title: ChIP-seq from A549 (ENCLB779YWU)

description:
https://www.encodeproject.org/experiments/ENCSR242TBH/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR242TBH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB779YWU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS774FRJ at ENCODE; https://www.encodeproject.org/ENCBS774FRJ/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: MeJA_1h_rep2

status: Public on Jan 10 2017

type: SRA

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

library_source: transcriptomic

data_processing:
Illumina Casava version 1.8 was used for basecalling
Quality assessment of the sequencing reads was performed using the FASTX-Toolkit version 0.0.13.2
cutadapt version 1.3 was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Arabidopsis thaliana TAIR10 genome using Tophat version 2.1.1 with parameters set to allow only one mismatch (-N 1)
The Python package HTSeq version 0.6.1p1 was used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Short day (9h of light at 21°C - 15h of dark at 18°C)

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings using the Qiagen Rneasy Minikit
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.

treatment_protocol: Two-week-old seedlings were sprayed with 50 μM MeJA (Sigma), 300 μM BTH (Actigard 50WG) or a mock solution (0.02% Silwet, 0.1% ethanol). Samples were harvested 1h, 5h and 8h after spraying. This experiment was repeated twice.

tag: ecotype

tag: age

value: 14 days

tag: treatment

value: MeJA

tag: time


title: BTH_8h_rep2

value: BTH


title: ChIP-seq from A549 (ENCLB689PUU)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR242TBH/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR242TBH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR548SPY
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB689PUU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 1 hour

tag: antibody

tag: line

value: immortalized cell line

tag: biosample encode accession

tag: dev stage

value: adult

value: 58 year

tag: Sex

value: male

tag: lab

value: Tim Reddy, Duke

tag: treatments

tag: link

value: ENCBS598CCT at ENCODE; https://www.encodeproject.org/ENCBS598CCT/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: coi1-16_DC3000cor-_rep3

treatment_protocol: Arabidopsis thaliana seedlings were grown under short day conditions (9h of light at 21°C - 15h of dark at 18°C) for two weeks. Plants were sprayed with the Pseudomonas syringae strain DC3000 cor- (OD600=0.2; 10mM MgCl2 and 0.04% Silwet L-77) and harvested after 24h for RNA extraction. A mock treatment  (10mM MgCl2 and 0.04% Silwet L-77) was also included. Lines Col-0 (3 replicates), UBQ10::YFP-TCP14-4 (3 replicates), tcp14-6 (3 replicates) and coi1-16 (3 replicates) were used in the experiment.

tag: genotype

value: DC3000 cor-


title: polyA mRNA RNA-seq from A549 (ENCLB565JKN)

description:
https://www.encodeproject.org/experiments/ENCSR224PTG/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR224PTG
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB565JKN
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 10 hours

extract_protocol:
general protocol: https://www.encodeproject.org/documents/5533fb32-41f1-4c7a-b62d-0095a33cab20/@@download/attachment/01_RNA_HARVEST_and_ISOLATION_Reddy_GGR.pdf
extraction protocol: https://www.encodeproject.org/documents/53726435-7acc-4248-a5df-3eef6ea3b422/@@download/attachment/02_Rev%20D%20Quick%20Reference%20Card%2C%20PrepX%20PolyA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/5f9d4f74-4e39-4818-9ee9-d8e9b8004ceb/@@download/attachment/03_RevC%20Quick%20Reference%20Card%2C%20PrepX%20mRNA%2048%20Protocol.pdf
extraction protocol: https://www.encodeproject.org/documents/c72e898e-82c7-478d-b043-8945133a7724/@@download/attachment/04_Rev%20C%20Quick%20Reference%20Card%2C%20PrepX%20PCR%20Cleanup%2048%20Protocol.pdf
general protocol: https://www.encodeproject.org/documents/7a683e77-85ac-45f9-b1fa-b6ceb50ca1bc/@@download/attachment/05_POST_RNA_LIB_PREP_Reddy_GGR.pdf
extraction method: RNeasy Plus Mini Kit Qiagen cat#74134 plus additional on column Dnase treatment

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS721HGM at ENCODE; https://www.encodeproject.org/ENCBS721HGM/


title: Col-0_DC3000cor-_rep3


title: tcp14-6_DC3000cor-_rep3


title: MeJA_1h_rep1


title: polyA mRNA RNA-seq from A549 (ENCLB101JNT)

description:
https://www.encodeproject.org/experiments/ENCSR224PTG/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR224PTG
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB101JNT
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS146CRN at ENCODE; https://www.encodeproject.org/ENCBS146CRN/


title: polyA mRNA RNA-seq from A549 (ENCLB451LSM)

description:
https://www.encodeproject.org/experiments/ENCSR224PTG/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR224PTG
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB451LSM
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS405EQX at ENCODE; https://www.encodeproject.org/ENCBS405EQX/


title: coi1-16_mock_rep3


title: ChIP-seq from A549 (ENCLB844GRC)

description:
https://www.encodeproject.org/experiments/ENCSR203XPU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR203XPU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR838ZAU
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB844GRC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line

value: ENCBS266ZMP at ENCODE; https://www.encodeproject.org/ENCBS266ZMP/


title: UBQ10::YFP-TCP14-3_mock_rep3


title: ChIP-seq from A549 (ENCLB047UWH)

description:
https://www.encodeproject.org/experiments/ENCSR180YHA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR180YHA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB047UWH
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS157YZR at ENCODE; https://www.encodeproject.org/ENCBS157YZR/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: MeJA_5h_rep2

value: 14 days

value: MeJA


title: tcp14-6_mock_rep3


title: UBQ10::YFP-TCP14-3_DC3000cor-_rep3


title: Col-0_mock_rep3


title: ChIP-seq from A549 (ENCLB353MPN)

description:
https://www.encodeproject.org/experiments/ENCSR180YHA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR180YHA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB353MPN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS851NMG at ENCODE; https://www.encodeproject.org/ENCBS851NMG/


title: UBQ10::YFP-TCP14-3_DC3000cor-_rep2


title: ChIP-seq from A549 (ENCLB532IEW)

description:
https://www.encodeproject.org/experiments/ENCSR171ZJG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR171ZJG
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR325PXS
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB532IEW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 3 hours

value: adult

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:3; duration_units:hour;

value: ENCBS640AFN at ENCODE; https://www.encodeproject.org/ENCBS640AFN/


title: coi1-16_DC3000cor-_rep2


title: ChIP-seq from A549 (ENCLB368XMA)

description:
https://www.encodeproject.org/experiments/ENCSR215DID/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR215DID
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR491TAD
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB368XMA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 30 minutes

value: male

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS553BBK at ENCODE; https://www.encodeproject.org/ENCBS553BBK/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: polyA mRNA RNA-seq from A549 (ENCLB071IVZ)

description:
https://www.encodeproject.org/experiments/ENCSR154TDP/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR154TDP
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB071IVZ
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 12 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS646TBQ at ENCODE; https://www.encodeproject.org/ENCBS646TBQ/


title: polyA mRNA RNA-seq from A549 (ENCLB752MHE)

description:
https://www.encodeproject.org/experiments/ENCSR154TDP/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR154TDP
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB752MHE
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS091SYA at ENCODE; https://www.encodeproject.org/ENCBS091SYA/


title: ChIP-seq from A549 (ENCLB183DEW)

description:
https://www.encodeproject.org/experiments/ENCSR225AOO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR225AOO
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR627RBH
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB183DEW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 5 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:hour;

value: ENCBS915DYB at ENCODE; https://www.encodeproject.org/ENCBS915DYB/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: polyA mRNA RNA-seq from A549 (ENCLB720ABS)

description:
https://www.encodeproject.org/experiments/ENCSR154TDP/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR154TDP
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB720ABS
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: immortalized cell line

value: ENCBS736RMD at ENCODE; https://www.encodeproject.org/ENCBS736RMD/


title: UBQ10::YFP-TCP14-3_mock_rep2

value: 14 days


title: coi1-16_mock_rep2


title: ChIP-seq from A549 (ENCLB431LIL)

description:
https://www.encodeproject.org/experiments/ENCSR139DGM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR139DGM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB431LIL
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: 58 year

value: ENCBS142GEF at ENCODE; https://www.encodeproject.org/ENCBS142GEF/


title: Col-0_mock_rep2


title: UBQ10::YFP-TCP14-3_DC3000cor-_rep1

value: DC3000 cor-


title: coi1-16_DC3000cor-_rep1


title: DNase-seq from A549 (ENCLB640BMZ)

description:
https://www.encodeproject.org/experiments/ENCSR136DNA/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR136DNA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB640BMZ

value: Control

value: male

value: Tim Reddy, Duke

value: ENCBS976TIO at ENCODE; https://www.encodeproject.org/ENCBS976TIO/


title: tcp14-6_mock_rep2


title: DNase-seq from A549 (ENCLB314IRK)

description:
https://www.encodeproject.org/experiments/ENCSR136DNA/
***************
biological replicate number: 3
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR136DNA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB314IRK
nucleic acid starting quantity: 85
nucleic acid starting quantity units: ng

value: ENCBS797SEZ at ENCODE; https://www.encodeproject.org/ENCBS797SEZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: DNase-seq from A549 (ENCLB674BXT)

description:
https://www.encodeproject.org/experiments/ENCSR128IVG/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR128IVG
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB674BXT
nucleic acid starting quantity: 32
nucleic acid starting quantity units: ng

value: ENCBS993AJE at ENCODE; https://www.encodeproject.org/ENCBS993AJE/


title: ChIP-seq from A549 (ENCLB501GWO)

