title: 10256_0_new onset T1D_10256 lib20908_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20901_CBG5GANXX_tophat_alignments

status: Public on Dec 15 2021

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

description: 10256_0_new onset T1D_10256

library_source: transcriptomic

data_processing:
The processing workflow was managed on the Galaxy platform. Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
Sequence alignment was performed using STAR aligner (v2.4.2a) with the GRCm38 reference genome and gene annotations from Ensembl release 91.
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), and HTSeq-count
Genome_build: GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: Islet-reactive CD4+ sorted T-cell

extract_protocol:
Single cells were captured on a C1 system or plate sorted. C1 capture was done using a 5-10 um mRNA Seq IFC according to manufacturer’s instructions (Fluidigm, South San Francisco, CA). Full-length cDNA was prepared using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech, Mountain View, CA). For plate sorting, single cells were sorted into wells of a 96-well plate. Full-length cDNA was prepared using a SMARTer V4 kit with half-volume reactions.
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).

tag: library id

tag: study group

value: new onset T1D

tag: donor

tag: age

tag: Sex

value: female

tag: lib prep method

value: Plate sort


title: 10256_0_new onset T1D_10256 lib20902_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20898_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20896_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20895_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20894_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20891_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20892_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20890_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20888_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20889_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20887_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20884_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20886_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20881_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20882_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20885_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20904_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20880_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20907_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20879_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20903_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20883_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20878_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10241_0_B12_new onset T1D_10241 lib20838_CBG5GANXX_tophat_alignments

description: 10241_0_B12_new onset T1D_10241

value: male


title: 10256_0_new onset T1D_10256 lib20900_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10241_0_A12_new onset T1D_10241 lib20837_CBG5GANXX_tophat_alignments

description: 10241_0_A12_new onset T1D_10241


title: 10256_0_new onset T1D_10256 lib20899_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10241_0_A11_new onset T1D_10241 lib20835_CBG5GANXX_tophat_alignments

description: 10241_0_A11_new onset T1D_10241


title: 10241_0_B10_new onset T1D_10241 lib20834_CBG5GANXX_tophat_alignments

description: 10241_0_B10_new onset T1D_10241


title: 10241_0_B11_new onset T1D_10241 lib20836_CBG5GANXX_tophat_alignments

description: 10241_0_B11_new onset T1D_10241


title: 10256_0_new onset T1D_10256 lib20893_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10256_0_new onset T1D_10256 lib20897_CBG5GANXX_tophat_alignments

