_gene_counts.gz
p2F4-RNAp2_AACGAGGCTA_S64


title: sciRNA_lib-p2F6

description:
rna_raw_cell_by_gene_counts.gz
p2F6-RNAp2_ACGAGGACCT_S66


title: Lineage_wRNA-p3A5

description:
lineage_profiles_wRNA.txt
p3A5-TARGp3_GCTCTAACGA_S101


title: sciRNA_lib-p2F12

description:
rna_raw_cell_by_gene_counts.gz
p2F12-RNAp2_CGAGCTGCCA_S72


title: sciRNA_lib-p2F3

description:
rna_raw_cell_by_gene_counts.gz
p2F3-RNAp2_GGTCCAGGAG_S63


title: 7Sc_h2D_7Sch5

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 7Lb_h2D_7Lbh42

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 8Lc_h2D_8Lch12

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3A2

description:
lineage_profiles_wRNA.txt
p3A2-TARGp3_CGACTACCAA_S98


title: 7Sc_h2D_7Sch11

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3B11

description:
lineage_profiles_wRNA.txt
p3B11-TARGp3_TTGAGTATCA_S119


title: 7Sc_h2D_7Sch1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3A6

description:
lineage_profiles_wRNA.txt
p3A6-TARGp3_TGATAGAACG_S102


title: sciRNA_lib-p2F10

description:
rna_raw_cell_by_gene_counts.gz
p2F10-RNAp2_AGTCCGCGGA_S70


title: sciRNA_lib-p2F1

description:
rna_raw_cell_by_gene_counts.gz
p2F1-RNAp2_AACTACCGAC_S61


title: Lineage_wRNA-p3A4

description:
lineage_profiles_wRNA.txt
p3A4-TARGp3_CTCGTCTAGG_S100


title: Lineage_wRNA-p3A12

description:
lineage_profiles_wRNA.txt
p3A12-TARGp3_AACGGACCAA_S108


title: 7Lb_h2D_7Lbh23

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2E9

description:
rna_raw_cell_by_gene_counts.gz
p2E9-RNAp2_TCCGTCGCCA_S57


title: sciRNA_lib-p2F11

description:
rna_raw_cell_by_gene_counts.gz
p2F11-RNAp2_ACTATCCGCA_S71


title: 6Lc_h2D_6Lch9

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-6Lc)


title: Lineage_wRNA-p3A11

description:
lineage_profiles_wRNA.txt
p3A11-TARGp3_TTGGTCATAA_S107


title: Lineage_wRNA-p2H8

description:
lineage_profiles_wRNA.txt
p2H8-TARGp2_CCTATAAGCT_S92


title: sciRNA_lib-p2E8

description:
rna_raw_cell_by_gene_counts.gz
p2E8-RNAp2_ACCGTTACGA_S56


title: Lineage_wRNA-p2H9

description:
lineage_profiles_wRNA.txt
p2H9-TARGp2_GATTGCAGAC_S93


title: 6Lc_h2D_6Lch29

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2H6

description:
lineage_profiles_wRNA.txt
p2H6-TARGp2_TCATCTAATC_S90


title: sciRNA_lib-p2E6

description:
rna_raw_cell_by_gene_counts.gz
p2E6-RNAp2_CATGCATCTC_S54


title: Lineage_wRNA-p2H7

description:
lineage_profiles_wRNA.txt
p2H7-TARGp2_AGATCCTATA_S91


title: 7Lb_h2D_7Lbh41

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p3A3

description:
lineage_profiles_wRNA.txt
p3A3-TARGp3_GTTGACGGCC_S99


title: 6Lc_h2D_6Lch18

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2E7

description:
rna_raw_cell_by_gene_counts.gz
p2E7-RNAp2_TCCGGTAATC_S55


title: Lineage_wRNA-p3A1

description:
lineage_profiles_wRNA.txt
p3A1-TARGp3_CTCGATGGAG_S97


title: Lineage_wRNA-p2H5

description:
lineage_profiles_wRNA.txt
p2H5-TARGp2_AACTTATAAG_S89


title: Lineage_wRNA-p2H2

description:
lineage_profiles_wRNA.txt
p2H2-TARGp2_TGGCCGCAAT_S86


title: sciRNA_lib-p2E5

description:
rna_raw_cell_by_gene_counts.gz
p2E5-RNAp2_CTCCGGTTCT_S53


title: Lineage_wRNA-p2H4

description:
lineage_profiles_wRNA.txt
p2H4-TARGp2_TGCCAGATGG_S88


title: 5Sc_h2D_5Sch5

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-5Sc)


title: Lineage_wRNA-p2H3

description:
lineage_profiles_wRNA.txt
p2H3-TARGp2_CCAAGCTGAA_S87


title: sciRNA_lib-p2E4

description:
rna_raw_cell_by_gene_counts.gz
p2E4-RNAp2_AAGCCGGCTG_S52


title: Lineage_wRNA-p3A10

description:
lineage_profiles_wRNA.txt
p3A10-TARGp3_CCAGGTCTAC_S106


title: Lineage_wRNA-p2H12

description:
lineage_profiles_wRNA.txt
p2H12-TARGp2_CTGCAATCGC_S96


title: Lineage_wRNA-p2H1

description:
lineage_profiles_wRNA.txt
p2H1-TARGp2_TTCTACGCCA_S85


title: 5Sc_h2D_5Sch10

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2E3

description:
rna_raw_cell_by_gene_counts.gz
p2E3-RNAp2_AGGTCAATTA_S51


title: 5Sc_h2D_5Sch14

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2H11

description:
lineage_profiles_wRNA.txt
p2H11-TARGp2_AAGATCCAAC_S95


title: Lineage_wRNA-p2H10

description:
lineage_profiles_wRNA.txt
p2H10-TARGp2_ATAAGAGGCG_S94


title: sciRNA_lib-p2E2

description:
rna_raw_cell_by_gene_counts.gz
p2E2-RNAp2_ACTATCTTGA_S50


title: 5Sc_h2D_5Sch7

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2E1

description:
rna_raw_cell_by_gene_counts.gz
p2E1-RNAp2_GCTCTCGCCT_S49


title: Lineage_wRNA-p2G9

description:
lineage_profiles_wRNA.txt
p2G9-TARGp2_CAAGCTTGGC_S81


title: 5Sc_h1D_5Sch6

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 5Sc_h1D_5Sch4

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2G8

description:
lineage_profiles_wRNA.txt
p2G8-TARGp2_TTGGAGTCGG_S80


title: Lineage_wRNA-p2G3

description:
lineage_profiles_wRNA.txt
p2G3-TARGp2_CAAGATTAAG_S75


title: Lineage_wRNA-p2G4

description:
lineage_profiles_wRNA.txt
p2G4-TARGp2_ACGCAACTCC_S76


title: sciRNA_lib-p2E11

description:
rna_raw_cell_by_gene_counts.gz
p2E11-RNAp2_TGGACTTGAC_S59


title: Lineage_wRNA-p2G5

description:
lineage_profiles_wRNA.txt
p2G5-TARGp2_TGATACGAGT_S77


title: 5Sc_h1D_5Sch18

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2G2

description:
lineage_profiles_wRNA.txt
p2G2-TARGp2_GTCATTGCGC_S74


title: sciRNA_lib-p2E10

description:
rna_raw_cell_by_gene_counts.gz
p2E10-RNAp2_GGCTATGACT_S58


title: Lineage_wRNA-p2G1

description:
lineage_profiles_wRNA.txt
p2G1-TARGp2_GACCGTAGCA_S73


title: Lineage_wRNA-p2G12

description:
lineage_profiles_wRNA.txt
p2G12-TARGp2_ACTGAATTCC_S84


title: 5Lb_h2D_5Lbh9

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-5Lb)