description:
https://www.encodeproject.org/experiments/ENCSR180YHA/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR180YHA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB501GWO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS962DEK at ENCODE; https://www.encodeproject.org/ENCBS962DEK/


title: Col-0_DC3000cor-_rep1


title: DNase-seq from A549 (ENCLB874QCQ)

description:
https://www.encodeproject.org/experiments/ENCSR128IVG/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR128IVG
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB874QCQ

value: ENCBS570WAL at ENCODE; https://www.encodeproject.org/ENCBS570WAL/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: tcp14-6_DC3000cor-_rep1


title: coi1-16_mock_rep1


title: DNase-seq from A549 (ENCLB401EKI)

description:
https://www.encodeproject.org/experiments/ENCSR128IVG/
***************
biological replicate number: 3
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR128IVG
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB401EKI
nucleic acid starting quantity: 66
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS146CRN at ENCODE; https://www.encodeproject.org/ENCBS146CRN/


title: ChIP-seq from A549 (ENCLB498JMN)

description:
https://www.encodeproject.org/experiments/ENCSR139DGM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR139DGM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB498JMN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: ENCBS462SQL at ENCODE; https://www.encodeproject.org/ENCBS462SQL/


title: tcp14-6_DC3000cor-_rep2

value: 14 days


title: Col-0_DC3000cor-_rep2


title: ChIP-seq from A549 (ENCLB234PNI)

description:
https://www.encodeproject.org/experiments/ENCSR124YCC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR124YCC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR344ERJ
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB234PNI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 2 hours

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS508LJT at ENCODE; https://www.encodeproject.org/ENCBS508LJT/


title: Col-0_mock_rep1


title: tcp14-6_mock_rep1


title: ChIP-seq from A549 (ENCLB159YNE)

description:
https://www.encodeproject.org/experiments/ENCSR109KEL/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR109KEL
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR491TAD
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB159YNE
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS594NFK at ENCODE; https://www.encodeproject.org/ENCBS594NFK/


title: ChIP-seq from A549 (ENCLB538RWK)

description:
https://www.encodeproject.org/experiments/ENCSR102XUM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR102XUM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR491TAD
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB538RWK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS657XCY at ENCODE; https://www.encodeproject.org/ENCBS657XCY/


title: ChIP-seq from A549 (ENCLB566YYG)

description:
https://www.encodeproject.org/experiments/ENCSR109KEL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR109KEL
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR491TAD
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB566YYG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS087LLT at ENCODE; https://www.encodeproject.org/ENCBS087LLT/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB590VHF)

description:
https://www.encodeproject.org/experiments/ENCSR102XUM/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR102XUM
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR491TAD
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB590VHF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS790LFN at ENCODE; https://www.encodeproject.org/ENCBS790LFN/


title: DNase-seq from A549 (ENCLB867MDM)

description:
https://www.encodeproject.org/experiments/ENCSR077EYC/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR077EYC
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB867MDM
nucleic acid starting quantity: 56
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 6 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS330OQB at ENCODE; https://www.encodeproject.org/ENCBS330OQB/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: DNase-seq from A549 (ENCLB394VFL)

description:
https://www.encodeproject.org/experiments/ENCSR077EYC/
***************
biological replicate number: 3
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR077EYC
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB394VFL
nucleic acid starting quantity: 108
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: ENCBS004RKE at ENCODE; https://www.encodeproject.org/ENCBS004RKE/


title: DC3000 cor- EV_rep3

treatment_protocol: Arabidopsis thaliana seedlings (Col-0 ecotype) were grown under short day conditions (9h of light at 21°C - 15h of dark at 18°C) for two weeks. Plants were sprayed with a mock solution (10 mM MgCl2) or bacteria [Pto DC3000 (EV), Pto DC3000 cor- (EV); Pto DC3000 cor- (HopBB1); Pto DC3000 cor- (HopBB1G126D)] at OD600=0.2 with 10mM MgCl2 and 0.04% Silwet L-77. Samples were harvested 24 hours after infection. This experiment included three biological replicates.

value: DC3000 cor- EV

value: 14 days


title: DC3000 BB1_rep3


title: DNase-seq from A549 (ENCLB338FOG)

description:
https://www.encodeproject.org/experiments/ENCSR077EYC/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR077EYC
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR136DNA
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB338FOG

value: 58 year

value: ENCBS183GJP at ENCODE; https://www.encodeproject.org/ENCBS183GJP/


title: DC3000_rep3


title: DC3000 mBB1_rep2

value: DC3000 mBB1


title: MgCl2_rep3


title: polyA mRNA RNA-seq from A549 (ENCLB891DFN)

description:
https://www.encodeproject.org/experiments/ENCSR070IYV/
***************
biological replicate number: 1
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR070IYV
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB891DFN
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS643KEB at ENCODE; https://www.encodeproject.org/ENCBS643KEB/


title: DC3000 BB1_rep2


title: DC3000 mBB1_rep3


title: polyA mRNA RNA-seq from A549 (ENCLB969EVJ)

description:
https://www.encodeproject.org/experiments/ENCSR070IYV/
***************
biological replicate number: 2
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR070IYV
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB969EVJ
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: Tim Reddy, Duke

value: ENCBS570ODA at ENCODE; https://www.encodeproject.org/ENCBS570ODA/


title: UBQ10::YFP-TCP14-3_mock_rep1


title: polyA mRNA RNA-seq from A549 (ENCLB293NNT)

description:
https://www.encodeproject.org/experiments/ENCSR070IYV/
***************
biological replicate number: 3
technical replicate number: 1
description: mRNA-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR070IYV
assay title: polyA mRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR632DQP
encode release date: 2016-05-05
lab: Tim Reddy, Duke
library encode accession: ENCLB293NNT
size range: >200
spikeins used: /references/ENCSR866KGS/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: ENCBS241DOQ at ENCODE; https://www.encodeproject.org/ENCBS241DOQ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: DC3000 cor- EV_rep2


title: DC3000_rep2


title: MgCl2_rep2


title: DC3000 mBB1_rep1


title: ChIP-seq from A549 (ENCLB452LBO)

description:
https://www.encodeproject.org/experiments/ENCSR037DAC/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR037DAC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB452LBO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 4 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS181LVW at ENCODE; https://www.encodeproject.org/ENCBS181LVW/


title: ChIP-seq from A549 (ENCLB375RCT)

description:
https://www.encodeproject.org/experiments/ENCSR032SCO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR032SCO
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR887SZF
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB375RCT
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS792THF at ENCODE; https://www.encodeproject.org/ENCBS792THF/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB624YOD)

description:
https://www.encodeproject.org/experiments/ENCSR037DAC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR037DAC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR872BBM
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB624YOD
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: ENCBS015HRP at ENCODE; https://www.encodeproject.org/ENCBS015HRP/


title: DC3000_rep1

value: 14 days


title: ChIP-seq from A549 (ENCLB898RLD)

description:
https://www.encodeproject.org/experiments/ENCSR016PSC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR016PSC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR317VER
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB898RLD
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line treated with 100 nM dexamethasone for 7 hours

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS979STP at ENCODE; https://www.encodeproject.org/ENCBS979STP/


title: ChIP-seq from A549 (ENCLB154QAU)

description:
https://www.encodeproject.org/experiments/ENCSR013RTF/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR013RTF
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB154QAU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS844JPS at ENCODE; https://www.encodeproject.org/ENCBS844JPS/


title: MgCl2_rep1


title: DC3000 cor- EV_rep1

value: DC3000 cor- EV


title: ChIP-seq from A549 (ENCLB534SDI)

description:
https://www.encodeproject.org/experiments/ENCSR013RTF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR013RTF
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB534SDI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS933PFW at ENCODE; https://www.encodeproject.org/ENCBS933PFW/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: DC3000 BB1_rep1


title: ChIP-seq from A549 (ENCLB078RTZ)

description:
https://www.encodeproject.org/experiments/ENCSR013RTF/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR013RTF
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR310TYO
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB078RTZ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: immortalized cell line

value: ENCBS734NQI at ENCODE; https://www.encodeproject.org/ENCBS734NQI/


title: Type 1 skeletal muscle fibers

city: Muncie

first: Scott

last: Trappe

state: IN

address: 2000 W University Ave

institute: Ball State University

data_processing:
Sequence reads from bisulfite treated libraries were identified using standard Illumina base-calling software.
Residual Cs in each read were converted to Ts. A reference sequence database was constructed from the 50 bp ends of each computationally predicted MspI-TaqI fragment in the 40–350 bp size range.
Following Cs to Ts conversion, adapter trimming using Trim Galore was performed prior to the alignment.
Bismark software (v0.11.1) was used for the read alignment and the best alignment for each was kept.
Minimum sequencing read coverage of 5 (5x) was used as the cutoff for inclusion in the DNA methylation analysis.
hg19
Supplementary_files_format_and_content: [.csv] file includes the annotated differentially CpG-sites (5x coverage, p<0.05) between the Type 1 and Type 2a samples.

source_name: vastus lateralis muscle, type 1 fibers

extract_protocol:
DNA extraction was carried out using the QIAamp® DNA micro kit (Qiagen).
Libraries were prepared from 32 ng of genomic DNA digested with 40 units of BfaI, 40 units of MseI, and 80 units of MspI and the fragments produced were ligated to pre-annealed adapters containing 5’-methylcytosine instead of cytosine. Adapter-ligated fragments were filled in and 3’ terminal-A extended, and then purified using the Zymo Research DNA Clean & Concentrator™– 5 kit (D4003). Size-selected DNA fragments of 40-350 bp were bisulfite treated using the EZ DNA Methylation– Lightning kit (Zymo Research, D5030). PCR was performed and the size and concentration of the fragments were confirmed on the Agilent 2200 TapeStation.

