title: Pn-0 infected by S. sclerotiorum rep 2

tag: tissue

value: Leaves of 5-week old plants

tag: genotype

tag: treatment

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: T2

status: Public on Feb 27 2024

type: SRA

city: Shanghai

first: Zeng

last: Ye

address: 270 Dongan Road, Xuhui District

country: China

institute: Fudan University Shanghai Cancer Center

description: 10x Genomincs

library_source: transcriptomic

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

organism: Homo sapiens

source_name: pancreatic neuroendocrine tumor

extract_protocol:
During surgery, immediately after the tissue specimens were isolated, the tissue specimens were cuted and kept in MACS Tissue Storage Solution (Miltenyi Biotec) for further processing. Tissue specimens were processed as described below. Briefly, specimen was first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1 mm3) on ice and enzymatically digested with collagenase I (Worthington) and DNase I (Worthington) for 45 min at 37°C, with agitation. After digestion, specimen was sieved through a 70 µm cell strainer, and centrifuged at 300 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
The scRNA-seq libraries and V(D)J libraries were generated using the 10x Genomics Chromium Controller Instrument and Chromium Single Cell 5’ library & gel bead kit, along with the V(D)J enrichment kit (10x Genomics). Briefly, cells were concentrated to 1000 cells/µL and approximately 10,000 cells were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which resulted in expected mRNA barcoding of 6,000 single-cells for each specimen. After the reverse transcription step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was used to construct 5’ gene expression libraries and TCR and BCR enriched libraries. For 5’ library construction, the amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by a NextSeq2000 sequencer (Illumina) on a 150 bp paired-end run.

value: pancreatic neuroendocrine tumor

value: transcriptomics

value: no


title: Rub infected by S. sclerotiorum rep 1

city: Castanet-Tolosan

first: Florent

last: Delplace

address: 24 chemin de Borde Rouge

country: France

institute: INRAe

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function described in the pipeline https://doi.org/10.5281/zenodo.1400710) using the nf-core framework (https://github.com/nf-core/rnaseq). Raw counts were normalized by edgeR.
Assembly: Arabidopsis thalinia (Araport11), Sclerotinia sclerotiorum strain 1980 (Derbyshire et al., 2017)
Supplementary files format and content: tab-delimited text files includes CPM values for all Samples

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Leaves of 5-week old plants

growth_protocol: Plants were grown in Jiffy pots under controlled conditions at 22°C, with a 9 hour light period at intensity of 120 μmol/m²/s.

extract_protocol:
Samples were ground using glass beads (2.5 mm) and RNA was extracted using NucleoSpin RNA PLUS extraction kits (Macherey-Nagel) following the manufacturer’s protocols. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves on 5-week old plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.

value: Rub

tag: time


title: T7

description: 10x Genomincs


title: Pn-0 infected by S. sclerotiorum rep 1


title: TF ChIP-seq from whole organism (ENCLB872JWN)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR321VWM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-47-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR321VWM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR251RZP
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB872JWN
fragmentation methods: sonication (generic microtip)

library_source: genomic

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

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain OP481 (unc-119(tm4063) III; wgIs481) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-47

tag: antibody

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-47

tag: Sex

value: hermaphrodite

tag: dev stage

value: L1 larva

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

tag: link

value: ENCBS980ZRH at ENCODE; https://www.encodeproject.org/ENCBS980ZRH/


title: TF ChIP-seq from whole organism (ENCLB211QLI)

description:
https://www.encodeproject.org/experiments/ENCSR139BJY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Oli-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR139BJY
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR203PPN
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB211QLI
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

organism: Drosophila melanogaster

source_name: Drosophila melanogaster mixed sex embryo (6-18 hours) insertion targeting D. melanogaster Oli

value: Oli

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Oli

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS162VYP at ENCODE; https://www.encodeproject.org/ENCBS162VYP/


title: T15

description: 10x Genomincs

tag: tissue

value: pancreatic neuroendocrine tumor

tag: genotype

value: transcriptomics

tag: treatment

value: no


title: Control ChIP-seq from whole organism (ENCLB416MPL)

description:
https://www.encodeproject.org/experiments/ENCSR225ALY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing DAO-5-eGFP fusion proteins.
experiment encode accession: ENCSR225ALY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB416MPL
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP252 hermaphrodite L4/young adult insertion targeting C. elegans dao-5