description: 10256_0_new onset T1D_10256


title: 10241_0_B9_new onset T1D_10241 lib20832_CBG5GANXX_tophat_alignments

description: 10241_0_B9_new onset T1D_10241


title: 10241_0_A10_new onset T1D_10241 lib20833_CBG5GANXX_tophat_alignments

description: 10241_0_A10_new onset T1D_10241


title: 10241_0_A9_new onset T1D_10241 lib20831_CBG5GANXX_tophat_alignments

description: 10241_0_A9_new onset T1D_10241


title: 10241_0_B8_new onset T1D_10241 lib20830_CBG5GANXX_tophat_alignments

description: 10241_0_B8_new onset T1D_10241


title: 10241_0_A7_new onset T1D_10241 lib20827_CBG5GANXX_tophat_alignments

description: 10241_0_A7_new onset T1D_10241


title: 10241_0_B7_new onset T1D_10241 lib20828_CBG5GANXX_tophat_alignments

description: 10241_0_B7_new onset T1D_10241


title: 10241_0_A8_new onset T1D_10241 lib20829_CBG5GANXX_tophat_alignments

description: 10241_0_A8_new onset T1D_10241


title: 10241_0_A6_new onset T1D_10241 lib20825_CBG5GANXX_tophat_alignments

description: 10241_0_A6_new onset T1D_10241


title: 10241_0_B5_new onset T1D_10241 lib20824_CBG5GANXX_tophat_alignments

description: 10241_0_B5_new onset T1D_10241


title: 10241_0_B4_new onset T1D_10241 lib20822_CBG5GANXX_tophat_alignments

description: 10241_0_B4_new onset T1D_10241


title: 10241_0_B3_new onset T1D_10241 lib20820_CBG5GANXX_tophat_alignments

description: 10241_0_B3_new onset T1D_10241


title: 10241_0_A5_new onset T1D_10241 lib20823_CBG5GANXX_tophat_alignments

description: 10241_0_A5_new onset T1D_10241


title: 10241_0_B2_new onset T1D_10241 lib20818_CBG5GANXX_tophat_alignments

description: 10241_0_B2_new onset T1D_10241


title: 10241_0_A3_new onset T1D_10241 lib20819_CBG5GANXX_tophat_alignments

description: 10241_0_A3_new onset T1D_10241


title: 10059_0_D12_new onset T1D_10059 lib20773_CBG5GANXX_tophat_alignments

description: 10059_0_D12_new onset T1D_10059


title: 10241_0_A2_new onset T1D_10241 lib20817_CBG5GANXX_tophat_alignments

description: 10241_0_A2_new onset T1D_10241


title: 10241_0_A1_new onset T1D_10241 lib20815_CBG5GANXX_tophat_alignments

description: 10241_0_A1_new onset T1D_10241


title: 10059_0_C12_new onset T1D_10059 lib20770_CBG5GANXX_tophat_alignments

description: 10059_0_C12_new onset T1D_10059


title: 10241_0_B1_new onset T1D_10241 lib20816_CBG5GANXX_tophat_alignments

description: 10241_0_B1_new onset T1D_10241


title: 10059_0_D10_new onset T1D_10059 lib20771_CBG5GANXX_tophat_alignments

description: 10059_0_D10_new onset T1D_10059


title: 10059_0_C11_new onset T1D_10059 lib20769_CBG5GANXX_tophat_alignments

description: 10059_0_C11_new onset T1D_10059


title: 10059_0_C7_new onset T1D_10059 lib20765_CBG5GANXX_tophat_alignments

description: 10059_0_C7_new onset T1D_10059


title: 10059_0_C8_new onset T1D_10059 lib20766_CBG5GANXX_tophat_alignments

description: 10059_0_C8_new onset T1D_10059


title: 10059_0_C10_new onset T1D_10059 lib20768_CBG5GANXX_tophat_alignments

description: 10059_0_C10_new onset T1D_10059


title: 10059_0_C6_new onset T1D_10059 lib20764_CBG5GANXX_tophat_alignments

description: 10059_0_C6_new onset T1D_10059


title: 10059_0_C3_new onset T1D_10059 lib20761_CBG5GANXX_tophat_alignments

description: 10059_0_C3_new onset T1D_10059


title: 10059_0_C4_new onset T1D_10059 lib20762_CBG5GANXX_tophat_alignments

description: 10059_0_C4_new onset T1D_10059


title: 10059_0_C2_new onset T1D_10059 lib20760_CBG5GANXX_tophat_alignments

description: 10059_0_C2_new onset T1D_10059


title: 10241_0_B6_new onset T1D_10241 lib20826_CBG5GANXX_tophat_alignments

description: 10241_0_B6_new onset T1D_10241


title: 10059_0_C5_new onset T1D_10059 lib20763_CBG5GANXX_tophat_alignments

description: 10059_0_C5_new onset T1D_10059


title: 10059_0_B12_new onset T1D_10059 lib20758_CBG5GANXX_tophat_alignments

description: 10059_0_B12_new onset T1D_10059


title: 10059_0_B11_new onset T1D_10059 lib20757_CBG5GANXX_tophat_alignments

description: 10059_0_B11_new onset T1D_10059


title: 10059_0_C1_new onset T1D_10059 lib20759_CBG5GANXX_tophat_alignments

description: 10059_0_C1_new onset T1D_10059


title: 10241_0_A4_new onset T1D_10241 lib20821_CBG5GANXX_tophat_alignments

description: 10241_0_A4_new onset T1D_10241


title: 10059_0_B9_new onset T1D_10059 lib20755_CBG5GANXX_tophat_alignments

description: 10059_0_B9_new onset T1D_10059


title: 10059_0_B10_new onset T1D_10059 lib20756_CBG5GANXX_tophat_alignments

description: 10059_0_B10_new onset T1D_10059


title: 10059_0_B8_new onset T1D_10059 lib20754_CBG5GANXX_tophat_alignments

description: 10059_0_B8_new onset T1D_10059


title: 10059_0_B6_new onset T1D_10059 lib20752_CBG5GANXX_tophat_alignments

description: 10059_0_B6_new onset T1D_10059


title: 10059_0_B5_new onset T1D_10059 lib20751_CBG5GANXX_tophat_alignments

description: 10059_0_B5_new onset T1D_10059


title: 10059_0_B4_new onset T1D_10059 lib20750_CBG5GANXX_tophat_alignments

description: 10059_0_B4_new onset T1D_10059


title: 10059_0_B7_new onset T1D_10059 lib20753_CBG5GANXX_tophat_alignments

description: 10059_0_B7_new onset T1D_10059


title: 10059_0_B3_new onset T1D_10059 lib20749_CBG5GANXX_tophat_alignments

description: 10059_0_B3_new onset T1D_10059


title: 10059_0_B1_new onset T1D_10059 lib20747_CBG5GANXX_tophat_alignments

description: 10059_0_B1_new onset T1D_10059


title: 10059_0_A12_new onset T1D_10059 lib20746_CBG5GANXX_tophat_alignments

description: 10059_0_A12_new onset T1D_10059


title: 10059_0_D11_new onset T1D_10059 lib20772_CBG5GANXX_tophat_alignments

description: 10059_0_D11_new onset T1D_10059


title: 10059_0_B2_new onset T1D_10059 lib20748_CBG5GANXX_tophat_alignments

description: 10059_0_B2_new onset T1D_10059


title: 10059_0_A10_new onset T1D_10059 lib20744_CBG5GANXX_tophat_alignments

description: 10059_0_A10_new onset T1D_10059


title: 10059_0_A9_new onset T1D_10059 lib20743_CBG5GANXX_tophat_alignments

description: 10059_0_A9_new onset T1D_10059


title: 10059_0_A8_new onset T1D_10059 lib20742_CBG5GANXX_tophat_alignments

description: 10059_0_A8_new onset T1D_10059


title: 10059_0_A11_new onset T1D_10059 lib20745_CBG5GANXX_tophat_alignments

description: 10059_0_A11_new onset T1D_10059


title: 10059_0_A4_new onset T1D_10059 lib20738_CBG5GANXX_tophat_alignments

description: 10059_0_A4_new onset T1D_10059


title: 10059_0_A6_new onset T1D_10059 lib20740_CBG5GANXX_tophat_alignments

description: 10059_0_A6_new onset T1D_10059


title: 10059_0_A7_new onset T1D_10059 lib20741_CBG5GANXX_tophat_alignments

description: 10059_0_A7_new onset T1D_10059


title: 10059_0_A3_new onset T1D_10059 lib20737_CBG5GANXX_tophat_alignments

description: 10059_0_A3_new onset T1D_10059


title: 10059_0_A2_new onset T1D_10059 lib20736_CBG5GANXX_tophat_alignments

description: 10059_0_A2_new onset T1D_10059


title: 10010_0_D12_new onset T1D_10010 lib20519_CBG5GANXX_tophat_alignments

description: 10010_0_D12_new onset T1D_10010


title: 10059_0_A5_new onset T1D_10059 lib20739_CBG5GANXX_tophat_alignments

description: 10059_0_A5_new onset T1D_10059


title: 10010_0_B12_new onset T1D_10010 lib20517_CBG5GANXX_tophat_alignments

description: 10010_0_B12_new onset T1D_10010


title: 10010_0_C11_new onset T1D_10010 lib20514_CBG5GANXX_tophat_alignments

description: 10010_0_C11_new onset T1D_10010


title: 10010_0_A11_new onset T1D_10010 lib20512_CBG5GANXX_tophat_alignments

description: 10010_0_A11_new onset T1D_10010


title: 10010_0_C12_new onset T1D_10010 lib20518_CBG5GANXX_tophat_alignments

description: 10010_0_C12_new onset T1D_10010


title: 10010_0_A12_new onset T1D_10010 lib20516_CBG5GANXX_tophat_alignments

description: 10010_0_A12_new onset T1D_10010


title: 10010_0_B11_new onset T1D_10010 lib20513_CBG5GANXX_tophat_alignments

description: 10010_0_B11_new onset T1D_10010


title: 10010_0_C9_new onset T1D_10010 lib20506_CBG5GANXX_tophat_alignments

description: 10010_0_C9_new onset T1D_10010


title: 10059_0_C9_new onset T1D_10059 lib20767_CBG5GANXX_tophat_alignments

description: 10059_0_C9_new onset T1D_10059


title: 10010_0_A9_new onset T1D_10010 lib20504_CBG5GANXX_tophat_alignments

description: 10010_0_A9_new onset T1D_10010


title: 10010_0_A10_new onset T1D_10010 lib20508_CBG5GANXX_tophat_alignments

description: 10010_0_A10_new onset T1D_10010


title: 10010_0_B10_new onset T1D_10010 lib20509_CBG5GANXX_tophat_alignments

description: 10010_0_B10_new onset T1D_10010


title: 10010_0_B9_new onset T1D_10010 lib20505_CBG5GANXX_tophat_alignments

description: 10010_0_B9_new onset T1D_10010


title: 10010_0_C10_new onset T1D_10010 lib20510_CBG5GANXX_tophat_alignments

description: 10010_0_C10_new onset T1D_10010


title: 10010_0_D8_new onset T1D_10010 lib20503_CBG5GANXX_tophat_alignments

description: 10010_0_D8_new onset T1D_10010


title: 10010_0_A8_new onset T1D_10010 lib20500_CBG5GANXX_tophat_alignments

description: 10010_0_A8_new onset T1D_10010


title: 10010_0_B8_new onset T1D_10010 lib20501_CBG5GANXX_tophat_alignments

description: 10010_0_B8_new onset T1D_10010


title: 10010_0_C7_new onset T1D_10010 lib20498_CBG5GANXX_tophat_alignments

description: 10010_0_C7_new onset T1D_10010


title: 10010_0_C8_new onset T1D_10010 lib20502_CBG5GANXX_tophat_alignments

description: 10010_0_C8_new onset T1D_10010


title: 10010_0_D7_new onset T1D_10010 lib20499_CBG5GANXX_tophat_alignments

description: 10010_0_D7_new onset T1D_10010


title: 10059_0_A1_new onset T1D_10059 lib20735_CBG5GANXX_tophat_alignments

description: 10059_0_A1_new onset T1D_10059


title: 10010_0_A7_new onset T1D_10010 lib20496_CBG5GANXX_tophat_alignments

description: 10010_0_A7_new onset T1D_10010


title: 10010_0_D6_new onset T1D_10010 lib20495_CBG5GANXX_tophat_alignments

description: 10010_0_D6_new onset T1D_10010


title: 10010_0_B6_new onset T1D_10010 lib20493_CBG5GANXX_tophat_alignments

description: 10010_0_B6_new onset T1D_10010


title: 10010_0_A6_new onset T1D_10010 lib20492_CBG5GANXX_tophat_alignments

description: 10010_0_A6_new onset T1D_10010


title: 10010_0_D11_new onset T1D_10010 lib20515_CBG5GANXX_tophat_alignments

description: 10010_0_D11_new onset T1D_10010


title: 10010_0_D5_new onset T1D_10010 lib20491_CBG5GANXX_tophat_alignments

description: 10010_0_D5_new onset T1D_10010


title: 10010_0_C5_new onset T1D_10010 lib20490_CBG5GANXX_tophat_alignments

description: 10010_0_C5_new onset T1D_10010


title: 10010_0_D10_new onset T1D_10010 lib20511_CBG5GANXX_tophat_alignments

description: 10010_0_D10_new onset T1D_10010