title: Lineage_wRNA-p2G11

description:
lineage_profiles_wRNA.txt
p2G11-TARGp2_TGGCGTAGGT_S83


title: sciRNA_lib-p2D8

description:
rna_raw_cell_by_gene_counts.gz
p2D8-RNAp2_CGATCATTAC_S44


title: sciRNA_lib-p2D9

description:
rna_raw_cell_by_gene_counts.gz
p2D9-RNAp2_GACCTCTCTG_S45


title: Lineage_wRNA-p2G10

description:
lineage_profiles_wRNA.txt
p2G10-TARGp2_ATAGGATATG_S82


title: 5Lb_h2D_5Lbh8

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2F9

description:
lineage_profiles_wRNA.txt
p2F9-TARGp2_AACCTAGCTT_S69


title: 5Lb_h2D_5Lbh6

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2G7

description:
lineage_profiles_wRNA.txt
p2G7-TARGp2_TCTATAAGGA_S79


title: sciRNA_lib-p2D7

description:
rna_raw_cell_by_gene_counts.gz
p2D7-RNAp2_ACCAAGATCT_S43


title: Lineage_wRNA-p2F8

description:
lineage_profiles_wRNA.txt
p2F8-TARGp2_AGGATTACCA_S68


title: 5Sc_h1D_5Sch11

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2E12

description:
rna_raw_cell_by_gene_counts.gz
p2E12-RNAp2_ACTTCCGAAT_S60


title: Lineage_wRNA-p2F5

description:
lineage_profiles_wRNA.txt
p2F5-TARGp2_ACGTTCAACC_S65


title: 5Lb_h2D_5Lbh17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2G6

description:
lineage_profiles_wRNA.txt
p2G6-TARGp2_CATTATTACC_S78


title: Lineage_wRNA-p2F6

description:
lineage_profiles_wRNA.txt
p2F6-TARGp2_ACGAGGACCT_S66


title: Lineage_wRNA-p2F7

description:
lineage_profiles_wRNA.txt
p2F7-TARGp2_TATAACTTCC_S67


title: 4Sa_h2D_4Sah8

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-4Sa)


title: sciRNA_lib-p2D6

description:
rna_raw_cell_by_gene_counts.gz
p2D6-RNAp2_CTAACTCCAA_S42


title: sciRNA_lib-p2D5

description:
rna_raw_cell_by_gene_counts.gz
p2D5-RNAp2_TCTAGAACTA_S41


title: 4Sa_h2D_4Sah5

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2F2

description:
lineage_profiles_wRNA.txt
p2F2-TARGp2_CGTCCGTCCT_S62


title: Lineage_wRNA-p2F1

description:
lineage_profiles_wRNA.txt
p2F1-TARGp2_AACTACCGAC_S61


title: 4Sa_h2D_4Sah3

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2F4

description:
lineage_profiles_wRNA.txt
p2F4-TARGp2_AACGAGGCTA_S64


title: sciRNA_lib-p2D4

description:
rna_raw_cell_by_gene_counts.gz
p2D4-RNAp2_GACCTCCGCC_S40


title: Lineage_wRNA-p2F12

description:
lineage_profiles_wRNA.txt
p2F12-TARGp2_CGAGCTGCCA_S72


title: Lineage_wRNA-p2F11

description:
lineage_profiles_wRNA.txt
p2F11-TARGp2_ACTATCCGCA_S71


title: sciRNA_lib-p2D3

description:
rna_raw_cell_by_gene_counts.gz
p2D3-RNAp2_CGGCGAGACC_S39


title: 4Lb_h2D_4Lbh52

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-4Lb)


title: Lineage_wRNA-p2F10

description:
lineage_profiles_wRNA.txt
p2F10-TARGp2_AGTCCGCGGA_S70


title: sciRNA_lib-p2D2

description:
rna_raw_cell_by_gene_counts.gz
p2D2-RNAp2_CAAGTACTGG_S38


title: Lineage_wRNA-p2E9

description:
lineage_profiles_wRNA.txt
p2E9-TARGp2_TCCGTCGCCA_S57


title: Lineage_wRNA-p2E6

description:
lineage_profiles_wRNA.txt
p2E6-TARGp2_CATGCATCTC_S54


title: sciRNA_lib-p2D1

description:
rna_raw_cell_by_gene_counts.gz
p2D1-RNAp2_CGCCGCCTCC_S37


title: Lineage_wRNA-p2E7

description:
lineage_profiles_wRNA.txt
p2E7-TARGp2_TCCGGTAATC_S55


title: Lineage_wRNA-p2F3

description:
lineage_profiles_wRNA.txt
p2F3-TARGp2_GGTCCAGGAG_S63


title: Lineage_wRNA-p2E8

description:
lineage_profiles_wRNA.txt
p2E8-TARGp2_ACCGTTACGA_S56


title: 4Lb_h2D_4Lbh48

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2D11

description:
rna_raw_cell_by_gene_counts.gz
p2D11-RNAp2_CGAGTTAGAG_S47


title: sciRNA_lib-p2D10

description:
rna_raw_cell_by_gene_counts.gz
p2D10-RNAp2_GGCTAATTAA_S46


title: Lineage_wRNA-p2E3

description:
lineage_profiles_wRNA.txt
p2E3-TARGp2_AGGTCAATTA_S51


title: 4Lb_h2D_4Lbh34

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2E5

description:
lineage_profiles_wRNA.txt
p2E5-TARGp2_CTCCGGTTCT_S53


title: sciRNA_lib-p2D12

description:
rna_raw_cell_by_gene_counts.gz
p2D12-RNAp2_GATGATCGTA_S48


title: 3Sb_h2D_3Sbh28

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-3Sb)


title: Lineage_wRNA-p2E2

description:
lineage_profiles_wRNA.txt
p2E2-TARGp2_ACTATCTTGA_S50


title: Lineage_wRNA-p2E4

description:
lineage_profiles_wRNA.txt
p2E4-TARGp2_AAGCCGGCTG_S52


title: 3Sb_h2D_3Sbh26

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2E10

description:
lineage_profiles_wRNA.txt
p2E10-TARGp2_GGCTATGACT_S58


title: Lineage_wRNA-p2E11

description:
lineage_profiles_wRNA.txt
p2E11-TARGp2_TGGACTTGAC_S59


title: Lineage_wRNA-p2E1

description:
lineage_profiles_wRNA.txt
p2E1-TARGp2_GCTCTCGCCT_S49


title: sciRNA_lib-p2C8

description:
rna_raw_cell_by_gene_counts.gz
p2C8-RNAp2_AATTGCCTAC_S32


title: sciRNA_lib-p2C9

description:
rna_raw_cell_by_gene_counts.gz
p2C9-RNAp2_GCAACTGGCA_S33


title: Lineage_wRNA-p2E12

description:
lineage_profiles_wRNA.txt
p2E12-TARGp2_ACTTCCGAAT_S60


title: 4Lb_h2D_4Lbh50

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2C7

description:
rna_raw_cell_by_gene_counts.gz
p2C7-RNAp2_TCGTAGGCTT_S31


title: Lineage_wRNA-p2D9

description:
lineage_profiles_wRNA.txt
p2D9-TARGp2_GACCTCTCTG_S45


title: Lineage_wRNA-p2D7

description:
lineage_profiles_wRNA.txt
p2D7-TARGp2_ACCAAGATCT_S43


title: 3Sb_h2D_3Sbh25

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2C6

description:
rna_raw_cell_by_gene_counts.gz
p2C6-RNAp2_AGTTGCATCT_S30


title: Lineage_wRNA-p2D8

description:
lineage_profiles_wRNA.txt
p2D8-TARGp2_CGATCATTAC_S44


title: Lineage_wRNA-p2D5

description:
lineage_profiles_wRNA.txt
p2D5-TARGp2_TCTAGAACTA_S41


title: sciRNA_lib-p2C5

description:
rna_raw_cell_by_gene_counts.gz
p2C5-RNAp2_CCTAGCGCCT_S29


title: Lineage_wRNA-p2D3

description:
lineage_profiles_wRNA.txt
p2D3-TARGp2_CGGCGAGACC_S39


title: 4Lb_h2D_4Lbh49

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2D4

description:
lineage_profiles_wRNA.txt
p2D4-TARGp2_GACCTCCGCC_S40


title: sciRNA_lib-p2C4

description:
rna_raw_cell_by_gene_counts.gz
p2C4-RNAp2_CTGCTTCGAC_S28


title: 3Sb_h2D_3Sbh20

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 3Sb_h2D_3Sbh24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 3La_h2D_3Lah9