value: whole organism

value: whole organisms

tag: biosample encode accession

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to DAO-5

value: hermaphrodite

value: L4/young adult

value: ENCBS577ICI at ENCODE; https://www.encodeproject.org/ENCBS577ICI/


title: TF ChIP-seq from whole organism (ENCLB325PAQ)

description:
https://www.encodeproject.org/experiments/ENCSR139BJY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Oli-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR139BJY
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR203PPN
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB325PAQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: Oli

tag: collection date

value: ENCBS986CWO at ENCODE; https://www.encodeproject.org/ENCBS986CWO/


title: TF ChIP-seq from whole organism (ENCLB512EBZ)

description:
https://www.encodeproject.org/experiments/ENCSR321VWM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-47-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR321VWM
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR251RZP
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB512EBZ
fragmentation methods: sonication (generic microtip)

tag: geographic location

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-47

value: L1 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS040NLB at ENCODE; https://www.encodeproject.org/ENCBS040NLB/


title: Oy-0 infected by S. sclerotiorum rep 3

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB684NFS)

description:
https://www.encodeproject.org/experiments/ENCSR038HZR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CoRest-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR038HZR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR073DRW
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB684NFS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CoRest

value: CoRest

value: whole organism

value: whole organisms

value: not applicable

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to coRest

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS429YAN at ENCODE; https://www.encodeproject.org/ENCBS429YAN/


title: Control ChIP-seq from whole organism (ENCLB940VWI)

description:
https://www.encodeproject.org/experiments/ENCSR324PNK/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing NHR-102-eGFP fusion proteins.
experiment encode accession: ENCSR324PNK
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB940VWI
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP463 (unc-119(tm4063) III; wgIs463) hermaphrodite L4 larva 50 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-102

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-102

value: hermaphrodite

value: L4 larva

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

value: L1 larva starved after bleaching

value: ENCBS666ZWT at ENCODE; https://www.encodeproject.org/ENCBS666ZWT/


title: Oy-0 infected by S. sclerotiorum rep 2

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: T14

description: 10x Genomincs

value: pancreatic neuroendocrine tumor

value: transcriptomics

value: no


title: T13

description: 10x Genomincs


title: TF ChIP-seq from whole organism (ENCLB367BBI)

description:
https://www.encodeproject.org/experiments/ENCSR311NAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-90-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR311NAQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR792LGD
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB367BBI
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP483 (unc-119(tm4063) III; wgIs483) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-90

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-90

value: L1 larva

tag: worm synchronization stage

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS395UOV at ENCODE; https://www.encodeproject.org/ENCBS395UOV/


title: TF ChIP-seq from whole organism (ENCLB874OFW)

description:
https://www.encodeproject.org/experiments/ENCSR138MDE/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Rel-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR138MDE
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR749JEF
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB874OFW
size range: 200-800

source_name: Drosophila melanogaster strain Rel mixed sex wandering third instar larva insertion targeting D. melanogaster Rel

value: Rel

value: Transgenic D. mel line, stably expressing a N-terminal GFP fused to Rel

value: pooled male and female

value: wandering third instar larva

value: unknown

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS785YCE at ENCODE; https://www.encodeproject.org/ENCBS785YCE/


title: Oy-0 infected by S. sclerotiorum rep 1

tag: tissue

value: Leaves of 5-week old plants

tag: genotype

tag: treatment

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: T3

description: 10x Genomincs

value: pancreatic neuroendocrine tumor

value: transcriptomics

value: no


title: T12

description: 10x Genomincs


title: Nok-3 infected by S. sclerotiorum rep 3


title: TF ChIP-seq from whole organism (ENCLB782SQV)

description:
https://www.encodeproject.org/experiments/ENCSR138MDE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Rel-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR138MDE
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR749JEF
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB782SQV
size range: 200-800

tag: antibody

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

value: ENCBS027ICA at ENCODE; https://www.encodeproject.org/ENCBS027ICA/


title: TF ChIP-seq from whole organism (ENCLB442QOJ)

description:
https://www.encodeproject.org/experiments/ENCSR138MDE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Rel-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR138MDE
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR749JEF
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB442QOJ
size range: 200-800

value: Rel

tag: geographic location

tag: encode accession

value: Transgenic D. mel line, stably expressing a N-terminal GFP fused to Rel

value: ENCBS475XIC at ENCODE; https://www.encodeproject.org/ENCBS475XIC/


title: TF ChIP-seq from whole organism (ENCLB933QXX)

description:
https://www.encodeproject.org/experiments/ENCSR311NAQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-90-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR311NAQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR792LGD
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB933QXX
fragmentation methods: sonication (generic microtip)