title: 10010_0_B5_new onset T1D_10010 lib20489_CBG5GANXX_tophat_alignments

description: 10010_0_B5_new onset T1D_10010


title: 10010_0_A5_new onset T1D_10010 lib20488_CBG5GANXX_tophat_alignments

description: 10010_0_A5_new onset T1D_10010


title: 10010_0_C4_new onset T1D_10010 lib20487_CBG5GANXX_tophat_alignments

description: 10010_0_C4_new onset T1D_10010


title: 10010_0_B4_new onset T1D_10010 lib20486_CBG5GANXX_tophat_alignments

description: 10010_0_B4_new onset T1D_10010


title: 10010_0_B3_new onset T1D_10010 lib20483_CBG5GANXX_tophat_alignments

description: 10010_0_B3_new onset T1D_10010


title: 10010_0_A3_new onset T1D_10010 lib20482_CBG5GANXX_tophat_alignments

description: 10010_0_A3_new onset T1D_10010


title: 10010_0_C2_new onset T1D_10010 lib20481_CBG5GANXX_tophat_alignments

description: 10010_0_C2_new onset T1D_10010


title: 10010_0_A2_new onset T1D_10010 lib20479_CBG5GANXX_tophat_alignments

description: 10010_0_A2_new onset T1D_10010


title: 10010_0_B2_new onset T1D_10010 lib20480_CBG5GANXX_tophat_alignments

description: 10010_0_B2_new onset T1D_10010


title: 10010_0_C3_new onset T1D_10010 lib20484_CBG5GANXX_tophat_alignments

description: 10010_0_C3_new onset T1D_10010


title: Control_11 _F5_HC_HC11 lib18474_CB6LAANXX_tophat_alignments

description: Control_11 _F5_HC_HC11

value: HC


title: 10010_0_B1_new onset T1D_10010 lib20477_CBG5GANXX_tophat_alignments

description: 10010_0_B1_new onset T1D_10010


title: Control_11 _F3_HC_HC11 lib18472_CB6LAANXX_tophat_alignments

description: Control_11 _F3_HC_HC11


title: 10010_0_C6_new onset T1D_10010 lib20494_CBG5GANXX_tophat_alignments

description: 10010_0_C6_new onset T1D_10010


title: Control_11 _F1_HC_HC11 lib18470_CB6LAANXX_tophat_alignments

description: Control_11 _F1_HC_HC11


title: Control_11 _F4_HC_HC11 lib18473_CB6LAANXX_tophat_alignments

description: Control_11 _F4_HC_HC11


title: Control_11 _E12_HC_HC11 lib18469_CB6LAANXX_tophat_alignments

description: Control_11 _E12_HC_HC11


title: Control_11 _E11_HC_HC11 lib18468_CB6LAANXX_tophat_alignments

description: Control_11 _E11_HC_HC11


title: Control_11 _E10_HC_HC11 lib18467_CB6LAANXX_tophat_alignments

description: Control_11 _E10_HC_HC11


title: Control_11 _E4_HC_HC11 lib18461_CB6LAANXX_tophat_alignments

description: Control_11 _E4_HC_HC11


title: Control_11 _E5_HC_HC11 lib18462_CB6LAANXX_tophat_alignments

description: Control_11 _E5_HC_HC11


title: Control_11 _E6_HC_HC11 lib18463_CB6LAANXX_tophat_alignments

description: Control_11 _E6_HC_HC11


title: 10010_0_D9_new onset T1D_10010 lib20507_CBG5GANXX_tophat_alignments

description: 10010_0_D9_new onset T1D_10010


title: Control_11 _E8_HC_HC11 lib18465_CB6LAANXX_tophat_alignments

description: Control_11 _E8_HC_HC11


title: Control_11 _E7_HC_HC11 lib18464_CB6LAANXX_tophat_alignments

description: Control_11 _E7_HC_HC11


title: Control_11 _E9_HC_HC11 lib18466_CB6LAANXX_tophat_alignments

description: Control_11 _E9_HC_HC11


title: Control_11 _E2_HC_HC11 lib18459_CB6LAANXX_tophat_alignments

description: Control_11 _E2_HC_HC11


title: Control_11 _E3_HC_HC11 lib18460_CB6LAANXX_tophat_alignments

description: Control_11 _E3_HC_HC11


title: 10010_0_A4_new onset T1D_10010 lib20485_CBG5GANXX_tophat_alignments

description: 10010_0_A4_new onset T1D_10010


title: Control_11 _E1_HC_HC11 lib18458_CB6LAANXX_tophat_alignments

description: Control_11 _E1_HC_HC11


title: 10010_0_C1_new onset T1D_10010 lib20478_CBG5GANXX_tophat_alignments

description: 10010_0_C1_new onset T1D_10010


title: 10010_0_A1_new onset T1D_10010 lib20476_CBG5GANXX_tophat_alignments

description: 10010_0_A1_new onset T1D_10010


title: Control_11 _D12_HC_HC11 lib18457_CB6LAANXX_tophat_alignments

description: Control_11 _D12_HC_HC11


title: Control_11 _D11_HC_HC11 lib18456_CB6LAANXX_tophat_alignments

description: Control_11 _D11_HC_HC11


title: Control_11 _D10_HC_HC11 lib18455_CB6LAANXX_tophat_alignments

description: Control_11 _D10_HC_HC11


title: Control_11 _D8_HC_HC11 lib18453_CB6LAANXX_tophat_alignments

description: Control_11 _D8_HC_HC11


title: Control_11 _F2_HC_HC11 lib18471_CB6LAANXX_tophat_alignments

description: Control_11 _F2_HC_HC11


title: Control_11 _D7_HC_HC11 lib18452_CB6LAANXX_tophat_alignments

description: Control_11 _D7_HC_HC11


title: Control_11 _D6_HC_HC11 lib18451_CB6LAANXX_tophat_alignments

description: Control_11 _D6_HC_HC11


title: Control_11 _D5_HC_HC11 lib18450_CB6LAANXX_tophat_alignments

description: Control_11 _D5_HC_HC11


title: Control_11 _D4_HC_HC11 lib18449_CB6LAANXX_tophat_alignments

description: Control_11 _D4_HC_HC11


title: Control_11 _D9_HC_HC11 lib18454_CB6LAANXX_tophat_alignments

description: Control_11 _D9_HC_HC11


title: 10010_0_B7_new onset T1D_10010 lib20497_CBG5GANXX_tophat_alignments

description: 10010_0_B7_new onset T1D_10010


title: Control_11 _D3_HC_HC11 lib18448_CB6LAANXX_tophat_alignments

description: Control_11 _D3_HC_HC11


title: Control_11 _D2_HC_HC11 lib18447_CB6LAANXX_tophat_alignments

description: Control_11 _D2_HC_HC11


title: T1D1_H10_T1D_T1D1 lib18295_CB6LAANXX_tophat_alignments


title: T1D1_H11_T1D_T1D1 lib18296_CB6LAANXX_tophat_alignments


title: Control_11 _D1_HC_HC11 lib18446_CB6LAANXX_tophat_alignments

description: Control_11 _D1_HC_HC11


title: T1D1_H12_T1D_T1D1 lib18297_CB6LAANXX_tophat_alignments


title: T1D1_H8_T1D_T1D1 lib18293_CB6LAANXX_tophat_alignments


title: T1D1_H4_T1D_T1D1 lib18289_CB6LAANXX_tophat_alignments


title: T1D1_H5_T1D_T1D1 lib18290_CB6LAANXX_tophat_alignments


title: T1D1_H9_T1D_T1D1 lib18294_CB6LAANXX_tophat_alignments


title: T1D1_H7_T1D_T1D1 lib18292_CB6LAANXX_tophat_alignments


title: T1D1_H3_T1D_T1D1 lib18288_CB6LAANXX_tophat_alignments


title: T1D1_H2_T1D_T1D1 lib18287_CB6LAANXX_tophat_alignments


title: T1D1_G12_T1D_T1D1 lib18285_CB6LAANXX_tophat_alignments


title: T1D1_H1_T1D_T1D1 lib18286_CB6LAANXX_tophat_alignments


title: T1D1_G10_T1D_T1D1 lib18283_CB6LAANXX_tophat_alignments


title: T1D1_G9_T1D_T1D1 lib18282_CB6LAANXX_tophat_alignments


title: T1D1_G7_T1D_T1D1 lib18280_CB6LAANXX_tophat_alignments


title: T1D1_G6_T1D_T1D1 lib18279_CB6LAANXX_tophat_alignments


title: T1D1_G5_T1D_T1D1 lib18278_CB6LAANXX_tophat_alignments


title: T1D1_G2_T1D_T1D1 lib18275_CB6LAANXX_tophat_alignments


title: T1D1_G1_T1D_T1D1 lib18274_CB6LAANXX_tophat_alignments


title: T1D1_F9_T1D_T1D1 lib18272_CB6LAANXX_tophat_alignments


title: T1D1_F10_T1D_T1D1 lib18273_CB6LAANXX_tophat_alignments


title: T1D1_G4_T1D_T1D1 lib18277_CB6LAANXX_tophat_alignments


title: T1D1_G3_T1D_T1D1 lib18276_CB6LAANXX_tophat_alignments


title: T1D1_F6_T1D_T1D1 lib18269_CB6LAANXX_tophat_alignments


title: T1D1_F8_T1D_T1D1 lib18271_CB6LAANXX_tophat_alignments


title: T1D1_F7_T1D_T1D1 lib18270_CB6LAANXX_tophat_alignments


title: T1D1_H6_T1D_T1D1 lib18291_CB6LAANXX_tophat_alignments


title: T1D1_F5_T1D_T1D1 lib18268_CB6LAANXX_tophat_alignments


title: T1D1_F2_T1D_T1D1 lib18265_CB6LAANXX_tophat_alignments


title: T1D1_F4_T1D_T1D1 lib18267_CB6LAANXX_tophat_alignments


title: T1D1_F1_T1D_T1D1 lib18264_CB6LAANXX_tophat_alignments


title: T1D1_G11_T1D_T1D1 lib18284_CB6LAANXX_tophat_alignments


title: T1D1_E9_T1D_T1D1 lib18260_CB6LAANXX_tophat_alignments


title: T1D1_F3_T1D_T1D1 lib18266_CB6LAANXX_tophat_alignments


title: T1D1_E10_T1D_T1D1 lib18261_CB6LAANXX_tophat_alignments


title: T1D1_E8_T1D_T1D1 lib18259_CB6LAANXX_tophat_alignments


title: T1D1_E6_T1D_T1D1 lib18257_CB6LAANXX_tophat_alignments


title: T1D1_E11_T1D_T1D1 lib18262_CB6LAANXX_tophat_alignments


title: T1D1_E7_T1D_T1D1 lib18258_CB6LAANXX_tophat_alignments


title: T1D1_E4_T1D_T1D1 lib18255_CB6LAANXX_tophat_alignments


title: T1D1_E12_T1D_T1D1 lib18263_CB6LAANXX_tophat_alignments


title: T1D1_E3_T1D_T1D1 lib18254_CB6LAANXX_tophat_alignments


title: T1D1_G8_T1D_T1D1 lib18281_CB6LAANXX_tophat_alignments


title: T1D1_E5_T1D_T1D1 lib18256_CB6LAANXX_tophat_alignments


title: T1D1_E2_T1D_T1D1 lib18253_CB6LAANXX_tophat_alignments


title: T1D1_D12_T1D_T1D1 lib18251_CB6LAANXX_tophat_alignments


title: T1D1_D11_T1D_T1D1 lib18250_CB6LAANXX_tophat_alignments


title: T1D1_E1_T1D_T1D1 lib18252_CB6LAANXX_tophat_alignments


title: T1D1_D6_T1D_T1D1 lib18245_CB6LAANXX_tophat_alignments


title: T1D1_D8_T1D_T1D1 lib18247_CB6LAANXX_tophat_alignments


title: T1D1_D7_T1D_T1D1 lib18246_CB6LAANXX_tophat_alignments


title: T1D1_D5_T1D_T1D1 lib18244_CB6LAANXX_tophat_alignments


title: T1D1_D4_T1D_T1D1 lib18243_CB6LAANXX_tophat_alignments


title: T1D1_D9_T1D_T1D1 lib18248_CB6LAANXX_tophat_alignments


title: T1D1_D3_T1D_T1D1 lib18242_CB6LAANXX_tophat_alignments


title: T1D1_D2_T1D_T1D1 lib18241_CB6LAANXX_tophat_alignments


title: T1D1_D1_T1D_T1D1 lib18240_CB6LAANXX_tophat_alignments


title: T1D1_C9_T1D_T1D1 lib18236_CB6LAANXX_tophat_alignments


title: T1D1_C11_T1D_T1D1 lib18238_CB6LAANXX_tophat_alignments


title: T1D1_C7_T1D_T1D1 lib18234_CB6LAANXX_tophat_alignments


title: T1D1_C6_T1D_T1D1 lib18233_CB6LAANXX_tophat_alignments


title: T1D1_C5_T1D_T1D1 lib18232_CB6LAANXX_tophat_alignments


title: T1D1_C4_T1D_T1D1 lib18231_CB6LAANXX_tophat_alignments


title: T1D1_C10_T1D_T1D1 lib18237_CB6LAANXX_tophat_alignments


title: T1D1_C3_T1D_T1D1 lib18230_CB6LAANXX_tophat_alignments


title: T1D1_C2_T1D_T1D1 lib18229_CB6LAANXX_tophat_alignments


title: T1D1_D10_T1D_T1D1 lib18249_CB6LAANXX_tophat_alignments


title: T1D1_B10_T1D_T1D1 lib18225_CB6LAANXX_tophat_alignments


title: T1D1_B12_T1D_T1D1 lib18227_CB6LAANXX_tophat_alignments


title: T1D1_C1_T1D_T1D1 lib18228_CB6LAANXX_tophat_alignments


title: T1D1_B9_T1D_T1D1 lib18224_CB6LAANXX_tophat_alignments


title: T1D1_B8_T1D_T1D1 lib18223_CB6LAANXX_tophat_alignments


title: T1D1_B11_T1D_T1D1 lib18226_CB6LAANXX_tophat_alignments


title: T1D1_B6_T1D_T1D1 lib18221_CB6LAANXX_tophat_alignments


title: T1D1_B4_T1D_T1D1 lib18219_CB6LAANXX_tophat_alignments


title: T1D1_B5_T1D_T1D1 lib18220_CB6LAANXX_tophat_alignments


title: T1D1_C12_T1D_T1D1 lib18239_CB6LAANXX_tophat_alignments


title: T1D1_B2_T1D_T1D1 lib18217_CB6LAANXX_tophat_alignments


title: T1D1_A11_T1D_T1D1 lib18214_CB6LAANXX_tophat_alignments


title: T1D1_B1_T1D_T1D1 lib18216_CB6LAANXX_tophat_alignments


title: T1D1_B3_T1D_T1D1 lib18218_CB6LAANXX_tophat_alignments


title: T1D1_A12_T1D_T1D1 lib18215_CB6LAANXX_tophat_alignments


title: T1D1_C8_T1D_T1D1 lib18235_CB6LAANXX_tophat_alignments


