April 2008
Lihua Julie Zhu and Jianhong Ou
ATACseqQC for quality assessment of ATACseq datasetNADfinder for identifying Nucleoli Associated Domain (NAD)
July 26th 2017
Adapted from Nature Methods10, 1213–1218, 2013By Buenrostro and Greenleaf et al.
Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq)
• 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.
Expected patterns of nucleosome occupancy and depletion at the TSS
Density Plot Flanking TSS
- Nucleosome free-- Nucleosome bound
Generate footprints for DNA-binding proteins
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
NADfinderWorkflow
• 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
• 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