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-3La)


title: Lineage_wRNA-p2D2

description:
lineage_profiles_wRNA.txt
p2D2-TARGp2_CAAGTACTGG_S38


title: 3La_h2D_3Lah33

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2D1

description:
lineage_profiles_wRNA.txt
p2D1-TARGp2_CGCCGCCTCC_S37


title: sciRNA_lib-p2C2

description:
rna_raw_cell_by_gene_counts.gz
p2C2-RNAp2_TCATCTCGAT_S26


title: 3La_h2D_3Lah10

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 3La_h2D_3Lah36

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2D11

description:
lineage_profiles_wRNA.txt
p2D11-TARGp2_CGAGTTAGAG_S47


title: Lineage_wRNA-p2D10

description:
lineage_profiles_wRNA.txt
p2D10-TARGp2_GGCTAATTAA_S46


title: sciRNA_lib-p2C1

description:
rna_raw_cell_by_gene_counts.gz
p2C1-RNAp2_GTTCCGACGA_S25


title: sciRNA_lib-p2C3

description:
rna_raw_cell_by_gene_counts.gz
p2C3-RNAp2_GACTAGTCTA_S27


title: 2Sanormal_h2D_2Sah9

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-2Sa)


title: Lineage_wRNA-p2C6

description:
lineage_profiles_wRNA.txt
p2C6-TARGp2_AGTTGCATCT_S30


title: Lineage_wRNA-p2D6

description:
lineage_profiles_wRNA.txt
p2D6-TARGp2_CTAACTCCAA_S42


title: Lineage_wRNA-p2C8

description:
lineage_profiles_wRNA.txt
p2C8-TARGp2_AATTGCCTAC_S32


title: Lineage_wRNA-p2C7

description:
lineage_profiles_wRNA.txt
p2C7-TARGp2_TCGTAGGCTT_S31


title: Lineage_wRNA-p2C9

description:
lineage_profiles_wRNA.txt
p2C9-TARGp2_GCAACTGGCA_S33


title: Lineage_wRNA-p2D12

description:
lineage_profiles_wRNA.txt
p2D12-TARGp2_GATGATCGTA_S48


title: Lineage_wRNA-p2C3

description:
lineage_profiles_wRNA.txt
p2C3-TARGp2_GACTAGTCTA_S27


title: 2Sanormal_h2D_2Sah16

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2C5

description:
lineage_profiles_wRNA.txt
p2C5-TARGp2_CCTAGCGCCT_S29


title: Lineage_wRNA-p2C4

description:
lineage_profiles_wRNA.txt
p2C4-TARGp2_CTGCTTCGAC_S28


title: sciRNA_lib-p2B9

description:
rna_raw_cell_by_gene_counts.gz
p2B9-RNAp2_AGCGTCAATG_S21


title: 2Sanormal_h2D_2Sah17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2C2

description:
lineage_profiles_wRNA.txt
p2C2-TARGp2_TCATCTCGAT_S26


title: sciRNA_lib-p2C11

description:
rna_raw_cell_by_gene_counts.gz
p2C11-RNAp2_GGTAGGTCTC_S35


title: sciRNA_lib-p2C10

description:
rna_raw_cell_by_gene_counts.gz
p2C10-RNAp2_GATACCTAAG_S34


title: Lineage_wRNA-p2C1

description:
lineage_profiles_wRNA.txt
p2C1-TARGp2_GTTCCGACGA_S25


title: sciRNA_lib-p2B8

description:
rna_raw_cell_by_gene_counts.gz
p2B8-RNAp2_CCGTCGGAGG_S20


title: Lineage_wRNA-p2C11

description:
lineage_profiles_wRNA.txt
p2C11-TARGp2_GGTAGGTCTC_S35


title: 2Sanormal_h2D_2Sah10

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2C10

description:
lineage_profiles_wRNA.txt
p2C10-TARGp2_GATACCTAAG_S34


title: sciRNA_lib-p2B7

description:
rna_raw_cell_by_gene_counts.gz
p2B7-RNAp2_TGATTCCTCA_S19


title: sciRNA_lib-p2C12

description:
rna_raw_cell_by_gene_counts.gz
p2C12-RNAp2_CTCGGTCAAT_S36


title: Lineage_wRNA-p2B7

description:
lineage_profiles_wRNA.txt
p2B7-TARGp2_TGATTCCTCA_S19


title: Lineage_wRNA-p2B9

description:
lineage_profiles_wRNA.txt
p2B9-TARGp2_AGCGTCAATG_S21


title: 2Sadeletion_h2D_2Sahde5

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-2Sa_deletion)


title: 2Sadeletion_h2D_2Sahde8

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2C12

description:
lineage_profiles_wRNA.txt
p2C12-TARGp2_CTCGGTCAAT_S36


title: 2Sadeletion_h2D_2Sahde7

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2B8

description:
lineage_profiles_wRNA.txt
p2B8-TARGp2_CCGTCGGAGG_S20


title: sciRNA_lib-p2B5

description:
rna_raw_cell_by_gene_counts.gz
p2B5-RNAp2_ACTCTCTCAA_S17


title: 1Sb_h2D_1Sbh9

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-1Sb)


title: Lineage_wRNA-p2B3

description:
lineage_profiles_wRNA.txt
p2B3-TARGp2_GAACTGCATC_S15


title: Lineage_wRNA-p2B5

description:
lineage_profiles_wRNA.txt
p2B5-TARGp2_ACTCTCTCAA_S17


title: Lineage_wRNA-p2B6

description:
lineage_profiles_wRNA.txt
p2B6-TARGp2_GTCGCTCAGT_S18


title: Lineage_wRNA-p2B1

description:
lineage_profiles_wRNA.txt
p2B1-TARGp2_TTAACGTACC_S13


title: 1Sb_h2D_1Sbh170

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2B2

description:
lineage_profiles_wRNA.txt
p2B2-TARGp2_GGACTCATTG_S14


title: sciRNA_lib-p2B6

description:
rna_raw_cell_by_gene_counts.gz
p2B6-RNAp2_GTCGCTCAGT_S18


title: sciRNA_lib-p2B4

description:
rna_raw_cell_by_gene_counts.gz
p2B4-RNAp2_GGAACGATGG_S16


title: Lineage_wRNA-p2B4

description:
lineage_profiles_wRNA.txt
p2B4-TARGp2_GGAACGATGG_S16


title: Lineage_wRNA-p2B12

description:
lineage_profiles_wRNA.txt
p2B12-TARGp2_TGAGGTAGAA_S24


title: Lineage_wRNA-p2B11

description:
lineage_profiles_wRNA.txt
p2B11-TARGp2_TTGAGTATCA_S23


title: sciRNA_lib-p2B3

description:
rna_raw_cell_by_gene_counts.gz
p2B3-RNAp2_GAACTGCATC_S15


title: 1Sb_h2D_1Sbh169

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2B10

description:
lineage_profiles_wRNA.txt
p2B10-TARGp2_CGAAGGACGA_S22


title: 1Sb_h2D_1Sbh158

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2A9

description:
lineage_profiles_wRNA.txt
p2A9-TARGp2_TCGATATTGA_S9


title: 1Sb_h2D_1Sbh168

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2B2

description:
rna_raw_cell_by_gene_counts.gz
p2B2-RNAp2_GGACTCATTG_S14


title: Lineage_wRNA-p2A8

description:
lineage_profiles_wRNA.txt
p2A8-TARGp2_GATCAGTCAT_S8


title: sciRNA_lib-p2B1

description:
rna_raw_cell_by_gene_counts.gz
p2B1-RNAp2_TTAACGTACC_S13


title: Lineage_wRNA-p2A7

description:
lineage_profiles_wRNA.txt
p2A7-TARGp2_TTAGATTCCG_S7


title: 1Sb_h2D_1Sbh154

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2B12

description:
rna_raw_cell_by_gene_counts.gz
p2B12-RNAp2_TGAGGTAGAA_S24


title: 1La_h2D_1Lah5

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-1La)


title: Lineage_wRNA-p2A5

description:
lineage_profiles_wRNA.txt
p2A5-TARGp2_GCTCTAACGA_S5


title: sciRNA_lib-p2B11

description:
rna_raw_cell_by_gene_counts.gz
p2B11-RNAp2_TTGAGTATCA_S23


title: Lineage_wRNA-p2A6

description:
lineage_profiles_wRNA.txt
p2A6-TARGp2_TGATAGAACG_S6


title: Lineage_wRNA-p2A4

description:
lineage_profiles_wRNA.txt
p2A4-TARGp2_CTCGTCTAGG_S4


title: Lineage_wRNA-p2A3

description:
lineage_profiles_wRNA.txt
p2A3-TARGp2_GTTGACGGCC_S3


title: 1La_h2D_1Lah19

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p2A1

description:
lineage_profiles_wRNA.txt
p2A1-TARGp2_CTCGATGGAG_S1


title: 1La_h2D_1Lah11

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2A9

description:
rna_raw_cell_by_gene_counts.gz
p2A9-RNAp2_TCGATATTGA_S9


title: sciRNA_lib-p2B10

description:
rna_raw_cell_by_gene_counts.gz
p2B10-RNAp2_CGAAGGACGA_S22


title: Lineage_wRNA-p2A2

description:
lineage_profiles_wRNA.txt
p2A2-TARGp2_CGACTACCAA_S2


title: Lineage_wRNA-p2A12

description:
lineage_profiles_wRNA.txt
p2A12-TARGp2_AACGGACCAA_S12


title: Lineage_wRNA-p2A11

description:
lineage_profiles_wRNA.txt
p2A11-TARGp2_TTGGTCATAA_S11


title: 1La_h2D_1Lah10

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2A8

description:
rna_raw_cell_by_gene_counts.gz
p2A8-RNAp2_GATCAGTCAT_S8


title: Lineage_wRNA-p2A10

description:
lineage_profiles_wRNA.txt
p2A10-TARGp2_CCAGGTCTAC_S10


title: 10L19_h2D_10L19h62

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: disomy comparison (TB-10L19)