title: T1D1_A9_T1D_T1D1 lib18212_CB6LAANXX_tophat_alignments


title: T1D1_A8_T1D_T1D1 lib18211_CB6LAANXX_tophat_alignments


title: T1D1_A10_T1D_T1D1 lib18213_CB6LAANXX_tophat_alignments


title: T1D1_A7_T1D_T1D1 lib18210_CB6LAANXX_tophat_alignments


title: T1D1_A4_T1D_T1D1 lib18207_CB6LAANXX_tophat_alignments


title: T1D6_H12_T1D_T1D6 lib17877_CB6LAANXX_tophat_alignments


title: T1D1_A3_T1D_T1D1 lib18206_CB6LAANXX_tophat_alignments


title: T1D1_A5_T1D_T1D1 lib18208_CB6LAANXX_tophat_alignments


title: T1D6_H11_T1D_T1D6 lib17876_CB6LAANXX_tophat_alignments


title: T1D1_A2_T1D_T1D1 lib18205_CB6LAANXX_tophat_alignments


title: T1D1_A1_T1D_T1D1 lib18204_CB6LAANXX_tophat_alignments


title: T1D6_H10_T1D_T1D6 lib17875_CB6LAANXX_tophat_alignments


title: T1D6_H8_T1D_T1D6 lib17873_CB6LAANXX_tophat_alignments


title: T1D6_H9_T1D_T1D6 lib17874_CB6LAANXX_tophat_alignments


title: T1D1_B7_T1D_T1D1 lib18222_CB6LAANXX_tophat_alignments


title: T1D6_H4_T1D_T1D6 lib17869_CB6LAANXX_tophat_alignments


title: T1D6_H5_T1D_T1D6 lib17870_CB6LAANXX_tophat_alignments


title: T1D6_H7_T1D_T1D6 lib17872_CB6LAANXX_tophat_alignments


title: T1D6_H3_T1D_T1D6 lib17868_CB6LAANXX_tophat_alignments


title: T1D6_H2_T1D_T1D6 lib17867_CB6LAANXX_tophat_alignments


title: T1D6_G12_T1D_T1D6 lib17865_CB6LAANXX_tophat_alignments


title: T1D6_H1_T1D_T1D6 lib17866_CB6LAANXX_tophat_alignments


title: T1D6_G10_T1D_T1D6 lib17863_CB6LAANXX_tophat_alignments


title: T1D6_G11_T1D_T1D6 lib17864_CB6LAANXX_tophat_alignments


title: T1D6_G9_T1D_T1D6 lib17862_CB6LAANXX_tophat_alignments


title: T1D6_G6_T1D_T1D6 lib17859_CB6LAANXX_tophat_alignments


title: T1D6_G7_T1D_T1D6 lib17860_CB6LAANXX_tophat_alignments


title: T1D6_G5_T1D_T1D6 lib17858_CB6LAANXX_tophat_alignments


title: T1D6_G8_T1D_T1D6 lib17861_CB6LAANXX_tophat_alignments


title: T1D1_A6_T1D_T1D1 lib18209_CB6LAANXX_tophat_alignments


title: T1D6_G3_T1D_T1D6 lib17856_CB6LAANXX_tophat_alignments


title: T1D6_G2_T1D_T1D6 lib17855_CB6LAANXX_tophat_alignments


title: T1D6_H6_T1D_T1D6 lib17871_CB6LAANXX_tophat_alignments


title: T1D6_F12_T1D_T1D6 lib17853_CB6LAANXX_tophat_alignments


title: T1D6_F4_T1D_T1D6 lib17845_CB6LAANXX_tophat_alignments


title: T1D6_F10_T1D_T1D6 lib17851_CB6LAANXX_tophat_alignments


title: T1D6_F5_T1D_T1D6 lib17846_CB6LAANXX_tophat_alignments


title: T1D6_F7_T1D_T1D6 lib17848_CB6LAANXX_tophat_alignments


title: T1D6_G1_T1D_T1D6 lib17854_CB6LAANXX_tophat_alignments


title: T1D6_F8_T1D_T1D6 lib17849_CB6LAANXX_tophat_alignments


title: T1D6_F9_T1D_T1D6 lib17850_CB6LAANXX_tophat_alignments


title: T1D6_F3_T1D_T1D6 lib17844_CB6LAANXX_tophat_alignments


title: T1D6_F11_T1D_T1D6 lib17852_CB6LAANXX_tophat_alignments


title: T1D6_F6_T1D_T1D6 lib17847_CB6LAANXX_tophat_alignments


title: T1D6_E12_T1D_T1D6 lib17841_CB6LAANXX_tophat_alignments


title: T1D6_E10_T1D_T1D6 lib17839_CB6LAANXX_tophat_alignments


title: T1D6_F1_T1D_T1D6 lib17842_CB6LAANXX_tophat_alignments


title: T1D6_F2_T1D_T1D6 lib17843_CB6LAANXX_tophat_alignments


title: T1D6_E9_T1D_T1D6 lib17838_CB6LAANXX_tophat_alignments


title: T1D6_E6_T1D_T1D6 lib17835_CB6LAANXX_tophat_alignments


title: T1D6_E7_T1D_T1D6 lib17836_CB6LAANXX_tophat_alignments


title: T1D6_G4_T1D_T1D6 lib17857_CB6LAANXX_tophat_alignments


title: T1D6_E5_T1D_T1D6 lib17834_CB6LAANXX_tophat_alignments


title: T1D6_E4_T1D_T1D6 lib17833_CB6LAANXX_tophat_alignments


title: T1D6_E2_T1D_T1D6 lib17831_CB6LAANXX_tophat_alignments


title: T1D6_D11_T1D_T1D6 lib17828_CB6LAANXX_tophat_alignments


title: T1D6_D12_T1D_T1D6 lib17829_CB6LAANXX_tophat_alignments


title: T1D6_E3_T1D_T1D6 lib17832_CB6LAANXX_tophat_alignments


title: T1D6_D10_T1D_T1D6 lib17827_CB6LAANXX_tophat_alignments


title: T1D6_D9_T1D_T1D6 lib17826_CB6LAANXX_tophat_alignments


title: T1D6_D8_T1D_T1D6 lib17825_CB6LAANXX_tophat_alignments


title: T1D6_E11_T1D_T1D6 lib17840_CB6LAANXX_tophat_alignments


title: T1D6_D6_T1D_T1D6 lib17823_CB6LAANXX_tophat_alignments


title: T1D6_D4_T1D_T1D6 lib17821_CB6LAANXX_tophat_alignments


title: T1D6_D2_T1D_T1D6 lib17819_CB6LAANXX_tophat_alignments


title: T1D6_C11_T1D_T1D6 lib17816_CB6LAANXX_tophat_alignments


title: T1D6_D1_T1D_T1D6 lib17818_CB6LAANXX_tophat_alignments


title: T1D6_C12_T1D_T1D6 lib17817_CB6LAANXX_tophat_alignments


title: T1D6_D5_T1D_T1D6 lib17822_CB6LAANXX_tophat_alignments


title: T1D6_D3_T1D_T1D6 lib17820_CB6LAANXX_tophat_alignments


title: T1D6_D7_T1D_T1D6 lib17824_CB6LAANXX_tophat_alignments


title: T1D6_E8_T1D_T1D6 lib17837_CB6LAANXX_tophat_alignments


title: T1D6_C10_T1D_T1D6 lib17815_CB6LAANXX_tophat_alignments


title: T1D6_C6_T1D_T1D6 lib17811_CB6LAANXX_tophat_alignments


title: T1D6_C9_T1D_T1D6 lib17814_CB6LAANXX_tophat_alignments


title: T1D6_E1_T1D_T1D6 lib17830_CB6LAANXX_tophat_alignments


title: T1D6_C1_T1D_T1D6 lib17806_CB6LAANXX_tophat_alignments


title: T1D6_C2_T1D_T1D6 lib17807_CB6LAANXX_tophat_alignments


title: T1D6_B12_T1D_T1D6 lib17805_CB6LAANXX_tophat_alignments


title: T1D6_B11_T1D_T1D6 lib17804_CB6LAANXX_tophat_alignments


title: T1D6_B10_T1D_T1D6 lib17803_CB6LAANXX_tophat_alignments


title: T1D6_C5_T1D_T1D6 lib17810_CB6LAANXX_tophat_alignments


title: T1D6_C4_T1D_T1D6 lib17809_CB6LAANXX_tophat_alignments


title: T1D6_B9_T1D_T1D6 lib17802_CB6LAANXX_tophat_alignments


title: T1D6_B8_T1D_T1D6 lib17801_CB6LAANXX_tophat_alignments


title: T1D6_B6_T1D_T1D6 lib17799_CB6LAANXX_tophat_alignments


title: T1D6_B7_T1D_T1D6 lib17800_CB6LAANXX_tophat_alignments


title: T1D6_B4_T1D_T1D6 lib17797_CB6LAANXX_tophat_alignments


title: T1D6_B5_T1D_T1D6 lib17798_CB6LAANXX_tophat_alignments


title: T1D6_B1_T1D_T1D6 lib17794_CB6LAANXX_tophat_alignments


title: T1D6_B2_T1D_T1D6 lib17795_CB6LAANXX_tophat_alignments


title: T1D6_C8_T1D_T1D6 lib17813_CB6LAANXX_tophat_alignments


title: T1D6_A10_T1D_T1D6 lib17791_CB6LAANXX_tophat_alignments


title: T1D6_A8_T1D_T1D6 lib17789_CB6LAANXX_tophat_alignments


title: T1D6_C7_T1D_T1D6 lib17812_CB6LAANXX_tophat_alignments


title: T1D6_C3_T1D_T1D6 lib17808_CB6LAANXX_tophat_alignments


title: T1D6_A5_T1D_T1D6 lib17786_CB6LAANXX_tophat_alignments


title: T1D6_A12_T1D_T1D6 lib17793_CB6LAANXX_tophat_alignments


title: T1D6_A7_T1D_T1D6 lib17788_CB6LAANXX_tophat_alignments


title: T1D6_A6_T1D_T1D6 lib17787_CB6LAANXX_tophat_alignments


title: T1D6_A3_T1D_T1D6 lib17784_CB6LAANXX_tophat_alignments


title: T1D6_A2_T1D_T1D6 lib17783_CB6LAANXX_tophat_alignments


title: T1D6_A4_T1D_T1D6 lib17785_CB6LAANXX_tophat_alignments


title: T1D8_2_H11_T1D_T1D8 lib17684_CB5F8ANXX_tophat_alignments


title: T1D8_2_H12_T1D_T1D8 lib17685_CB5F8ANXX_tophat_alignments


title: T1D6_A1_T1D_T1D6 lib17782_CB6LAANXX_tophat_alignments


title: T1D8_2_H10_T1D_T1D8 lib17683_CB5F8ANXX_tophat_alignments


title: T1D6_B3_T1D_T1D6 lib17796_CB6LAANXX_tophat_alignments


title: T1D8_2_H9_T1D_T1D8 lib17682_CB5F8ANXX_tophat_alignments


title: T1D6_A11_T1D_T1D6 lib17792_CB6LAANXX_tophat_alignments


title: T1D8_2_H8_T1D_T1D8 lib17681_CB5F8ANXX_tophat_alignments


title: T1D8_2_H6_T1D_T1D8 lib17679_CB5F8ANXX_tophat_alignments


title: T1D8_2_H7_T1D_T1D8 lib17680_CB5F8ANXX_tophat_alignments


title: T1D6_A9_T1D_T1D6 lib17790_CB6LAANXX_tophat_alignments


title: T1D8_2_H4_T1D_T1D8 lib17677_CB5F8ANXX_tophat_alignments


title: T1D8_2_H3_T1D_T1D8 lib17676_CB5F8ANXX_tophat_alignments


title: T1D8_2_H5_T1D_T1D8 lib17678_CB5F8ANXX_tophat_alignments


title: T1D8_2_H2_T1D_T1D8 lib17675_CB5F8ANXX_tophat_alignments


title: T1D8_2_G11_T1D_T1D8 lib17672_CB5F8ANXX_tophat_alignments


title: T1D8_2_H1_T1D_T1D8 lib17674_CB5F8ANXX_tophat_alignments


title: T1D8_2_G6_T1D_T1D8 lib17667_CB5F8ANXX_tophat_alignments


title: T1D8_2_G10_T1D_T1D8 lib17671_CB5F8ANXX_tophat_alignments


title: T1D8_2_F12_T1D_T1D8 lib17661_CB5F8ANXX_tophat_alignments


title: T1D8_2_G12_T1D_T1D8 lib17673_CB5F8ANXX_tophat_alignments


title: T1D8_2_G9_T1D_T1D8 lib17670_CB5F8ANXX_tophat_alignments


title: T1D8_2_F11_T1D_T1D8 lib17660_CB5F8ANXX_tophat_alignments


title: T1D8_2_G1_T1D_T1D8 lib17662_CB5F8ANXX_tophat_alignments


title: T1D8_2_G7_T1D_T1D8 lib17668_CB5F8ANXX_tophat_alignments


title: T1D8_2_G5_T1D_T1D8 lib17666_CB5F8ANXX_tophat_alignments


title: T1D8_2_G3_T1D_T1D8 lib17664_CB5F8ANXX_tophat_alignments


title: T1D8_2_F10_T1D_T1D8 lib17659_CB5F8ANXX_tophat_alignments


title: T1D8_2_F9_T1D_T1D8 lib17658_CB5F8ANXX_tophat_alignments


title: T1D8_2_G2_T1D_T1D8 lib17663_CB5F8ANXX_tophat_alignments


title: T1D8_2_F5_T1D_T1D8 lib17654_CB5F8ANXX_tophat_alignments


title: T1D8_2_F8_T1D_T1D8 lib17657_CB5F8ANXX_tophat_alignments


title: T1D8_2_F7_T1D_T1D8 lib17656_CB5F8ANXX_tophat_alignments


title: T1D8_2_F6_T1D_T1D8 lib17655_CB5F8ANXX_tophat_alignments


title: T1D8_2_F2_T1D_T1D8 lib17651_CB5F8ANXX_tophat_alignments


title: T1D8_2_F3_T1D_T1D8 lib17652_CB5F8ANXX_tophat_alignments


title: T1D8_2_F1_T1D_T1D8 lib17650_CB5F8ANXX_tophat_alignments


title: T1D8_2_G4_T1D_T1D8 lib17665_CB5F8ANXX_tophat_alignments


title: T1D8_2_F4_T1D_T1D8 lib17653_CB5F8ANXX_tophat_alignments


title: T1D8_2_E12_T1D_T1D8 lib17649_CB5F8ANXX_tophat_alignments


title: T1D8_2_G8_T1D_T1D8 lib17669_CB5F8ANXX_tophat_alignments


title: T1D8_2_E10_T1D_T1D8 lib17647_CB5F8ANXX_tophat_alignments


title: T1D8_2_E11_T1D_T1D8 lib17648_CB5F8ANXX_tophat_alignments


title: T1D8_2_E8_T1D_T1D8 lib17645_CB5F8ANXX_tophat_alignments


title: T1D8_2_E7_T1D_T1D8 lib17644_CB5F8ANXX_tophat_alignments


title: T1D8_2_E3_T1D_T1D8 lib17640_CB5F8ANXX_tophat_alignments


title: T1D8_2_E5_T1D_T1D8 lib17642_CB5F8ANXX_tophat_alignments


title: T1D8_2_E6_T1D_T1D8 lib17643_CB5F8ANXX_tophat_alignments


title: T1D8_2_D10_T1D_T1D8 lib17635_CB5F8ANXX_tophat_alignments


title: T1D8_2_E4_T1D_T1D8 lib17641_CB5F8ANXX_tophat_alignments


title: T1D8_2_D6_T1D_T1D8 lib17631_CB5F8ANXX_tophat_alignments


title: T1D8_2_D5_T1D_T1D8 lib17630_CB5F8ANXX_tophat_alignments


title: T1D8_2_D7_T1D_T1D8 lib17632_CB5F8ANXX_tophat_alignments


title: T1D8_2_E2_T1D_T1D8 lib17639_CB5F8ANXX_tophat_alignments


title: T1D8_2_D12_T1D_T1D8 lib17637_CB5F8ANXX_tophat_alignments


title: T1D8_2_D1_T1D_T1D8 lib17626_CB5F8ANXX_tophat_alignments


title: T1D8_2_E1_T1D_T1D8 lib17638_CB5F8ANXX_tophat_alignments


title: T1D8_2_C10_T1D_T1D8 lib17623_CB5F8ANXX_tophat_alignments


title: T1D8_2_D9_T1D_T1D8 lib17634_CB5F8ANXX_tophat_alignments


title: T1D8_2_E9_T1D_T1D8 lib17646_CB5F8ANXX_tophat_alignments


title: T1D8_2_D11_T1D_T1D8 lib17636_CB5F8ANXX_tophat_alignments