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-90

tag: Sex

value: hermaphrodite

value: L1 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS677MSB at ENCODE; https://www.encodeproject.org/ENCBS677MSB/


title: T11

description: 10x Genomincs

value: pancreatic neuroendocrine tumor

value: transcriptomics

value: no


title: Nok-3 infected by S. sclerotiorum rep 1

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB062VRU)

description:
https://www.encodeproject.org/experiments/ENCSR137DAC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR137DAC
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB062VRU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG12299 embryo (0-24 hours) insertion targeting D. melanogaster CG12299

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG12299

value: not collected

tag: dev stage

value: embryonic

tag: age

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

value: Kevin White

value: ENCBS019HSC at ENCODE; https://www.encodeproject.org/ENCBS019HSC/


title: TF ChIP-seq from whole organism (ENCLB517JHT)

description:
https://www.encodeproject.org/experiments/ENCSR133RTP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing MADF-10-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR133RTP
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR555GJK
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB517JHT
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP508 (unc-119(tm4063) III; wgIs508) hermaphrodite young adult 68 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans madf-10

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to MADF-10

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

tag: post synchronization time

value: hour

value: ENCBS672SLN at ENCODE; https://www.encodeproject.org/ENCBS672SLN/


title: Nok-3 infected by S. sclerotiorum rep 2

tag: tissue

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: Mt-0 infected by S. sclerotiorum rep 3

tag: genotype


title: Control ChIP-seq from whole organism (ENCLB856FWQ)

description:
https://www.encodeproject.org/experiments/ENCSR308YQB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR308YQB
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB856FWQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain nerfin-1 mixed sex embryo (4-16 hours) insertion targeting D. melanogaster nerfin-1

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to nerfin-1

value: pooled male and female

value: embryonic

tag: link

value: ENCBS021TZF at ENCODE; https://www.encodeproject.org/ENCBS021TZF/


title: T10

description: 10x Genomincs

value: pancreatic neuroendocrine tumor

value: transcriptomics

tag: treatment

value: no


title: TF ChIP-seq from whole organism (ENCLB993BYZ)

description:
https://www.encodeproject.org/experiments/ENCSR213XFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing DAO-5-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR213XFQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR225ALY
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB993BYZ
fragmentation methods: sonication (generic microtip)

tag: antibody

tag: biosample encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to DAO-5

value: hermaphrodite

value: L4/young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: ENCBS810FJH at ENCODE; https://www.encodeproject.org/ENCBS810FJH/


title: Mt-0 infected by S. sclerotiorum rep 2

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB476NLU)

description:
https://www.encodeproject.org/experiments/ENCSR213XFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing DAO-5-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR213XFQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR225ALY
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB476NLU
fragmentation methods: sonication (generic microtip)

value: whole organism

value: whole organisms

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS577ICI at ENCODE; https://www.encodeproject.org/ENCBS577ICI/


title: N10

description: 10x Genomincs

source_name: adjacent pancreas

value: adjacent pancreas


title: Mt-0 infected by S. sclerotiorum rep 1


title: Control ChIP-seq from whole organism (ENCLB088ZPY)

description:
https://www.encodeproject.org/experiments/ENCSR215MXM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG8359-eGFP fusion proteins.
experiment encode accession: ENCSR215MXM
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB088ZPY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG8359-GFP mixed sex embryo (0-14 hours) insertion targeting D. melanogaster hng2

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG8359

value: pooled male and female

value: embryonic

value: 0-14 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS478IOF at ENCODE; https://www.encodeproject.org/ENCBS478IOF/


title: N3

description: 10x Genomincs

value: transcriptomics

value: no


title: TF ChIP-seq from whole organism (ENCLB194ELK)

description:
https://www.encodeproject.org/experiments/ENCSR133PLZ/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing LIN-40-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR133PLZ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR866EST
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB194ELK
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP485 hermaphrodite young adult 57.25 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans lin-40