title: Lineage_wRNA-p1H8

description:
lineage_profiles_wRNA.txt
p1H8-TARG-AGCTTATAGG_S92_L001


title: Lineage_wRNA-p1H9

description:
lineage_profiles_wRNA.txt
p1H9-TARG-GTCTGCAATC_S93_L001


title: Lineage_wRNA-p1H6

description:
lineage_profiles_wRNA.txt
p1H6-TARG-GATTAGATGA_S90_L001


title: Lineage_wRNA-p1H5

description:
lineage_profiles_wRNA.txt
p1H5-TARG-CTTATAAGTT_S89_L001


title: sciRNA_lib-p2A6

description:
rna_raw_cell_by_gene_counts.gz
p2A6-RNAp2_TGATAGAACG_S6


title: Lineage_wRNA-p1H7

description:
lineage_profiles_wRNA.txt
p1H7-TARG-TATAGGATCT_S91_L001


title: sciRNA_lib-p2A4

description:
rna_raw_cell_by_gene_counts.gz
p2A4-RNAp2_CTCGTCTAGG_S4


title: sciRNA_lib-p2A5

description:
rna_raw_cell_by_gene_counts.gz
p2A5-RNAp2_GCTCTAACGA_S5


title: Lineage_wRNA-p1H4

description:
lineage_profiles_wRNA.txt
p1H4-TARG-CCATCTGGCA_S88_L001


title: Lineage_wRNA-p1H2

description:
lineage_profiles_wRNA.txt
p1H2-TARG-ATTGCGGCCA_S86_L001


title: Lineage_wRNA-p1H1

description:
lineage_profiles_wRNA.txt
p1H1-TARG-TGGCGTAGAA_S85_L001


title: 10L19_h2D_10L19h35

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1H12

description:
lineage_profiles_wRNA.txt
p1H12-TARG-GCGATTGCAG_S96_L001


title: 10L19_h2D_10L19h60

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1H3

description:
lineage_profiles_wRNA.txt
p1H3-TARG-TTCAGCTTGG_S87_L001


title: 10L19_h2D_10L19h34

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2A2

description:
rna_raw_cell_by_gene_counts.gz
p2A2-RNAp2_CGACTACCAA_S2


title: Lineage_wRNA-p1G9

description:
lineage_profiles_wRNA.txt
p1G9-TARG-GCCAAGCTTG_S81_L001


title: Lineage_wRNA-p1H10

description:
lineage_profiles_wRNA.txt
p1H10-TARG-CGCCTCTTAT_S94_L001


title: sciRNA_lib-p2A7

description:
rna_raw_cell_by_gene_counts.gz
p2A7-RNAp2_TTAGATTCCG_S7


title: 3X_2C_3N7

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: whole-ploidy comparison(triploid)


title: Lineage_wRNA-p1G7

description:
lineage_profiles_wRNA.txt
p1G7-TARG-TCCTTATAGA_S79_L001


title: 10L19_h2D_10L19h61

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1G8

description:
lineage_profiles_wRNA.txt
p1G8-TARG-CCGACTCCAA_S80_L001


title: sciRNA_lib-p2A1

description:
rna_raw_cell_by_gene_counts.gz
p2A1-RNAp2_CTCGATGGAG_S1

value: sci-RNA-seq


title: Lineage_wRNA-p1G5

description:
lineage_profiles_wRNA.txt
p1G5-TARG-ACTCGTATCA_S77_L001

value: Targeted lineage amplicon captured alongside sci-RNA-seq


title: Lineage_wRNA-p1G6

description:
lineage_profiles_wRNA.txt
p1G6-TARG-GGTAATAATG_S78_L001


title: 3X_2C_3N4

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1G4

description:
lineage_profiles_wRNA.txt
p1G4-TARG-GGAGTTGCGT_S76_L001


title: Lineage_wRNA-p1G3

description:
lineage_profiles_wRNA.txt
p1G3-TARG-CTTAATCTTG_S75_L001


title: sciRNA_lib-p2A11

description:
rna_raw_cell_by_gene_counts.gz
p2A11-RNAp2_TTGGTCATAA_S11


title: 3X_3C_3N3

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 3X_3C_3N1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p2A3

description:
rna_raw_cell_by_gene_counts.gz
p2A3-RNAp2_GTTGACGGCC_S3


title: Lineage_wRNA-p1G12

description:
lineage_profiles_wRNA.txt
p1G12-TARG-GGAATTCAGT_S84_L001


title: Dp4_4D_5

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (Dp4)