title: T1D8_2_D8_T1D_T1D8 lib17633_CB5F8ANXX_tophat_alignments


title: T1D8_2_C6_T1D_T1D8 lib17619_CB5F8ANXX_tophat_alignments


title: T1D8_2_C5_T1D_T1D8 lib17618_CB5F8ANXX_tophat_alignments


title: T1D8_2_C3_T1D_T1D8 lib17616_CB5F8ANXX_tophat_alignments


title: T1D8_2_D4_T1D_T1D8 lib17629_CB5F8ANXX_tophat_alignments


title: T1D8_2_D2_T1D_T1D8 lib17627_CB5F8ANXX_tophat_alignments


title: T1D8_2_C12_T1D_T1D8 lib17625_CB5F8ANXX_tophat_alignments


title: T1D8_2_B10_T1D_T1D8 lib17611_CB5F8ANXX_tophat_alignments


title: T1D8_2_C11_T1D_T1D8 lib17624_CB5F8ANXX_tophat_alignments


title: T1D8_2_C9_T1D_T1D8 lib17622_CB5F8ANXX_tophat_alignments


title: T1D8_2_B9_T1D_T1D8 lib17610_CB5F8ANXX_tophat_alignments


title: T1D8_2_C8_T1D_T1D8 lib17621_CB5F8ANXX_tophat_alignments


title: T1D8_2_B6_T1D_T1D8 lib17607_CB5F8ANXX_tophat_alignments


title: T1D8_2_C7_T1D_T1D8 lib17620_CB5F8ANXX_tophat_alignments


title: T1D8_2_C4_T1D_T1D8 lib17617_CB5F8ANXX_tophat_alignments


title: T1D8_2_B12_T1D_T1D8 lib17613_CB5F8ANXX_tophat_alignments


title: T1D8_2_C1_T1D_T1D8 lib17614_CB5F8ANXX_tophat_alignments


title: T1D8_2_B3_T1D_T1D8 lib17604_CB5F8ANXX_tophat_alignments


title: T1D8_2_B7_T1D_T1D8 lib17608_CB5F8ANXX_tophat_alignments


title: T1D8_2_A12_T1D_T1D8 lib17601_CB5F8ANXX_tophat_alignments


title: T1D8_2_D3_T1D_T1D8 lib17628_CB5F8ANXX_tophat_alignments


title: T1D8_2_A10_T1D_T1D8 lib17599_CB5F8ANXX_tophat_alignments


title: T1D8_2_B5_T1D_T1D8 lib17606_CB5F8ANXX_tophat_alignments


title: T1D8_2_A11_T1D_T1D8 lib17600_CB5F8ANXX_tophat_alignments


title: T1D8_2_B8_T1D_T1D8 lib17609_CB5F8ANXX_tophat_alignments


title: T1D8_2_C2_T1D_T1D8 lib17615_CB5F8ANXX_tophat_alignments


title: T1D8_2_B2_T1D_T1D8 lib17603_CB5F8ANXX_tophat_alignments


title: T1D8_2_B11_T1D_T1D8 lib17612_CB5F8ANXX_tophat_alignments


title: T1D8_2_A6_T1D_T1D8 lib17595_CB5F8ANXX_tophat_alignments


title: T1D8_2_B1_T1D_T1D8 lib17602_CB5F8ANXX_tophat_alignments


title: T1D8_2_B4_T1D_T1D8 lib17605_CB5F8ANXX_tophat_alignments


title: T1D8_2_A8_T1D_T1D8 lib17597_CB5F8ANXX_tophat_alignments


title: T1D8_2_A9_T1D_T1D8 lib17598_CB5F8ANXX_tophat_alignments


title: T1D8_2_A2_T1D_T1D8 lib17591_CB5F8ANXX_tophat_alignments


title: T1D8_2_A1_T1D_T1D8 lib17590_CB5F8ANXX_tophat_alignments


title: H10_Wb366624175_T1D_T1D2 lib17166_CAU0CANXX_tophat_alignments


title: H9_Wb366624175_T1D_T1D2 lib17165_CAU0CANXX_tophat_alignments


title: T1D8_2_A7_T1D_T1D8 lib17596_CB5F8ANXX_tophat_alignments


title: H6_Wb366624175_T1D_T1D2 lib17162_CAU0CANXX_tophat_alignments


title: H8_Wb366624175_T1D_T1D2 lib17164_CAU0CANXX_tophat_alignments


title: H4_Wb366624175_T1D_T1D2 lib17160_CAU0CANXX_tophat_alignments


title: T1D8_2_A4_T1D_T1D8 lib17593_CB5F8ANXX_tophat_alignments


title: H12_Wb366624175_T1D_T1D2 lib17168_CAU0CANXX_tophat_alignments


title: H3_Wb366624175_T1D_T1D2 lib17159_CAU0CANXX_tophat_alignments


title: H11_Wb366624175_T1D_T1D2 lib17167_CAU0CANXX_tophat_alignments


title: H7_Wb366624175_T1D_T1D2 lib17163_CAU0CANXX_tophat_alignments


title: G10_Wb366624175_T1D_T1D2 lib17154_CAU0CANXX_tophat_alignments


title: H2_Wb366624175_T1D_T1D2 lib17158_CAU0CANXX_tophat_alignments


title: T1D8_2_A3_T1D_T1D8 lib17592_CB5F8ANXX_tophat_alignments


title: H5_Wb366624175_T1D_T1D2 lib17161_CAU0CANXX_tophat_alignments


title: H1_Wb366624175_T1D_T1D2 lib17157_CAU0CANXX_tophat_alignments


title: G1_Wb366624175_T1D_T1D2 lib17145_CAU0CANXX_tophat_alignments


title: F11_Wb366624175_T1D_T1D2 lib17143_CAU0CANXX_tophat_alignments


title: G8_Wb366624175_T1D_T1D2 lib17152_CAU0CANXX_tophat_alignments


title: T1D8_2_A5_T1D_T1D8 lib17594_CB5F8ANXX_tophat_alignments


title: G9_Wb366624175_T1D_T1D2 lib17153_CAU0CANXX_tophat_alignments


title: F7_Wb366624175_T1D_T1D2 lib17139_CAU0CANXX_tophat_alignments


title: G7_Wb366624175_T1D_T1D2 lib17151_CAU0CANXX_tophat_alignments


title: G6_Wb366624175_T1D_T1D2 lib17150_CAU0CANXX_tophat_alignments


title: G12_Wb366624175_T1D_T1D2 lib17156_CAU0CANXX_tophat_alignments


title: G11_Wb366624175_T1D_T1D2 lib17155_CAU0CANXX_tophat_alignments


title: F2_Wb366624175_T1D_T1D2 lib17134_CAU0CANXX_tophat_alignments


title: F1_Wb366624175_T1D_T1D2 lib17133_CAU0CANXX_tophat_alignments


title: G5_Wb366624175_T1D_T1D2 lib17149_CAU0CANXX_tophat_alignments


title: E12_Wb366624175_T1D_T1D2 lib17132_CAU0CANXX_tophat_alignments


title: F6_Wb366624175_T1D_T1D2 lib17138_CAU0CANXX_tophat_alignments


title: F12_Wb366624175_T1D_T1D2 lib17144_CAU0CANXX_tophat_alignments


title: E7_Wb366624175_T1D_T1D2 lib17127_CAU0CANXX_tophat_alignments


title: G2_Wb366624175_T1D_T1D2 lib17146_CAU0CANXX_tophat_alignments


title: E6_Wb366624175_T1D_T1D2 lib17126_CAU0CANXX_tophat_alignments


title: F10_Wb366624175_T1D_T1D2 lib17142_CAU0CANXX_tophat_alignments


title: F9_Wb366624175_T1D_T1D2 lib17141_CAU0CANXX_tophat_alignments


title: E4_Wb366624175_T1D_T1D2 lib17124_CAU0CANXX_tophat_alignments


title: E2_Wb366624175_T1D_T1D2 lib17122_CAU0CANXX_tophat_alignments


title: F8_Wb366624175_T1D_T1D2 lib17140_CAU0CANXX_tophat_alignments


title: D11_Wb366624175_T1D_T1D2 lib17119_CAU0CANXX_tophat_alignments


title: D12_Wb366624175_T1D_T1D2 lib17120_CAU0CANXX_tophat_alignments


title: F5_Wb366624175_T1D_T1D2 lib17137_CAU0CANXX_tophat_alignments


title: F4_Wb366624175_T1D_T1D2 lib17136_CAU0CANXX_tophat_alignments


title: D9_Wb366624175_T1D_T1D2 lib17117_CAU0CANXX_tophat_alignments


title: D6_Wb366624175_T1D_T1D2 lib17114_CAU0CANXX_tophat_alignments


title: F3_Wb366624175_T1D_T1D2 lib17135_CAU0CANXX_tophat_alignments


title: D3_Wb366624175_T1D_T1D2 lib17111_CAU0CANXX_tophat_alignments


title: D1_Wb366624175_T1D_T1D2 lib17109_CAU0CANXX_tophat_alignments


title: E11_Wb366624175_T1D_T1D2 lib17131_CAU0CANXX_tophat_alignments


title: C10_Wb366624175_T1D_T1D2 lib17106_CAU0CANXX_tophat_alignments


title: E10_Wb366624175_T1D_T1D2 lib17130_CAU0CANXX_tophat_alignments


title: E9_Wb366624175_T1D_T1D2 lib17129_CAU0CANXX_tophat_alignments


title: G4_Wb366624175_T1D_T1D2 lib17148_CAU0CANXX_tophat_alignments


title: G3_Wb366624175_T1D_T1D2 lib17147_CAU0CANXX_tophat_alignments


title: C6_Wb366624175_T1D_T1D2 lib17102_CAU0CANXX_tophat_alignments


title: C5_Wb366624175_T1D_T1D2 lib17101_CAU0CANXX_tophat_alignments


title: E8_Wb366624175_T1D_T1D2 lib17128_CAU0CANXX_tophat_alignments


title: B12_Wb366624175_T1D_T1D2 lib17096_CAU0CANXX_tophat_alignments


title: E5_Wb366624175_T1D_T1D2 lib17125_CAU0CANXX_tophat_alignments


title: E3_Wb366624175_T1D_T1D2 lib17123_CAU0CANXX_tophat_alignments


title: B10_Wb366624175_T1D_T1D2 lib17094_CAU0CANXX_tophat_alignments


title: E1_Wb366624175_T1D_T1D2 lib17121_CAU0CANXX_tophat_alignments


title: D10_Wb366624175_T1D_T1D2 lib17118_CAU0CANXX_tophat_alignments


title: D8_Wb366624175_T1D_T1D2 lib17116_CAU0CANXX_tophat_alignments


title: B9_Wb366624175_T1D_T1D2 lib17093_CAU0CANXX_tophat_alignments


title: B7_Wb366624175_T1D_T1D2 lib17091_CAU0CANXX_tophat_alignments


title: D7_Wb366624175_T1D_T1D2 lib17115_CAU0CANXX_tophat_alignments


title: B6_Wb366624175_T1D_T1D2 lib17090_CAU0CANXX_tophat_alignments


title: B5_Wb366624175_T1D_T1D2 lib17089_CAU0CANXX_tophat_alignments


title: C3_Wb366624175_T1D_T1D2 lib17099_CAU0CANXX_tophat_alignments


title: B3_Wb366624175_T1D_T1D2 lib17087_CAU0CANXX_tophat_alignments


title: D5_Wb366624175_T1D_T1D2 lib17113_CAU0CANXX_tophat_alignments


title: D2_Wb366624175_T1D_T1D2 lib17110_CAU0CANXX_tophat_alignments


title: D4_Wb366624175_T1D_T1D2 lib17112_CAU0CANXX_tophat_alignments


title: A12_Wb366624175_T1D_T1D2 lib17084_CAU0CANXX_tophat_alignments


title: B1_Wb366624175_T1D_T1D2 lib17085_CAU0CANXX_tophat_alignments


title: A11_Wb366624175_T1D_T1D2 lib17083_CAU0CANXX_tophat_alignments


title: C11_Wb366624175_T1D_T1D2 lib17107_CAU0CANXX_tophat_alignments


title: A9_Wb366624175_T1D_T1D2 lib17081_CAU0CANXX_tophat_alignments


title: A8_Wb366624175_T1D_T1D2 lib17080_CAU0CANXX_tophat_alignments


title: A7_Wb366624175_T1D_T1D2 lib17079_CAU0CANXX_tophat_alignments


title: A6_Wb366624175_T1D_T1D2 lib17078_CAU0CANXX_tophat_alignments


title: C9_Wb366624175_T1D_T1D2 lib17105_CAU0CANXX_tophat_alignments


title: C8_Wb366624175_T1D_T1D2 lib17104_CAU0CANXX_tophat_alignments


title: A3_Wb366624175_T1D_T1D2 lib17075_CAU0CANXX_tophat_alignments


title: C2_Wb366624175_T1D_T1D2 lib17098_CAU0CANXX_tophat_alignments


title: C4_Wb366624175_T1D_T1D2 lib17100_CAU0CANXX_tophat_alignments


title: A2_Wb366624175_T1D_T1D2 lib17074_CAU0CANXX_tophat_alignments


title: C1_Wb366624175_T1D_T1D2 lib17097_CAU0CANXX_tophat_alignments


title: 1D_T1D10_C94_T1D_T1D10 lib15714_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C54_T1D_T1D10 lib15710_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C89_T1D_T1D10 lib15708_CAHY7ANXX_tophat_alignments


title: 1D_T1D10_C95_T1D_T1D10 lib15709_CAHY7ANXX_tophat_alignments


title: B11_Wb366624175_T1D_T1D2 lib17095_CAU0CANXX_tophat_alignments


title: C12_Wb366624175_T1D_T1D2 lib17108_CAU0CANXX_tophat_alignments


title: 1_T1D10_C48_T1D_T1D10 lib15703_CAHY7ANXX_tophat_alignments


title: C7_Wb366624175_T1D_T1D2 lib17103_CAU0CANXX_tophat_alignments


title: 1_T1D10_C47_T1D_T1D10 lib15700_CAHY7ANXX_tophat_alignments


title: 1D_T1D10_C30_T1D_T1D10 lib15702_CAHY7ANXX_tophat_alignments


title: B4_Wb366624175_T1D_T1D2 lib17088_CAU0CANXX_tophat_alignments


title: A10_Wb366624175_T1D_T1D2 lib17082_CAU0CANXX_tophat_alignments


title: 1_T1D10_C29_T1D_T1D10 lib15698_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C18_T1D_T1D10 lib15697_CAHY7ANXX_tophat_alignments


title: B8_Wb366624175_T1D_T1D2 lib17092_CAU0CANXX_tophat_alignments


title: 1_T1D10_C91_T1D_T1D10 lib15696_CAHY7ANXX_tophat_alignments


title: B2_Wb366624175_T1D_T1D2 lib17086_CAU0CANXX_tophat_alignments


title: A5_Wb366624175_T1D_T1D2 lib17077_CAU0CANXX_tophat_alignments


title: 1_T1D10_C88_T1D_T1D10 lib15713_CAHY7ANXX_tophat_alignments


title: A1_Wb366624175_T1D_T1D2 lib17073_CAU0CANXX_tophat_alignments


title: 1_T1D10_C76_T1D_T1D10 lib15712_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C92_T1D_T1D10 lib15693_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C86_T1D_T1D10 lib15692_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C68_T1D_T1D10 lib15691_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C66_T1D_T1D10 lib15711_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C96_T1D_T1D10 lib15706_CAHY7ANXX_tophat_alignments