treatment_protocol: After the muscle biopsy, each muscle sample was immediately divided into longitudinal bundles, placed in 0.5 ml RNAlater solution (Ambion), stored at 4°C overnight, and subsequently stored at -20 °C until muscle fiber isolation and subsequent DNA extraction.

tag: tissue

value: pool of isolated muscle fibers

tag: cell type

value: slow-twitch (MHC I)

tag: subject

value: Young Active Healthy Males


title: Type 2a skeletal muscle fibers

source_name: vastus lateralis muscle, type 2a fibers

value: fast-twitch (MHC IIa)


title: RIP_2

city: Edinburgh

first: Roseanne

last: Rosario

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

data_processing:
Reads were mapped to human genome hg19 using gsnap version 2013-11-27 and only reads that mapped uniquely were considered for transcript counting purpose.
Counts on individual samples were performed using version HTSeq 0.6.0 and the mode of counting was "union"
Raw counts were normalized based on the total number of reads mapped uniquely.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized reads based on the total number of reads mapped uniquely.

source_name: fetal ovary_DAZL RIP

extract_protocol:
DAZL-bound RNA's were purified using the RNeasy Micro Kit (Qiagen, Crawley, UK)
Ovation® RNA-Seq system V2 was used to amplify RNA prior to sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols
Paired-end RNA seq Illumuni Hi-Seq

value: 17weeks gestational age (wga)

value: fetal ovarian tissue

value: DAZL antibody #8042 CST


title: RIP_1


title: RIP_3


title: control_1

source_name: fetal ovary_control IgG

value: control rabbit IgG


title: control_3


title: ChIP-seq from A549 (ENCLB606QTY)

description:
https://www.encodeproject.org/experiments/ENCSR032SCO/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K9me3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR032SCO
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR887SZF
encode release date: 2016-07-21
lab: Tim Reddy, Duke
library encode accession: ENCLB606QTY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS431FWG at ENCODE; https://www.encodeproject.org/ENCBS431FWG/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: Pt control 1

city: Tianjin

first: Si

last: Li

address: Guangrong Dao 8

country: China

institute: Hebei University of Technology

data_processing:
We use BWA to map clean reads to genome reference and use Bowtie to gene reference.
Bowtie 2 version 2.2.5 ：parameter：-q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200
BWA (alignment via Burrows-Wheeler transformation) Version: 0.7.10-r789 ：parameter： -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
Genes and isoforms expression level are quantified by a software package: RSEM v1.2.12  rsem-calculate-expression --paired-end –bam Phaeodactylum-tricornutum-control-1.bam -p 8  rsem-reference/refMrna.fa  outdir/ Phaeodactylum-tricornutum-control-1
transcript are blasted to the  Gene IDs are screened on KEGG, gene ontology, and GenBank to find the Kegg orthology,GO terms,and blast nr the software is blastall,version 2.2.23,the parameters are blastall -d  KEGG/59.3/plant.fa  -i GCF_000150955.2_ASM15095v2_rna.fna -o GCF_000150955.2_ASM15095v2_rna.fna.ko -blast blastx -e 1e-05 -m 8
Genome_build: Genome reference : GCF_000150955.2_ASM15095v2_genomic.fna Gene reference:GCF_000150955.2_ASM15095v2_rna.fna
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, Kegg orthology,GO terms,and blast nr for each Sample

organism: Phaeodactylum tricornutum CCAP 1055/1

source_name: diatom cells

growth_protocol: The culture medium was prepared with sterile-filtered natural seawater from the North Sea (Minisart High-Flow 0.1μm syringe filter; Sartorius Stedim Biotech GmbH, Goettingen, Germany), and enrichment nutrient solutions (macronutrients and micronutrients) based on a modified Provasoli medium. P. tricornutum cells were grown at 18°C in a temperature-controlled room. The light intensity was constant at 100 μmol photons·m-2·s-1 at a light:dark cycle of 12:12 h with 2 hours sunrise and 2 hours sunset phase simulations via irradiance profiles as typical at this latitude.

extract_protocol:
The total RNA was extracted with RNeasy® Plant Mini Kit (QIAGEN, Hilden, Germany).5µg total RNA was treated with Ribo-Zero™Magnetic Kit (Plant Leaf)) （Epicentre）to depleterRNA.
The retrieved RNA is fragmented by adding First Strand Master Mix（Invitrogen）. First-strand cDNA is generated by First Strand Master Mix and Super Script II reverse transcription (Invitrogen) (Reaction condition：25℃for 10 min；42℃for 50 min；70℃for 15 min).Purify the product(Agencourt RNAClean XP Beads，AGENCOURT), then add Second Strand Master Mix and dATP,dGTP, dCTP, dUTP mix to synthesize the second-strand cDNA (16℃for 1h).Then the purified cDNA combine with End Repair Mix, incubate at 30℃for 30min. After purification with beads, add A-Tailing Mix , incubate at 37℃for 30 min. Combine the Adenylate 3'Ends DNA, Index Adapter and Ligation Mix, incubate at 30℃for 10 min. After that, add the Uracil-N-Glycosylase enzyme into the purified ligation product, incubate at 37℃for 10min. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the cDNA fragments. Then thePCR products are purified with Ampure XP Beads.The final library is quantitated in two ways:determine the average molecule length using the Agilent 2100 bioanalyzer instrument (Agilent DNA 1000 Reagents), and quantify the library by real-time quantitative PCR (QPCR) (TaqMan Probe).The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3–cBot–HS，Illumina). And the amplified flowcell will be sequenced pairend on the HiSeq 2000 System (TruSeq SBS KIT-HS V3，Illumina), read length 90 are the most common sequencing strategy.

treatment_protocol: To generate grazing effect, over 2000 individuals of Acartia tonsa in 25 L  seawater were fed with 1×107 P. tricornutum cells per day. Acartia was cultured in two nesting buckets of with the bottom of the inner one replaced by a sieve with mesh size of 300 μm. Seawater was changed every day in the outer bucket with the feces and eggs of Acartia removed. The culture medium of Acartia was filtered with a 0.1 μm syringe filter to P. tricornutum grazing treatment groups, while the same amount of sterile-filtered seawater (for culturing Acartia) with the same ratio of the pure medium (for culturing P. tricornutum) was added to the control groups.

tag: strain

value: diatom cells


title: Pt grazing 1


title: Pt control 2


title: Pt control 3


title: MVV___in_vitro_control

city: London

first: Peter

middle: P

last: Cherepanov

address: 1 Midland Road

institute: The Francis Crick Institute

description: Genomic DNA was fragmented by sonication, end-repaired, and A-tailed as described in Serrao et al., J. Vis. Exp. 2016 (109). Resulting DNA was ligated to an asymmetric linker made by annealing synthetic oligonucleotides 5'-GTC CCT TAA GCG GAG-3' (with 3´ end blocked by an amino group modifier) and 5'-GTA ATA CGA CTC ACT ATA GGG CCT CCG CTT AAG GGA CT-3'. MVV U5-chromsomal DNA junctions were recovered using linker-mediated PCR and sequenced on an Illumina platform as previously described. The first round and the nested MVV U5 primers were 5'-CTA ATT CCG TGC AAC ACC G-3' and 5'-AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TNN NNN NCA ACA CCG GAG CGG ATC-3', respectively (the stretch of random nucleotides represents the Illumina index, not relevant to this study). Linker-specific primer used in both PCR steps was 5´- CAA GCA GAA GAC GGC ATA CGA GAT CGG TCT CGG CAT TCC TGC TGA ACC GCT CTT CCG ATC TGT AAT ACG ACT CAC TAT AGG GC-3'.

data_processing:
Paired-end reads were cropped to remove linker and virus LTR sequences. Cropped paired reads were aligned to sheep genome oviAri3 using BWA MEM. High-quality alignemnts were selected with samtools view -F 4 -F 256 -q 1. The remaining alignements were parsed to select unique integration sites and extract coordinates of the central base pair step for each site.
Genome_build: oviAri (https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.1/)
Supplementary_files_format_and_content: processed data files are in standard bed format with the following 6 columns of data:
chromosome (chr1, chr2, etc)
interval start
interval end
sequence read ID
confidence value (100)
chromosome strand (+ or -)

organism: Ovis aries

source_name: deproteinized sheep genomic DNA reacted with recombinant MVV intasome

extract_protocol: DNA was extracted from infected cells 40 h post-infection prior to the onset of the cytopathic effect using a Gentra Puregene kit (Qiagen).

treatment_protocol:
MVV intasomes were assembled using MVV IN and DNA fragments mimicking processed U5 MVV vDNA ends, obtained by annealing  5’-CTAATTCCGTGCAACACCGGAGCGGATCTCGCA and 5’-GCTGCGAGATCCGCTCCGGTGTTGCACGGAATTAG.
The intasomes were purified by size exclusion chromatography and allowed to react with deproteinized sheep genomic DNA. Reaction products were repaired with Phi29 DNA polymerase and processed for linker-mediated PCR as for the infection sample.

