title: GB941915_S166

description: iscChIC-seq


title: GB941919_S170

status: Public on Dec 14 2020

type: SRA

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

country: USA

institute: national Institute of Health

description: iscChIC-seq

library_source: genomic

data_processing:
Library strategy: iChiC-seq
Basecalls performed
Each raw fastq file are reads corresponding to 96 cell barcodes . The 96 pairs are shown in barcode_96.txt. Read 1 is considered  to belong to one of the barcodes if  it corresponding read 2 contains  that barcode.  After separting each set of fastq files into 96 files, read 1 is mapped to the human genome hg18 using bowtie2.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910?914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 3000 (4000)reads for H3K4me3 (H3K27me3)  With these requirements, 7798 (9207) cells were obtained . From the bulk-cell ENCODE data, we obtaind a set of H3K4me3 peaks  (52798 peaks) that are shown in peakname3.txt and a set of H3K27me3 peaks (79100 peaks ) that are shown in combined_sicer_E100_peaks.sort.merge.txt. Using  BedTools and the H3K4me3 and H3K27me3 peak files, we obtained a set of bivalent domains (25951 bivalent domains) that are shown in K4_K27_bivalent_domain.txt.   For each H3K4me3 cell, we calculated the reads that were located within the H3K4me3 peaks and stored the results in a matrix, which can be found from the file 'scH3K4me3_7798_cell_counts_at_WBCpeaks.txt.gz' . We also calculated the reads that were located within the bivalent domains and stored the results in a matrix, which can be found from the file 'scK4_rc_at_25951_bipeaks.txt.gz' .   For each H3K27me3 cell, we calculated the reads that were located within the H3K27me3 peaks and stored the results in a matrix, which can be found from the file 'scK27_4lanes_rc_at_79100peaks_width10k.txt.gz' . We also calculated the reads that were located within the bivalent domains and stored the results in a matrix, which can be found from the file 'scK27_4lanes_rc_at_25951_bipeaks.txt.gz' .
Genome_build: hg18
Supplementary_files_format_and_content:
barcode_96.txt: one column  refers to a DNA barcode starting from the 3'
combined_sicer_E100_peaks.sort.merge.txt:first column is for chromsome, second column is for H3K27me3 peak start site, and third column is for H3K27me3 peak end site
K4_K27_bivalent_domain.txt: first column is for chromsome, second column is for bivalent domain start site, and third column is for bivalent domain end site
peakname3.txt: first column is for chromsome, second column is for H3K4me3 peak start site, and third column is for H3K4me3 peak end site
scH3K4me3_7798_cell_counts_at_WBCpeaks.txt.gz: This file contains read count data for single cells in text format. The rows refer to H3K4me3 peaks while the column refer to single cells. Reading the matrix results in a 52798 x 7798 matrix.
scK27_4lanes_rc_at_25951_bipeaks.txt.gz: This file contains read count data for single cells in text format. The rows refer to bivalent domains while the column refer to single cells. Reading the matrix results in a 25951 x 9207 matrix.
scK27_4lanes_rc_at_79100peaks_width10k.txt.gz:This file contains read count data for single cells in text format. The rows refer to H3K27me3 peaks while the column refer to single cells. Reading the matrix results in a 79100 x 9207matrix
scK4_rc_at_25951_bipeaks.txt.gz: This file contains read count data for single cells in text format. The rows refer to bivalent domains while the column refer to single cells. Reading the matrix results in a 25951 x 7798 matrix.

molecule: genomic DNA

organism: Homo sapiens

source_name: human WBC H3K27me3

extract_protocol:
iscChIC-seq human 1.25M 2-step crosslink human healthy WBC, TdT&T4 methods adding P7 barcode adaptor (12.5μl volumn/well 37°C 60 minutes), pool, dilution, counting and redistribute into 96-well plate, total 30 nuclei per well seal completely, 65°C overnight; direct PCR1 (12 cycles), pool all the DNA, EXO I 30 minutes, A-tailing and P5 ligation(rt overnight) , column purification and PCR2(16 cycles), run-e-gel and cut from 200-500bp rc#1 i5-01
The isolated 50M of WBCsuspended by 50ml PBS /MgCl2 are firstly fixed by adding 400μl freshly prepared 0.25M Disuccinimidyl glutarate (DSG, ThermoFisher Scientific, catalog no.20593) and incubate at room temperature for 45 minutes with rotation. After protein-protein fixation by DSG and washing three times by PBS, cells suspended by culture medium DMEM supplemented with 10% FBS are further fixed by the addition of 1:15 volume of 16% (w/v) methanol-free formaldehyde solution (Thermo Fisher Scientific) and incubate at room temperature for 10 minutes. The fixing reaction is terminated by a 1:10 volume of 1.25 M glycine and incubate at room temperature for 5 minutes. The fixed cells are collected by centrifugation at 1320rpm for 7 minutes and washed with PBS. The cells are stored in aliquots (1 × 106 cells per tube) at −80°C until use.

tag: cell type

value: WBC


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


title: GB941628_S124

description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


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description: iscChIC-seq


title: GB941585_S85

description: iscChIC-seq


title: GB941584_S84

description: iscChIC-seq


title: GB941583_S83

description: iscChIC-seq


title: GB941582_S82

description: iscChIC-seq


title: GB941605_S101

description: iscChIC-seq


title: GB941581_S81

description: iscChIC-seq


title: GB941591_S91

description: iscChIC-seq


title: GB941578_S78

description: iscChIC-seq


title: GB941580_S80

description: iscChIC-seq


title: GB941574_S74

description: iscChIC-seq


title: GB941573_S73

description: iscChIC-seq


title: GB941601_S97

description: iscChIC-seq


title: GB941575_S75

description: iscChIC-seq


title: GB941579_S79

description: iscChIC-seq


title: GB941572_S72

description: iscChIC-seq


title: GB941571_S71

description: iscChIC-seq


title: GB941570_S70

description: iscChIC-seq


title: GB941569_S69

description: iscChIC-seq


title: GB941586_S86

description: iscChIC-seq


title: GB941564_S64

description: iscChIC-seq


title: GB941566_S66

description: iscChIC-seq


title: GB941567_S67

description: iscChIC-seq


title: GB941565_S65

description: iscChIC-seq


title: GB941563_S63

description: iscChIC-seq


title: GB941561_S61

description: iscChIC-seq


title: GB941562_S62

description: iscChIC-seq


title: GB941576_S76

description: iscChIC-seq


title: GB941558_S58

description: iscChIC-seq


title: GB941559_S59

description: iscChIC-seq


title: GB941557_S57

description: iscChIC-seq


title: GB941560_S60

description: iscChIC-seq


title: GB941577_S77

description: iscChIC-seq


title: GB941552_S52

description: iscChIC-seq


title: GB941556_S56

description: iscChIC-seq


title: GB941555_S55

description: iscChIC-seq


title: GB941553_S53

description: iscChIC-seq


title: GB941551_S51

description: iscChIC-seq


title: GB941550_S50

description: iscChIC-seq


title: GB941554_S54

description: iscChIC-seq


title: GB941549_S49

description: iscChIC-seq


title: GB941548_S48

description: iscChIC-seq


title: GB941547_S47

description: iscChIC-seq


title: GB941544_S44

description: iscChIC-seq


title: GB941546_S46

description: iscChIC-seq


title: GB941543_S43

description: iscChIC-seq


title: GB941542_S42

description: iscChIC-seq


title: GB941545_S45

description: iscChIC-seq


title: GB941568_S68

description: iscChIC-seq


title: GB941541_S41

description: iscChIC-seq


title: GB941539_S39

description: iscChIC-seq


title: GB941540_S40

description: iscChIC-seq


title: GB941536_S36

description: iscChIC-seq


title: GB941538_S38

description: iscChIC-seq


title: GB941537_S37

description: iscChIC-seq


title: GB941535_S35

description: iscChIC-seq


title: GB941534_S34

description: iscChIC-seq


title: GB941530_S30

description: iscChIC-seq


title: GB941533_S33

description: iscChIC-seq


title: GB941532_S32

description: iscChIC-seq


title: GB941531_S31

description: iscChIC-seq


title: GB941529_S29

description: iscChIC-seq


title: GB941527_S27

description: iscChIC-seq


title: GB941526_S26

description: iscChIC-seq


title: GB941520_S20

description: iscChIC-seq


title: GB941528_S28

description: iscChIC-seq


title: GB941518_S18

description: iscChIC-seq


title: GB941525_S25

description: iscChIC-seq


title: GB941523_S23

description: iscChIC-seq


title: GB941522_S22

description: iscChIC-seq


title: GB941524_S24

description: iscChIC-seq


title: GB941521_S21

description: iscChIC-seq


title: GB941519_S19

description: iscChIC-seq


title: GB941516_S16

description: iscChIC-seq


title: GB941517_S17

description: iscChIC-seq


title: GB941513_S13

description: iscChIC-seq


title: GB941512_S12

description: iscChIC-seq


title: GB941514_S14

description: iscChIC-seq


title: GB941515_S15

description: iscChIC-seq


title: GB941511_S11

description: iscChIC-seq


title: GB941509_S9

description: iscChIC-seq


title: GB941510_S10

description: iscChIC-seq


title: GB941508_S8

description: iscChIC-seq


title: GB941503_S3

description: iscChIC-seq


title: GB941504_S4

description: iscChIC-seq


title: GB941505_S5

description: iscChIC-seq


title: GB941502_S2

description: iscChIC-seq


title: GB941501_S1

description: iscChIC-seq


title: human WBC GB930595

source_name: human WBC H3K4me3

extract_protocol:
iChIC-seq human 1.25M 2-step crosslink human healthy WBC, TdT&T4 methods adding P7 barcode adaptor (12.5μl volumn/well 37°C 60 minutes), pool, dilution, counting and redistribute into 96-well plate, total 30 nuclei per well seal completely, 65°C overnight; direct PCR1 (12 cycles), pool all the DNA, EXO I 30 minutes, A-tailing and P5 ligation(rt overnight) , column purification and PCR2(16 cycles), run-e-gel and cut from 200-500bp rc#1 i5-01
The isolated 50M of WBC suspended by 50ml PBS /MgCl2 are firstly fixed by adding 400μl freshly prepared 0.25M Disuccinimidyl glutarate (DSG, ThermoFisher Scientific, catalog no.20593) and incubate at room temperature for 45 minutes with rotation. After protein-protein fixation by DSG and washing three times by PBS, cells suspended by culture medium DMEM supplemented with 10% FBS are further fixed by the addition of 1:15 volume of 16% (w/v) methanol-free formaldehyde solution (Thermo Fisher Scientific) and incubate at room temperature for 10 minutes. The fixing reaction is terminated by a 1:10 volume of 1.25 M glycine and incubate at room temperature for 5 minutes. The fixed cells are collected by centrifugation at 1320rpm for 7 minutes and washed with PBS. The cells are stored in aliquots (1 × 10e6 cells per tube) at −80°C until use.