title: A4_Wb366624175_T1D_T1D2 lib17076_CAU0CANXX_tophat_alignments


title: 1_T1D10_C78_T1D_T1D10 lib15705_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C81_T1D_T1D10 lib15688_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C70_T1D_T1D10 lib15704_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C75_T1D_T1D10 lib15687_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C10_T1D_T1D10 lib15701_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C35_T1D_T1D10 lib15699_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C85_T1D_T1D10 lib15695_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C79_T1D_T1D10 lib15694_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C33_T1D_T1D10 lib15684_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C19_T1D_T1D10 lib15683_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C87_T1D_T1D10 lib15689_CAHY7ANXX_tophat_alignments


title: 1D_T1D10_C37_T1D_T1D10 lib15680_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C93_T1D_T1D10 lib15690_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C09_T1D_T1D10 lib15675_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C13_T1D_T1D10 lib15682_CAHY7ANXX_tophat_alignments


title: 1D_T1D10_C45_T1D_T1D10 lib15686_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C77_T1D_T1D10 lib15707_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C39_T1D_T1D10 lib15685_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C26_T1D_T1D10 lib15681_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C21_T1D_T1D10 lib15677_CAHY7ANXX_tophat_alignments


title: 1P_Ctl10_C83_HC_HC10 lib15671_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C15_T1D_T1D10 lib15676_CAHY7ANXX_tophat_alignments


title: 1D_Ctl10_C48_HC_HC10 lib15670_CAHY7ANXX_tophat_alignments


title: 1_Ctl10_C42_HC_HC10 lib15669_CAHY7ANXX_tophat_alignments


title: 1P_Ctl10_C45_HC_HC10 lib15665_CAHY7ANXX_tophat_alignments


title: 1_Ctl10_C17_HC_HC10 lib15668_CAHY7ANXX_tophat_alignments


title: 1_HC11_C66_HC_HC11 lib15626_CAHY7ANXX_tophat_alignments


title: 1_Ctl10_C43_HC_HC10 lib15661_CAHY7ANXX_tophat_alignments


title: 1P_Ctl10_C28_HC_HC10 lib15666_CAHY7ANXX_tophat_alignments


title: 1D_HC11_C94_HC_HC11 lib15629_CAHY7ANXX_tophat_alignments


title: 1D_HC11_C60_HC_HC11 lib15625_CAHY7ANXX_tophat_alignments


title: 1_Ctl10_C14_HC_HC10 lib15662_CAHY7ANXX_tophat_alignments


title: 1_Ctl10_C11_HC_HC10 lib15667_CAHY7ANXX_tophat_alignments


title: 1P_Ctl10_C39_HC_HC10 lib15664_CAHY7ANXX_tophat_alignments


title: 1D_HC11_C88_HC_HC11 lib15628_CAHY7ANXX_tophat_alignments


title: 1_Ctl10_C26_HC_HC10 lib15663_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C25_T1D_T1D10 lib15678_CAHY7ANXX_tophat_alignments


title: 1_T1D10_C31_T1D_T1D10 lib15679_CAHY7ANXX_tophat_alignments


title: 1_Ctl10_C03_HC_HC10 lib15660_CAHY7ANXX_tophat_alignments


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title: 1D_HC11_C83_HC_HC11 lib15622_CAHY7ANXX_tophat_alignments


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title: 1D_HC11_C54_HC_HC11 lib15624_CAHY7ANXX_tophat_alignments


title: 1D_HC11_C90_HC_HC11 lib15618_CAHY7ANXX_tophat_alignments


title: 1D_HC11_C58_HC_HC11 lib15615_CAHY7ANXX_tophat_alignments


title: 1_HC11_C30_HC_HC11 lib15613_CAHY7ANXX_tophat_alignments


title: 1D_HC11_C71_HC_HC11 lib15621_CAHY7ANXX_tophat_alignments


title: 1D_HC11_C89_HC_HC11 lib15623_CAHY7ANXX_tophat_alignments


title: 1_HC11_C64_HC_HC11 lib15616_CAHY7ANXX_tophat_alignments


title: 1_HC11_C22_HC_HC11 lib15612_CAHY7ANXX_tophat_alignments


title: 1_HC11_C04_HC_HC11 lib15610_CAHY7ANXX_tophat_alignments


title: 1_HC11_C23_HC_HC11 lib15609_CAHY7ANXX_tophat_alignments


title: 1M_HC11_C11_HC_HC11 lib15608_CAHY7ANXX_tophat_alignments


title: 1_HC11_C05_HC_HC11 lib15607_CAHY7ANXX_tophat_alignments


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title: 1_HC11_C24_HC_HC11 lib15603_CAHY7ANXX_tophat_alignments


title: 1_HC11_C28_HC_HC11 lib15604_CAHY7ANXX_tophat_alignments


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title: 1_T1D8_C35_T1D_T1D8 lib14991_CAK30ANXX_tophat_alignments


title: 1D_Ctrl6_C88_HC_HC06 lib14698_CAC6PANXX_tophat_alignments


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title: 1_HC11_C37_HC_HC11 lib15579_CAHY7ANXX_tophat_alignments


title: 1_T1D8_C92_T1D_T1D8 lib14985_CAK30ANXX_tophat_alignments


title: 1_Ctrl6_C60_HC_HC06 lib14695_CAC6PANXX_tophat_alignments


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title: 2D_Ctrl6_C89_HC_HC06 lib14693_CAC6PANXX_tophat_alignments


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title: 1_Ctrl6_C66_HC_HC06 lib14696_CAC6PANXX_tophat_alignments


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title: 1D_Ctrl6_C90_HC_HC06 lib14688_CAC6PANXX_tophat_alignments


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title: 1_T1D2-REDRAW _C60_T1D_T1D2 lib10698_C81B3ANXX

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description: 1D_T1D2-REDRAW _C28_T1D_T1D2


title: 1_T1D2-REDRAW _C22_T1D_T1D2 lib10687_C81B3ANXX

description: 1_T1D2-REDRAW _C22_T1D_T1D2


title: 1_T1D2-REDRAW _C04_T1D_T1D2 lib10685_C81B3ANXX

description: 1_T1D2-REDRAW _C04_T1D_T1D2


title: 1_T1D6_C01_T1D_T1D6 lib14609_CAC6PANXX_tophat_alignments


title: 1_T1D2-REDRAW _C08_T1D_T1D2 lib10648_C81B3ANXX

description: 1_T1D2-REDRAW _C08_T1D_T1D2


title: 1D_T1D2-REDRAW _C85_T1D_T1D2 lib10671_C81B3ANXX

description: 1D_T1D2-REDRAW _C85_T1D_T1D2


title: 1_T1D2-REDRAW _C12_T1D_T1D2 lib10674_C81B3ANXX

description: 1_T1D2-REDRAW _C12_T1D_T1D2


title: 1_T1D2-REDRAW _C43_T1D_T1D2 lib10646_C81B3ANXX

description: 1_T1D2-REDRAW _C43_T1D_T1D2


title: 1D_T1D2-REDRAW _C79_T1D_T1D2 lib10670_C81B3ANXX

description: 1D_T1D2-REDRAW _C79_T1D_T1D2


title: 1D_T1D2-REDRAW _C21_T1D_T1D2 lib10643_C81B3ANXX

description: 1D_T1D2-REDRAW _C21_T1D_T1D2


title: 1D_T1D2-REDRAW _C92_T1D_T1D2 lib10667_C81B3ANXX

description: 1D_T1D2-REDRAW _C92_T1D_T1D2


title: 1D_T1D2-REDRAW _C80_T1D_T1D2 lib10666_C81B3ANXX

description: 1D_T1D2-REDRAW _C80_T1D_T1D2


title: 1D_T1D2-REDRAW _C75_T1D_T1D2 lib10661_C81B3ANXX

description: 1D_T1D2-REDRAW _C75_T1D_T1D2


title: 1_T1D2-REDRAW _C62_T1D_T1D2 lib10665_C81B3ANXX

description: 1_T1D2-REDRAW _C62_T1D_T1D2


title: 1_T1D2-REDRAW _C55_T1D_T1D2 lib10659_C81B3ANXX

description: 1_T1D2-REDRAW _C55_T1D_T1D2


title: 1_Ctl5_redraw_C72_HC_HC05 lib10631_C81B3ANXX


title: 1D_T1D2-REDRAW _C26_T1D_T1D2 lib10650_C81B3ANXX

description: 1D_T1D2-REDRAW _C26_T1D_T1D2


title: 1_T1D2-REDRAW _C63_T1D_T1D2 lib10669_C81B3ANXX

description: 1_T1D2-REDRAW _C63_T1D_T1D2


title: 1_T1D2-REDRAW _C49_T1D_T1D2 lib10658_C81B3ANXX

description: 1_T1D2-REDRAW _C49_T1D_T1D2


title: 1D_T1D2-REDRAW _C19_T1D_T1D2 lib10654_C81B3ANXX

description: 1D_T1D2-REDRAW _C19_T1D_T1D2


title: 1D_T1D2-REDRAW _C44_T1D_T1D2 lib10652_C81B3ANXX

description: 1D_T1D2-REDRAW _C44_T1D_T1D2


title: 1D_Ctl5_redraw_C96_HC_HC05 lib10628_C81B3ANXX


title: 1D_Ctl5_redraw_C90_HC_HC05 lib10627_C81B3ANXX


title: 1D_Ctl5_redraw_C84_HC_HC05 lib10626_C81B3ANXX


title: 1D_Ctl5_redraw_C42_HC_HC05 lib10624_C81B3ANXX


title: 1_Ctl5_redraw_C48_HC_HC05 lib10625_C81B3ANXX


title: 1_T1D2-REDRAW _C20_T1D_T1D2 lib10649_C81B3ANXX

description: 1_T1D2-REDRAW _C20_T1D_T1D2


title: 1_T1D2-REDRAW _C02_T1D_T1D2 lib10647_C81B3ANXX

description: 1_T1D2-REDRAW _C02_T1D_T1D2


title: 1D_Ctl5_redraw_C36_HC_HC05 lib10623_C81B3ANXX


title: 1D_T1D2-REDRAW _C31_T1D_T1D2 lib10644_C81B3ANXX

description: 1D_T1D2-REDRAW _C31_T1D_T1D2


title: 1D_T1D2-REDRAW _C37_T1D_T1D2 lib10645_C81B3ANXX

description: 1D_T1D2-REDRAW _C37_T1D_T1D2


title: 1D_Ctl5_redraw_C28_HC_HC05 lib10618_C81B3ANXX


title: 1D_T1D2-REDRAW _C38_T1D_T1D2 lib10651_C81B3ANXX

description: 1D_T1D2-REDRAW _C38_T1D_T1D2


title: 1_T1D2-REDRAW _C15_T1D_T1D2 lib10642_C81B3ANXX

description: 1_T1D2-REDRAW _C15_T1D_T1D2


title: 1_T1D2-REDRAW _C03_T1D_T1D2 lib10640_C81B3ANXX

description: 1_T1D2-REDRAW _C03_T1D_T1D2


title: 1_T1D2-REDRAW _C09_T1D_T1D2 lib10641_C81B3ANXX

description: 1_T1D2-REDRAW _C09_T1D_T1D2


title: 1_Ctl5_redraw_C86_HC_HC05 lib10613_C81B3ANXX


title: 1_Ctl5_redraw_C74_HC_HC05 lib10612_C81B3ANXX


title: 1D_Ctl5_redraw_C91_HC_HC05 lib10616_C81B3ANXX


title: 1D_Ctl5_redraw_C33_HC_HC05 lib10609_C81B3ANXX


title: 1_Ctl5_redraw_C45_HC_HC05 lib10611_C81B3ANXX


title: 1D_Ctl5_redraw_C95_HC_HC05 lib10630_C81B3ANXX


title: 1D_Ctl5_redraw_C44_HC_HC05 lib10606_C81B3ANXX


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title: 1D_Ctl5_redraw_C38_HC_HC05 lib10605_C81B3ANXX


title: 1_Ctl5_redraw_C83_HC_HC05 lib10629_C81B3ANXX


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title: 1D_Ctl5_redraw_C37_HC_HC05 lib10601_C81B3ANXX


title: 1D_Ctl5_redraw_C41_HC_HC05 lib10621_C81B3ANXX


title: 1D_Ctl5_redraw_C35_HC_HC05 lib10620_C81B3ANXX


title: 1D_Ctl5_redraw_C40_HC_HC05 lib10619_C81B3ANXX


title: 1D_Ctl5_redraw_C85_HC_HC05 lib10615_C81B3ANXX


title: 1D_Ctl5_redraw_C24_HC_HC05 lib10617_C81B3ANXX


title: D4 Replicate D

status: Public on Oct 22 2021

city: Maastricht

first: Tobias

last: Messmer

address: Watermolen 28

department: Cell Biology

country: Netherlands

institute: Mosa Meat

data_processing:
STAR aligner 2.7 was used to align single-end reads to the reference genome bosTau9 (ARS UCD1.2.98)
Gene counts based on the aligned reads were quantified using the FeatureCounts function of the Rsubread package
Genome_build: bosTau9
Supplementary_files_format_and_content: Comma-separated matrix table with raw gene counts for every gene (row) and every sample (column)

molecule: polyA RNA

organism: Bos taurus

source_name: Muscle progenitor cell

growth_protocol: Satellite cells were cultured on collagen-coated flasks in 20%-FBS growth medium.