tag: sample type


title: Pt grazing 2


title: HB-3_2_sRNA

status: Public on Jan 09 2017

city: Wu Han

first: Yan-ni

last: Fang

address: shizi mountain street

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, abandon seqences small than 18 nt, and masked for low-complexity or low-quality sequence, then mapped to ref2 database using soap -v 0 -r 2 -s 7 -p 7 -a clean.fa -d ref_genome.fa -o match_genome.soap
Supplementary_files_format_and_content: .txt file reports data cleaned by trimming adaptors and removing low-quality reads and other contaminants

organism: Citrus maxima

source_name: HB flowers

growth_protocol: grown under field conditions

extract_protocol:
Total RNA was isolated from all of the samples using modified trizol method according to Liu et al.,Journal of Huazhong Agricultural University,2006
Small RNA sequencing was carried out using Illumina sequencing technology by the Beijing Genomics institute (BGI). Firstly, RNAs of 18-30 nt long were isolated by size fraction with 15% Tris-borate-EDTA urea polyacrylamide gel. Subsequently, they were ligated to 5' and 3' RNA adaptors (Illumina) by T4 RNA ligase. After that, the adapter-ligated RNA molecules were reverse-transcribed into cDNA by Super Script III using a primer specific to the 3’ adapter, followed by PCR amplification with two primers that annealed to the ends of the adapters. These PCR products constituted the sequencing library.

value: HBP

value: floral tissue

tag: developmental stage

value: from the development of young microspores to the release of mature pollens


title: HB-1_2_sRNA

value: from floral bud differentiation to pollen mother stage


title: GH-1_1_sRNA

source_name: GH flowers


title: HB-2_1_sRNA

value: from the formation of tetrads to the release of microspores


title: GH-2_1_sRNA


title: HB-3_1_sRNA


title: HB-2_2_sRNA


title: GH-1_2_sRNA


title: Pummelo_degra

description: Library strategy: Degradome sequencing

value: mixed sample of three stages


title: GH-2_2_sRNA


title: GH-3_2_sRNA


title: control_2

tag: age

value: 17weeks gestational age (wga)


title: epi28

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

description: met1-3 derived epiRILs 28 F8

data_processing:
For image analysis and base calling, we used the Illumina OLB software version 1.8
The raw reads were trimmed using Trimmomatic (Bolger et al, 2014 Bioinformatics) in order to remove adapter sequences. Reads with an average quality value of at least 15 in a window of 4 nucleotides were trimmed from both ends. After trimming, reads shorter than 16 bases were discarded.
The remaining sequences were aligned against the Arabidopsis thaliana genome TAIR10 version using Bismark (Krueger et al. 2011, Bioinformatics). Duplicated reads were collapsed into one read.
Chloroplast sequences were used to estimate the bisulfite conversion. To account for non-converted DNA, we applied a correction according to (Lister et al. 2013 Science). Briefly, the number of methylated reads were decreased as: m*= max(0, m – nc) (where m* is the corrected number of methylated reads, m is the raw number of methylated reads, n is the total number of reads and c is the conversion rate).
Genome_build: TAIR10
Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is reported (Krueger et al. 2011, Bioinformatics), after correction for non-converted DNA has been applied.

source_name: whole seedling

growth_protocol: Plants were grown in plates under long-day conditions (21°C, 16 h light, 8 h dark)

extract_protocol:
Genomic DNA was extracted using the Qiagen Plant DNeasy kit (Qiagen), starting from purified nuclei.
Libraries were constructed starting from 0.5 - 1 μg of genomic DNA, using the NEBNext DNA Sample PrepReagentSet1 (New England Biolabs), following the Illumina Genomic Sample Prep Guide (Illumina).

tag: ecotype

value: seedling

value: 2 weeks

tag: genotype/variation

value: met1-3 derived epiRILs 28 F8


title: epi01

description: met1-3 derived epiRILs 01 F8

value: met1-3 derived epiRILs 01 F8


title: RS_GMI1000_methylome

city: Castanet-Tolosan

first: Ludovic

last: Legrand

address: 24 Chemin de Borde Rouge

country: France

institute: INRA/CNRS

data_processing:
Modifications and motifs detection was performed using RS_Modification_and_Motif_analysis protocol from SMRT Analysis 2.3 (min read quality = 80 ;  min modification QV = 30 )
Genome_build: GCA_000009125.1
Supplementary_files_format_and_content: RS-GMI1000_modifications.csv.gz file contains statistical analysis of each position in the reference. RS-GMI1000_motifs.gff.gz contains information about all sites detected as modified. RS-GMI1000_motif_summary.csv.gz contains the genome-wide summary of the methyltransferase recognition motifs discovered in this sample.

organism: Ralstonia solanacearum

growth_protocol: Bacteria were grown overnight in 50 ml MP minimal medium (FeSO4, 7H2O,1.25x10-4g/l; (NH4)2SO4, 0.5g/l; MgSO4, 7H2O, 0.05g/l; KH2PO4, 3.4g/l) supplemented with glucose 20 mM and a pH adjusted to 6.5 with KOH.

extract_protocol:
The protocol used to extract DNA from the GMI1000 strain was derived from the protocol described in (Mayjonade et al., 2016). When the culture reached an OD600nm of 0.5 (exponential phase), bacteria were centrifuged 10 min at 7000 rpm, the pellet was washed with 50 ml sterile water and centrifuged again to resuspend the pellet in 600 µl of lysis buffer (NaCl 2.5M, TrisHCl pH8 1M, EDTA pH8 0.5M, SDS 20%, Sodium Metabisulfite 0.1%) preheated at 72°C. A total of 6µl RNAse (100mg/ml) was added before incubation 30 min at 55°C with gentle agitation every 10 min. Then 200 µl potassium acetate 5M was added, mixed and the suspension was centrifuged 10 min 13000 rpm at 4°C. A total of 500 µl of supernatant was transferred in a new tube and 500 µl binding buffer (PEG8000 200mg/ml, NaCl 200mg/ml) was added. Then 30 µl of carboxylated magnetic beads (Thermo Fisher Scientific, RRID:SCR_013270) was added, and mixed before incubation for 1 hour at room temperature under gentle agitation. The tubes were transferred to a magnetic rack to wash the beads 3 times with 70% Ethanol. DNA was eluted from the beads by resuspension in 80 µl of elution buffer (TrisHCl pH8 1M) preheated at 55°C. DNA concentration and quality were measured by spectrometry (Nanodrop 2000, Thermo Fisher Scientific, RRID:SCR_013270) and fluorometry (Qubit 3.0 Fluorometer, Thermo Fisher Scientific, RRID:SCR_013270).
A 20 kb SMRTbell library was prepared according to manufacturer s protocols as described for the 20 kb template preparation with Blue Pippin size selections as follow: 5 µg of gDNA was sheared to an average length of 35 kb using Megaruptor system (Diagenode), treated with DNA damage repair mix, end repaired and ligated to hairpin adapters. Incompletely formed SMRTbell templates were digested using Exonuclease III and VII. Finally, the library was size selected with a 12 kb cutoff using BluePippin electrophoresis. Sequencing was carried out on the PacBio RS II (INRA, Toulouse, France) from 0.25 nM of library loading on 3 SMRTCells, and using OneCellPerWell protocol on P6/C4 chemistry for six hours movies.


title: Pt grazing 3


title: HB-1_1_sRNA

tag: line


title: epi12

description: met1-3 derived epiRILs 12 F8

value: met1-3 derived epiRILs 12 F8


title: C57_CTL_F1_3

city: Geneva

first: Ludwig

last: Stenz

address: Rue Michel-Servet 1

department: Department of Genetic Medecine and Development

country: Switzerland

institute: University of Geneva

data_processing:
Base-calling (HiSeq Control Software 2.2.58, RTA 1.18.64.0, CASAVA-1.8.2)
RA3 clipped and reads > 18 bp from Fastq files using fastx_clipper
mapping to mm10 using TopHat
differential analysis using CuffDiff
analysis using CummeRbund
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM

organism: Mus musculus

source_name: epididymis extracted sperm

growth_protocol: animal core facility of Geneva University under conventional accommodation.

extract_protocol:
TRIZOL
RiboZero, fragmentation, Pyrophosphatase, kinase, TruSeq small RNA

treatment_protocol: Prenatal exposure per os to 300 mg/kg/day of bis(2-ethylhexyl)phthalate (D300) or corn oil vehicle (CTL) was administered to pregnant mice during embryonic days 9th to 19th

tag: prenatal exposure

value: CTL

value: 14 weeks


title: C57_CTL_F1_5


title: C57_CTL_F1_2


title: MVV___infection

data_processing:
Paired-end reads were cropped to remove linker and virus LTR sequences. Cropped paired reads were aligned to sheep genome oviAri3 using BWA MEM. High-quality alignemnts were selected with samtools view -F 4 -F 256 -q 1. The remaining alignements were parsed to select unique integration sites and extract coordinates of the central base pair step for each site.
Genome_build: oviAri (https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.1/)
Supplementary_files_format_and_content: processed data files are in standard bed format with the following 6 columns of data:
chromsome (chr1, chr2, etc)
interval start
interval end
sequence read ID
confidence value (100)
chromosome strand (+ or -)

source_name: sheep choroid plexus cells infected with MVV strain KV1772

growth_protocol: Sheep choroid plexus cells were established from healthy animals by explants of choroid plexus. The cells were grown at 37 °C in Dulbecco’s modified Eagles medium supplemented with 200 U/ml penicillin, 100 U/ml streptomycin, 2 mM glutamine and either 10% lamb serum (growth medium) or 1% lamb serum (maintenance medium).

treatment_protocol: Cells were infected with pathogenic MVV molecular clone KV1772 at a multiplicity of infection of 5.

value: sheep choroid plexus cells, infected with MVV strain KV1772.


