lihuajulie zhu and jianhongou - bioconductor · adapted from nature methods 10,1213–1218, 2013 by...
TRANSCRIPT
![Page 1: LihuaJulie Zhu and JianhongOu - Bioconductor · Adapted from Nature Methods 10,1213–1218, 2013 By Buenrostroand Greenleaf et al. Assay for Transposase- Accessible Chromatin using](https://reader034.vdocument.in/reader034/viewer/2022050211/5f5d8b9c4609d860030a5ddf/html5/thumbnails/1.jpg)
April 2008
Lihua Julie Zhu and Jianhong Ou
ATACseqQC for quality assessment of ATACseq datasetNADfinder for identifying Nucleoli Associated Domain (NAD)
July 26th 2017
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Adapted from Nature Methods10, 1213–1218, 2013By Buenrostro and Greenleaf et al.
Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq)
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• Provide quick assessment of the quality of the ATAC-seq data– diagnostic plot of insert size distribution of sequenced fragments
(periodicity)
– proportion of mitochondria reads (< 5%)
– genome-wide nucleosome positioning pattern at TSS
– CTCF or other Transcript Factor footprints (depleted signals)
ATACseqQC Package
Adapted from Nature Methods 10, 1213–1218, 2013By Buenrostro and Greenleaf et al.
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Expected patterns of nucleosome occupancy and depletion at the TSS
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Density Plot Flanking TSS
- Nucleosome free-- Nucleosome bound
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Generate footprints for DNA-binding proteins
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NADFINDERNUCLEOLI ARE THE LARGEST NUCLEAR BODIES AND
ARE SURROUNDED BY HETEROCHROMATIN
van Koningsbruggen et al… Lamond, MBoC 2010http://schoolbag.info/chemistry/mcat_biochemistry/mcat_biochemistry.files/image140.jpg
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NADfinderWorkflow
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• Workshop By J Ou and LJ Zhu on July 28th, 3:15 - 5:00 Smith 309
– ChIPpeakAnno (BMC Bioinformatics 2010)
– GeneNetworkBuilder
– TrackViewer
• Workshop by LJ Zhu on July 27th , 1-2:45pm Smith 309
– CRISPRseek (PLoS One 2014)
– GUIDEseq (BMC Genomics 2017)
• NADFinder (Poster)
• ATACseqQC
• cleanUpdTseq (Bioinformatics 2013)
• REDseq (BMC Genomics 2014 )
• MotifStack (in prep)
• InPAS
• dagLogo
ctBARHL2Barhl1BARHL2Hoxd13 3HOXA13 1HOXC13 1HOXD13 1HOXA13 1HOXB13 1HOXA10Hoxa11HOXC12 1HOXD12 1HOXC11HOXD11HOXC11HOXC10 2Hoxc10 3HOXD12 2Hoxd9 2Hoxa11 1
H2 0HOXA10 1HOXD12 3
HOXC10 1Abd BcadCDX1
CDX2HOXA13
HOXB13HOXA13
HOXC13
HOXD13
Hoxd1
3 2
HOXC11 1
Hoxd9
1
Hoxc1
0 4
HOXC12
HOXD12
HOXC11
1
HOXD11
1
HOXC10
Hoxd
9
GSC2
DMBX
1
Gsc
GSC
PITX
1PI
TX1
PITX
3OT
X1 1
PITX
1 1
Ptx1bcd
ocOtx
1 3
OTX2
1DP
RX 1
RHOX
F1RH
OXF1
DPRX
RHOX
F1 1
RHOX
F1 1
OTX
2O
TX1
Otx
1 2
VEN
TXVE
NTX
1Si
x4O
ptix
soMEO
X2 2
HN
F1B
1H
NF1
AH
NF1
BH
OXD
8EV
X2EV
X1on
ecut
CG70
56CG
1342
4re
poC1
5CG
1236
1ab
d A
Ubx
HGTX
NKX6
1DL
X1AL
X3M
IXL1
HOXA
1Lh
x8 1
LMX1
BPr
rx2
Lim3
enDrexex
invOdsH
unc 4
slou
unpg
Lim1
CG3398
0
CG3210
5
CG4328
CG3253
2
CG4136
hbnCG11294
roapE5CG9876
RxotpPph13VAX1Lhx4LMX1AAlx1ALX3MNX1EMX1Hoxd3HOXB5HOXB3GSX1GSX2Hoxa2 1HOXB2HOXA2lbelblMeox2 3ftzems lab zen2 CG18599pbzen Dfd Antp Scr bsh btn NKX6 1 PDX1 1 Nkx6 1 1 NKX6 2 NKX6 2 MEOX2 EMX2 En2 1 VSX1 LHX2 NOTO LHX6 Ind VAX2 Awh eve al Uncx 3 VSX1 VSX2 LHX2 1