title: human WBC GB930596


title: human WBC GB930589


title: human WBC GB930593


title: human WBC GB930594


title: human WBC GB930592


title: human WBC GB930591


title: human WBC GB930582


title: human WBC GB930584


title: human WBC GB930586


title: human WBC GB930588


title: human WBC GB930587


title: human WBC GB930580


title: human WBC GB930579


title: GB941507_S7

description: iscChIC-seq


title: human WBC GB930583


title: human WBC GB930585


title: human WBC GB930577


title: human WBC GB930578


title: GB941506_S6

description: iscChIC-seq


title: human WBC GB930575


title: human WBC GB930574


title: human WBC GB930573


title: human WBC GB930590


title: human WBC GB930570


title: human WBC GB930572


title: human WBC GB930569


title: human WBC GB930568


title: human WBC GB930581


title: human WBC GB930567


title: human WBC GB930565


title: human WBC GB930566


title: human WBC GB930562


title: human WBC GB930563


title: human WBC GB930560


title: human WBC GB930558


title: human WBC GB930556


title: human WBC GB930557


title: human WBC GB930576


title: human WBC GB930553


title: human WBC GB930554


title: human WBC GB930559


title: human WBC GB930561


title: human WBC GB930551


title: human WBC GB930552


title: human WBC GB930549


title: human WBC GB930548


title: human WBC GB930571


title: human WBC GB930550


title: human WBC GB930546


title: human WBC GB930545


title: human WBC GB930544


title: human WBC GB930542


title: human WBC GB930541


title: human WBC GB930564


title: human WBC GB930540


title: human WBC GB930539


title: human WBC GB930538


title: human WBC GB930537


title: human WBC GB930535


title: human WBC GB930536


title: human WBC GB930555


title: human WBC GB930533


title: human WBC GB930534


title: human WBC GB930532


title: human WBC GB930547


title: human WBC GB930531


title: human WBC GB930529


title: human WBC GB930528


title: human WBC GB930530


title: human WBC GB930525


title: human WBC GB930523


title: human WBC GB930522


title: human WBC GB930520


title: human WBC GB930526


title: human WBC GB930519


title: human WBC GB930521


title: human WBC GB930524


title: human WBC GB930518


title: human WBC GB930517


title: human WBC GB930543


title: human WBC GB930514


title: human WBC GB930515


title: human WBC GB930512


title: human WBC GB930511


title: human WBC GB930513


title: human WBC GB930508


title: human WBC GB930509


title: human WBC GB930510


title: human WBC GB930507


title: human WBC GB930527


title: human WBC GB930503


title: human WBC GB930504


title: human WBC GB930505


title: human WBC GB930506


title: human WBC GB930502


title: human WBC GB930496


title: human WBC GB930501


title: human WBC GB930492


title: human WBC GB930494


title: human WBC GB930495


title: human WBC GB930491


title: human WBC GB930490


title: human WBC GB930489


title: human WBC GB930488


title: human WBC GB930486


title: human WBC GB930485


title: human WBC GB930487


title: human WBC GB930493


title: human WBC GB930484


title: human WBC GB930482


title: human WBC GB930516


title: human WBC GB930480


title: human WBC GB930479


title: human WBC GB930478


title: human WBC GB930476


title: human WBC GB930477


title: human WBC GB930483


title: human WBC GB930474


title: human WBC GB930475


title: human WBC GB930471


title: human WBC GB930472


title: human WBC GB930473


title: human WBC GB930469


title: human WBC GB930467


title: human WBC GB930468


title: human WBC GB930466


title: human WBC GB930465


title: human WBC GB930463


title: human WBC GB930464


title: human WBC GB930462


title: human WBC GB930458


title: human WBC GB930457


title: human WBC GB930456


title: human WBC GB930460


title: human WBC GB930481


title: human WBC GB930455


title: human WBC GB930459


title: human WBC GB930453


title: human WBC GB930454


title: human WBC GB930452


title: human WBC GB930449


title: human WBC GB930450


title: human WBC GB930448


title: human WBC GB930451


title: human WBC GB930470


title: human WBC GB930447


title: human WBC GB930446


title: human WBC GB930445


title: human WBC GB930442


title: human WBC GB930443


title: human WBC GB930444


title: human WBC GB930461


title: human WBC GB930440


title: human WBC GB930439


title: human WBC GB930437


title: human WBC GB930434


title: human WBC GB930435


title: human WBC GB930433


title: human WBC GB930436


title: human WBC GB930430


title: human WBC GB930429


title: human WBC GB930431


title: human WBC GB930428


title: human WBC GB930427


title: human WBC GB930425


title: human WBC GB930426


title: human WBC GB930422


title: human WBC GB930423


title: human WBC GB930420


title: human WBC GB930419


title: human WBC GB930418


title: human WBC GB930413


title: human WBC GB930417


title: human WBC GB930416


title: human WBC GB930441


title: human WBC GB930438


title: human WBC GB930421


title: human WBC GB930415


title: human WBC GB930432


title: human WBC GB930414


title: human WBC GB930409


title: human WBC GB930408


title: human WBC GB930412


title: human WBC GB930424


title: human WBC GB930410


title: human WBC GB930407


title: human WBC GB930402


title: human WBC GB930404


title: human WBC GB930406


title: human WBC GB930403


title: human WBC GB930394


title: human WBC GB930401


title: human WBC GB930396


title: human WBC GB930393


title: human WBC GB930391


title: human WBC GB930390


title: human WBC GB930392


title: human WBC GB930389


title: human WBC GB930388


title: human WBC GB930384


title: human WBC GB930386


title: human WBC GB930385


title: human WBC GB930411


title: human WBC GB930380


title: human WBC GB930382


title: human WBC GB930381


title: human WBC GB930387


title: human WBC GB930405


title: human WBC GB930379


title: human WBC GB930395


title: human WBC GB930377


title: human WBC GB930376


title: human WBC GB930375


title: human WBC GB930374


title: human WBC GB930373


title: human WBC GB930370


title: human WBC GB930371


title: human WBC GB930372


title: human WBC GB930368


title: human WBC GB930369


title: human WBC GB930367


title: human WBC GB930383


title: human WBC GB930366


title: human WBC GB930365


title: human WBC GB930364


title: human WBC GB930359


title: human WBC GB930360


title: human WBC GB930362


title: human WBC GB930356


title: human WBC GB930357


title: human WBC GB930355


title: human WBC GB930352


title: human WBC GB930358


title: human WBC GB930350


title: human WBC GB930354


title: human WBC GB930378


title: human WBC GB930353


title: human WBC GB930346


title: human WBC GB930361


title: human WBC GB930339


title: human WBC GB930349


title: human WBC GB930348


title: human WBC GB930338


title: human WBC GB930347


title: human WBC GB930363


title: human WBC GB930351


title: human WBC GB930345


title: human WBC GB930344


title: human WBC GB930341


title: human WBC GB930340


title: human WBC GB930342


title: human WBC GB930325


title: human WBC GB930324


title: human WBC GB930335


title: human WBC GB930336


title: human WBC GB930333


title: human WBC GB930337


title: human WBC GB930334


title: human WBC GB930332


title: human WBC GB930320


title: human WBC GB930319


title: human WBC GB930321


title: human WBC GB930317


title: human WBC GB930331


title: human WBC GB930329


title: human WBC GB930327


title: human WBC GB930328


title: human WBC GB930326


title: human WBC GB930314


title: human WBC GB930330


title: human WBC GB930313


title: human WBC GB930343


title: human WBC GB930323


title: human WBC GB930322


title: human WBC GB930308


title: human WBC GB930306


title: human WBC GB930318


title: human WBC GB930316


title: human WBC GB930315


title: human WBC GB930302


title: human WBC GB930301


title: human WBC GB930303


title: human WBC GB930296


title: human WBC GB930312


title: human WBC GB930293


title: human WBC GB930290


title: human WBC GB930310


title: human WBC GB930311


title: human WBC GB930289


title: human WBC GB930309


title: human WBC GB930288


title: human WBC GB930286


title: human WBC GB930305


title: human WBC GB930304


title: human WBC GB930307


title: human WBC GB930295


title: human WBC GB930283


title: human WBC GB930282


title: human WBC GB930280


title: human WBC GB930294


title: human WBC GB930279


title: human WBC GB930292


title: human WBC GB930276


title: human WBC GB930275


title: human WBC GB930278


title: human WBC GB930277


title: human WBC GB930287


title: human WBC GB930291


title: human WBC GB930285


title: human WBC GB930284


title: human WBC GB930271


title: human WBC GB930272


title: human WBC GB930269


title: human WBC GB930281


title: human WBC GB930270


title: human WBC GB930268


title: human WBC GB930274


title: human WBC GB930266


title: human WBC GB930267


title: human WBC GB930265


title: human WBC GB930262


title: human WBC GB930264


title: human WBC GB930261


title: human WBC GB930273


title: human WBC GB930263


title: human WBC GB930256


title: human WBC GB930257


title: human WBC GB930254


title: human WBC GB930260


title: human WBC GB930255


title: human WBC GB930259


title: human WBC GB930250


title: human WBC GB930249


title: human WBC GB930246


title: human WBC GB930258


title: human WBC GB930252


title: human WBC GB930253


title: human WBC GB930248


title: human WBC GB930240


title: human WBC GB930245


title: human WBC GB930244


title: human WBC GB930243


title: human WBC GB930239


title: human WBC GB930242


title: human WBC GB930238


title: human WBC GB930241


title: human WBC GB930237


title: human WBC GB930251


title: human WBC GB930236


title: human WBC GB930234


title: human WBC GB930235


title: human WBC GB930247


title: human WBC GB930233


title: human WBC GB930232


title: human WBC GB930230


title: human WBC GB930227


title: human WBC GB930228


title: human WBC GB930225


title: human WBC GB930226


title: human WBC GB930229


title: human WBC GB930224


title: human WBC GB930223


title: human WBC GB930222


title: human WBC GB930216


title: human WBC GB930214


title: human WBC GB930215


title: human WBC GB930213


title: human WBC GB930212


title: human WBC GB930208


title: human WBC GB930218


title: human WBC GB930205


title: human WBC GB930203


title: human WBC GB930202


title: human WBC GB930210


title: human WBC GB930201


title: human WBC GB930196


title: human WBC GB930221


title: human WBC GB930194


title: human WBC GB930192


title: human WBC GB930219


title: human WBC GB930209


title: human WBC GB930207


title: human WBC GB930190


title: human WBC GB930211


title: human WBC GB930189


title: human WBC GB930181


title: human WBC GB930206