title: GH-3_1_sRNA


title: C57_D300_F1_1

value: DEHP 300mg/kg/day


title: C57_D300_F1_5


title: C57_D300_F1_3


title: C57_D300_F1_4


title: C57_D300_F1_2


title: RNAseq_wt_glucose_NH4Cl_O2_2

city: La Jolla

first: Haythem

last: Latif

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

data_processing:
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing
bowtie2 v2.2.3 was used for alignment
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013).
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format

organism: Escherichia coli

source_name: E. coli K12 MG1655

growth_protocol: Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample.

extract_protocol:
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit.
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies).

treatment_protocol: Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment.

value: wt


title: RNAseq_wt_glycerol_NH4Cl_O2_2


title: RNAseq_wt_fructose_NH4Cl_O2_2


title: RNAseq_wt_glucose_NH4Cl_O2_3


title: MET1+ rep2

description: WT F2 pool from met1-3 and WT cross, replicate 2

source_name: rosette leaves

value: leaves


title: RNAseq_wt_glucose_NH4Cl_O2_1


title: WT

description: wild type

value: wild type


title: RNAseq_delta-crp_glycerol_NH4Cl_O2_2

value: delta Crp


title: RNAseq_delta-crp_glucose_NH4Cl_O2_3


title: MET1+ rep1

description: WT F2 pool from met1-3 and WT cross, replicate 1


title: RNAseq_wt_fructose_NH4Cl_O2_1


title: met1-1

description: met1-1 mutant

value: met1-1 mutant


title: RNAseq_delta-crp_fructose_NH4Cl_O2_3


title: RNAseq_delta-crp_glucose_NH4Cl_O2_2


title: RNAseq_delta-crp_fructose_NH4Cl_O2_2


title: RNAseq_delta-crp_glycerol_NH4Cl_O2_3


title: RNAseq_delta-crp_glycerol_NH4Cl_O2_1


title: RNAseq_delta-crp_glucose_NH4Cl_O2_1


title: RNAseq_delta-crp_fructose_NH4Cl_O2_1


title: RNAseq_delAr2_glycerol_NH4Cl_O2_3


title: RNAseq_delAr2_glycerol_NH4Cl_O2_2


title: RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_1


title: RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_2


title: RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_3


title: C57_CTL_F1_4


title: RNAseq_delAr2_glycerol_NH4Cl_O2_1


title: RNAseq_delAr1_glycerol_NH4Cl_O2_2


title: RNAseq_wt_glycerol_NH4Cl_O2_1


title: C57_CTL_F1_1


title: ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod

description:
Immunoprecipitated DNA
E. coli K12 MG1655

data_processing:
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing
bowtie2 v2.2.3 was used for alignment
Peak-calls were done using GPS within the GEMS software package (v2.3) adapted for ChIP-exo data
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Processed data is presented in gff files containing a pileup of 5' tags. GFF column headers "Genbank fna ID, file name, left genomic position, right genomic position, value, strand, extra value, information"

source_name: Chromosomal DNA

extract_protocol:
Cells were enyzmatically lysed in the presence of protease inhibitors prior to fragmentation using sonication. Protein/DNA complexes were recovered using an appropriate mouse monoclonal antibody followed by recovery using Pan Mouse IgG Dynabeads. While complexed on the magnetic bead, a series of enzymatic reactions were performed to 1) end repair, fragmented DNA, 2) ligate sequencing adpator 2, 3) nick repair, 4) lambda exonuclease treatment, 5) RecJ nuclease treatment. This was based on the method developed by Rhee et al. (doi:10.1016/j.cell.2011.11.013). IP DNA was then rleased from the complex and recovered.
Library construction was based on the method described by Rhee et al. (doi:10.1016/j.cell.2011.11.013).

treatment_protocol: Cells were crosslinked in 1% formadehyde for 25 min at room temperature followed by 5 minutes of quenching with glycine. Cells were washed 3X with ice cold TBS. Cell pellets were stored at -80 C.

tag: chip antibody

value: E. coli RNA Sigma 70 Monoclonal Antibody, Neoclone, #WP004


title: RNAseq_delAr1_glycerol_NH4Cl_O2_1


title: ChIPExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod


title: ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod


title: ChIPExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod


title: ChIPExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod


title: ChIPExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp

value: E. coli CRP Monoclonal Antibody, Neoclone, #N0004


title: ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc

value: c-Myc Antibody (9E10), Santa Cruz Biotech, sc-40


title: ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc


title: ChIPExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp


title: ChIPExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp


title: ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif


title: ChIPExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod


title: ChIPExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod


title: ChIPExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_1_anti-myc


title: RNAseq_delAr1_glycerol_NH4Cl_O2_3


title: ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif


title: ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif


title: ChIPExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp


title: ChIPExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp


title: ChIPExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp


title: ChIPExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp


title: ChIPExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp


title: ChIPExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp


title: ChIPExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp


title: ChIPExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp


title: ChIPExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp


title: ChIPExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp


title: ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp


title: ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp


title: ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp


title: ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp


title: ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp


title: ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp


title: ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc


title: ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_1_anti-myc


title: ChIPExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc


title: ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp


title: T-MET1a

description: MET1 complemented met1-1 line 1

value: seedling

value: MET1 complemented met1-1 line 1


title: ChIPExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp


title: ChIPExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod


title: T-MET1b

description: MET1 complemented met1-1 line 2

value: 2 weeks

value: MET1 complemented met1-1 line 2


title: ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp


title: met1-3

description: met1-3 mutant

value: met1-3 mutant


title: ChIPExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp


title: ChIPExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp


title: ChIPExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod


title: 6C_TP

city: College Station

first: Rodolfo

last: Aramayo

state: Texas

address: Room 412, Biological Sciences Building West (BSBW)

institute: Texas A&M University

description: Transcriptional Profiling

data_processing:
Sample libraries were sequenced using the Illumina HiSeq 2500 in High Output mode. Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.58 and RTA 1.18.64 software with default parameter settings. Sequencer .bcl basecall files were de-multiplexed, allowing a 1bp mismatch, and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl. Cutadapt 1.8 was used to identify reads that contained >5bp of sequence adaptor and binned but not processed to remove adaptor.
bowtie version 1.1.2
TopHat v2.1.0
rsem-1.2.20
samtools 1.3-1-g493b1ca
Genome_build: S288C_reference_sequence_R64-2-1_20150113
Supplementary_files_format_and_content: Dataset01.txt: Log2-transformed mRNA values for periodic expression (.txt)
Supplementary_files_format_and_content: Dataset02.txt: The 144 mRNAs that are cell cycle regulated in elutriation datasets but not in the Spellman core dataset (.txt)
Supplementary_files_format_and_content: Dataset03.txt: Input mRNA values for babel package (.txt)
Supplementary_files_format_and_content: Dataset04.txt: Input ribosome footprint values for babel package (.txt)
Supplementary_files_format_and_content: Dataset05.txt: mRNAs under translational control from babel package (.txt)
Supplementary_files_format_and_content: Dataset06.txt: Input values for anota package (.txt)
Supplementary_files_format_and_content: Dataset07.txt: mRNAs under translational control from anota package (.txt)
Supplementary_files_format_and_content: Dataset08.txt: mRNAs under translational control identified in common between the babel and anota packages (.txt)

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Growth at 30°C in YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose)

extract_protocol:
For the mRNA libraries, cells were lysed and total RNA isolated using the RNeasy kit (Qiagen, Cat#: 74104), which was then used to isolate poly(A)+ RNA with the Oligotex kit (Qiagen, Cat#: 70022). The purified mRNA from each sample was then used with the ScriptSeq v2 RNA-Seq library preparation kit (Illumina, Cat#: SSV21124), exactly according to the manufacturer’s instructions. In the final PCR amplification of the libraries, the forward primer was the one included in the ScriptSeq v2 RNA-Seq kit, while the reverse index PCR primers used for the mRNA libraries were primers 1 through 8, from the ScriptSeq Set 1 (Illumina, Cat#: RSBC10948)
For the ribosome footprint libraries, the cell extracts were prepared as follows: The cell pellets were in 1.5 ml screw-cap microcentrifuge tubes and they were washed once with 1 ml ice-cold DEPC-treated water, centrifuged at 13,000 g for 1 min and the supernatant was aspirated. To each tube we added 0.25 ml glass beads (425-600 μm; Sigma-Aldrich, Cat#: G9268) and 0.4 ml ice-cold lysis buffer, which is described in Ingolia et al(Ingolia et al., 2012). The cells were broken by vortexing at full speed eight times, for 15 sec each time. The samples were placed in ice for at least 30 sec between each vortexing. The extracts were clarified by centrifugation at 5,000 g for 5 min, at 4 °C. The supernatant was clarified in a second centrifugation, at 13,000 g for 10 min, at 4 °C. All subsequent steps for the ribosome footprint libraries were performed as described in Ingolia et al(Ingolia et al., 2012), except step 7, where we used 1.875 μl of RNase I (100 U μl-1) per reaction. For all gel extractions, we used the overnight protocol described in(Ingolia et al., 2012). Depletion of rRNA was done as described in (Ingolia et al., 2012). In the final PCR amplification and barcode addition step, we amplified each library for 12 cycles