MEOX2 1LBX2 MEOX1
Dll DUXAALX4
Alx4 1Alx1 1
PROP1
PROP1
PHOX2B
PHOX2B
ALX3 1
PHOX2A
ARX Arx 1UNCXUncx 2
ISX DRGXCART1
PRRX1 1
HMX3
BapHM
X2HM
X1tup CG
34031
Hmx
Barhl1 1BARHL2 1
BARHL2 1
EN2G
BX2BARX1 1BSXB H1B H2CG
11085DLX2M
SX2 1M
SX1M
SX1 1M
sx3 1EN
2G
BX1LH
X9ISX 1D
LX3D
LX4C
G15696
NK7 1PRRX2Dlx2 1Dlx1 1DLX6PRRX1RAXL1SHOX2Vsx1 1LM
X1BDLX5ISXSHOXShox2 1EN1PRRX1UNCX 1
RAXLBX2 1
EN1GBX2
Gbx2 2HESX1
PHDPGbx1 1
BARHL2 2
Barhl1 2BARHL2 2
PDX1LHX6 1
Lhx8
LHX6 2
Lhx8 2
Msx3MSX2
BARX1
MSX1
HESX1 1
LHX9 1
HMBOX1
Lag1EMX1 1
EMX2 1
GBX2 1
EN1 1EN1 1tinvndNKX2 3NKX2 3NKX2 8NKX2 8Nkx3 1NKX3 1ISL2NKX3 2Irx3IRX2IRX5exdvisachihthRhox11araCG11617caupmirr
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C02F5.5
mi r -46C33D9.9
C01B10.4
mi r -52
mi r -53
C17A2.4
mi r -228
F01D5.1
srd-16
mb f - 1
mi r -74
mi r -229Y37D8A.5
lsy-2
mi r -75
C50F4.9
mi r -73
hpd -1
F32A5.4
C08E8.3
K10C2.3
Y69E1A.5
mi r -76
htas-1
Y59E9AL.3
dod-24
R10H10.3
sss-1
mi r -240
K09H11.7
pos-1
mi r -43
F55G11.7T01D3.6
cdh-5
T05E12.6
mi r -788
F57G8.7
C33F10.1
F01D5.3
K03H1.12
scl-27
m i r - 2
mi r -242
bre-1
mi r -63nhr -86
hpo-28
Y106G6A.4
F35H8.4
msp-51
clec-66
mi r -72
F44A2.5
ZK1248.17
msp-76
mir-239.1
mi r -87
B0507.10
T11B7.5
pho-1
clec-52
f l i - 1
T05C3.6
nspd-10
Y54G11A.14F21C10.11
Y49G5A.1
F36D1.4
K10D3.6
C27F2.7
nspd-1
ceh-45
meg-2
col-172
z ip -2
tbc -7
mi r -230
wago-9col -19
m i r - 1clec-4
g rd -5
gst -11
dyc-1
nhr -20
T22B7.7
F35E12.5
mi r -243
mi r -44
m ig -5
mi r -80
nhr -42
h lh-30
mi r -40
C24B9.3
i lys-2
mi r -58Y44A6D.1
Y75B8A.23
gst -27
cyp-14A5
col-20
C53A5.2
mi r -34far -3
msp-38
Y67A6A.1
W10C8.5
nhr -10
a t f -6
W01B6.4
ces-2mi r -237
l i n -4
nh r -1
daf -12
grd-10
C12D5.4
F09F7.4
mi r -84
sre-13lnp -1
msp-56
mi r -261
pho-12 T01B11.2
C36C9.1
mi r -42
msp-142le t -7
mi r -795
mi r -37
ug t -6
F11G11.4
ssq-2msp-63
C27D6.3
mi r -51
clec-76
msp-50
fu t - 1
mi r -39
Y40C5A.1
mi r -355
pd i -2
mi r -38
daf -3
mi r -41
l in -13mi r -241
mi r -35
mi r -36
scd-1
C32H11.4
K12H4.7
Bioconductor Packages By MCCB
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• University of Massachusetts Medical School– Usha Acharya & Niraj Nirala (dagLogo)
– Neil Aronin (CRISPRseek)
– Michael Brodsky (CRISPRseek & MotifStack)
– Tom Fazio and Benson Chen (REDseq)
– Claude Gazin & Chris Hull (ChIPpeakAnno)
– Michael Green (ChIPpeakAnno & InPAS)
– Alper Kucukural & Manuel Garber (GUIDEseq)
– Nathan Lawson (ChIPpeakAnno, ATACseqQC & cleanUpdTSeq)
– Jianhong Ou (ChIPpeakAnno, dagLogo, NADfinder, ATACseqQC, GeneNetworkBuilder, MotifStack, TrackViewer, InPAS)
– Sungmi Park ( InPAS) Lucio Castilla (ATACseqQC)
– Sarah Sheppard (cleanUpdTSeq) Paul Kaufman (NADfinder)
– Heidi Tissenbaum (GeneNetworkBuilder)
– Yongxu Wang (TrackViewer) Michelle Kelliher (ATACseqQC)
– Scot Wolfe (GUIDEseq and motifStack)
– Jun Yu (ChIPpeakAnno, NADfinder, ATACseqQC)
• Broad Institute of MIT and Harvard
• Feng Zhang (CRISPRseek)
– Benjamin Holmes
• Genentech
- Michael Lawrence(GUIDEseq)
• The Bioconductor core members
– Hervé Pagès (ChIPpeakAnno, CRISPRseek & GUIDEseq)
– Martin Morgan (CRISPRseek)
– Valerie Obenchain
– Dan Tenenbaum
• The Bioconductor community
• Ryan Thompson (ChIPpeakAnno)
• Nationwide Children's Hospital
• Simon Lin (ChIPpeakAnno)
• Tufts University
• David Lapointe (ChIPpeakAnno)
Acknowledgement