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to LIN-40

tag: Sex

value: hermaphrodite

value: young adult

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

tag: post synchronization time units

value: hour

value: ENCBS787LNU at ENCODE; https://www.encodeproject.org/ENCBS787LNU/


title: Control ChIP-seq from whole organism (ENCLB990KMS)

description:
https://www.encodeproject.org/experiments/ENCSR216KNP/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG4318-eGFP fusion proteins.
experiment encode accession: ENCSR216KNP
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB990KMS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG4318-GFP mixed sex prepupa (48 days) insertion targeting D. melanogaster CG4318

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG4318

value: pooled male and female

tag: dev stage

value: prepupa

tag: age

value: 48 day

value: ENCBS161DTJ at ENCODE; https://www.encodeproject.org/ENCBS161DTJ/


title: Ll-0 infected by S. sclerotiorum rep 3

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB906LCH)

description:
https://www.encodeproject.org/experiments/ENCSR214WCZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing dmrt99B-eGFP fusion proteins.
experiment encode accession: ENCSR214WCZ
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB906LCH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex embryo (6-16 hours) insertion targeting D. melanogaster dmrt99B

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to dmrt99B

value: embryonic

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS671WAS at ENCODE; https://www.encodeproject.org/ENCBS671WAS/


title: TF ChIP-seq from whole organism (ENCLB507DXX)

description:
https://www.encodeproject.org/experiments/ENCSR214LWK/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR214LWK
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR774SAN
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB507DXX
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG33557-GFP mixed sex embryo (4-10 hours) insertion targeting D. melanogaster CG33557

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG33557

value: ENCBS832CHR at ENCODE; https://www.encodeproject.org/ENCBS832CHR/


title: N2

description: 10x Genomincs

tag: tissue

value: adjacent pancreas

value: transcriptomics

value: no


title: Control ChIP-seq from whole organism (ENCLB974LJU)

description:
https://www.encodeproject.org/experiments/ENCSR139CXE/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing F13H6.1-eGFP fusion proteins.
experiment encode accession: ENCSR139CXE
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB974LJU
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP471 (unc-119(tm4063) III; wgIs471) hermaphrodite late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans bcl-11

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F13H6.1

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: egg bleaching

tag: post synchronization time

value: hour

value: ENCBS108AKX at ENCODE; https://www.encodeproject.org/ENCBS108AKX/


title: TF ChIP-seq from whole organism (ENCLB288RWE)

description:
https://www.encodeproject.org/experiments/ENCSR032FII/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing SNPC-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR032FII
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR814NFI
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB288RWE
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL487 hermaphrodite young adult 60 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans snpc-4

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SNPC-4

value: young adult

value: L1 larva starved after bleaching

tag: link

value: ENCBS507ODV at ENCODE; https://www.encodeproject.org/ENCBS507ODV/


title: TF ChIP-seq from whole organism (ENCLB925BHF)

description:
https://www.encodeproject.org/experiments/ENCSR214LWK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR214LWK
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR774SAN
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB925BHF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG33557

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS650LPV at ENCODE; https://www.encodeproject.org/ENCBS650LPV/


title: Ll-0 infected by S. sclerotiorum rep 2

source_name: Leaves of 5-week old plants

value: Leaves of 5-week old plants

tag: genotype

tag: treatment

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: RELA-KO human CD8+ T cells, donor 5

city: Lyon

first: Yenkel

last: Grinberg-Bleyer

address: 28 rue Laennec

department: Immunity, viruses and inflammation

institute: Cancer Research Center of Lyon

data_processing:
Bcl files were converted to fastq using Bcl2fastq (2.20.0).
Gene expression was quantified using Salmon (0.14.1) and the annotation of protein coding genes from gencode v29.
Transcription matrix was done using R package tximport on the salmon results.
Assembly: hg38
Supplementary files format and content: tab delimited file with samples in columns, genes in rows, and estimated raw counts.

source_name: Human blood

extract_protocol:
RNA was isolated with Nucleospin RNA extraction kits (Macherey Nagel)
libraries were prepared using an Illumina TruSeq Library Kit

value: Human blood

tag: cell type

value: CD8+ T cells

value: RELA-/-


title: TF ChIP-seq from whole organism (ENCLB472SOM)

description:
https://www.encodeproject.org/experiments/ENCSR133PLZ/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing LIN-40-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR133PLZ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR866EST
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB472SOM
fragmentation methods: sonication (generic microtip)