title: sciRNA_lib-p2A10

description:
rna_raw_cell_by_gene_counts.gz
p2A10-RNAp2_CCAGGTCTAC_S10


title: Lineage_wRNA-p1G2

description:
lineage_profiles_wRNA.txt
p1G2-TARG-GCGCAATGAC_S74_L001


title: Lineage_wRNA-p1G11

description:
lineage_profiles_wRNA.txt
p1G11-TARG-ACCTACGCCA_S83_L001


title: sciRNA_lib-p1H9

description:
rna_raw_cell_by_gene_counts.gz
p1H9-RNA_GATTGCAGAC_S93


title: Dp4_4D_1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1H11

description:
lineage_profiles_wRNA.txt
p1H11-TARG-GTTGGATCTT_S95_L001


title: Lineage_wRNA-p1G10

description:
lineage_profiles_wRNA.txt
p1G10-TARG-CATATCCTAT_S82_L001


title: sciRNA_lib-p1H8

description:
rna_raw_cell_by_gene_counts.gz
p1H8-RNA_CCTATAAGCT_S92


title: Dp4_4D_13

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 3X_2C_3N6

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1F9

description:
lineage_profiles_wRNA.txt
p1F9-TARG-AAGCTAGGTT_S69_L001


title: sciRNA_lib-p2A12

description:
rna_raw_cell_by_gene_counts.gz
p2A12-RNAp2_AACGGACCAA_S12


title: Lineage_wRNA-p1F8

description:
lineage_profiles_wRNA.txt
p1F8-TARG-TGGTAATCCT_S68_L001


title: Lineage_wRNA-p1F7

description:
lineage_profiles_wRNA.txt
p1F7-TARG-GGAAGTTATA_S67_L001


title: sciRNA_lib-p1H7

description:
rna_raw_cell_by_gene_counts.gz
p1H7-RNA_AGATCCTATA_S91


title: Lineage_wRNA-p1F6

description:
lineage_profiles_wRNA.txt
p1F6-TARG-AGGTCCTCGT_S66_L001


title: Lineage_wRNA-p1F5

description:
lineage_profiles_wRNA.txt
p1F5-TARG-GGTTGAACGT_S65_L001


title: sciRNA_lib-p1H6

description:
rna_raw_cell_by_gene_counts.gz
p1H6-RNA_TCATCTAATC_S90


title: Dp4_3D_6

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1F4

description:
lineage_profiles_wRNA.txt
p1F4-TARG-TAGCCTCGTT_S64_L001


title: Dp4_3D_14

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1G1

description:
lineage_profiles_wRNA.txt
p1G1-TARG-TGCTACGGTC_S73_L001


title: Lineage_wRNA-p1F3

description:
lineage_profiles_wRNA.txt
p1F3-TARG-CTCCTGGACC_S63_L001


title: sciRNA_lib-p1H5

description:
rna_raw_cell_by_gene_counts.gz
p1H5-RNA_AACTTATAAG_S89


title: sciRNA_lib-p1H4

description:
rna_raw_cell_by_gene_counts.gz
p1H4-RNA_TGCCAGATGG_S88


title: Dp4_3D_10

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1F12

description:
lineage_profiles_wRNA.txt
p1F12-TARG-TGGCAGCTCG_S72_L001


title: Lineage_wRNA-p1F2

description:
lineage_profiles_wRNA.txt
p1F2-TARG-AGGACGGACG_S62_L001


title: Lineage_wRNA-p1F1

description:
lineage_profiles_wRNA.txt
p1F1-TARG-GTCGGTAGTT_S61_L001


title: sciRNA_lib-p1H3

description:
rna_raw_cell_by_gene_counts.gz
p1H3-RNA_CCAAGCTGAA_S87


title: Lineage_wRNA-p1F11

description:
lineage_profiles_wRNA.txt
p1F11-TARG-TGCGGATAGT_S71_L001


title: Lineage_wRNA-p1F10

description:
lineage_profiles_wRNA.txt
p1F10-TARG-TCCGCGGACT_S70_L001


title: Dp4_2D_7

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Dp4_2D_4

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1E8

description:
lineage_profiles_wRNA.txt
p1E8-TARG-TCGTAACGGT_S56_L001


title: Lineage_wRNA-p1E9

description:
lineage_profiles_wRNA.txt
p1E9-TARG-TGGCGACGGA_S57_L001


title: sciRNA_lib-p1H1

description:
rna_raw_cell_by_gene_counts.gz
p1H1-RNA_TTCTACGCCA_S85


title: sciRNA_lib-p1H12

description:
rna_raw_cell_by_gene_counts.gz
p1H12-RNA_CTGCAATCGC_S96


title: Lineage_wRNA-p1E6

description:
lineage_profiles_wRNA.txt
p1E6-TARG-GAGATGCATG_S54_L001


title: Dp4_2D_16

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Dp4_2D_3

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1E5

description:
lineage_profiles_wRNA.txt
p1E5-TARG-AGAACCGGAG_S53_L001


title: Lineage_wRNA-p1E7

description:
lineage_profiles_wRNA.txt
p1E7-TARG-GATTACCGGA_S55_L001


title: sciRNA_lib-p1H11

description:
rna_raw_cell_by_gene_counts.gz
p1H11-RNA_AAGATCCAAC_S95


title: Lineage_wRNA-p1E3

description:
lineage_profiles_wRNA.txt
p1E3-TARG-TAATTGACCT_S51_L001


title: Lineage_wRNA-p1E2

description:
lineage_profiles_wRNA.txt
p1E2-TARG-TCAAGATAGT_S50_L001


title: Dp4_3D_11

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 1La_3D_1La45

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-1La)


title: sciRNA_lib-p1H10

description:
rna_raw_cell_by_gene_counts.gz
p1H10-RNA_ATAAGAGGCG_S94


title: Lineage_wRNA-p1E1

description:
lineage_profiles_wRNA.txt
p1E1-TARG-AGGCGAGAGC_S49_L001


title: 1La_3D_1La42

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1G9

description:
rna_raw_cell_by_gene_counts.gz
p1G9-RNA_CAAGCTTGGC_S81


title: Lineage_wRNA-p1E12

description:
lineage_profiles_wRNA.txt
p1E12-TARG-ATTCGGAAGT_S60_L001


title: sciRNA_lib-p1G8

description:
rna_raw_cell_by_gene_counts.gz
p1G8-RNA_TTGGAGTCGG_S80


title: 1La_3D_1La40

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1H2

description:
rna_raw_cell_by_gene_counts.gz
p1H2-RNA_TGGCCGCAAT_S86


title: Lineage_wRNA-p1D8

description:
lineage_profiles_wRNA.txt
p1D8-TARG-GTAATGATCG_S44_L001


title: Lineage_wRNA-p1D9

description:
lineage_profiles_wRNA.txt
p1D9-TARG-CAGAGAGGTC_S45_L001


title: sciRNA_lib-p1G7

description:
rna_raw_cell_by_gene_counts.gz
p1G7-RNA_TCTATAAGGA_S79


title: Lineage_wRNA-p1E4

description:
lineage_profiles_wRNA.txt
p1E4-TARG-CAGCCGGCTT_S52_L001


title: 1La_1D_1La30

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1D6

description:
lineage_profiles_wRNA.txt
p1D6-TARG-TTGGAGTTAG_S42_L001


title: sciRNA_lib-p1G6

description:
rna_raw_cell_by_gene_counts.gz
p1G6-RNA_CATTATTACC_S78


title: Lineage_wRNA-p1D7

description:
lineage_profiles_wRNA.txt
p1D7-TARG-AGATCTTGGT_S43_L001


title: 1La_1D_1La29

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1D5

description:
lineage_profiles_wRNA.txt
p1D5-TARG-TAGTTCTAGA_S41_L001


title: Lineage_wRNA-p1D4

description:
lineage_profiles_wRNA.txt
p1D4-TARG-GGCGGAGGTC_S40_L001


title: 1La_1D_1La27

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1D2

description:
lineage_profiles_wRNA.txt
p1D2-TARG-CCAGTACTTG_S38_L001


title: sciRNA_lib-p1G5

description:
rna_raw_cell_by_gene_counts.gz
p1G5-RNA_TGATACGAGT_S77


title: Lineage_wRNA-p1E11

description:
lineage_profiles_wRNA.txt
p1E11-TARG-GTCAAGTCCA_S59_L001


title: Lineage_wRNA-p1D1

description:
lineage_profiles_wRNA.txt
p1D1-TARG-GGAGGCGGCG_S37_L001


title: 1La_1D_1La21

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1G3

description:
rna_raw_cell_by_gene_counts.gz
p1G3-RNA_CAAGATTAAG_S75


title: 1La_3D_1La41

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1E10

description:
lineage_profiles_wRNA.txt
p1E10-TARG-AGTCATAGCC_S58_L001


title: Lineage_wRNA-p1D12

description:
lineage_profiles_wRNA.txt
p1D12-TARG-TACGATCATC_S48_L001


title: Lineage_wRNA-p1D11

description:
lineage_profiles_wRNA.txt
p1D11-TARG-CTCTAACTCG_S47_L001


title: 1La_2D_1La20

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1G2

description:
rna_raw_cell_by_gene_counts.gz
p1G2-RNA_GTCATTGCGC_S74


title: Lineage_wRNA-p1C8

description:
lineage_profiles_wRNA.txt
p1C8-TARG-GTAGGCAATT_S32_L001


title: Lineage_wRNA-p1C9

description:
lineage_profiles_wRNA.txt
p1C9-TARG-TGCCAGTTGC_S33_L001


title: Lineage_wRNA-p1D10

description:
lineage_profiles_wRNA.txt
p1D10-TARG-TTAATTAGCC_S46_L001


title: Lineage_wRNA-p1C7

description:
lineage_profiles_wRNA.txt
p1C7-TARG-AAGCCTACGA_S31_L001


title: Lineage_wRNA-p1D3

description:
lineage_profiles_wRNA.txt
p1D3-TARG-GGTCTCGCCG_S39_L001


title: sciRNA_lib-p1G12

description:
rna_raw_cell_by_gene_counts.gz
p1G12-RNA_ACTGAATTCC_S84


title: sciRNA_lib-p1G4

description:
rna_raw_cell_by_gene_counts.gz
p1G4-RNA_ACGCAACTCC_S76


title: Lineage_wRNA-p1C3

description:
lineage_profiles_wRNA.txt
p1C3-TARG-TAGACTAGTC_S27_L001


title: Lineage_wRNA-p1C4

description:
lineage_profiles_wRNA.txt
p1C4-TARG-GTCGAAGCAG_S28_L001


title: Lineage_wRNA-p1C5

description:
lineage_profiles_wRNA.txt
p1C5-TARG-AGGCGCTAGG_S29_L001


title: Lineage_wRNA-p1C6

description:
lineage_profiles_wRNA.txt
p1C6-TARG-AGATGCAACT_S30_L001


title: 1La_2D_1La14

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1C2

description:
lineage_profiles_wRNA.txt
p1C2-TARG-ATCGAGATGA_S26_L001


title: sciRNA_lib-p1G11

description:
rna_raw_cell_by_gene_counts.gz
p1G11-RNA_TGGCGTAGGT_S83


title: Lineage_wRNA-p1C1

description:
lineage_profiles_wRNA.txt
p1C1-TARG-TCGTCGGAAC_S25_L001


title: 9Sd_2D_9Sd7

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-9Sd)