title: human WBC GB930204


title: human WBC GB930180


title: human WBC GB930178


title: human WBC GB930231


title: human WBC GB930186


title: human WBC GB930176


title: human WBC GB930179


title: human WBC GB930171


title: human WBC GB930170


title: human WBC GB930195


title: human WBC GB930169


title: human WBC GB930193


title: human WBC GB930220


title: human WBC GB930217


title: human WBC GB930191


title: human WBC GB930188


title: human WBC GB930187


title: human WBC GB930182


title: human WBC GB930185


title: human WBC GB930184


title: human WBC GB930168


title: human WBC GB930167


title: human WBC GB930183


title: human WBC GB930166


title: human WBC GB930164


title: human WBC GB930163


title: human WBC GB930160


title: human WBC GB930174


title: human WBC GB930162


title: human WBC GB930158


title: human WBC GB930173


title: human WBC GB930177


title: human WBC GB930175


title: human WBC GB930172


title: human WBC GB930165


title: human WBC GB930161


title: human WBC GB930159


title: human WBC GB930157


title: human WBC GB930152


title: human WBC GB930156


title: human WBC GB930155


title: human WBC GB930147


title: human WBC GB930154


title: human WBC GB930144


title: human WBC GB930146


title: human WBC GB930140


title: human WBC GB930153


title: human WBC GB930142


title: human WBC GB930149


title: human WBC GB930137


title: human WBC GB930145


title: human WBC GB930143


title: human WBC GB930136


title: human WBC GB930141


title: human WBC GB930150


title: human WBC GB930135


title: human WBC GB930131


title: human WBC GB930133


title: human WBC GB930139


title: human WBC GB930132


title: human WBC GB930129


title: human WBC GB930130


title: human WBC GB930127


title: human WBC GB930148


title: human WBC GB930124


title: human WBC GB930151


title: human WBC GB930126


title: human WBC GB930123


title: human WBC GB930125


title: human WBC GB930121


title: human WBC GB930138


title: human WBC GB930120


title: human WBC GB930122


title: human WBC GB930119


title: human WBC GB930117


title: human WBC GB930116


title: human WBC GB930118


title: human WBC GB930115


title: human WBC GB930134


title: human WBC GB930128


title: human WBC GB930110


title: human WBC GB930113


title: human WBC GB930108


title: human WBC GB930107


title: human WBC GB930106


title: human WBC GB930109


title: human WBC GB930105


title: human WBC GB930102


title: human WBC GB930104


title: human WBC GB930103


title: human WBC GB930101


title: ATC3

status: Public on Dec 03 2020

city: Houston

first: Nicholas

last: Navin

state: tx

address: 6767Bertner AVE

institute: UT MD Anderson

description:
10X genomics
3'-scRNAseq

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger V3.0 mkfastq
cellranger V3.0 count
reads are mapped to hg20
UMI counts are summarized are gene expression levels
Genome_build: hg20
Supplementary_files_format_and_content: tab-delimited text files include cell type prediction and UMI values for each Sample

molecule: total RNA

growth_protocol: Single cell suspensions are made from fresh tumors

extract_protocol:
RNAs are extracted from single cell suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)
single cell 3' RNAseq

treatment_protocol: samples are collected before treatment

tag: tissue

value: fresh tumor

tag: sample type

value: surgical sample


title: ATC5

description:
10X genomics
3'-scRNAseq


title: human WBC GB930114


title: ATC2

description:
10X genomics
3'-scRNAseq


title: ATC1

description:
10X genomics
3'-scRNAseq


title: TNBC5

description:
10X genomics
3'-scRNAseq

value: biopsy


title: TNBC3

description:
10X genomics
3'-scRNAseq


title: TNBC4

description:
10X genomics
3'-scRNAseq


title: human WBC GB930112


title: human WBC GB930111


title: TNBC2

description:
10X genomics
3'-scRNAseq


title: DCIS1

description:
10X genomics
3'-scRNAseq


title: TNBC1

description:
10X genomics
3'-scRNAseq


title: Insulin alone

status: Public on Nov 21 2020

city: Québec

first: Patricia

middle: G

last: Tremblay

state: Québec

address: 2440 Hochelaga Blvd

department: Sciences animales

country: Canada

institute: Laval University

description: CTRL-FAT-Ins

data_processing:
Using Trimmomatic, sequencing adapters were removed and base calls with a quality score below 30 were removed from the end of the reads. Reads with a minimum length of 32nt were kept for further processing. The abundances for all transcripts described in release 91 of ENSEMBL cdna gene annotation were estimated using kallisto . Differential expression of genes were then assessed using pairwise comparisons in edgeR . Lacking replicates, dispersion within edgeR was evaluated by grouping samples for similar comparisons (First for control, then for FSH, FSK, PMA and SC79 samples) and dropping the factor with the lowest impact, as suggested by the edgeR manual.
Genome_build: Ensembl (release 91)
Supplementary_files_format_and_content: tab-delimited text files include  transcript tsl, log Fold change, p-value, adjsuted p-value for each Sample ...
Supplementary_files_format_and_content: raw reads counts
Supplementary_files_format_and_content: nornalized reads counts

molecule: polyA RNA

source_name: KGN cell line

growth_protocol: KGN cells were thawed on day 1, placed in a cell culture flask (25 cm3, Sigma-Aldrich) and sub-cultured on day 3. Confluence was never over 80%. On day 6, viable cells were placed in a 6-well dish at the density of 3x10^5 per well in 3 ml of medium and grown for 72 h.

extract_protocol:
Total RNA was isolated with AllPrep DNA/RNA Mini Kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instructions. Total RNA integrity and concentration were evaluated on a 2100-Bioanalyzer (Agilent Technologies, Palo Alto, CA). For all samples RNA Integrity Number was 10.
The total RNA input used for sequencing was 270 ng for each treatment, a pool of 90 ng for each biological replicates. mRNA was isolated from total RNA using NEBNext Poly (A) mRNA Magnetic Isolation Module (E7490S; NEB). PolyA-selected mRNA was fragmented to a mean size of 200 nt, reverse transcribed to generate double-stranded cDNA, and converted to a paired-end library using NEBNext Ultra RNA Library Prep kit for Illumina (E7530S; NEB) according to the manufacturer’s instructions, using Agencourt AMPure XP beads and NEBNext Mutliplex Oligos for Illumina (set1, E7335S; NEB).

treatment_protocol: For all experimental conditions, the medium was replaced with charcoal-stripped (SVFA) DMEM/F12 containing antibiotics and 100 nmol L-1 of 4-androstene-3,17-dione and 1% of low fatty acid BSA. Plates were incubated for 24 h in a humidified incubator at 37 °C in 5% CO2:95% air after adding either ethanol (less than 0.1% of the culture volume) as a control or the fatty acid combination PA 75 uM + SA 25 uM + OA 100 uM with or without the addition of human insulin 100 ng/mL. Control wells received the same volume of ethanol as the test groups. The experiment was repeated 3 times (3 different weeks) for the RNAseq analysis.

value: granulosa cells

tag: cell line

value: KGN

tag: concentrations

value: 100 ng/mL insulin


title: High fat (high concentration of fatty acids)

description: H-FAT

value: PA 75 microM + SA 25 microM + OA 100 microM


title: High fat Insulin (High concentration of fatty acids added with insulin)

description: H-FAT-Ins

value: PA 75 microM + SA 25 microM + OA 100 microM +100 ng/mL insulin


title: Control (no treatment)

description: CTRL


title: Ileum uninjected rep2

status: Public on Nov 04 2020

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description:
FPKM_VDR_Ileum_TGuninjectedvsTGandTreatment.txt
FPKM_VDR_Ileum_KOvsTGuninjected.txt

data_processing:
Alignment: RNA-seq: Kallisto v0.45.0.
RNA-seq Transcript Import: tximport 1.26.0
DESeq 1.14.0
Genome_build: RefSeq mm9
Supplementary_files_format_and_content: RNA-Seq: fpkm table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments

organism: Mus musculus

source_name: Ileum uninjected

extract_protocol:
Total RNA was isolated from mouse tissues, isolated mouse villus and crypt epithelium and human organoids using RiboZol RNA extraction reagent (Amresco, Solon, OH) or TRIzol reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions and subsequently purified with RNeasy Plus Universal Kit (Qiagen, Hilden, Germany) using on column DNAse digestion (Qiagen, Hilden, Germany). RNA concentration was measured with a NanoDrop spectrophotometer ND-1000 (Isogen Life Science, Utrecht, The Netherlands). RNA integrity was assessed using a denaturing agarose gel stained with ethidium bromide (EtBr) or by using an Agilent (Agilent Technologies, Santa Clara, CA) Bioanalyzer nanochip. For quantitative real time PCR (qRT-PCR), 2 µg of total RNA were used to synthesize complementary DNA using Superscript III First Strand synthesis system (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions. Relative quantification of target gene expression was performed using Taqman analyses. Taqman Gene Expression Probes (Applied Biosystems, Foster City, CA) used for qRT-PCR are the following: Cyp24a1 (Mm00487244-m1), S100g (Mm00486654-m1), Slc30a10 (Mm00437377-m1), Slc37a2 (Mm00451435_m1), Trpv5 (Mm01166037_m1), Trpv6 (Mm00499069-m1). Reactions were performed in a 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA). The cycle steps as follow: an initial 3-min incubation at 95 °C, followed by 40 cycles of 95 °C for 10 s, 60 °C for 30 s, and 72 °C for 30 s. Expressions of gene of interest were normalized to Gapdh (Mm999999-g1). The 2-ΔΔCt method was used to calculate relative gene expression.
The kit used to prepare the library include the following: NEBNext Ultra II RNA Library Prep with Sample Purification Beads Cat# E7775L, NEBNext Poly(A) mRNA Magnetic Isolation Module Cat# E7490L, and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) Cat# E7600S. CLC genomics workbench from Qiagen was utilized to map samples to the mouse genome, create transcript IDs, count reads, and normalization. For global assessment of mouse RNA levels, total RNA was subjected to ribosomal RNA (rRNA) depletion using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Ipswich, MA, USA). Libraries were constructed using the TruSeqRNA Sample Prep Kit (Illumina Inc, San Diego, CA) according to the manufacturer’s instructions. rRNA depletion and library quality were assessed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). The prepared libraries were sequenced on an Illumina NextSeq 500 instrument. (Illumina, San Diego, CA). Over 60 M reads per sample were obtained. The raw reads were aligned to the Mus musculus reference genome build 9 (mm9) using Kallisto. Differential gene expression was assessed using DESeq2 in R and transcript levels were obtained using a false discovery rate of 0.05.