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to LIN-40

value: hermaphrodite

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: hour

value: ENCBS019ZKR at ENCODE; https://www.encodeproject.org/ENCBS019ZKR/


title: T1

description: 10x Genomincs

source_name: pancreatic neuroendocrine tumor

value: pancreatic neuroendocrine tumor

value: transcriptomics

value: no


title: Ll-0 infected by S. sclerotiorum rep 1

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB882FYC)

description:
https://www.encodeproject.org/experiments/ENCSR036PHI/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing BtbVII-eGFP fusion proteins.
experiment encode accession: ENCSR036PHI
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB882FYC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain BtbVII-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster BtbVII

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to BtbVII

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS821ATF at ENCODE; https://www.encodeproject.org/ENCBS821ATF/


title: RELA-KO human CD8+ T cells, donor 4

value: Human blood

value: CD8+ T cells

value: RELA-/-


title: Kyoto infected by S. sclerotiorum rep 3

value: Kyoto

tag: time


title: TF ChIP-seq from whole organism (ENCLB603ORD)

description:
https://www.encodeproject.org/experiments/ENCSR032FII/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing SNPC-4-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR032FII
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR814NFI
encode release date: 2017-11-22
lab: Valerie Reinke, Yale
library encode accession: ENCLB603ORD
fragmentation methods: sonication (generic microtip)

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SNPC-4

value: hermaphrodite

value: young adult

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

value: L1 larva starved after bleaching

tag: post synchronization time units

value: hour

value: ENCBS710QFW at ENCODE; https://www.encodeproject.org/ENCBS710QFW/


title: RELA-KO human CD8+ T cells, donor 6

tag: tissue


title: Control ChIP-seq from whole organism (ENCLB541VYE)

description:
https://www.encodeproject.org/experiments/ENCSR136DEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR136DEQ
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB541VYE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain gcm-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster gcm

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to gcm

value: pooled male and female

value: embryonic

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS759UWP at ENCODE; https://www.encodeproject.org/ENCBS759UWP/


title: TF ChIP-seq from whole organism (ENCLB892KXV)

description:
https://www.encodeproject.org/experiments/ENCSR292NVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HLH-12-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR292NVQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR745OUC
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB892KXV
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP538 (unc-119(tm4063) III; wgIs538) hermaphrodite young adult 64 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans hlh-12

tag: antibody

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HLH-12

tag: worm synchronization stage

tag: post synchronization time

value: ENCBS246BHR at ENCODE; https://www.encodeproject.org/ENCBS246BHR/


title: Kyoto infected by S. sclerotiorum rep 2

value: Leaves of 5-week old plants

tag: genotype

value: Kyoto

tag: treatment

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: RELA-KO human CD8+ T cells, donor 3

value: Human blood

tag: cell type

value: CD8+ T cells

value: RELA-/-


title: TF ChIP-seq from whole organism (ENCLB196CZY)

description:
https://www.encodeproject.org/experiments/ENCSR035GCI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing nau-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR035GCI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR292YZL
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB196CZY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain nau-GFP mixed sex embryo (4-24 hours) insertion targeting D. melanogaster nau

value: nau

tag: biosample encode accession

tag: collection date

tag: geographic location

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to nau

value: pooled male and female

value: embryonic

value: ENCBS988RAJ at ENCODE; https://www.encodeproject.org/ENCBS988RAJ/


title: TF ChIP-seq from whole organism (ENCLB444EKY)

description:
https://www.encodeproject.org/experiments/ENCSR035GCI/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing nau-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR035GCI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR292YZL
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB444EKY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: note

tag: Sex

tag: dev stage

value: Kevin White, UChicago

value: Kevin White

value: ENCBS501JAQ at ENCODE; https://www.encodeproject.org/ENCBS501JAQ/


title: TF ChIP-seq from whole organism (ENCLB536VHL)

description:
https://www.encodeproject.org/experiments/ENCSR292NVQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HLH-12-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR292NVQ
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR745OUC
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB536VHL
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HLH-12

value: hermaphrodite

value: young adult

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

value: L1 larva starved after bleaching

value: hour

value: ENCBS803EZP at ENCODE; https://www.encodeproject.org/ENCBS803EZP/


title: RELA-KO human CD8+ T cells, donor 1

tag: tissue

value: Human blood

value: CD8+ T cells

value: RELA-/-


title: TF ChIP-seq from whole organism (ENCLB003RVL)

description:
https://www.encodeproject.org/experiments/ENCSR035GCI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing nau-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR035GCI
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR292YZL
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB003RVL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: nau