title: Lineage_wRNA-p1C12

description:
lineage_profiles_wRNA.txt
p1C12-TARG-ATTGACCGAG_S36_L001


title: sciRNA_lib-p1G10

description:
rna_raw_cell_by_gene_counts.gz
p1G10-RNA_ATAGGATATG_S82


title: Lineage_wRNA-p1B9

description:
lineage_profiles_wRNA.txt
p1B9-TARG-CATTGACGCT_S21_L001


title: Lineage_wRNA-p1C11

description:
lineage_profiles_wRNA.txt
p1C11-TARG-GAGACCTACC_S35_L001


title: 9Sd_2D_9Sd4

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1F8

description:
rna_raw_cell_by_gene_counts.gz
p1F8-RNA_AGGATTACCA_S68


title: Lineage_wRNA-p1C10

description:
lineage_profiles_wRNA.txt
p1C10-TARG-CTTAGGTATC_S34_L001


title: 1La_2D_1La17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1G1

description:
rna_raw_cell_by_gene_counts.gz
p1G1-RNA_GACCGTAGCA_S73


title: Lineage_wRNA-p1B7

description:
lineage_profiles_wRNA.txt
p1B7-TARG-TGAGGAATCA_S19_L001


title: 1La_2D_1La16

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1F7

description:
rna_raw_cell_by_gene_counts.gz
p1F7-RNA_TATAACTTCC_S67


title: Lineage_wRNA-p1B8

description:
lineage_profiles_wRNA.txt
p1B8-TARG-CCTCCGACGG_S20_L001


title: Lineage_wRNA-p1B6

description:
lineage_profiles_wRNA.txt
p1B6-TARG-ACTGAGCGAC_S18_L001


title: 9Sd_2D_9Sd8

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1F5

description:
rna_raw_cell_by_gene_counts.gz
p1F5-RNA_ACGTTCAACC_S65


title: sciRNA_lib-p1F6

description:
rna_raw_cell_by_gene_counts.gz
p1F6-RNA_ACGAGGACCT_S66


title: Lineage_wRNA-p1B4

description:
lineage_profiles_wRNA.txt
p1B4-TARG-CCATCGTTCC_S16_L001


title: 9Sd_1D_9Sd40

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1B5

description:
lineage_profiles_wRNA.txt
p1B5-TARG-TTGAGAGAGT_S17_L001


title: 9Sd_1D_9Sd39

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1F4

description:
rna_raw_cell_by_gene_counts.gz
p1F4-RNA_AACGAGGCTA_S64


title: 9Sd_3D_9Sd31

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1F3

description:
rna_raw_cell_by_gene_counts.gz
p1F3-RNA_GGTCCAGGAG_S63


title: Lineage_wRNA-p1B12

description:
lineage_profiles_wRNA.txt
p1B12-TARG-TTCTACCTCA_S24_L001


title: sciRNA_lib-p1F9

description:
rna_raw_cell_by_gene_counts.gz
p1F9-RNA_AACCTAGCTT_S69


title: Lineage_wRNA-p1B1

description:
lineage_profiles_wRNA.txt
p1B1-TARG-GGTACGTTAA_S13_L001


title: sciRNA_lib-p1F2

description:
rna_raw_cell_by_gene_counts.gz
p1F2-RNA_CGTCCGTCCT_S62


title: 9Sd_3D_9Sd24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1B10

description:
lineage_profiles_wRNA.txt
p1B10-TARG-TCGTCCTTCG_S22_L001


title: 9Sd_1D_9Sd41

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1A9

description:
lineage_profiles_wRNA.txt
p1A9-TARG-TCAATATCGA_S9_L001


title: Lineage_wRNA-p1A8

description:
lineage_profiles_wRNA.txt
p1A8-TARG-ATGACTGATC_S8_L001


title: 9Sd_3D_9Sd23

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 9Sd_3D_9Sd22

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1A7

description:
lineage_profiles_wRNA.txt
p1A7-TARG-CGGAATCTAA_S7_L001


title: Lineage_wRNA-p1A6

description:
lineage_profiles_wRNA.txt
p1A6-TARG-CGTTCTATCA_S6_L001


title: 9Sd_1D_9Sd43

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1F1

description:
rna_raw_cell_by_gene_counts.gz
p1F1-RNA_AACTACCGAC_S61


title: Lineage_wRNA-p1B2

description:
lineage_profiles_wRNA.txt
p1B2-TARG-CAATGAGTCC_S14_L001


title: Lineage_wRNA-p1A5

description:
lineage_profiles_wRNA.txt
p1A5-TARG-TCGTTAGAGC_S5_L001


title: Lineage_wRNA-p1B3

description:
lineage_profiles_wRNA.txt
p1B3-TARG-GATGCAGTTC_S15_L001


title: Lineage_wRNA-p1A2

description:
lineage_profiles_wRNA.txt
p1A2-TARG-TTGGTAGTCG_S2_L001


title: 9Sd_2D_9Sd1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1F11

description:
rna_raw_cell_by_gene_counts.gz
p1F11-RNA_ACTATCCGCA_S71


title: Lineage_wRNA-p1B11

description:
lineage_profiles_wRNA.txt
p1B11-TARG-TGATACTCAA_S23_L001


title: sciRNA_lib-p1F10

description:
rna_raw_cell_by_gene_counts.gz
p1F10-RNA_AGTCCGCGGA_S70


title: Lineage_wRNA-p1A12

description:
lineage_profiles_wRNA.txt
p1A12-TARG-TTGGTCCGTT_S12_L001


title: 9Lc_2D_9Lc66

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-9Lc)


title: 9Lc_3D_9Lc5

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1E9

description:
rna_raw_cell_by_gene_counts.gz
p1E9-RNA_TCCGTCGCCA_S57


title: Lineage_wRNA-p1A1

description:
lineage_profiles_wRNA.txt
p1A1-TARG-CTCCATCGAG_S1_L001


title: Lineage_wRNA-p1A3

description:
lineage_profiles_wRNA.txt
p1A3-TARG-GGCCGTCAAC_S3_L001


title: sciRNA_lib-p1F12

description:
rna_raw_cell_by_gene_counts.gz
p1F12-RNA_CGAGCTGCCA_S72


title: Lineage_wRNA-p1A11

description:
lineage_profiles_wRNA.txt
p1A11-TARG-TTATGACCAA_S11_L001


title: sciRNA_lib-p1E8

description:
rna_raw_cell_by_gene_counts.gz
p1E8-RNA_ACCGTTACGA_S56


title: 9Lc_1D_9Lc47

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1A10

description:
lineage_profiles_wRNA.txt
p1A10-TARG-GTAGACCTGG_S10_L001


title: sciRNA_lib-p1E7

description:
rna_raw_cell_by_gene_counts.gz
p1E7-RNA_TCCGGTAATC_S55


title: 9Lc_1D_9Lc43

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1E6

description:
rna_raw_cell_by_gene_counts.gz
p1E6-RNA_CATGCATCTC_S54


title: 9Lc_3D_9Lc3

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Lineage_wRNA-p1A4

description:
lineage_profiles_wRNA.txt
p1A4-TARG-CCTAGACGAG_S4_L001


title: 9Lc_1D_9Lc40

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 9Lc_2D_9Lc36

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 9Lc_2D_9Lc34

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1E4

description:
rna_raw_cell_by_gene_counts.gz
p1E4-RNA_AAGCCGGCTG_S52


title: sciRNA_lib-p1E3

description:
rna_raw_cell_by_gene_counts.gz
p1E3-RNA_AGGTCAATTA_S51


title: 9Lc_3D_9Lc2

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1E5

description:
rna_raw_cell_by_gene_counts.gz
p1E5-RNA_CTCCGGTTCT_S53


title: sciRNA_lib-p1E1

description:
rna_raw_cell_by_gene_counts.gz
p1E1-RNA_GCTCTCGCCT_S49


title: 9Lc_3D_9Lc1

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 9Lc_1D_9Lc21

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: HPJP26-rep1 - native

city: Houston

first: Tao

middle: P.

last: Wu

state: TX

address: One Baylor Plaza, MS BCM225

department: Molecular and Human Genetics

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Library strategy: NT-seq
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3)
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated values

molecule: genomic DNA

organism: Helicobacter pylori

source_name: H. pylori

extract_protocol:
Genomic DNA was extrated using DNeasy Blood and Tissue Kit according to the manufacturer's instructions (Qiagen, 69506)
Genomic DNA was fragmentized to 100-300 bp using Covaris S220 Focused-ultrasonicator. Fragmented gDNA was ligated to TruSeq adaptor using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S). Unmodified control DNA was made by amplifying adaptor-ligated DNA using Q5 DNA polymerase (NEB, M0492S). Nitrite treatment was performed in both native and amplified DNA. Indexed libraries were constructed using NEB ultra ii library prep kit.