treatment_protocol: 3-time injection of 1,25D3 (1 ng/g bw, 48h, 24h, 6h injection before termination)

tag: genotype

value: CDX2-VDR transgenic (no endrogenous VDR, but only express human VDR in the distal intestine)

tag: background strain

tag: Sex

value: female

value: Intestinal Epithelium

tag: age (weeks)

tag: treatment

value: No treatment


title: Ileum uninjected rep3

value: male


title: Ileum KO rep4

description:
FPKM_VDR_Ileum_KOvsTGandTreatment.txt
FPKM_VDR_Ileum_KOvsTGuninjected.txt

source_name: Ileum KO

value: Villin-CreERT2 VDR f/f


title: Ileum treated rep1

description:
FPKM_VDR_Ileum_TGuninjectedvsTGandTreatment.txt
FPKM_VDR_Ileum_KOvsTGandTreatment.txt

source_name: Ileum treated

value: 3-time injection of 1,25D3 (1 ng/g bw, 48h, 24h, 6h injection before termination)


title: Ileum treated rep3


title: Ileum treated rep2


title: Ileum KO rep1


title: Ileum uninjected rep1


title: Ileum KO rep3


title: Colon uninjected rep4

description:
FPKM_VDR_Colon_KOvsTGuninjected.txt
FPKM_VDR_Colon_TGuninjectedvsTGandTreatment.txt

source_name: Colon uninjected


title: Colon uninjected rep3


title: Colon uninjected rep2


title: Colon uninjected rep1


title: Colon treated rep2

description:
FPKM_VDR_Colon_KOvsTGandTreatment.txt
FPKM_VDR_Colon_TGuninjectedvsTGandTreatment.txt

source_name: Colon treated


title: Colon KO rep4

description:
FPKM_VDR_Colon_KOvsTGandTreatment.txt
FPKM_VDR_Colon_KOvsTGuninjected.txt

source_name: Colon KO


title: Colon KO rep3


title: Colon KO rep2


title: Colon KO rep1


title: R1_4d_RA_Single_Cell_RNAseq

status: Public on Sep 23 2020

city: Jerusalem

first: Adi

last: Alajem

state: Israel

address: Givat Ram Campus

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
for ChIP-Seq analysis:
Basecalls were performed using illumina nextseq and bcl2fastq
ChIP-seq reads were aligned to the mm9 genome assembly using Bismark and bowtie
Data were aligned single ended (SE)
Single CpGs were extracted using Bismark_methylation_extractor program.
We counted the number of methylated vs. non methylated CpGs within 200-bp bins.
mm9
Supplementary_files_format_and_content: We applied HOMER to find peaks and used bedtools to intersect peaks with reads
Supplementary_files_format_and_content: We counted the number of methylated vs. non methylated CpGs within 200-bp bins.
for single cell analysis:
In house perl based pipeline for generating single cell matrix bed file:  1. Deconvolution to single cell fastq files  2. Single cell alignment using RSEM + Bowtie  3. Matrix generator

source_name: Retinoic acid-induced differentiated cells

growth_protocol: R1 ESCs were grown on 0.1% gelatin-coated dishes and maintained in ESC medium (DMEM, 15% ESC-grade fetal calf serum, 50 μg/mL penicillin, 50 μg/mL streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1000 U/ml LIF), supplemented with 1 μM PD0325901, an inhibitor of MEK/ERK pathway, and 3 μM CHIR99021, an inhibitor of GSK3.

extract_protocol:
Cells were lysed, treated with MNAse, and histone-DNA complexes were isolated with antibody.
DNA samples were converted to blunt-ended, phosphorylated DNA using End-It™ DNA End-Repair Kit. DNA was purified using ratio of 1:1.8 sample:AMPure XP beads. An adenosine was added to the 3’ end of the DNA fragments using Klenow (3’-5’ exo-) (New England Biolabs, M0212L). DNA was purified using ratio of 1:1.8 sample:AMPure XP beads. Methylated adapters were added by ligation using DNA ligase (New England Biolabs, M2200S). DNA was purified using ratio of 1:1.2 sample:AMPure XP beads. Next the DNA was subjected to bisulfite conversion using the EZ DNA Methylation Gold kit (Zymo Research) according to the manufacturer’s instructions. The bisulfite-converted DNA samples were amplified using KAPA HiFi HotStart Uracil (KK2801) with 25 μM full-length primer mix containing Illumina library indices for multiplexing. Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads and eluted in 10 mM Tris-HCl [pH 8]. Library fragments were selected and isolated using the PureLink DNA gel extraction kit (Invitrogen). The resulting libraries had an average size of 350-550 bp. Size-selected libraries were diluted to 4 nM concentration and combined for paired end, single index sequencing on the Illumina NextSeq 550 instrument, using an illumina 550 High Output v2 (75 cycles) kit. Cycle distribution was 45 cycles for Read 1, 35 cycles for Read 2, and 8 cycles for the library index read.
ChIP-Bisulfite-Seq, single cell RNA-Seq

treatment_protocol: For "2 days no 2i" the cells were grown with ESC medium without 2i. For retinoic acid-induced differentiation, cells were grown on 0.1% gelatin-coated dishes for 4 days in ESC medium (10% fetal calf serum without LIF) supplemented with 1 µM retinoic acid. For XEN differentiation,R1 cells were grown on 0.1% gelatin-coated dishes for 9 days in RPMI 1640 with 15% ESC-grade fetal calf serum, 0.1 mM β-mercaptoethanol, Penicillin/Streptomycin 100 U/mL, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 10 ng/mL Activin A and 0.1 µM Retinoic acid.

tag: strain

tag: passages


title: mpimg_L12301-1_WTBL6-FL-E9-5-scRNAseq

status: Public on Oct 25 2020

city: Berlin

first: Lila

last: Allou

address: 63-73 Ihnestrasse

department: FG Development and Disease

country: Germany

institute: Max Planck Institute For Molecular Genetics

description:
barcode_metadata.txt
genes.txt
umi_count_matrix.mtx

data_processing:
The Cell Ranger pipeline version 3 (10x Genomics lnc.) was used for each scRNA-seq sample to de-multiplex the raw base call files, generate the fastq files, and perform the alignment against a custom mouse reference genome mm10, including Maenli coordinates (ENSMUSG00000099336.2), to create the UMI count matrix.
Only cells with a detected number of UMI counts among 500 and 40,000, a detected number of genes among 200 and 5,000, and less than 10% of mitochondrial UMI counts were considered for further analysis.
We used scrublet (https://doi.org/10.1016/j.cels.2018.11.005) to identify potential duplets in our dataset. We filtered out cells with a scrublet score higher than 0.2.
Each sample dataset was normalized independently using the SCT method (10.1186/s13059-019-1874-1) implemented in Seurat3 (10.1038/nbt.4096) R package and then integrated the datasets using the Seurat3 IntegrateData function and considering the top 6000 most variable genes.
The first 20 Principal Components of this joint dataset were calculated and used for UMAP projection and cell clustering. To delimitate the major forelimb bud cell types, we used the Louvain algorithm implemented in the Seurat3 function FindClusters with resolution equal 0.02. We identified marker genes for each of the main cell types using the ROC method of the Seurat3 FindAllMarkers function. We only considered genes expressed in at least 10% of each cell-cluster and a log2 fold-change average higher than 0.25.
Genome_build: Mm10
Supplementary_files_format_and_content: barcode_metadata.txt, genes.txt, umi_count_matrix.mtx

source_name: Forelimb

extract_protocol:
The cell concentration was determined using an automated cell counter (Bio-Rad) and cells were subjected to single-cell RNA-sequencing (10x Genomic, ChromiumTM Single Cell 3’ v2; one reaction per time point and per strain has been used) aiming for a target cell recovery of up to 10,000 sequenced cells per sequencing library (time point and strain). Single-cell libraries were generated according to the manufacturer’s instructions with the following conditions: 8 PCR cycles were ran during cDNA amplification and 12 PCR cycles were ran during library generation/sample indexing to increase library complexity. Libraries were sequenced with a minimum of 230 million paired end reads.
scRNA-seq 10X Genomics

treatment_protocol: Limbs from E9.5 and E10.5 mouse embryos were dissected in PBS. A single-cell suspension was obtained by incubating the tissue for 10 min at 37 °C in 200 µL Gibco trypsin-EDTA 0.05% (Thermo Fisher Scientific) and 20 µL 5% BSA (Sigma-Aldrich). Digestion was then blocked by adding 400 µL of BSA 5%. Cells were then resuspended by pipetting and filtered using a 0.40 µm cell strainer (Falcon). Cells were washed once with 0.04% BSA with a centrifugation step performed for 5 min at 1200 r.p.m then resuspended in 0.04% BSA.