extract_protocol:
Cell lysates were harvested by adding TRK lysis buffer (Omega Bio-tek) to tissue culture samples after removing culture media and washing with PBS. RNA was purified using the Omega MicroElute Total RNA Kit (Omega Bio-tek).
Sequencing libraries were prepared from harvested RNA samples using the TruSeq stranded mRNA kit (Illumina) and sequenced on a high-output 75bp NextSeq 500/550 (Illumina)

treatment_protocol: Satellite cells were differentiated by switching to 2%-FBS differentiation medium (serum-starvation) and harvested every 24 h.

tag: source breed

value: Belgian Blue

tag: cell type

value: Satellite cells

tag: sampling time

tag: batch


title: D4 Replicate C


title: 1D_Ctl5_redraw_C39_HC_HC05 lib10610_C81B3ANXX


title: 1_Ctl5_redraw_C14_HC_HC05 lib10603_C81B3ANXX


title: 1_Ctl5_redraw_C13_HC_HC05 lib10607_C81B3ANXX


title: 1D_Ctl5_redraw_C43_HC_HC05 lib10602_C81B3ANXX


title: 1D_Ctl5_redraw_C27_HC_HC05 lib10608_C81B3ANXX


title: D4 Replicate A


title: D3 Replicate B


title: 1D_Ctl5_redraw_C31_HC_HC05 lib10600_C81B3ANXX


title: D3 Replicate C


title: D2 Replicate D


title: D2 Replicate B


title: D2 Replicate A


title: D1 Replicate D


title: D4 Replicate B


title: 1_Ctl5_redraw_C51_HC_HC05 lib10614_C81B3ANXX


title: D3 Replicate A


title: D1 Replicate C


title: D0 Replicate C

value: 0 h


title: D1 Replicate A


title: D2 Replicate C


title: D0 Replicate D


title: D1 Replicate B


title: D3 Replicate D


title: D0 Replicate A


title: D0 Replicate B


title: DM Replicate B

growth_protocol: Satellite cells were cultured on collagen-coated flasks in either growth medium (GM) or serum-free growth medium (SFGM).

treatment_protocol: Satellite cells were differentiated for 72h in either serum-free base medium (SFB), DMEM/F-12-based serum-free differentiation medium (SFDM) or DMEM-based serum-free differentiation medium (DMEM)

tag: medium

value: DM


title: SFDM Replicate A

value: DMEM/F-12-based SFDM


title: DMEM Replicate A

value: DMEM-based SFDM


title: SFB Replicate C

value: SFB


title: SFDM Replicate C


title: DM Replicate C


title: DM Replicate A


title: DMEM Replicate B


title: SFGM Replicate C

value: SFGM


title: SFDM Replicate B


title: SFB Replicate A


title: SFB Replicate B


title: SFGM Replicate A


title: GM Replicate C

value: GM


title: GM Replicate B


title: GM Replicate A


title: DMEM Replicate C


title: P1_Treated_VDJ

status: Public on Oct 15 2021

city: Pittsburgh

first: Mark

middle: E

last: Snyder

state: PA

address: 200 Lothrop Street, BST12

department: Medicine

institute: University of Pittsburgh

description: single cell RNA_VDJ

data_processing:
Allignment, Filtering: CellRanger, CellRanger VDJ
Genome_build: GRCh38

source_name: BAL

growth_protocol: Primary cells from BAL of lung transplant recipients

extract_protocol:
FACS sorted - recipient-derived T cells based on recipient / donor HLA discrepancies
10x Genomics, 5' v1

treatment_protocol: Mixed lymphocyte reaction with irradiated donor cells for 5 hours in complete RPMI with human serum

value: T cell

tag: origin

value: Recipient

value: Treated


title: SFGM Replicate B


title: VISIUM Spatial

status: Public on Oct 13 2021

city: Toronto

first: Tallulah

middle: Suzanne

last: Andrews

state: Ontario

address: MARS Building

country: Canada

institute: UHN Research

data_processing:
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files contain compressed folders of the raw count matrices from cell ranger, and the final metadata table for the retained cells with their complete manual annotation and sample metadata.

source_name: Liver Caudate Lobe

extract_protocol:
During organ retrieval, donor liver grafts were perfused in situ with cold (HTK) solution (Methapharm) to thoroughly flush circulating cells, leaving only tissue resident cells that are then used to prepare a single-cell suspension for scRNA-seq analysis. At our institute, the caudate lobe (segment 1) of the liver is often removed in preparation of the organ for implantation. The removed caudate lobe was then dissociated using the protocol as fully described in [https://doi.org/10.17504/protocols.io.m9sc96e] and detailed below.
Samples were prepared as outlined by the 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Sample viability was assessed via Trypan Blue (Thermo Fisher) and using a haemocytometer (Thermo Fisher). Following counting, the appropriate volume for each sample was calculated for a target capture of 6000 cells. Samples below the required cell concentration as defined by the user guide (i.e., <400 cells/µl) were pelleted and re-suspended in a reduced volume and counted again using a haemocytometer prior to loading onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche). Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles. A median sequencing depth of 60,000 reads/cell was targeted for each sample.

value: M

tag: time frozen

tag: age (years)


title: P3_ACR_VDJ

description: single cell RNA_VDJ

value: Rejection


title: scRNA-seq of notum-1-treatment embryo replicate 4

status: Public on Aug 18 2021

city: New Haven

first: Scott

middle: A.

last: Holley

state: CT

address: 219 Prospect St

department: Department of Molecular, Cellular and Developmental Biology

institute: Yale University

description: No other description

data_processing:
We aligned the scRNA-seq data to Grcz11 and demultiplexed using Cell Ranger (10X Genomics, version 3.0).
Genome_build: Grcz11
Supplementary_files_format_and_content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes (column labels for MTX file) and gene names (row labels for MTX file).

organism: Danio rerio

source_name: tail

extract_protocol:
Cells were dissociated by incubation in 20 U/mL papain solution (Worthing Biochemical) for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required.
Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead has primers containing (i) an Illumina R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence. Upon dissolution of the Gel Beads in a GEM, the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina-ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired-end Read 1 (containing the 16 bp 10x Barcode and 10 bp UMI) and Read 2 and the sample index in the i7 index read.

treatment_protocol: Embryos were incubated until the 10-12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild-type, FGF, or BMP inhibition or twelve tails for Wnt inhibition were pooled together.

tag: treatment


title: scRNA-seq of  SU5402-treatment embryo replicate 2

description: No other description


title: scRNA-seq of  SU5402-treatment embryo replicate 4

description: No other description


title: scRNA-seq of notum-1-treatment embryo replicate 3

description: No other description


title: scRNA-seq of Wild type embryo replicate 3

description: No other description

value: WT


title: scRNA-seq of  DMH1-treatment embryo replicate 1

description: No other description


title: scRNA-seq of Wild type embryo replicate 1

description: No other description


title: scRNA-seq of  DMH1-treatment embryo replicate 2

description: No other description


title: scRNA-seq of  SU5402-treatment embryo replicate 1

description: No other description


title: scRNA-seq of  DMH1-treatment embryo replicate 3

description: No other description


title: scRNA-seq of  SU5402-treatment embryo replicate 3

description: No other description


title: scRNA-seq of notum-1-treatment embryo replicate 2

description: No other description


title: scRNA-seq of Wild type embryo replicate 4

description: No other description


title: colorectal cancer sample AUS2_891

status: Public on Jul 27 2021

type: RNA

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: Gene-level expression values derived using Transcriptome Analysis Console (TAC 4.0) software.

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing: Gene-level expression signals were obtained from raw data CEL files by the RMA procedure implemented in the Transcriptome Analysis Console (TAC 4.0) software using defult settings.

label: biotin

source_name: Colorectal cancer patient

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

tag: tissue

value: colorectal cancer tissue sample


title: colorectal cancer sample AUS2_885


title: colorectal cancer sample AUS2_892


title: colorectal cancer sample AUS2_886


title: Gar15-13 Decitabine 4_methylation

status: Public on Dec 12 2021

type: genomic

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw intensity data (IDAT) files were imported and quality controlled using minfi package (v.1.34.0) (Aryee et al., 2014). Data was then normalised with background correction. To reduce the risk of false discoveries, we removed probes affected for cross-hybridization to multiple locations on the genome or overlapped SNPs, as previously described (Pidsley et al., 2016). Beta (β) values were calculated from unmethylated (U) and methylated (M) signal [M/(U + M + 100)] and ranged from 0 to 1 (0 to 100% methylation). β values of loci whose detection P values were > 0.01 were assigned NA in the output file. To map EPIC arrays to hg38/GRCh38 assembly, all probes were annotated with the EPIC.hg38.manifest.tsv.gz files as described in (Zhou et al., 2017).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Gar15-13 Decitabine tumour

label_protocol: Standard Illumina Protocol

growth_protocol: A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet.

extract_protocol: Gernomic DNA from Decitabine-treated and Vehicle tumours from two PDX models (GAR15-13d and HCI-005) was isolated from snap-frozen tumour samples using the  QIAamp DNA Mini Kit (Qiagen).

treatment_protocol: Mice were randomly assigned to treatment groups and treated  with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC).

value: Breast cancer PDX model Gar15-13

value: Decitabine

tag: replicate


title: colorectal cancer sample AUS2_889


title: colorectal cancer sample AUS2_879


title: colorectal cancer sample AUS2_884


title: scRNA-seq of  DMH1-treatment embryo replicate 4

description: No other description


title: colorectal cancer sample AUS2_874


title: colorectal cancer sample AUS2_883


title: colorectal cancer sample AUS2_870


title: colorectal cancer sample AUS2_871


title: colorectal cancer sample AUS2_877


title: scRNA-seq of Wild type embryo replicate 2

description: No other description


title: colorectal cancer sample AUS2_876


title: colorectal cancer sample AUS2_875


title: colorectal cancer sample AUS2_873


title: colorectal cancer sample AUS2_878


title: HCI-005 Vehicle 3_methylation

source_name: HCI-005 Vehicle tumour

extract_protocol: Gernomic DNA from Decitabine-treated and Vehicle tumours from two PDX models (GAR15-13D and HCI-005) was isolated from snap-frozen tumour samples using the  QIAamp DNA Mini Kit (Qiagen).

treatment_protocol: Mice were randomly assigned to treatment groups and treated for 5 days with either a vehicle or Decitabine.