treatment_protocol: We used centrifugal elutriation to isolate growing, highly synchronous, unbudded, early G1 cell populations and scored the elutriated cultures over time microscopically, recording the percentage of budded cells with a particle counter that directly measures their volume (channelyzer). Generation of both the Ribosome Profile (RP) and Transcriptional Profile (TP) libraries require at least ≥2E+09 yeast cells per sample. Such sample size could not be collected following a typical time-series experiment because only a small minority of the total cell population is in early G1 at any given moment. Instead, we allowed the entire cell population of each elutriated fraction to progress in the cell cycle until it reached a given cell size (e.g., 40 fl), at which point the sample was harvested. Elutriated cells of the same size were pooled together until enough cells per sample were obtained. This pool of same-size cells defined one experimental replicate (e.g., Sample01A). We harvested cells with 5fl cell size increments, from the time they are born (40 fl -- Sample01), until the end of the cell cycle (75 fl -- Sample08)

tag: cell size

tag: ploidy

value: Diploid


title: 8A_TP

description: Transcriptional Profiling


title: 7B_TP

description: Transcriptional Profiling


title: 8B_TP

description: Transcriptional Profiling


title: 7C_TP

description: Transcriptional Profiling


title: 6B_TP

description: Transcriptional Profiling


title: ChIPExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp


title: 7A_TP

description: Transcriptional Profiling


title: 8C_TP

description: Transcriptional Profiling


title: 6A_TP

description: Transcriptional Profiling


title: 5B_TP

description: Transcriptional Profiling


title: 5C_TP

description: Transcriptional Profiling


title: 5A_TP

description: Transcriptional Profiling


title: 4C_TP

description: Transcriptional Profiling


title: 4B_TP

description: Transcriptional Profiling


title: 4A_TP

description: Transcriptional Profiling


title: 3C_TP

description: Transcriptional Profiling


title: 3B_TP

description: Transcriptional Profiling


title: 2C_TP

description: Transcriptional Profiling


title: 2A_TP

description: Transcriptional Profiling


title: 1B_TP

description: Transcriptional Profiling


title: 1C_TP

description: Transcriptional Profiling


title: 1A_TP

description: Transcriptional Profiling


title: 8B_RP

description:
Ribosome Profiling
Protected RNA

data_processing:
Library strategy: ribosome footprinting
Sample libraries were sequenced using the Illumina HiSeq 2500 in High Output mode. Sequence cluster identification, quality pre-filtering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.58 and RTA 1.18.64 software with default parameter settings. Sequencer .bcl basecall files were de-multiplexed, allowing a 1bp mismatch, and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl. Cutadapt 1.8 was used to identify reads that contained >5bp of sequence adaptor and binned but not processed to remove adaptor.
bowtie version 1.1.2
TopHat v2.1.0
rsem-1.2.20
samtools 1.3-1-g493b1ca
Genome_build: S288C_reference_sequence_R64-2-1_20150113
Supplementary_files_format_and_content: Dataset01.txt: Log2-transformed mRNA values for periodic expression (.txt)
Supplementary_files_format_and_content: Dataset02.txt: The 144 mRNAs that are cell cycle regulated in elutriation datasets but not in the Spellman core dataset (.txt)
Supplementary_files_format_and_content: Dataset03.txt: Input mRNA values for babel package (.txt)
Supplementary_files_format_and_content: Dataset04.txt: Input ribosome footprint values for babel package (.txt)
Supplementary_files_format_and_content: Dataset05.txt: mRNAs under translational control from babel package (.txt)
Supplementary_files_format_and_content: Dataset06.txt: Input values for anota package (.txt)
Supplementary_files_format_and_content: Dataset07.txt: mRNAs under translational control from anota package (.txt)
Supplementary_files_format_and_content: Dataset08.txt: mRNAs under translational control identified in common between the babel and anota packages (.txt)


title: 8A_RP

description:
Ribosome Profiling
Protected RNA


title: 2B_TP

description: Transcriptional Profiling


title: 7B_RP

description:
Ribosome Profiling
Protected RNA


title: 3A_TP

description: Transcriptional Profiling


title: 7A_RP

description:
Ribosome Profiling
Protected RNA


title: 6C_RP

description:
Ribosome Profiling
Protected RNA


title: 6A_RP

description:
Ribosome Profiling
Protected RNA


title: 6B_RP

description:
Ribosome Profiling
Protected RNA


title: 5C_RP

description:
Ribosome Profiling
Protected RNA


title: 5B_RP

description:
Ribosome Profiling
Protected RNA


title: 7C_RP

description:
Ribosome Profiling
Protected RNA


title: 4C_RP

description:
Ribosome Profiling
Protected RNA


title: 5A_RP

description:
Ribosome Profiling
Protected RNA


title: 4A_RP

description:
Ribosome Profiling
Protected RNA


title: 4B_RP

description:
Ribosome Profiling
Protected RNA


title: 2C_RP

description:
Ribosome Profiling
Protected RNA


title: 3C_RP

description:
Ribosome Profiling
Protected RNA


title: 3B_RP

description:
Ribosome Profiling
Protected RNA


title: 1B_RP

description:
Ribosome Profiling
Protected RNA


title: 1C_RP

description:
Ribosome Profiling
Protected RNA


title: 2A_RP

description:
Ribosome Profiling
Protected RNA


title: 1A_RP

description:
Ribosome Profiling
Protected RNA


title: 8C_RP

description:
Ribosome Profiling
Protected RNA


title: Non-Cachectic controls [7359]

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Ave

department: Laboratory medicine and pathology

country: Canada

institute: University of Alberta

description: Genomic small RNA (size selected from total RNA)

data_processing:
Base calling and demultiplexing was performed using MiSeq Reporter FastQ workflow
Cutadapt 1.4.1  was used to trim the adapters
Trimming of low quality reads were performed with a threshold of 30 on Sanger scale
Quality control for sequenced reads before and after adapter trimming was performed using FastQC v0.11.3 software
BWA aligner version 0.6.1 was used to align trimmed reads to the reference genome  human genome 19 build, downloaded from Illumina iGenome website
Samtools version 0.1.18 was used to convert aligned .sam files to .bam format which was used for downstream analyses
Genome_build: hg 19, miRBAse v 20 for annotating miRNAs
Supplementary_files_format_and_content: tab-delimited txt files containing RPKM normalized values for all miRs

source_name: Rectus abdominus

growth_protocol: Muscle biposies were preserved as Fresh frozen tissues

extract_protocol:
Total RNA was isolated using TRIzol and Qiagen Rneasy kit according to manufacturer's instructions
Small RNAs were sequenced using Truseq Small RNA sequencing kit(Illumina), TruSeq SR cluster kit v5-CS-GA (Illumina) and TruSeq SBS kit v5-GA(Illumina) according to manufacturer's instructions. All samples were sequenced using MiSeq platform with 36 cycles single end protocol

value: Fresh frozen (FF) Muscle biopsy

tag: tumor type

value: Pancreas


title: Non-Cachectic controls [7409]

value: Colorectal


title: Non-Cachectic controls [7347]


title: Non-Cachectic controls [7288]


title: Cachectic controls [7308]


title: Non-Cachectic controls [7257]


title: Non-Cachectic controls [7254]


title: Non-Cachectic controls [7227]


title: 2B_RP

description:
Ribosome Profiling
Protected RNA


title: Non-Cachectic controls [7212]


title: Cachectic controls [7156]


title: 3A_RP

description:
Ribosome Profiling
Protected RNA


title: Non-Cachectic controls [7192]


title: Non-Cachectic controls [7050]


title: Non-Cachectic controls [7135]


title: Non-Cachectic controls [6144]


title: Non-Cachectic controls [3016]


title: Non-Cachectic controls [3027]


title: Cachectic controls [7100]


title: Cachectic controls [6189]


title: Non-Cachectic controls [6142]


title: Non-Cachectic controls [6147]


title: Non-Cachectic controls [2066]


title: Cachectic cases [5159]


title: Cachectic cases [3053]


title: Cachectic cases [7183]


title: Non-Cachectic controls [7353]


title: Cachectic cases [7455]


title: Non-Cachectic controls [7245]


title: Cachectic cases [7173]


title: Cachectic cases [7180]


title: Cachectic cases [7147]


title: Cachectic cases [6181]


title: Cachectic cases [5211]


title: Cachectic cases [7056]


title: Non-Cachectic controls [7139]


title: Cachectic cases [5100]


title: Cachectic cases [5128]


title: Cachectic cases [5134]


title: Cachectic cases [5186]


title: Cachectic cases [4093]


title: Cachectic cases [4219]


title: Cachectic cases [3005]


title: UNC0379 replicate 2

city: Bethesda

first: Veronica

last: veschi

state: MD

address: 10 Center Dr. MSC-1105

department: NCI

institute: NIH

data_processing:
Illumina RTA 1.18.64 software used for basecalling.
Sequenced reads were trimmed with Trimmomatic (version 0.30), then mapped to hg19 using STAR (version 2.4.2a) with the quantMode option
The gene reads count data from STAR for UNC0379 and siSETD8 samples were analyzed separately with R Package edgeR (version 3.10.5).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads count for each sample

source_name: Neuroblastoma

extract_protocol:
SY5Y cells 36 hours after SETD8 genetic silencing and 12 hours after treatment with 4μM UNC0379 were harvested and cell pellets were collected. From these pellets total RNA extraction was carried out using an RNeasy Plus Kit. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor stage

value: high-risk

tag: genotype 1

value: MYCN wild type

tag: genotype 2

value: p53 wild type


title: non-silencing sample 1

city: West Haven

first: Sarah

middle: A

last: Slavoff

state: Connecticut

address: Yale University West Campus-Building 600

department: Chemistry

institute: Yale University- West Campus

description:
N1
N1_006_GCCAAT

data_processing:
Reads were aligned to the human genome (hg19, GRCh37) using STAR (version 2.4.0.k) (Dobin et al. 2013).  Only reads that aligned uniquely to a single genomic location were used for downstream analysis (MAPQ > 10).
Gene expression values were calculated for annotated RefSeq genes using HOMER by counting reads found overlapping exons of the major gene isofrom (Heinz et al. 2010). We report fragments per kilobase per million mapped reads (fpkm) normalized counts.
Log-transformed filtered FPKM expression values were used to perform hierarchical clustering assuming the modified Wald agglomeration technique, and 1-cor as a distance metric. Heatmaps of sorted expression values were generated with the heatmap.2 R function after normalizing across samples.
Differentially expressed genes were found using the R edgeR package (Robinson et al. 2010). Genes that were significantly misregulated (adj. p-value < 0.01 and log2fold change > 1) were used for analysis.
Pathway/Term enrichment analysis was carried out using the hypergeometric test with multiple testing correction using the Homer (Heinz et al. 2010) package which looks for significant overlaps in multiple public databases.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content:  ALL_gene_diff_exp.txt reports FPKMs

source_name: non-silencing sample

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS (no antibiotics) in 5% CO2 atmosphere in a 6-well plate.