value: Forelimb

value: Wild Type

tag: embryonic stage


title: ATC4

description:
10X genomics
3'-scRNAseq

value: fresh tumor


title: no_2i_2d_Single_Cell_RNAseq

data_processing:
for ChIP-Seq analysis:
Basecalls were performed using illumina nextseq and bcl2fastq
ChIP-seq reads were aligned to the mm9 genome assembly using Bismark and bowtie
Data were aligned single ended (SE)
Single CpGs were extracted using Bismark_methylation_extractor program.
We counted the number of methylated vs. non methylated CpGs within 200-bp bins.
mm9
Supplementary_files_format_and_content: We applied HOMER to find peaks and used bedtools to intersect peaks with reads
Supplementary_files_format_and_content: We counted the number of methylated vs. non methylated CpGs within 200-bp bins.
for single cell analysis:
In house perl based pipeline for generating single cell matrix bed file (available upon request):
1.      Deconvolution to single cell fastq files
Read1 (45bp): N(7-10)- GAGTGATTGCTTGTGACGCCTT-N{8}- N{5}
7-10 bp == Barcode1
22bp == spacer
8bp == Barcode2
5bp== UMI
Read2 (35bp):
Align to mRNA transcripts.
2.      Single cell alignment using RSEM + Bowtie2
rsem-calculate-expression --num-threads 1 --bowtie2 --single-cell-prior --estimate-rspd FASTQ REFERENCE OUTFOLDER
3.      Matrix generator

source_name: embryonic stem cells


title: R1_4days_RA_H3K36me_Bismark

tag: chip antibody


title: R1_4days_RA_WCE_Bismark


title: Ileum KO rep2


title: R1_4days_RA_H3K27Ac_Bismark


title: 2days_no_2i_H3K27Ac_Bismark


title: 2days_no_2i_WCE_Bismark


title: 2days_no_2i_H3K4me1_Bismark


title: LZ002 (AZFa_Del)

status: Public on Sep 04 2020

city: Zhuhai

first: Liangyu

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

country: China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

data_processing:
Cell Ranger software (version 2.2.0), provided by 10× Genomics, was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and downsample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Cells were further filtered according to the following threshold parameters: the total number of expressed genes, 500 to 9000; total UMI count, less than 35,000; and proportion of mitochondrial genes expressed, <40%.
Genome_build: hg38
Supplementary_files_format_and_content: UMI values for each cell

source_name: testis tissue

extract_protocol:
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit (P/N 120237, 10× Genomics) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina Novaseq 6000)

tag: disease state

value: Non -obstructive azoospermia (NOA)

value: testis

tag: condition

value: pathologic

tag: group


title: LZ003 (Adult_1)

value: normal spermatogenesis

value: physiologic


title: US-1596606

status: Public on Sep 01 2020

city: London

first: Christopher

last: Chiu

address: Hammersmith Campus, Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

data_processing:
Adaptors were removal by SeqPrep.
RNAseq reads were mapped to human B38 genome with Omicsoft OSA aligner.
Read counts mapped to the human ensemble genes (Release 75) were calculated with RSEM.
RNAseq that did not pass QC were exclude from downstream analysis. The gene count data were normalized and differential gene expression was calculated by DESeq2 (R package, version 1.18.1)
Genome_build: human B38
Supplementary_files_format_and_content: file contains gene counts for all genes in the samples submitted

source_name: Nasal Scrape

extract_protocol:
RNAseq cDNA library was prepared with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat Sample Prep Kit (Illumina, #RS-122-2203). Starting with 100 ng of total RNA, cytoplasmic ribosomal RNA was removed by hybridization to a biotinylated probe selective for ribosomal RNA species, followed by streptavidin bead binding and sample purification.  The resulting cytoplasmic rRNA-depleted sample was chemically fragmented and converted into single-stranded cDNA using reverse transcriptase and random hexamer primers, with the addition of Actinomycin D to suppress DNA-dependent synthesis of the second strand.  Double-stranded cDNA was created by removing the RNA template and synthesizing the second strand in the presence of dUTP in place of dTTP.  A single A base was added to the 3’ end to facilitate ligation of sequencing adapters, which contain a single T base overhang.  Adapter-ligated cDNA was amplified by polymerase chain reaction to increase the amount of sequence-ready library.  During this amplification the polymerase stalls when it encounters a U base, rendering the second strand a poor template.  Accordingly, amplified material used the first strand as a template, thereby preserving the strand information.  Final cDNA libraries were analyzed for size distribution using the Agilent Tapestation 2200 (D1000 kit, Agilent # 5067-5582 and 5067-5583), quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824), then normalized to 2 nM in preparation for sequencing. Prepared libraries were sequenced with 2 × 50 bp paired-end reads on the Illumina HiSeq 2500 sequencer with a minimum of 3 GB of raw RNA sequencing data (Illumina, San Diego, USA).
TruSeq Stranded Total RNA Ribo-Zero library preparation

tag: donor id

tag: batch

value: pilot

tag: timepoint

tag: outcome

value: Infected

tag: symptom

value: cold


title: Colon treated rep1

tag: genotype

value: CDX2-VDR transgenic (no endrogenous VDR, but only express human VDR in the distal intestine)

tag: tissue


title: Colon treated rep3

tag: background strain

tag: Sex

value: Intestinal Epithelium


title: US-1596576

value: Uninfected


title: CXCR2 neutrophils

status: Public on Sep 08 2020

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description: aCXCR2 treated

data_processing:
Cell Ranger Single Cell Software Suite was used to perform sample de-multiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) at the University of Michigan Biomedical Core Facilities DNA Sequencing Core
Genome_build: GRCh38
Supplementary_files_format_and_content: Seurat R package was used to perform unsupervised clustering and identification of cell-type specific markers. Used only  cells with > 500 genes and < 20% mitochondrial read content.

source_name: aCXCR2 treated

extract_protocol:
Eyes were dissected, and the vitreous fluid was collected
Retinas were rinsed with 200 ul of PBS and cells collected from rinse. Neutrophils were purified by MACS Ly6G bead purification. Cell purity and viability was confirmed by flow cytometry.
The cDNA libraries were constructed using the 10x ChromiumTM Single cell 3’ Library Kit according to the manufacturer’s original protocol.
Libraries were sequenced on an Illumina Novaseq paired-end kits using the following read length: 26bp Read1 for cell barcode and UMI, 8bp I7 index for sample index and 98bp Read2 for transcript.

value: vitreous fluid

tag: cell type

value: Ly6G+ cells


title: US-1596636


title: US-1596620


title: US-1635445

value: new


title: US-1635462


title: US-1635439


title: US-1635489


title: US-1635435


title: 2days_no_2i_H3K36me_Bismark

tag: strain


title: US-1635410


title: R1_4days_RA_H3K4me1_Bismark

tag: passages


title: WT_T47D_HiC

status: Public on Sep 15 2020

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

data_processing:
Hi-C data was processed with TADbit. Sequencing reads were mapped to the reference genome (GRCh37/hg19) applying a fragment-based strategy, dependent on the GEM mapper.
Mapped reads were filtered to remove those resulting from unspecified ligations, errors or experimental artefacts.
Hi-C data were normalized with OneD correction at a resolution of 100 kb to remove known biases.
Genome_build: hg19
Supplementary_files_format_and_content: BED files include TADs coordinates, border strength and interactions density or A/B compartments coordinates and identity.
Supplementary_files_format_and_content: The BDG file includes the differential interaction score (D) between WT and multiH1 KD conditions within bins of 100 kb. The D score is defined as the average value of differential interactions in a 20x20 box centred in that bin (only along the diagonal).

source_name: Breast cancer cell line

growth_protocol: Cells were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol:
For the in situ Hi-C, adherent cells were crosslinked with 1% formaldehyde in PBS for 10 min at room temperature. Glycine 0.125M was added for 5 min at room temperature and for 15 min at 4ºC to stop the crosslink reaction. Before permeabilization, cells were treated for 5 min with trypsin. Nuclei digestion was performed with 400 units of MboI restriction enzyme. The ends of the restriction fragments were labeled using biotinylated nucleotides and ligated with T4 DNA ligase. After reversal of crosslinks, DNA was purifed and sheared (Diagenode BioruptorPico) to obtain fragments of around 300-500 bp and ligation junctions were pull-down with streptavidin beads.
Hi-C libraries were finally amplified, controlled for quality and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. This cell line was subsequently infected with viruses for expression of the H1 variants shRNA (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Doxicycline treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Doxicycline (Sigma) was added at 2.5 µg/ml when indicated and cells were treated for 6 days.

value: Breast cancer ductal carcinoma

tag: cell line

tag: dox treatment

value: Untreated


title: US-1635407


title: US-1635426


title: US-1635406


title: US-1634291


title: US-1634188


title: US-1634187


title: US-1634380


title: US-1635397


title: US-1596618


title: US-1635405


title: US-1634341


title: US-1634172


title: US-1634178


title: US-1634156


title: US-1634170


title: US-1634140


title: US-1634163


title: US-1634159


title: US-1630699


title: US-1630698


title: US-1634152


title: US-1634145


title: US-1630689


title: US-1635420


title: US-1630686


title: US-1634138


title: US-1630680


title: US-1630677


title: US-1630678


title: US-1634177


title: US-1630671


title: US-1630660


title: US-1630673


title: US-1630672


title: US-1630661


title: US-1630667


title: US-1630663


title: US-1630657


title: US-1630656


title: US-1630648


title: US-1630652


title: US-1634115


title: US-1630651


title: US-1630646


title: US-1630643


title: US-1630638


title: US-1630645


title: US-1630633


title: US-1630627


title: US-1630628


title: US-1630631


title: US-1630630


title: US-1630670


title: US-1630624


title: US-1630615


title: US-1630621


title: US-1630620


title: US-1630612


title: US-1630609


title: US-1630602


title: US-1630601


title: US-1630606


title: US-1630605


title: US-1630608


title: US-1630603


title: L_W22_37R3

status: Public on Aug 31 2020

city: Ames

first: Stephen

middle: H

last: Howell

state: Iowa

address: 1111 WOI Road

department: Plant Sciences Institute Department of Genetics, Development and Cell Biology

institute: Iowa State University

description: W22 maize leaf (V5, maximum daily temperature 37°C) replicate 3

data_processing: Sequencing data were filtered with SOAPnuke (v1.5.2, github.com/BGI-flexlab/SOAPnuke) by removing reads (1) containing sequencing adapters, (2) in which more than 20% of the bases have a quality score less than 5 or (3) in which 5% or more of the bases are unknown (represented by N).  Clean reads were stored in FASTQ format and mapped to the reference maize B73 genome using HISAT2 (v2.0.4, http://www.ccb.jhu.edu/software/hisat/index.shtml). Bowtie2 (v2.2.5, http://bowtiebio.sourceforge.net/%20Bowtie2%20/index.shtml) was used to align the clean reads to the reference coding gene set (plants.ensembl.org/info/website/ftp/index.html),and gene expression levels were calculated by RSEM (v1.2.12, github.com/deweylab/RSEM).  Differential expression analysis was performed using DESeq2 (v1.4.5, www.bioconductor.org/packages/release/bioc/html/ DESeq2.html) using a Q value ≤ 0.05. GO (http://www.geneontology.org/) enrichment analysis of annotated DEGs was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution).  The significant levels of terms were corrected by Log2Ratio ≥ 1 and Q value with a threshold (Q value ≤ 0.05) by Bonferroni (Abdi, 2007).