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to nau

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

tag: link

value: ENCBS909QVL at ENCODE; https://www.encodeproject.org/ENCBS909QVL/


title: Control ChIP-seq from whole organism (ENCLB504KBA)

description:
https://www.encodeproject.org/experiments/ENCSR194OUP/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing LIM-6-eGFP fusion proteins.
experiment encode accession: ENCSR194OUP
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB504KBA
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP388 (unc-119(ed3) III; wgIs388) hermaphrodite late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans lim-6

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to LIM-6

value: hermaphrodite

value: late embryonic

tag: worm synchronization stage

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: ENCBS535IZX at ENCODE; https://www.encodeproject.org/ENCBS535IZX/


title: Hs-0 infected by S. sclerotiorum rep 2

value: Leaves of 5-week old plants

tag: genotype

tag: treatment

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB042VYW)

description:
https://www.encodeproject.org/experiments/ENCSR111NKF/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing SDC-2-eGFP fusion proteins.
experiment encode accession: ENCSR111NKF
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB042VYW
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP92 hermaphrodite late embryo 3.25 hours post synchronization using egg bleaching insertion targeting C. elegans sdc-2

tag: biosample encode accession

tag: collection date

tag: geographic location

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SDC-2

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: hour

value: ENCBS492MNG at ENCODE; https://www.encodeproject.org/ENCBS492MNG/


title: Control human CD8+ T cells, donor 6

value: Human blood

tag: cell type

value: CD8+ T cells

value: WT


title: Hs-0 infected by S. sclerotiorum rep 3


title: Control ChIP-seq from whole organism (ENCLB156GJE)

description:
https://www.encodeproject.org/experiments/ENCSR034KIV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG45071-eGFP fusion proteins.
experiment encode accession: ENCSR034KIV
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB156GJE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG6854-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CTPsyn

value: whole organism

value: whole organisms

value: not applicable

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG45071

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS588ILC at ENCODE; https://www.encodeproject.org/ENCBS588ILC/


title: TF ChIP-seq from whole organism (ENCLB991RKF)

description:
https://www.encodeproject.org/experiments/ENCSR111LGE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F13H6.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR111LGE
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR139CXE
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB991RKF
fragmentation methods: sonication (generic microtip)

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F13H6.1

value: hermaphrodite

value: late embryonic

tag: age

value: unknown

tag: lab

value: Valerie Reinke, Yale

tag: source

value: egg bleaching

value: ENCBS699ICR at ENCODE; https://www.encodeproject.org/ENCBS699ICR/


title: Control ChIP-seq from whole organism (ENCLB569FFQ)

description:
https://www.encodeproject.org/experiments/ENCSR030PDY/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing UNC-130-eGFP fusion proteins.
experiment encode accession: ENCSR030PDY
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB569FFQ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain AGK541 ((armSi1[Pmex5::UNC-130::GFP::tbb-2 3'UTR; cb-unc-119(+)II]; unc-119(ed3)III; niDf199IV)) hermaphrodite young adult 56 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. el...

value: whole organism

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to UNC-130

value: young adult

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: hour

tag: link

value: ENCBS180LTV at ENCODE; https://www.encodeproject.org/ENCBS180LTV/


title: Control human CD8+ T cells, donor 4

tag: tissue

value: Human blood

value: CD8+ T cells

value: WT


title: TF ChIP-seq from whole organism (ENCLB681PVW)

description:
https://www.encodeproject.org/experiments/ENCSR134NKA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR134NKA
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR640GRU
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB681PVW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Nf-YB-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Nf-YB

tag: antibody

value: Nf-YB

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Nf-YB

value: pooled male and female

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS893OCY at ENCODE; https://www.encodeproject.org/ENCBS893OCY/


title: Gy-0 infected by S. sclerotiorum rep 3

value: Leaves of 5-week old plants

tag: genotype

tag: treatment

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB555TCN)

description:
https://www.encodeproject.org/experiments/ENCSR134NKA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR134NKA
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR640GRU
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB555TCN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

tag: biosample encode accession

value: ENCBS087VZQ at ENCODE; https://www.encodeproject.org/ENCBS087VZQ/


title: TF ChIP-seq from whole organism (ENCLB441CIL)