extract_protocol:
Total RNA was isolated from each sample using an Rneasy kit according to the manufacturer's instructions. After RNA isolation, genomic DNA was removed via in-solution Dnase digest, followed by Rneasy column-based purification.  Prior to analysis, LOC550643 silencing was confirmed via RT-PCR.
mRNA-Seq libraries were prepared using the mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Briefly, RNA with poly-A tail was isolated using magnetic beads conjugated to poly-T oligos. mRNA was then fragmented and reverse-transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. dUTP-incorporated second strand was not amplified. cDNA was then end-repaired, index adapter-ligated and PCR amplified. Libraries were then quantified, pooled and sequenced at paired-end 75 base pair using the Illumina HiSeq platform at the Yale Center for Genomic Analysis Core. Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2). Sequenced reads were quality tested using FASTQC and aligned to the human hg19 genome using the STAR aligner version 2.4.0k. Raw gene expression was quantified across all annotated exons and differential gene expression was carried out using the edgeR package v3.6.8. using representative triplicates to compute within-group dispersion. Differentially expressed genes were defined as having an FDR < 0.05 and a log2 fold change greater than 1.

treatment_protocol: HEK293T cells at 50% confluency were transfected with a pool of 4 siRNA sequences targeting LOC550643 (Qiagen) or a human non-targeting (non-silencing) siRNA using Dharmafect I according to the manufacturer's instructions. 48 hours post-transfection, cells were washed 3X with DPBS prior to lysis and RNA extraction. 3 replicates of the silencing and non-silencing samples were prepared.

tag: cell line

tag: transfection

value: non-silencing siRNA


title: LOC550643 silencing sample 2

description:
S2
S2_004_TGACCA

source_name: LOC550643 silencing sample

value: LOC550643 siRNA


title: non-silencing sample 3

description:
N3
N3_012_CTTGTA


title: LOC550643 silencing sample 1

description:
S1
S1_002_CGATGT


title: siSETD8 replicate 2

tag: cell type


title: UNC0379 replicate 1


title: Cachectic cases [3003]

tag: tissue


title: siSETD8 replicate 1


title: non-silencing sample 2

description:
N2
N2_007_CAGATC


title: Cachectic cases [6170]


title: DMSO replicate 2


title: DMSO replicate 1


title: Mononuclear cells 60d (replacement BAM)

city: Vienna

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

country: Austria

institute: Children's Cancer Research Institute

description: mRNA profiles of the corresponding sample

data_processing:
RNA-seq reads were mapped with GSNAP v2014-12- 28 [20147302] (“-- maxsearch=100 -- npaths=1 -- max-mismatches=1 --novelsplicing=0 “) to human reference genome build GRCh37. Known SNPs and splice sites were extracted from dbSNP build 138 and Ensembl GRCh37 build 75, respectively.
DESeq2-normalized fragments per million (FPM), log2 scale
Genome_build: hg19
Supplementary_files_format_and_content: DESeq expression matrix (log2)

source_name: Tumor cells-depleted bone marrow-derived mono nuclear cells

growth_protocol: See SAMPLES section

extract_protocol:
miRNeasy Micro Kit
RNA-Seq, New England Biolab kit with polyA enrichment

treatment_protocol: No treatment

tag: growth

value: Samples were not cultivated


title: Mononuclear cells 59d (replacement BAM)


title: Mononuclear cells 33d (replacement BAM)


title: TSLPR– Treg_Mi2

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm9 or mm10 assembly of the mouse genome using either the Burrows-Wheeler or the STAR genome alignment algorithms.
Read normalization per sample was performed using the easyRNAseq algorithm and differential gene expression was performed with the Deseq2 algorithm implemented by the R platform.
Genome_build: mm9 or mm10
Supplementary_files_format_and_content: normalized read with annotation

source_name: skin draining LNs

extract_protocol:
Epidermis or Treg were purified by FACS sorting
NEXTflex RNAseq kit (BIOO scientific) or a Trueseq stranded mRNA sample prep kit (Illumina)

value: skin draining LNs

value: FACS sorted ex vivo regulatory T cells (Treg)


title: siCTR replicate 1


title: TSLPR WT Treg_Mi2 rep2


title: Mononuclear cells 01d (replacement BAM)


title: KPCS 520 Hx

city: zurich

first: Cédric

last: Cortijo

address: Otto-Stern-Weg 7

department: HPL

institute: ETHZ

description:
data_norm.txt
DEA_hits.txt

data_processing:
Starting from the raw .fastq files (1x81bp) the reads were mapped against the mouse reference genome and simultaneously soft‐clipped using the STAR aligner (version 2.4.2a).
Standard quality control (Picard, RSeQC, QoRTs was run to assess the quality of the resulting alignments. Subsequently, strand‐specific (reversely stranded) read counting was performed using featureCount (subread, version 1.5.0).
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files

source_name: pancreatic ductal adenocarcinoma

extract_protocol:
Organoids were collected in RA1 buffer + TCEP, RNA was harvested using MN kit.  Illumina TruSeq SR cluster kit v4-cBot-HS was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: KrasG12D; p53R172H, Sf3b1 fl/f, Ptf1aCre

tag: age

value: post natal 13 weeks


title: KPCS 530 Hx

description:
data_norm.txt
DEA_hits.txt


title: TSLPR WT Treg_Mi2 rep1


title: LOC550643 silencing sample 3

description:
S3
S3_005_ACAGTG


title: Ctl Treg rep2


title: Mononuclear cells 02d (replacement BAM)


title: KPCS 520 Nx

description:
data_norm.txt
DEA_hits.txt


title: Ctl Treg rep1


title: Mi2 epidermis rep1

source_name: adult skin epidermis

value: adult skin epidermis

value: FACS sorted ex vivo keratinocytes


title: Mi2 epidermis rep2


title: KPCS 530 Nx

description:
data_norm.txt
DEA_hits.txt


title: KPCS 528 Nx

description:
data_norm.txt
DEA_hits.txt


title: KPS 520 Hx

description:
data_norm.txt
DEA_hits.txt

value: KrasG12D; p53R172H, Sf3b1 fl/fl


title: siCTR replicate 2


title: KPS 528 Hx

description:
data_norm.txt
DEA_hits.txt


title: WT epidermis rep2


title: Neuroblastoma cell line STA-NB-6 (2) (replacement BAM)

source_name: Primary neuroblastoma cell line established at the Children's Cancer Research Institute

value: grown in MEMa


title: WT epidermis rep1


title: KPS 530 Hx

description:
data_norm.txt
DEA_hits.txt


title: Dgcr8-/- NSC_2

city: Rochester

first: Hu

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
alignment TopHat v2.0.6
feautureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited gene counts

source_name: Neural stem cells

growth_protocol: NSCs were maintained in Mouse Neural Stem Cell Expansion medium (EMD Millipore) on tissue culture plate coated with polyornithine (Sigma-Aldrich) and laminin (BD Biosciences).

extract_protocol:
Total RNA was from NSCs the DirectZol RNA Kit (Zymo Research). RNA integrity (RIN) was verified on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Paired-end sequencing libraries were prepared by the Genomic Services Lab at HudsonAlpha Institute for Biotechnology (Huntsville, AL) followed by quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina (by the Mayo Clinic core).

treatment_protocol: Dgcr8 heterozyous vs. null NSCs

tag: genotype/variation

value: Dgcr8 null NSCs

value: E13.5 embryonic brain


title: KPS 520 Nx

description:
data_norm.txt
DEA_hits.txt

value: Pancreas


title: Neuroblastoma cell line STA-NB-6 (1) (replacement BAM)


title: Mononuclear cells 08d (replacement BAM)


title: KPS 528 Nx

description:
data_norm.txt
DEA_hits.txt


title: Dgcr8-/- NSC_1


title: KPCS 528 Hx

description:
data_norm.txt
DEA_hits.txt


title: Peripheral nerve associated primary fibroblasts 2 (replacement BAM)

source_name: Collected during reconstructive surgery or amputations of male and female patients


title: Peripheral nerve associated primary fibroblasts 3 (replacement BAM)


title: KPS 530 Nx

description:
data_norm.txt
DEA_hits.txt


title: Dgcr8+/- NSC_2

value: Dgcr8 heterozygous NSCs


title: Dgcr8+/- NSC_1


title: Mononuclear cells 05d (replacement BAM)


title: Peripheral nerve associated primary fibroblasts 1 (replacement BAM)


title: KPC 571 Hx

description:
data_norm.txt
DEA_hits.txt

value: KrasG12D; p53R172H; Ptf1aCre


title: Neuroblastoma cell line STA-NB-2 (replacement BAM)


title: Peripheral nerve associated primary Schwann cells 5 (replacement BAM)

value: grown on PLL/Laminin in SC media


title: Mutant Endo 3

city: Aurora

first: Lori

last: Sussel

state: CO

address: 1775 Aurora Ct.