organism: Zea mays

growth_protocol: Seeds of maize W22 and bzip60 mutants were germinated in soil in small pots with 13h light/11h dark at 26°C.  For experiments in the Enviratron, 7 day-old plants were transplanted in 9 inch pots and randomly placed into 12 set positions within each chamber. The eight growth chambers in the Enviratron were used to simulate 4 different environmental conditions, i.e., with duplicate chambers for each condition. The performance of plants under these conditions was monitored by a robot, equipped with various sensors, that travels from chamber to chamber (Bao et al., 2019).  The temperature and light cycles were offset by 40 min from chamber to chamber to allow the robot to enter the different chambers at the same time of virtual day. The daytime temperatures were ramped up over 6 hr to a maximum daily temperature (MDT) of 31°C, 33°C, 35°C or 37°C.  Nightime temperatures were ramped down over 8 hr to 10°C below the MDT.  Light intensities in a 16 hr/8 hr photoperiod cycle were also ramped up to 1200 µmol/m²/sec (measured 60 cm from the LED light source) or down over 2 hr periods to simulate dawn and dusk.  Water potential in the soil (Sunshine SB300 or MM900 Universal potting soil) was maintained at 50% VWC (volumetric water content) and relative humidity was held at 60%.  Plant performance was assessed at three different stages of vegetative growth, V4, V5 and V13-R1 stages (He et al., 2010), with the most extensive analysis carried out at the mid vegetative stages (V4 and V5).  The stages are defined by the leaf numbers visible in the collars.  For example, the V4 stage has leaf 4 visible in the collar. (The leaf collar is the light-colored band located at the base of an exposed leaf blade, where the leaf blade attaches to the plant stem.)  The middle part of the first (newest) fully expanded leaf from plants at the V4 (20 DAG) and V5 (27 DAG) stages were collected for RNAseq analysis.

extract_protocol:
RNA was extracted from small samples (0.1 g) of leaf lamina (avoiding the midrib) obtained from the middle of the first fully expanded leaves. The samples were taken in triplicate, one sample from each of three different plants, in the two chambers set for the same conditions.  The samples obtained from the plants in the two different chambers were taken at the same time of virtual day, because the temperature and light cycles are offset to allow for sampling at the same time of day. The samples were separately ground to a powder in liquid nitrogen, and RNA was isolated using a Plant RNeasy Mini Kit and treated with DNase (Qiagen, www.qiagen.com/us/) according to the manufacturer’s instructions. RNA quality and quantity were determined by the UV absorbance spectra, gel electrophoresis and Agilent 2000 BioAnalyzer (http://www.agilent.com).
For RNAseq analysis, poly A RNA was isolated from the purified RNA using oligo(dT)-attached magnetic beads and fragmented at elevated temperature with NEBNext RNA fragmentation buffer (New England BioLabs).  cDNA library construction, sequencing, and primary bioinformatics analysis were performed by BGI Tech Solutions Co., Ltd. (Beijing Genomic Institute (www.genomics.org.cn, BGI)) as follows:  First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis.  cDNA ends were repaired by A-Tailing followed by adding RNA Index Adapters. The cDNA fragments were amplified by PCR, and the products purified by Ampure XP Beads (Beckman Coulter).  The products were validated for quality control using an Agilent Technologies 2100 bioanalyzer. The double stranded PCR products were heat denatured and circularized using splint oligos (Diegelman and Kool, 2000). The single strand circular DNAs (ssCir DNAs) were amplified with phi29 (Blanco et al., 1989) to make DNA nanoballs (DNBs) (Porreca, 2010).  DNBs were loaded into the patterned nanoarray and single end 50 base reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Seeds of maize W22 and bzip60 mutants were germinated in soil in small pots with 13h light/11h dark at 26°C.  For experiments in the Enviratron, 7 day-old plants were transplanted in 9 inch pots and randomly placed into 12 set positions within each chamber. The eight growth chambers in the Enviratron were used to simulate 4 different environmental conditions, i.e., with duplicate chambers for each condition.  The daytime temperatures were ramped up over 6 hr to a maximum daily temperature (MDT) of 31°C, 33°C, 35°C or 37°C.  Nightime temperatures were ramped down over 8 hr to 10°C below the MDT.  Light intensities in a 16 hr/8 hr photoperiod cycle were also ramped up to 1200 µmol/m²/sec (measured 60 cm from the LED light source) or down over 2 hr periods to simulate dawn and dusk.  Water potential in the soil (Sunshine SB300 or MM900 Universal potting soil) was maintained at 50% VWC (volumetric water content) and relative humidity was held at 60%.  The V4 stage has leaf 4 visible in the collar. (The leaf collar is the light-colored band located at the base of an exposed leaf blade, where the leaf blade attaches to the plant stem.)  The middle part of the first (newest) fully expanded leaf from plants at the V4 (20 DAG) and V5 (27 DAG) stages were collected for RNAseq analysis.

value: leaf

tag: vegetative stage

value: V5 stage

tag: treatment

value: maximum daily temperature 37°C


title: US-1630632


title: L_W22_35R3

description: W22 maize leaf (V5, maximum daily temperature 35°C) replicate 3

value: maximum daily temperature 35°C


title: L_W22_37R1

description: W22 maize leaf (V5, maximum daily temperature 37°C) replicate 1


title: L_W22_37R2

description: W22 maize leaf (V5, maximum daily temperature 37°C) replicate 2


title: US-1630636


title: L_W22_35R2

description: W22 maize leaf (V5, maximum daily temperature 35°C) replicate 2


title: L_W22_33R3

description: W22 maize leaf (V5, maximum daily temperature 33°C) replicate 3

value: maximum daily temperature 33°C


title: L_W22_31R1

description: W22 maize leaf (V5, maximum daily temperature 31°C) replicate 1

value: maximum daily temperature 31°C


title: L_W22_31R2

description: W22 maize leaf (V5, maximum daily temperature 31°C) replicate 2


title: L_W22_31R3

description: W22 maize leaf (V5, maximum daily temperature 31°C) replicate 3


title: L_W22_33R1

description: W22 maize leaf (V5, maximum daily temperature 33°C) replicate 1


title: E_W22_37R1

description: W22 maize leaf (V4, maximum daily temperature 37°C) replicate 1

value: V4 stage


title: L_W22_33R2

description: W22 maize leaf (V5, maximum daily temperature 33°C) replicate 2


title: E_W22_35R3

description: W22 maize leaf (V4, maximum daily temperature 35°C) replicate 3


title: E_W22_37R2

description: W22 maize leaf (V4, maximum daily temperature 37°C) replicate 2


title: L_W22_35R1

description: W22 maize leaf (V5, maximum daily temperature 35°C) replicate 1


title: E_W22_37R3

description: W22 maize leaf (V4, maximum daily temperature 37°C) replicate 3


title: E_W22_35R1

description: W22 maize leaf (V4, maximum daily temperature 35°C) replicate 1


title: E_W22_31R3

description: W22 maize leaf (V4, maximum daily temperature 31°C) replicate 3


title: E_W22_33R1

description: W22 maize leaf (V4, maximum daily temperature 33°C) replicate 1


title: US-1630610


title: E_W22_35R2

description: W22 maize leaf (V4, maximum daily temperature 35°C) replicate 2


title: E_W22_31R2

description: W22 maize leaf (V4, maximum daily temperature 31°C) replicate 2


title: Ume6_delta_2-508_FLAG_ChIP_Replicate_1

city: Eugene

first: Laura

middle: Emily

last: McKnight

state: Oregon

address: 1318 Franklin Blvd Room 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Data were normalized such that average value at a genomic position was 1.0
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts; coverage file (chr, position, count)

organism: Saccharomyces cerevisiae

source_name: exponentially-growing W303 yeast cells

growth_protocol: grown to mid-log

extract_protocol:
cells were crosslinked with 1% formaldehyde for 20 min, lysed by bead beating for 4 minutes, chromatin was sheared to ~300bp mean fragment length using Bioruptor high setting, ChIP was performed, crosslinks were reversed, protein was digested, RNA was degraded, DNA was recovered by Qiagen PCR Purification
Libraries were made with NuGEN Ovation Ultralow kit V2

tag: strain background

value: W303 WT

tag: mutations

value: N-terminal Truncation of Ume6 to residue 508

tag: epitope tag

value: FLAG


title: E_W22_33R3

description: W22 maize leaf (V4, maximum daily temperature 33°C) replicate 3


title: Itc1_E33R_E40H_E43R_D70K_Replicate_1

description: Nucleosomal DNA

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts; coverage file (chr, position, count)

extract_protocol:
cells were crosslinked with 1% formaldehyde for 20 min, spheroplasted, digested with micrococcal nuclease, quenched, treated with RNase for 40 minutes, crosslinks reversed for 1 hour at 65 degrees with proteinase K treatment, purified by MinElute (PCR clean-up) column, CIP-treated, and mononucleosome band was gel-extracted
CIP-treated nucleosome-sized DNA footprints were converted to libraries with NuGEN Ovation Ultralow kit

tag: strain background (not specified elsewhere)