value: Breast cancer PDX model HCI-005

value: Vehicle


title: colorectal cancer sample AUS2_868


title: colorectal cancer sample AUS2_869


title: colorectal cancer sample AUS2_867


title: HCI-005 Decitabine 4_methylation

source_name: HCI-005 Decitabine tumour


title: colorectal cancer sample AUS2_865


title: colorectal cancer sample AUS2_862


title: HCI-005 Vehicle 4_methylation


title: colorectal cancer sample AUS2_866


title: colorectal cancer sample AUS2_860


title: Gar15-13 Decitabine 5_methylation


title: Gar15-13 Vehicle 4_methylation

source_name: Gar15-13 Vehicle tumour


title: colorectal cancer sample AUS2_861


title: colorectal cancer sample AUS2_859


title: Gar15-13 Vehicle 3_methylation


title: HCI-005 Decitabine 2_methylation


title: colorectal cancer sample AUS2_840


title: colorectal cancer sample AUS2_854


title: colorectal cancer sample AUS2_849


title: colorectal cancer sample AUS2_822


title: colorectal cancer sample AUS2_828


title: colorectal cancer sample AUS2_853


title: colorectal cancer sample AUS2_827


title: colorectal cancer sample AUS2_809


title: colorectal cancer sample AUS2_858


title: colorectal cancer sample AUS2_852


title: colorectal cancer sample AUS2_847


title: colorectal cancer sample AUS2_812


title: colorectal cancer sample AUS2_837


title: colorectal cancer sample AUS2_815


title: colorectal cancer sample AUS2_846


title: colorectal cancer sample AUS2_842


title: colorectal cancer sample AUS2_821


title: colorectal cancer sample AUS2_823


title: colorectal cancer sample AUS2_851


title: colorectal cancer sample AUS2_830


title: colorectal cancer sample AUS2_816


title: colorectal cancer sample AUS2_835


title: colorectal cancer sample AUS2_805


title: colorectal cancer sample AUS2_834


title: colorectal cancer sample AUS2_855


title: colorectal cancer sample AUS2_825


title: colorectal cancer sample AUS2_807


title: colorectal cancer sample AUS2_802


title: colorectal cancer sample AUS2_800


title: colorectal cancer sample AUS2_804


title: colorectal cancer sample AUS2_799


title: colorectal cancer sample AUS2_784


title: colorectal cancer sample AUS2_790


title: colorectal cancer sample AUS2_774


title: colorectal cancer sample AUS2_778


title: colorectal cancer sample AUS2_792


title: colorectal cancer sample AUS2_794


title: colorectal cancer sample AUS2_786


title: colorectal cancer sample AUS2_776


title: colorectal cancer sample AUS2_785


title: colorectal cancer sample AUS2_797


title: colorectal cancer sample AUS2_793


title: colorectal cancer sample AUS2_771


title: colorectal cancer sample AUS2_773


title: colorectal cancer sample AUS2_795


title: colorectal cancer sample AUS2_788


title: colorectal cancer sample AUS2_780


title: colorectal cancer sample AUS2_770


title: colorectal cancer sample AUS2_769


title: colorectal cancer sample AUS2_767


title: colorectal cancer sample AUS2_791


title: colorectal cancer sample AUS2_781


title: colorectal cancer sample AUS2_763


title: ATRT, INI296

status: Public on Jun 02 2021

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Quality control: sequenced reads quality were assessed using fastqc v0.11.5
Mapping: sequenced reads were aligned with hg19 human genome reference using STAR v2.5.3a
Reads counting: reads aligned in each gene are counted using STAR v2.5.3a and the and the refFlat table gene annotation (downloaded in GTF format on October 2nd, 2018 from UCSC website)
Transcript Per Million (TPM) normalized count were calculated based on library size and gene length using an in-house script
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with TPM normalized gene count for every gene and every sample in tab-delimited text file
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in tab-delimited text file

source_name: tumor sample

extract_protocol:
Total RNAs were obtained from tumor frozen samples using Qiagen RNAeasy kit, according to the manufacturer's procedures (Qiage, Venlo, Netherlands)
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.)
Library werer sequenced using the Illumina HiSeq 2500 platform in the 100 bp paired-end mode

tag: tumor type

value: ATRT

value: CNS

tag: genotype

value: F


title: ATRT, INI267


title: Xuebin#8

status: Public on Jun 04 2021

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

institute: Tulane University

description: Infected

data_processing:
bcl2fast2/2.17.1 and 10x Cellranger-4.0.0 were used to generate Fastq files, perform alignment,filtering,barcode counting,UMI counting and aggregation.
Seurat V.3.0.0 for scRNA QC and further analysis

organism: Mus musculus

source_name: Lung

growth_protocol: All mice were obtained from Jax farm and maintained in specific pathogen-free rooms at Tulane University. Experiment were preformed when mice were at age of six to ten weeks.

extract_protocol:
mRNA was extracted from lung single cell suspension using the 10X Genomics Chromium™ Single Cell G Chip Kit
Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v3.1 protocol

tag: strain

value: K18 hACE2 transgenic mice

tag: time point of infection

value: SARS-CoV2_4 days post infection

value: lung


title: ATRT, INI228

tag: age

tag: Sex


title: colorectal cancer sample AUS2_766


title: ATRT, INI293


title: ATRT, INI153


title: ATRT, INI159


title: ATRT, INI301


title: ATRT, INI165

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC Beadchip using Illumina protocol

data_processing:
RnBeads Bioconductor R package (version 1.6.1)
matrix processed value definition: beta-value

label: cy3, cy5

source_name: Fresh frozen sample

label_protocol: Illumina Protocol

extract_protocol: Illumina Protocol

tag: gender

value: Female

tag: sample type

tag: disease state

value: tumour


title: ATRT, INI287


title: ATRT, INI286


title: ATRT, INI162


title: ATRT, INI302


title: ATRT, INI158


title: ATRT, INI147

value: Male


title: colorectal cancer sample AUS2_759


title: colorectal cancer sample AUS2_762


title: colorectal cancer sample AUS2_760


title: colorectal cancer sample AUS2_755


title: colorectal cancer sample AUS2_750


title: colorectal cancer sample AUS2_748


title: colorectal cancer sample AUS2_753


title: colorectal cancer sample AUS2_751


title: colorectal cancer sample AUS2_754


title: colorectal cancer sample AUS2_752


title: ATRT, INI239


title: ATRT, INI232


title: ATRT, INI293


title: colorectal cancer sample AUS2_746


title: ATRT, INI246


title: ATRT, INI292


title: ATRT, INI301


title: ATRT, INI295


title: ATRT, INI266


title: ATRT, INI296


title: ATRT, INI286


title: ATRT, INI159


title: ATRT, INI206


title: ATRT, INI104


title: ATRT, INI258


title: ATRT, INI227


title: ATRT, INI226


title: colorectal cancer sample AUS2_756


title: colorectal cancer sample AUS2_796


title: ATRT, INI240


title: ATRT, INI153


title: ATRT, INI254


title: ATRT, INI235


title: ATRT, INI228


title: ATRT, INI256


title: ATRT, INI255


title: ATRT, INI251


title: MC7 [miRNA]

status: Public on Mar 13 2021

city: Copenhagen

first: Reza

last: Yarani

address: Emdrupvej 111, 1-1

country: Denmark

institute: Steno Diabetes Center Copenhagen

description: Small RNA

data_processing:
Raw fastq files were trimmed with Flexbar for the specific adapter sequence (“AGATCGGAAGAGCACACGTCT")
Cleaned reads were collapsed using fastx-toolkit and mature mouse miRNAs annotated in miRBAse version 22 were quantified using the quantifier.pl module from the miRDeep2 software, version 2.0.1.0, default options.
Quantification output was filtered such that If two or more miRNAs had identical mature miRNA sequences, only the highest expressed of them was retained.
Normalization and differential expression was performed in each tissue using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: raw mature miRNA counts across all samples in csv format, produced using quantifier.pl script from miRDeep2 software, and post-processed to remove miRNAs with identical mature sequences
Supplementary_files_format_and_content: miRNA counts normalized to library sizes in colon or blood, in tsv format, produced using DESeq2

source_name: blood

extract_protocol:
Total RNA (including miRNA) from blood was isolated using RNeasy Protect Animal Blood Kit (Cat No./ID: 73224, Qiagen) with Buffer RWT (cat. no. 1067933, Qiagen). Colon total RNA was isolated using miRNeasy Mini Kit (Cat No./ID: 217004, Qiagen) after simultaneous tissue disruption and homogenization using TissueLyser LT (Cat No./ID: 85600, Qiagen) and Stainless-Steel Beads, 5 mm (Cat No./ID: 69989, Qiagen).
Library preparation for colon RNA samples was performed using Ribo-Zero™ Magnetic Gold rRNA Removal Kit (Epidemiology, MRZE724, illumina) and for blood, using Globin-Zero Gold rRNA Removal Kit (GZG1224, illumine) based on the standard kits protocol.

treatment_protocol: Acute ulcerative colitis was induced using dextran sulfate sodium salt (DSS), colitis grade (mw: 36 kDa, CAS Number 9011-18-1, MP Biomedicals, Soho, OH, USA) by administration in the drinking water at a final concentration of 1.5% (wt/vol) for 7 days and then replaced by regular water. Control group was time-matched and received the same drinking water without DSS. If mice weight loss exceeded 20% of the initial weight, they were sacrificed by cervical dislocation. All animals were sacrificed by the same procedure on day 8.

value: Control

value: COLON


title: MC4 [miRNA]

description: Small RNA

value: ulcerative colitis


title: MC7

description: Total RNA (minus small RNA)

data_processing:
Fastq files were cleaned for adapters, low quality ends and ribosomal content. Illumina TruSeq adapters and low quality tails were trimmed using Flexbar. Reads of ribosomal origin were removed using the bbduk software (with k=31) from the bbmap library (https://sourceforge.net/projects/bbmap/), by matching reads to a rRNA collection of sequences extracted from the SILVA database.
Cleaned reads were aligned to the mouse genome (GRCm38) using STAR version 2.5.2a.4 (options: --outSAMstrandField intronMotif; --outSAMunmapped Within; --outSAMattrIHstart 0; --outFilterType BySJout; --outFilterIntronMotifs RemoveNoncanonical; --alignSoftClipAtReferenceEnds No)
Transcript and gene level quantification was obtained using Stringtie (version 1.3.4c)5 in estimate mode (-e option) with gtf annotation files corresponding to Ensembl (release 92)6 and default options. Gene-level and transcript raw counts were obtained using the prepDE.py script provided together with Stringtie.
Normalization and differential expression was performed in each tissue using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: raw gene counts across all samples in csv format, output from the Stringtie prepDE.py script
Supplementary_files_format_and_content: gene counts normalized to library sizes across samples from blood or colon in csv format, normalized using DESeq2


title: MC4

description: Total RNA (minus small RNA)


title: MC8

description: Total RNA (minus small RNA)


title: MC9

description: Total RNA (minus small RNA)


title: M8-3 [miRNA]

description: Small RNA

source_name: colon

value: BLOOD


title: M7-3 [miRNA]

description: Small RNA


title: MC2 [miRNA]

description: Small RNA


title: M1-3 [miRNA]

description: Small RNA


title: M2-3 [miRNA]

description: Small RNA


title: M4-3 [miRNA]

description: Small RNA


title: M9-3 [miRNA]

description: Small RNA


title: MC1

description: Total RNA (minus small RNA)


title: M9-3

description: Total RNA (minus small RNA)


title: MC8 [miRNA]

description: Small RNA


title: MC9 [miRNA]

description: Small RNA


title: M8-3

description: Total RNA (minus small RNA)


title: MC1 [miRNA]

description: Small RNA


title: M7-3

description: Total RNA (minus small RNA)


title: M2-3

description: Total RNA (minus small RNA)


title: M4-3

description: Total RNA (minus small RNA)


title: RNAseq_11

status: Public on Feb 02 2021

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
Peaks were called using MACS2 peak caller
ATACseq an RNAseq reads were aligned to the hg19 human genome using Bowtie2
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq: bw; RNA-seq: raw counts

source_name: Human ALL Clinical Sample

growth_protocol: Cryopreserved patient samples were thawed using RPMI + 20% FBS and flow sorted for viable cells

extract_protocol:
DNA was transposed using the FAST-ATAC protocol and mini-elute reaction cleanup kit was used to isolate the transposed  DNA and RNA was collected using the Norgen RNA Isolation Kit
Library was constructed using illumina barcodes and SPRI bead size selection

tag: cancer type

value: Human ALL Clinical Sample

tag: cell type

value: primary acute lymphoblastic leukemia cells


title: MC2

description: Total RNA (minus small RNA)


title: RNAseq_9


title: RNAseq_12


title: RNAseq_19


title: RNAseq_7


title: RNAseq_17


title: RNAseq_16


title: RNAseq_10


title: RNAseq_4


title: RNAseq_1


title: RNAseq_15


title: RNAseq_3


title: RNAseq_13


title: RNAseq_8


title: RNAseq_6


title: RNAseq_2


title: RNAseq_5


title: M1-3

description: Total RNA (minus small RNA)


title: ATACseq_24

description: Transposed DNA

library_source: genomic


title: ATACseq_23

description: Transposed DNA


title: ATACseq_20

description: Transposed DNA


title: ATACseq_21

description: Transposed DNA


title: ATACseq_14

description: Transposed DNA


title: RNAseq_14


title: ATACseq_11

description: Transposed DNA


title: RNAseq_18


title: ATACseq_4

description: Transposed DNA


title: ATACseq_9

description: Transposed DNA


title: ATACseq_19

description: Transposed DNA


title: ATACseq_12

description: Transposed DNA


title: ATACseq_3

description: Transposed DNA


title: ATACseq_15

description: Transposed DNA