institute: University of Colorado

data_processing:
RTA (Illumina) was used for base calling
CASAVA (version 1.8.2) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were mapped to a reference genome (Mouse: UCSC/mm9) using Tophat (Trapnell C et al 2009 Bioinformatics) (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
Relative abundance (aka expression level) of genes and splice isoforms was determined using cufflinks (Trapnell C et al 2010 Nature Biotech) (version 2.0.2) with default settings.
Differentially expressed genes were calculated using Deseq (Anders S et al 2010 Genome Biology).
Genome_build: mm9
Supplementary_files_format_and_content: csv-files includse FPKM values for all genes/isoforms in a sample
Supplementary_files_format_and_content: csv-file includes DESeq analysis for mutant samples and respective controls

source_name: whole pancreas

extract_protocol:
Embryonic pancreata were dissected and total RNA was isolated using QIAGEN RNeasy Mini kit. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample name

tag: genotype

value: Ngn3-Cre/+; Nkx2.2-flox/flox

value: whole pancreas


title: Mutant Endo 2


title: Peripheral nerve associated primary Schwann cells 4 (replacement BAM)


title: Peripheral nerve associated primary Schwann cells 3 (replacement BAM)


title: Mutant Endo 1


title: Peripheral nerve associated primary Schwann cells 2 (replacement BAM)


title: Control Endo 3

value: Nkx2.2-flox/+; Rosa26-Tomato/+


title: KPC 616 Nx

description:
data_norm.txt
DEA_hits.txt


title: KPC 571 Nx

description:
data_norm.txt
DEA_hits.txt


title: Control Endo 2


title: Peripheral nerve fascicle injured 3 (replacement BAM)

value: Samples were kept in MEMa medium for 8 days. Not grown.


title: Peripheral nerve associated primary Schwann cells 1 (replacement BAM)


title: KP 571 Hx

description:
data_norm.txt
DEA_hits.txt

value: KrasG12D; p53R172H


title: Control Endo 1


title: KPC 625 Nx

description:
data_norm.txt
DEA_hits.txt


title: Mutant KO 3


title: ZMELR1 - rep3

city: New York

first: Richard

middle: Mark

last: White

state: NY

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
TopHot2 alignment to Zv9
Read counts extracted with HTSeq
Differential expression with limma
Zebrafish genes converted to human orthologs using DIOPT
Mutations called on RNA-seq using Strelka
Genome_build: Zv9
Supplementary_files_format_and_content: XLSX sheet with normalized read counts output from HTSeq

organism: Danio rerio

source_name: BRAF inhibitor resistant ZMEL-R1 cells in vitro

growth_protocol: ZMEL1: DMEM/10% FCS/1X glutamax/28.5C     ZMELR1: DMEM/10% FCS/1X glutamax/28.5C  + PLX4032 1uM

extract_protocol:
Cells were trypsinized and total RNA isolated with Zymo kits
Illumina TruSeq

tag: tissue type

value: melanoma


title: Peripheral nerve fascicle injured 2 (replacement BAM)


title: ZMELR1 - rep1


title: Peripheral nerve fascicle injured 1 (replacement BAM)


title: KP 616 Hx

description:
data_norm.txt
DEA_hits.txt

value: post natal 13 weeks


title: Mutant KO 1


title: KP 625 Hx

description:
data_norm.txt
DEA_hits.txt


title: Peripheral nerve fascicle CTRL 3 (replacement BAM)

value: Samples were fresh frozen. Not grown.


title: KPC 625 Hx

description:
data_norm.txt
DEA_hits.txt


title: KPC 616 Hx

description:
data_norm.txt
DEA_hits.txt


title: ZMEL1 - rep3

source_name: ZMEL1 cells in vitro


title: KP 571 Nx

description:
data_norm.txt
DEA_hits.txt


title: Peripheral nerve fascicle CTRL 2 (replacement BAM)


title: KP 616 Nx

description:
data_norm.txt
DEA_hits.txt


title: Control KO 3


title: ZMEL1 - rep2


title: Control KO 2


title: Peripheral nerve fascicle CTRL 1 (replacement BAM)


title: ZMEL1 - rep1


title: Control KO 1


title: shRNA-Ctrl_E1_rep3 RNA-seq

status: Public on Jan 08 2017

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat2 using default setting
Genome_build: mm9
Supplementary_files_format_and_content: DESeq2 output

extract_protocol:
mice dentate gyrus were microdisected, RNA was harvested using RNeasy Kit (Qiagen), RNA-seq libraries were generated from each individuals
libraries were prepared for sequencing using standard Illumina protocols

value: dentate gyrus

value: adult 8 wks old


title: KP 625 Nx

description:
data_norm.txt
DEA_hits.txt


title: ZMELR1 - rep2


title: Mutant KO 2


title: shRNA-Ctrl_E0_rep2 RNA-seq


title: shRNA-Ctrl_E0_rep3 RNA-seq


title: shRNA-Ctrl_E1_rep2 RNA-seq


title: shRNA-Ctrl_E0_rep1 RNA-seq


title: shRNA-cFos_E1_rep2 RNA-seq


title: shRNA-cFos_E0_rep3 RNA-seq


title: shRNA-cFos_E0_rep2 RNA-seq


title: shRNA-cFos_E0_rep1 RNA-seq


title: shRNA-cFos_E1_rep1 RNA-seq


title: shRNA-Ctrl_E1_rep1 RNA-seq


title: shRNA-cFos_E1_rep3 RNA-seq


title: E24_rep3 (ATAC-Seq)

data_processing:
Illumina Casava1.7 software used for basecalling.
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtie2 using default setting
peaks were called using MACS
Genome_build: mm9
Supplementary_files_format_and_content: peak/bed file

extract_protocol:
mice dentate gyrus were microdisected, ATAC-seq libraries were generated from each individuals
libraries were prepared for sequencing using standard Illumina protocols


title: E24_rep2 (ATAC-Seq)


title: E24_rep1 (ATAC-Seq)


title: cFos_OE_rep2 RNA-seq


title: cFos_OE_rep1 RNA-seq


title: cFos_OE_rep3 RNA-seq


title: EYFP_OE_rep3 RNA-seq


title: EYFP_OE_rep2 RNA-seq


title: shRNA-cFos_E1_rep2 ATAC-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtie2 using default setting
peaks were called using MACS
Genome_build: mm9
Supplementary_files_format_and_content: bed/peak file

extract_protocol:
mice dentate gyrus infected with AAV expressing shRNA-Ctrl or shRNA-cFos were microdisected, ATAC-seq libraries were generated from each individuals
libraries were prepared for sequencing using standard Illumina protocols


title: EYFP_OE_rep1 RNA-seq


title: shRNA-cFos_E0_rep3 ATAC-seq


title: shRNA-cFos_E0_rep1 ATAC-seq


title: shRNA-Ctrl_E1_rep2 ATAC-seq


title: shRNA-Ctrl_E1_rep3 ATAC-seq


title: shRNA-Ctrl_E0_rep1 ATAC-seq


title: cFos_OE_rep3 ATAC-seq

extract_protocol:
mice dentate gyrus infected with AAV expressing EYFP and/or cFos were microdisected, ATAC-seq libraries were generated from each individuals
libraries were prepared for sequencing using standard Illumina protocols


title: shRNA-Ctrl_E0_rep2 ATAC-seq


title: shRNA-Ctrl_E0_rep3 ATAC-seq


title: cFos_OE_rep2 ATAC-seq


title: E24_rep3 (RNA-Seq)

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat2 using default setting
peaks were called using MACS
Genome_build: mm9
Supplementary_files_format_and_content: cufflinks output file (RPKM)


title: EYFP_OE_rep2 ATAC-seq


title: cFos_OE_rep1 ATAC-seq


title: EYFP_OE_rep3 ATAC-seq


title: E1_rep4 ATAC-seq


title: E4_rep3 RNA-seq


title: E4_rep1 ATAC-seq


title: E24_rep2 (RNA-Seq)


title: E4_rep4 ATAC-seq


title: EYFP_OE_rep1 ATAC-seq


title: E4_rep2 RNA-seq


title: E4_rep1 RNA-seq


title: E24_rep1 (RNA-Seq)


title: E1_rep3 ATAC-seq


title: shRNA-cFos_E1_rep1 ATAC-seq


title: E1_rep3 RNA-seq


title: E1_rep1 ATAC-seq


title: shRNA-cFos_E0_rep2 ATAC-seq


title: shRNA-Ctrl_E1_rep1 ATAC-seq


title: E1_rep2 RNA-seq


title: E0_rep4 ATAC-seq


title: E1_rep1 RNA-seq


title: E4_rep3 ATAC-seq


title: E0_rep3 RNA-seq


title: E0_rep2 ATAC-seq


title: E4_rep2 ATAC-seq


title: E0_rep2 RNA-seq


title: E0_rep1 RNA-seq


title: E0_rep3 ATAC-seq


title: E0_rep1 ATAC-seq