tag: mutations present

value: Itc1 E33R, E40H, E43R, delta_70K

tag: spytagged-factor

tag: expression promoter


title: Itc1_E43R_D70K_Replicate_2

description: Nucleosomal DNA

value: Itc1 E43R, delta_70K


title: Ume6_FLAG_ChIP_Replicate_1


title: Mbp1_1-561_Replicate_1

description: Nucleosomal DNA

value: Deletion of Mbp1 residues 562-833


title: Mbp1_1-561_Replicate_2

description: Nucleosomal DNA


title: E_W22_33R2

description: W22 maize leaf (V4, maximum daily temperature 33°C) replicate 2

tag: genotype

tag: tissue


title: E_W22_31R1

description: W22 maize leaf (V4, maximum daily temperature 31°C) replicate 1


title: Ume6_delta_2-479_FLAG_ChIP_Replicate_1

value: N-terminal Truncation of Ume6 to residue 479


title: Itc1_E43R_D70K_Replicate_1

description: Nucleosomal DNA


title: Itc1_E33R_E40H_Replicate_2

description: Nucleosomal DNA

value: Itc1 E33R, E40H


title: Itc1_E33R_E40H_Replicate_1

description: Nucleosomal DNA


title: Itc1_delta_9-374_Replicate_2

description: Nucleosomal DNA


title: Mbp1_1-136_SpyTag_with_SpyCatcher-Ume6_479-508_Replicate_3

description: Nucleosomal DNA

value: Mbp1 truncated to only residues 1-136


title: Itc1_delta_22-200_Replicate_1

description: Nucleosomal DNA


title: Itc1_delta_24-130_Replicate_1

description: Nucleosomal DNA


title: Itc1_delta_22-273_Replicate_1

description: Nucleosomal DNA


title: Itc1_delta_9-374_Replicate_1

description: Nucleosomal DNA


title: Mbp1_1-136_SpyTag_with_SpyCatcher-Ume6_479-508_Replicate_1

description: Nucleosomal DNA


title: Mbp1_1-136_SpyTag_with_SpyCatcher-Ume6_479-508_Replicate_2

description: Nucleosomal DNA


title: delta_swi6_Replicate_1

description: Nucleosomal DNA


title: Mbp1_1-136_SpyTag_Replicate_1

description: Nucleosomal DNA


title: Mbp1_1-136_SpyTag_Replicate_2

description: Nucleosomal DNA


title: delta_swi4_Replicate_2

description: Nucleosomal DNA


title: delta_swi4_Replicate_1

description: Nucleosomal DNA


title: delta_swi6_Replicate_2

description: Nucleosomal DNA


title: delta_mbp1_Replicate_1

description: Nucleosomal DNA


title: wild_type_Replicate_2

description: Nucleosomal DNA


title: delta_isw2_Replicate_1

description: Nucleosomal DNA


title: delta_isw2_Replicate_2

description: Nucleosomal DNA


title: delta_chd1_delta_isw1_delta_isw2_Replicate_2

description: Nucleosomal DNA

value: delta_chd_1, delta_isw1, delta_isw2


title: delta_chd1_delta_isw1_ISW2+_Replicate_1

description: Nucleosomal DNA

value: delta_chd_1, delta_isw1


title: delta_chd1_delta_isw1_ISW2+_Replicate_2

description: Nucleosomal DNA


title: delta_chd1_delta_isw1_delta_isw2_Replicate_1

description: Nucleosomal DNA


title: delta_chd1_delta_isw2_ISW1+_Replicate_1

description: Nucleosomal DNA

value: delta_chd_1, delta_isw2


title: delta_isw1_delta_isw2_CHD1+_Replicate_1

description: Nucleosomal DNA

value: delta_isw1, delta_isw2


title: Ume6_delta_2-596_SpyTag_with_SpyCatcher-Ume6_479-508_Replicate_2

description: Nucleosomal DNA


title: Ume6_delta_480-507_Replicate_1

description: Nucleosomal DNA


title: Ume6_delta_2-596_SpyTag_with_SpyCatcher-Ume6_479-508_Replicate_1

description: Nucleosomal DNA


title: Ume6_delta_2-596_Replicate_1

description: Nucleosomal DNA


title: Ume6_delta_2-508_Replicate_2

description: Nucleosomal DNA


title: Ume6_delta_2-596_Replicate_2

description: Nucleosomal DNA


title: Ume6_delta_2-322_Replicate_1

description: Nucleosomal DNA


title: Ume6_delta_2-175_Replicate_3

description: Nucleosomal DNA


title: Ume6_delta_2-175_Replicate_2

description: Nucleosomal DNA


title: wild_type_Replicate_1

description: Nucleosomal DNA


title: Ume6_delta_2-508_Replicate_1

description: Nucleosomal DNA


title: Ume6_delta_2-97_Replicate_1

description: Nucleosomal DNA


title: Ume6_delta_2-97_Replicate_2

description: Nucleosomal DNA


title: Ume6_delta_2-763_Replicate_1

description: Nucleosomal DNA

value: delta_ume6, Ume6(delta_2-763) on expression plasmid


title: Ume6_delta_2-763_Replicate_2

description: Nucleosomal DNA


title: Ume6_delta_2-175_Replicate_1

description: Nucleosomal DNA


title: rpd3_delta_ume6_delta_2-479_Replicate_2

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Strands were separated into Watson and Crick strands using SAMtools filtering
Read counts were piled up across the yeast genome
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/RNA read counts; coverage file (chr, position, count)

extract_protocol:
NuGEN Universal mRNA Kit
RNA was extracted using hot-acid phenol ; rRNA was depleted using Illumina Ribo-Zero Gold (Yeast)
cDNA libraries were constructed with the NuGEN Universal mRNA Library Kit as per instructions

value: W303 rpd3

tag: isw2 recruitment status

value: loses rpd3 repression at Ume6 targets


title: rpd3_delta_ume6_delta_2-508_Replicate_2

value: loses rpd3 and Isw2 repression at Ume6 targets


title: rpd3_delta_Replicate_2


title: rpd3_delta_ume6_delta_2-508_Replicate_1


title: rpd3_delta_ume6_delta_2-479_Replicate_1


title: ume6_delta_2-479_Replicate_1

value: W303 WT

value: maintains Isw2 recruitment


title: ume6_delta_2-479_Replicate_2


title: Ume6_delta_2-596_SpyTag_with_SpyCatcher-Ume6_479-508_Replicate_3

description: Nucleosomal DNA


title: rpd3_delta_Replicate_1


title: ume6_delta_2-508_Replicate_2

value: loses Isw2 recruitment


title: ume6_delta_2-508_Replicate_1


title: ume6_delta_2-763_FLAG_Replicate_2

extract_protocol:
cells were crosslinked with 1% formaldehyde for 20 min, lysed by bead beating for 4 minutes, chromatin was sheared to ~300bp mean fragment length using Bioruptor high setting, ChIP was performed, crosslinks were reversed, protein was digested, RNA was degraded, DNA was recovered by Qiagen PCR Purification
Libraries were made with NuGEN Ovation Ultralow kit

value: ume6 delta 2-763 ; leaves DNA binding domain intact

value: FLAG


title: WT_Replicate_2

extract_protocol:
Illumina TruSeq Stranded Kit
RNA was extracted using hot-acid phenol ; rRNA was depleted using Illumina Ribo-Zero Gold (Yeast)

value: wild type


title: WT_Replicate_1


title: Ume6_delta_2-479_Replicate_1

description: Nucleosomal DNA


title: ume6_delta_2-763_FLAG_Replicate_1


title: Itc1_1-73_FLAG_Replicate_2

value: Itc1 C-terminal Deletion Leaving only Residues 1-73


title: Itc1_1-130_FLAG_Replicate_1

value: Itc1 C-terminal Deletion Leaving only Residues 1-130


title: Isw2_K215R_FLAG_Replicate_1

value: Isw2 K215R Mutation


title: Isw2_K215R_FLAG_Replicate_2


title: ovary-tumor-1 [ID99]

status: Public on Aug 20 2020

type: RNA

city: Kensington

first: Susan

last: Ramus

state: NSW

address: High Street

department: School of Women's and Children's Health

country: Australia

institute: UNSW Sydney

description:
ID99
FFPE-derived total RNA

hyb_protocol: 500 ng of total RNA was mixed with hybridization buffer and hybridized at 65°C overnight.

scan_protocol: The sample, wash reagents and imaging cartridges were processed on the nCounter Prep Station and imaged on the Digital Analyzer.

data_processing: We used batch effects adjustment, quality control, and normalisation techniques that are applied one patient at a time, single-patient processing [Talhouk et al. 2016]. After quality control assessments, the count data were log2 transformed and centered by the arithmetic mean of the selected housekeeping genes, RPL19, ACTB, PGK1, SDHA, and POLR1B.

label: barcode

label_protocol: Proprietary 'barcode' for each target sequence.

extract_protocol: RNA was extracted from FFPE tumor samples using the Qiagen miRNeasy FFPE kit.

tag: diagnosis

value: High-grade serous ovarian cancer (HGSOC)

tag: Sex

value: Female

value: adnexal

tag: status

tag: Stage

tag: signature

tag: age

tag: site

value: VAN


title: ovary-tumor-1 [ID993]

description:
ID993
FFPE-derived total RNA

value: MAY


title: ovary-tumor-1 [ID999]

description:
ID999
FFPE-derived total RNA

value: presumed adnexal

value: AOC


title: ovary-tumor-1 [ID991]

description:
ID991
FFPE-derived total RNA

value: TRI


title: ovary-tumor-1 [ID998]

description:
ID998
FFPE-derived total RNA

value: UKO


title: Itc1_1-130_FLAG_Replicate_2

tag: strain background

value: W303 WT


title: ovary-tumor-1 [ID995]

description:
ID995
FFPE-derived total RNA

value: SEA


title: ovary-tumor-1 [ID992]

description:
ID992
FFPE-derived total RNA


title: ovary-tumor-1 [ID997]

description:
ID997
FFPE-derived total RNA

value: SRF


title: ovary-tumor-1 [ID987]

description:
ID987
FFPE-derived total RNA

value: DOV


title: ovary-tumor-1 [ID996]

description:
ID996
FFPE-derived total RNA

value: HAW


title: ovary-tumor-1 [ID985]

description:
ID985
FFPE-derived total RNA


title: ovary-tumor-1 [ID98]

description:
ID98
FFPE-derived total RNA


title: ovary-tumor-1 [ID988]

description:
ID988
FFPE-derived total RNA


title: ovary-tumor-1 [ID984]

description:
ID984
FFPE-derived total RNA

value: NCO


title: ovary-tumor-1 [ID989]

description:
ID989
FFPE-derived total RNA

value: BRO


title: ovary-tumor-1 [ID981]

description:
ID981
FFPE-derived total RNA


title: ovary-tumor-1 [ID9]

description:
ID9
FFPE-derived total RNA


title: ovary-tumor-1 [ID979]

description:
ID979
FFPE-derived total RNA


title: ovary-tumor-1 [ID977]

description:
ID977
FFPE-derived total RNA


title: ovary-tumor-1 [ID97]

description:
ID97
FFPE-derived total RNA


title: ovary-tumor-1 [ID983]

description:
ID983
FFPE-derived total RNA

value: POC


title: ovary-tumor-1 [ID986]

description:
ID986
FFPE-derived total RNA

value: High-grade serous ovarian cancer (HGSOC)


title: ovary-tumor-1 [ID980]

description:
ID980
FFPE-derived total RNA

value: Female


title: ovary-tumor-1 [ID976]

description:
ID976
FFPE-derived total RNA

value: adnexal


title: omentum-tumor-1 [ID978]

description:
ID978
FFPE-derived total RNA

value: omentum


title: Itc1_1-73_FLAG_Replicate_1

tag: mutations

value: Itc1 C-terminal Deletion Leaving only Residues 1-73

value: FLAG


title: ovary-tumor-1 [ID990]

description:
ID990
FFPE-derived total RNA


title: ovary-tumor-1 [ID975]

description:
ID975
FFPE-derived total RNA

value: WMH


title: ovary-tumor-1 [ID994]

description:
ID994
FFPE-derived total RNA

value: AOC


title: omentum-tumor-1 [ID973]

description:
ID973
FFPE-derived total RNA

value: VAN


title: ovary-tumor-1 [ID982]

description:
ID982
FFPE-derived total RNA


title: ovary-tumor-1 [ID972]

description:
ID972
FFPE-derived total RNA

value: presumed adnexal

value: MAY


title: ovary-tumor-1 [ID968]

description:
ID968
FFPE-derived total RNA


title: ovary-tumor-1 [ID969]

description:
ID969
FFPE-derived total RNA


title: other-tumor-1 [ID974]