tag: strain

tag: genotype

value: wild-type


title: HPJP26-rep2 - native

data_processing:
sequencing reads were trimmed using cutadapt (v1.18) to remove adaptors. Duplicated reads were removed using BBMAP (v38.84)34 clumpify package.
Fastq reads and fasta reference were converted to AT-only format (convert all purine to A and all thymine to T). Converted fastq reads were aligned to reference using bowtie2 (v2.3.5.1)
AT only sam files were converted back to sam files with original reads using custom python scripts. NM and MD tags were recalculated using samtools (1.9) calmd. The alignments in sam files were filtered by recreated MD tag to keep allowed base mutation (A to G and C to T)
Base count at each genomic location was generated by igvtools (v2.5.3)
Assembly: NC_000913.3
Supplementary files format and content: Comma-separated values
Library strategy: NT-seq


title: HPJP26-rep2 - PCR


title: Oxytricha Mut DIP

data_processing:
Library strategy: DIP-seq
Raw reads were first trimmed using cutadapt (1.18) for illumina TruSeq adatper
Trimmed reads were aligned to the reference genome using bowtie2 (v2.3.5.1) with default parameters
6mA peaks were identified using MACS3 (3.0.0a6) using input as control
Supplementary_files_format_and_content: peak text files

organism: Oxytricha trifallax

source_name: Oxytricha

extract_protocol:
Genomic DNA was extrated using DNeasy Blood and Tissue Kit according to the manufacturer's instructions (Qiagen, 69506)
Genomic DNA was fragmentized to 100-300 bp using Covaris S220 Focused-ultrasonicator. Fragmented gDNA was ligated to TruSeq adaptor using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S). 6mA DIP enrichemnt was performed using anti-6mA antibody (CST, D9D9W). Unmodified control DNA was made by amplifying DIP enriched DNA using Q5 DNA polymerase (NEB, M0492S). Nitrite treatment was performed with both native and amplified DNA. Indexed librarier were constructed using NEB ultra ii library prep kit.

value: MTA1 mutant

tag: dip antibody

value: 6mA (CST D9D9W)


title: sciRNA_lib-p1E11

description:
rna_raw_cell_by_gene_counts.gz
p1E11-RNA_TGGACTTGAC_S59


title: sciRNA_lib-p1E12

description:
rna_raw_cell_by_gene_counts.gz
p1E12-RNA_ACTTCCGAAT_S60


title: HPJP26-rep1 - PCR


title: Oxytricha Mut Input


title: 9Lc_2D_9Lc15

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 8Lc_3D_8Lc9

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-8Lc)


title: Oxytricha WT Input


title: sciRNA_lib-p1E2

description:
rna_raw_cell_by_gene_counts.gz
p1E2-RNA_ACTATCTTGA_S50


title: Oxytricha WT DIP


title: Rat thymus Cocaine

city: Tokyo

first: Toshihiko

last: Aki

address: 1-5-45 Yushima

department: Forensic medicine

country: Japan

institute: Tokyo Medical and Dental University

hyb_protocol: Hybridization was performed according to the manufacturer's instruction.

scan_protocol: Array scanning was performed according to the manufacturer's instruction.

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization.

organism: Rattus norvegicus

source_name: thymus

label_protocol: Labeling was performed according to the manufacturer's instruction.

extract_protocol: RNA was isolated from rat spleen with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: 20 mg/kg cocaine was injected i.v. to rats daily for 7 days.

tag: Sex

value: male


title: sciRNA_lib-p1D9

description:
rna_raw_cell_by_gene_counts.gz
p1D9-RNA_GACCTCTCTG_S45


title: Oxytricha Mut DIP - native


title: Oxytricha Mut DIP - PCR


title: Oxytricha WT DIP - PCR


title: Rat thymus No Stimulation


title: sciRNA_lib-p1D8

description:
rna_raw_cell_by_gene_counts.gz
p1D8-RNA_CGATCATTAC_S44


title: Oxytricha WT DIP - native


title: 8Lc_2D_8Lc66

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 8Lc_1D_8Lc37

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1D6

description:
rna_raw_cell_by_gene_counts.gz
p1D6-RNA_CTAACTCCAA_S42


title: 8Lc_3D_8Lc8

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 8Lc_1D_8Lc35

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 8Lc_1D_8Lc36

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1D7

description:
rna_raw_cell_by_gene_counts.gz
p1D7-RNA_ACCAAGATCT_S43


title: sciRNA_lib-p1D4

description:
rna_raw_cell_by_gene_counts.gz
p1D4-RNA_GACCTCCGCC_S40


title: 8Lc_1D_8Lc28

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 8Lc_2D_8Lc24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1D3

description:
rna_raw_cell_by_gene_counts.gz
p1D3-RNA_CGGCGAGACC_S39


title: MGC_derived exosome_rep1

city: Zhengzhou

first: peiming

last: zheng

address: 7 Weiwu Road

institute: People’s Hospital of Zhengzhou University

description: Exosome derived from MGC culture media

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: MGC derived exosome

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Four human GCC lines (MGC803, BGC823, SGC7901, and AGS) and one normal human gastric (GES-1) cell line were  cultured at 37 °C with 5% CO2 in 1640/DMEM containing 10% exosome-depleted FBS. Exosomes from the culture media (CM) of four GC cells (GCCs) and human gastric epithelial cells were isolated using ExoQuick solution kit.

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified byRNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

tag: cell


title: SGC_derived exosome_rep1

description: Exosome derived from SGC culture media

source_name: SGC derived exosome


title: BGC_derived exosome_rep1

description: Exosome derived from BGC culture media

source_name: BGC derived exosome


title: AGS_derived exosome_rep1

description: Exosome derived from AGS culture media

source_name: AGS derived exosome

value: AGS


title: Healthy Volunteer 2 - TRUNK R3

city: New York

first: Shruti

last: Naik

state: NY

address: 435 East 30th Street

department: Pathology

institute: NYU Langone Health

description:
st_images.gz
Sample name: HV2_S2
sample id v2: ST-HF-1T

data_processing:
Sequencing output and the histology images were processed using space ranger software (10X Genomics).  The space ranger mkfastq function was used for sample demultiplexing and to converting spatial barcodes and reads into FASTQ format.
The space ranger count function was used to align reads from FASTQ files to human genome (hg38) and then align microscopic slide image and transcriptome to generate barcode/UMI counts, feature spot matrices, cluster data, and perform gene expression analysis.
Assembly: hg38
Supplementary files format and content: Filtered feature-barcode matrices (filtered_feature_bc_matrix) containing only spot barcodes in MEX format for each sample. Spatial folder output from space ranger count function containing QC images for aligned fiducials and detetected tissue in jpg format, scalefactors_json.json, high and low resolution versions of the input image in png format, and tissue_positions_list.csv.  All spatial outputs (Spatial image data) are stored in st_images.tar.gz.
Library strategy: spatial transcriptomics

source_name: Skin

growth_protocol: Three to four millimeter skin punch biopsies were obtained from lesional and non-lesional skin of healthy controls and subjects with psoriatic disease.

extract_protocol: Tissues were embedded in OCT and frozen in liquid nitrogen-chilled isopentane within 5 minutes of devascularization. 10-µm cryosections were mounted onto the ST arrays (10X Visium)  where reverse transcription of cellular transcripts took place in situ after tissue permeabilization.

treatment_protocol: Subjects were biologic-naïve (untreated)

tag: individual

value: Healthy Volunteer 2

tag: tissue

value: Skin punch biopsy

tag: sequencing run / batch

tag: disease state

value: control

tag: disease status

value: Healthy

tag: pasi score


title: Healthy Volunteer 1 - TRUNK R2

description:
st_images.gz
Sample name: HV1_S1_R2
sample id v2: ST-HM-1 R2

value: Healthy Volunteer 1


title: Healthy Volunteer 3 - TRUNK R2

description:
st_images.gz
Sample name: HV3_S2
sample id v2: ST-HF-2T

value: Healthy Volunteer 3


title: Healthy Volunteer 3 - FA R1

description:
st_images.gz
Sample name: HV3_S1
sample id v2: ST-HF-2E


title: Healthy Volunteer 2 - FA R2

description:
st_images.gz
Sample name: HV2_S1_R2
sample id v2: ST-HF-1 R2


title: Healthy Volunteer 1 - TRUNK R1

description:
st_images.gz
Sample name: HV1_S1_R1
sample id v2: ST-HM-1


title: PSA Lesional Patient 4

description:
st_images.gz
Sample name: PSA_LES_P4
sample id v2: ST-22-L

value: patient 4

value: Psoriatic Arthritis (PsA)

value: Lesional


title: PSO Lesional Patient 6

description:
st_images.gz
Sample name: PSO_LES_P6
sample id v2: ST-L-RP1

value: patient 6

value: Psoriasis (PsO)


title: sciRNA_lib-p1D2

description:
rna_raw_cell_by_gene_counts.gz
p1D2-RNA_CAAGTACTGG_S38

tag: cell type

tag: data type

value: sci-RNA-seq


title: 8Lc_2D_8Lc17

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: PSO Non-Lesional Patient 5

description:
st_images.gz
Sample name: PSO_NON_LES_P5
sample id v2: ST-21 NL

value: patient 5

value: Non-Lesional


title: 8Lc_3D_8Lc11

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-8Lc)