description:
ID974
FFPE-derived total RNA

value: peritoneal


title: ovary-tumor-1 [ID971]

description:
ID971
FFPE-derived total RNA

value: SEA


title: ovary-tumor-1 [ID967]

description:
ID967
FFPE-derived total RNA


title: ovary-tumor-1 [ID96]

description:
ID96
FFPE-derived total RNA

value: SRF


title: ovary-tumor-1 [ID970]

description:
ID970
FFPE-derived total RNA


title: omentum-tumor-1 [ID966]

description:
ID966
FFPE-derived total RNA


title: ovary-tumor-1 [ID965]

description:
ID965
FFPE-derived total RNA


title: omentum-tumor-1 [ID964]

description:
ID964
FFPE-derived total RNA


title: ovary-tumor-1 [ID962]

description:
ID962
FFPE-derived total RNA


title: ovary-tumor-1 [ID959]

description:
ID959
FFPE-derived total RNA

value: DOV


title: ovary-tumor-1 [ID955]

description:
ID955
FFPE-derived total RNA


title: ovary-tumor-1 [ID956]

description:
ID956
FFPE-derived total RNA

value: TRI


title: ovary-tumor-1 [ID953]

description:
ID953
FFPE-derived total RNA


title: ovary-tumor-1 [ID963]

description:
ID963
FFPE-derived total RNA


title: ovary-tumor-1 [ID954]

description:
ID954
FFPE-derived total RNA


title: ovary-tumor-1 [ID957]

description:
ID957
FFPE-derived total RNA


title: ovary-tumor-1 [ID95]

description:
ID95
FFPE-derived total RNA


title: ovary-tumor-1 [ID952]

description:
ID952
FFPE-derived total RNA


title: ovary-tumor-1 [ID960]

description:
ID960
FFPE-derived total RNA

value: NCO


title: ovary-tumor-1 [ID951]

description:
ID951
FFPE-derived total RNA

value: High-grade serous ovarian cancer (HGSOC)


title: ovary-tumor-1 [ID958]

description:
ID958
FFPE-derived total RNA

value: Female


title: ovary-tumor-1 [ID950]

description:
ID950
FFPE-derived total RNA

value: adnexal

value: UKO


title: other-tumor-1 [ID947]

description:
ID947
FFPE-derived total RNA


title: ovary-tumor-1 [ID945]

description:
ID945
FFPE-derived total RNA


title: omentum-tumor-1 [ID949]

description:
ID949
FFPE-derived total RNA

value: omentum


title: omentum-tumor-1 [ID94]

description:
ID94
FFPE-derived total RNA


title: ovary-tumor-1 [ID946]

description:
ID946
FFPE-derived total RNA

value: HAW


title: ovary-tumor-1 [ID961]

description:
ID961
FFPE-derived total RNA


title: ovary-tumor-1 [ID941]

description:
ID941
FFPE-derived total RNA


title: ovary-tumor-1 [ID943]

description:
ID943
FFPE-derived total RNA


title: ovary-tumor-1 [ID942]

description:
ID942
FFPE-derived total RNA

value: RTR


title: ovary-tumor-1 [ID93]

description:
ID93
FFPE-derived total RNA

value: BRO


title: ovary-tumor-1 [ID940]

description:
ID940
FFPE-derived total RNA


title: other-tumor-1 [ID944]

description:
ID944
FFPE-derived total RNA

value: AOC


title: ovary-tumor-1 [ID938]

description:
ID938
FFPE-derived total RNA


title: ovary-tumor-1 [ID939]

description:
ID939
FFPE-derived total RNA

value: presumed adnexal


title: ovary-tumor-1 [ID937]

description:
ID937
FFPE-derived total RNA

value: MAY


title: ovary-tumor-1 [ID936]

description:
ID936
FFPE-derived total RNA


title: ovary-tumor-1 [ID927]

description:
ID927
FFPE-derived total RNA

value: AOV


title: other-tumor-1 [ID926]

description:
ID926
FFPE-derived total RNA

value: other

value: VAN


title: ovary-tumor-1 [ID92]

description:
ID92
FFPE-derived total RNA


title: ovary-tumor-1 [ID948]

description:
ID948
FFPE-derived total RNA

value: POC


title: ovary-tumor-1 [ID929]

description:
ID929
FFPE-derived total RNA

value: DOV


title: ovary-tumor-1 [ID930]

description:
ID930
FFPE-derived total RNA

value: POL


title: ovary-tumor-1 [ID928]

description:
ID928
FFPE-derived total RNA

value: High-grade serous ovarian cancer (HGSOC)

value: SEA


title: ovary-tumor-1 [ID925]

description:
ID925
FFPE-derived total RNA

value: Female

value: NCO


title: ovary-tumor-1 [ID924]

description:
ID924
FFPE-derived total RNA

value: adnexal


title: ovary-tumor-1 [ID931]

description:
ID931
FFPE-derived total RNA


title: ovary-tumor-1 [ID923]

description:
ID923
FFPE-derived total RNA

value: UKO


title: ovary-tumor-1 [ID922]

description:
ID922
FFPE-derived total RNA


title: ovary-tumor-1 [ID921]

description:
ID921
FFPE-derived total RNA


title: ovary-tumor-1 [ID920]

description:
ID920
FFPE-derived total RNA


title: ovary-tumor-1 [ID933]

description:
ID933
FFPE-derived total RNA


title: ovary-tumor-1 [ID934]

description:
ID934
FFPE-derived total RNA

value: SRF


title: ovary-tumor-1 [ID919]

description:
ID919
FFPE-derived total RNA


title: ovary-tumor-1 [ID932]

description:
ID932
FFPE-derived total RNA


title: ovary-tumor-1 [ID918]

description:
ID918
FFPE-derived total RNA


title: ovary-tumor-1 [ID935]

description:
ID935
FFPE-derived total RNA


title: ovary-tumor-1 [ID913]

description:
ID913
FFPE-derived total RNA


title: ovary-tumor-1 [ID915]

description:
ID915
FFPE-derived total RNA


title: ovary-tumor-1 [ID914]

description:
ID914
FFPE-derived total RNA


title: ovary-tumor-1 [ID912]

description:
ID912
FFPE-derived total RNA

value: CNI


title: ovary-tumor-1 [ID911]

description:
ID911
FFPE-derived total RNA


title: ovary-tumor-1 [ID917]

description:
ID917
FFPE-derived total RNA


title: ovary-tumor-1 [ID916]

description:
ID916
FFPE-derived total RNA


title: ovary-tumor-1 [ID910]

description:
ID910
FFPE-derived total RNA


title: ovary-tumor-1 [ID908]

description:
ID908
FFPE-derived total RNA


title: other-tumor-1 [ID909]

description:
ID909
FFPE-derived total RNA

value: peritoneal

value: AOC


title: ovary-tumor-1 [ID907]

description:
ID907
FFPE-derived total RNA

value: MAY


title: ovary-tumor-1 [ID902]

description:
ID902
FFPE-derived total RNA

value: presumed adnexal


title: ovary-tumor-1 [ID905]

description:
ID905
FFPE-derived total RNA


title: ovary-tumor-1 [ID91]

description:
ID91
FFPE-derived total RNA


title: ovary-tumor-1 [ID903]

description:
ID903
FFPE-derived total RNA


title: ovary-tumor-1 [ID900]

description:
ID900
FFPE-derived total RNA


title: ovary-tumor-1 [ID906]

description:
ID906
FFPE-derived total RNA


title: other-tumor-1 [ID904]

description:
ID904
FFPE-derived total RNA


title: ovary-tumor-1 [ID898]

description:
ID898
FFPE-derived total RNA


title: ovary-tumor-1 [ID896]

description:
ID896
FFPE-derived total RNA


title: ovary-tumor-1 [ID897]

description:
ID897
FFPE-derived total RNA


title: ovary-tumor-1 [ID890]

description:
ID890
FFPE-derived total RNA


title: ovary-tumor-1 [ID88]

description:
ID88
FFPE-derived total RNA


title: ovary-tumor-1 [ID891]

description:
ID891
FFPE-derived total RNA


title: ovary-tumor-1 [ID90]

description:
ID90
FFPE-derived total RNA


title: ovary-tumor-1 [ID89]

description:
ID89
FFPE-derived total RNA


title: ovary-tumor-1 [ID901]

description:
ID901
FFPE-derived total RNA


title: ovary-tumor-1 [ID8]

description:
ID8
FFPE-derived total RNA


title: ovary-tumor-1 [ID887]

description:
ID887
FFPE-derived total RNA

value: HAW


title: ovary-tumor-1 [ID899]

description:
ID899
FFPE-derived total RNA


title: ovary-tumor-1 [ID885]

description:
ID885
FFPE-derived total RNA


title: ovary-tumor-1 [ID892]

description:
ID892
FFPE-derived total RNA


title: other-tumor-1 [ID883]

description:
ID883
FFPE-derived total RNA


title: ovary-tumor-1 [ID895]

description:
ID895
FFPE-derived total RNA


title: ovary-tumor-1 [ID894]

description:
ID894
FFPE-derived total RNA


title: ovary-tumor-1 [ID889]

description:
ID889
FFPE-derived total RNA

value: GER


title: ovary-tumor-1 [ID880]

description:
ID880
FFPE-derived total RNA


title: omentum-tumor-1 [ID893]

description:
ID893
FFPE-derived total RNA

value: omentum


title: ovary-tumor-1 [ID87]

description:
ID87
FFPE-derived total RNA


title: omentum-tumor-1 [ID886]

description:
ID886
FFPE-derived total RNA


title: ovary-tumor-1 [ID884]

description:
ID884
FFPE-derived total RNA


title: ovary-tumor-1 [ID882]

description:
ID882
FFPE-derived total RNA


title: ovary-tumor-1 [ID888]

description:
ID888
FFPE-derived total RNA

value: DOV


title: ovary-tumor-1 [ID874]

description:
ID874
FFPE-derived total RNA


title: ovary-tumor-1 [ID872]

description:
ID872
FFPE-derived total RNA

value: WMH


title: omentum-tumor-1 [ID873]

description:
ID873
FFPE-derived total RNA

value: High-grade serous ovarian cancer (HGSOC)

value: VAN


title: ovary-tumor-1 [ID878]

description:
ID878
FFPE-derived total RNA

value: Female


title: ovary-tumor-1 [ID881]

description:
ID881
FFPE-derived total RNA

value: TRI


title: omentum-tumor-1 [ID866]

description:
ID866
FFPE-derived total RNA


title: ovary-tumor-1 [ID868]

description:
ID868
FFPE-derived total RNA

value: adnexal