title: sciRNA_lib-p1D1

description:
rna_raw_cell_by_gene_counts.gz
p1D1-RNA_CGCCGCCTCC_S37


title: PSO Lesional Patient 5

description:
st_images.gz
Sample name: PSO_LES_P5
sample id v2: ST-21 L


title: PSO Lesional Patient 4

description:
st_images.gz
Sample name: PSO_LES_P4
sample id v2: ST-20 L


title: PSO Non-Lesional Patient 4

description:
st_images.gz
Sample name: PSO_NON_LES_P4
sample id v2: ST-20-NL


title: PSA Non-Lesional Patient 4

description:
st_images.gz
Sample name: PSA_NON_LES_P4
sample id v2: ST-22-NL


title: PSA Non-Lesional Patient 3

description:
st_images.gz
Sample name: PSA_NON_LES_ P3
sample id v2: ST-18 NL

value: patient 3


title: sciRNA_lib-p1D12

description:
rna_raw_cell_by_gene_counts.gz
p1D12-RNA_GATGATCGTA_S48


title: PSA Lesional Patient 3 R2

description:
st_images.gz
Sample name: PSA_LES_P3_R2
sample id v2: ST-18 L R2


title: sciRNA_lib-p1E10

description:
rna_raw_cell_by_gene_counts.gz
p1E10-RNA_GGCTATGACT_S58


title: GES_derived exosome_rep1

description: Exosome derived from GES culture media

source_name: GES derived exosome


title: sciRNA_lib-p1D11

description:
rna_raw_cell_by_gene_counts.gz
p1D11-RNA_CGAGTTAGAG_S47


title: 7Lb_2D_7Lb6

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-7Lb)


title: 7Lb_2D_7Lb4

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 7Lb_2D_7Lb5

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: PSA Lesional Skin Patient 1

description:
st_images.gz
Sample name: PSA_LES_P1
sample id v2: ST-16 L

value: patient 1


title: PSO Lesional Skin Patient 3

description:
st_images.gz
Sample name: PSO_LES_P3
sample id v2: ST-17 L

value: Skin punch biopsy


title: sciRNA_lib-p1C9

description:
rna_raw_cell_by_gene_counts.gz
p1C9-RNA_GCAACTGGCA_S33


title: sciRNA_lib-p1D10

description:
rna_raw_cell_by_gene_counts.gz
p1D10-RNA_GGCTAATTAA_S46


title: 7Lb_2D_7Lb2

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: PSA Non-Lesional Skin Patient 1

description:
st_images.gz
Sample name: PSA_NON_LES_P1
sample id v2: ST-16 NL


title: PSA Non-Lesional Patient 2

description:
st_images.gz
Sample name: PSA_NON_LES_P2
sample id v2: ST-15 NL

value: patient 2


title: PSA Lesional Patient 2 R2

description:
st_images.gz
Sample name: PSA_LES_P2_R2
sample id v2: ST-15 L R2


title: sciRNA_lib-p1C8

description:
rna_raw_cell_by_gene_counts.gz
p1C8-RNA_AATTGCCTAC_S32


title: PSO Non-Lesional Skin Patient 3

description:
st_images.gz
Sample name: PSO_NON_LES_P3
sample id v2: ST-17 NL


title: PSO Non-Lesional Skin Patient 2

description:
st_images.gz
Sample name: PSO_NON_LES_P2
sample id v2: ST-14 NL


title: sciRNA_lib-p1C7

description:
rna_raw_cell_by_gene_counts.gz
p1C7-RNA_TCGTAGGCTT_S31


title: 7Lb_1D_7Lb27

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 7Lb_1D_7Lb24

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: PSO Lesional Skin Patient 2 R1

description:
st_images.gz
Sample name: PSO_LES_P2_R1
sample id v2: ST-14 L


title: PSO Lesional Skin Patient 2 R2

description:
st_images.gz
Sample name: PSO_LES_P2_R2
sample id v2: ST-14 L R2


title: PSA Lesional Patient 2 R1

description:
st_images.gz
Sample name: PSA_LES_P2_R1
sample id v2: ST-15 L


title: sciRNA_lib-p1C6

description:
rna_raw_cell_by_gene_counts.gz
p1C6-RNA_AGTTGCATCT_S30


title: PSO Non-Lesional Skin Patient 1

description:
st_images.gz
Sample name: PSO_NON_LES_P1
sample id v2: ST-13 NL


title: PSA Lesional Patient 3 R1

description:
st_images.gz
Sample name: PSA_LES_P3_R1
sample id v2: ST-18 L


title: sciRNA_lib-p1C5

description:
rna_raw_cell_by_gene_counts.gz
p1C5-RNA_CCTAGCGCCT_S29


title: 7Lb_1D_7Lb21

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1C4

description:
rna_raw_cell_by_gene_counts.gz
p1C4-RNA_CTGCTTCGAC_S28


title: HtrA2/Omi DelPDZ, bio rep 2

city: Chengdu

first: Haoran

last: Tai

state: Sichuan

address: #783 Xindu Avenue

department: Department of Histology and Embryology

institute: Chengdu Medical College

data_processing:
Paired-end sequence files were mapped to human reference genome using Hisat2 (version 2.0.5).
The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM).
Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCh38.100
Supplementary files format and content: tab-delimited text file includes FPKM & count for each Sample

source_name: HUVEC

extract_protocol:
RNA was extracted using a total RNA isolation kit (TR205-200, Tianmo). Agilent Bioanalyzer 2100 (Agilent Technologies, USA) was used for quality control and Qubit 3.0 Fluorometer (Life Technologies, USA) was used for quantification.
RNA was fragmented into small pieces using divalent cations under 94 °C for 8 min. Cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, and followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single A’ base, and then ligation of the adapters. The products were purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit 3.0 Fluorometer and validated by Agilent 2100 bioanalyzer to confirm the insert size and calculate the concentration.

tag: cell line

value: HUVEC

value: Endothelial cells

value: Tet-On HtrA2 DelPDZ

tag: treatment

value: 50 nM doxycycline for 24 h


title: HtrA2/Omi DelPDZ, bio rep 3


title: 7Lb_1D_7Lb19

description:
rpm_miRNA.txt
results_counts_miRNA.txt

tag: age


title: HtrA2/Omi DelPDZ, bio rep 1


title: sciRNA_lib-p1C3

description:
rna_raw_cell_by_gene_counts.gz
p1C3-RNA_GACTAGTCTA_S27


title: 7Lb_3D_7Lb17

description:
rpm_miRNA.txt
results_counts_miRNA.txt

tag: diploid aneuploids, disomy, whole-ploidy, or b chromosome


title: HtrA2/Omi G399S, bio rep 3

value: Tet-On HtrA2 G399S


title: HtrA2/Omi G399S, bio rep 2


title: sciRNA_lib-p1C2

description:
rna_raw_cell_by_gene_counts.gz
p1C2-RNA_TCATCTCGAT_S26


title: HtrA2/Omi G399S, bio rep 1


title: HtrA2/Omi WT, bio rep 3

value: Tet-On HtrA2 WT


title: HtrA2/Omi WT, bio rep 2


title: sciRNA_lib-p1C1

description:
rna_raw_cell_by_gene_counts.gz
p1C1-RNA_GTTCCGACGA_S25


title: HtrA2/Omi WT, bio rep 1


title: sciRNA_lib-p1C12

description:
rna_raw_cell_by_gene_counts.gz
p1C12-RNA_CTCGGTCAAT_S36


title: 7Lb_3D_7Lb14

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Ctrl, bio rep 2

value: Tet-On


title: 7Lb_3D_7Lb15

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: Ctrl, bio rep 1


title: sciRNA_lib-p1C11

description:
rna_raw_cell_by_gene_counts.gz
p1C11-RNA_GGTAGGTCTC_S35


title: PSO Lesional Skin Patient 1

description:
st_images.gz
Sample name: PSO_LES_P1
sample id v2: ST-13 L

value: Psoriasis (PsO)

value: Lesional


title: Ctrl, bio rep 3


title: 4Sa_3D_4Sa7

description:
rpm_miRNA.txt
results_counts_miRNA.txt

value: diploid aneuploids comparison (TB-4Sa)


title: sciRNA_lib-p1C10

description:
rna_raw_cell_by_gene_counts.gz
p1C10-RNA_GATACCTAAG_S34

value: sci-RNA-seq


title: 4Sa_2D_4Sa6

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: 7Lb_3D_7Lb16

description:
rpm_miRNA.txt
results_counts_miRNA.txt


title: sciRNA_lib-p1B9

description:
rna_raw_cell_by_gene_counts.gz
p1B9-RNA_AGCGTCAATG_S21