description:
https://www.encodeproject.org/experiments/ENCSR111LGE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing F13H6.1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR111LGE
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR139CXE
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB441CIL
fragmentation methods: sonication (generic microtip)

tag: collection date

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to F13H6.1

value: hermaphrodite

value: late embryonic

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS567JPD at ENCODE; https://www.encodeproject.org/ENCBS567JPD/


title: RELA-KO human CD8+ T cells, donor 2

value: Human blood

tag: cell type

value: CD8+ T cells

value: RELA-/-


title: TF ChIP-seq from whole organism (ENCLB327HTF)

description:
https://www.encodeproject.org/experiments/ENCSR110CKX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HIM-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR110CKX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR782TWP
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB327HTF
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL577 hermaphrodite young adult 47 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans him-1

value: whole organisms

value: not applicable

tag: geographic location

tag: encode accession

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HIM-1

value: young adult

value: L1 larva starved after bleaching

value: ENCBS043GBS at ENCODE; https://www.encodeproject.org/ENCBS043GBS/


title: TF ChIP-seq from whole organism (ENCLB592FCR)

description:
https://www.encodeproject.org/experiments/ENCSR134NKA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR134NKA
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR640GRU
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB592FCR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Nf-YB

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Nf-YB

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

tag: age

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS565YYS at ENCODE; https://www.encodeproject.org/ENCBS565YYS/


title: Gy-0 infected by S. sclerotiorum rep 2

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: Control human CD8+ T cells, donor 2

value: Human blood

value: CD8+ T cells

value: WT


title: Kyoto infected by S. sclerotiorum rep 1

value: Kyoto


title: Gy-0 infected by S. sclerotiorum rep 1


title: TF ChIP-seq from whole organism (ENCLB999ZZJ)

description:
https://www.encodeproject.org/experiments/ENCSR110CKX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing HIM-1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR110CKX
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR782TWP
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB999ZZJ
fragmentation methods: sonication (generic microtip)

value: whole organisms

value: not applicable

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to HIM-1

value: hermaphrodite

value: young adult

value: unknown

tag: lab

value: Valerie Reinke, Yale

tag: source

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: hour

tag: link

value: ENCBS740ICN at ENCODE; https://www.encodeproject.org/ENCBS740ICN/


title: Control ChIP-seq from whole organism (ENCLB213GMA)

description:
https://www.encodeproject.org/experiments/ENCSR107LHB/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing HIM-1-eGFP fusion proteins.
experiment encode accession: ENCSR107LHB
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB213GMA
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL576 hermaphrodite L4/young adult 51 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans him-1

value: whole organism

value: L4/young adult

value: ENCBS728WZW at ENCODE; https://www.encodeproject.org/ENCBS728WZW/


title: Es-0 infected by S. sclerotiorum rep 3

tag: tissue

value: Leaves of 5-week old plants

tag: genotype

tag: treatment

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB791IMZ)

description:
https://www.encodeproject.org/experiments/ENCSR033ZHC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR033ZHC
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR472BOK
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB791IMZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG7101 female adult insertion targeting D. melanogaster CG7101

tag: antibody

value: whole organisms

tag: biosample encode accession

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG7101

value: female

value: adult

value: Kevin White, UChicago

value: Kevin White

value: ENCBS455DKA at ENCODE; https://www.encodeproject.org/ENCBS455DKA/


title: TF ChIP-seq from whole organism (ENCLB683PLU)

description:
https://www.encodeproject.org/experiments/ENCSR033ZHC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR033ZHC
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR472BOK
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB683PLU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

tag: geographic location

value: unknown

value: ENCBS007WFE at ENCODE; https://www.encodeproject.org/ENCBS007WFE/


title: Control human CD8+ T cells, donor 1

value: Human blood

tag: cell type

value: CD8+ T cells

value: WT


title: Es-0 infected by S. sclerotiorum rep 2


title: Control ChIP-seq from whole organism (ENCLB708MEO)

description:
https://www.encodeproject.org/experiments/ENCSR033NNL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR033NNL
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB708MEO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain stwl embryo (0-10 hours) insertion targeting D. melanogaster stwl

value: whole organism

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to stwl

value: not collected

value: embryonic

value: 0-10 hour

value: ENCBS826SLY at ENCODE; https://www.encodeproject.org/ENCBS826SLY/


title: Control human CD8+ T cells, donor 5


title: TF ChIP-seq from whole organism (ENCLB441ODB)

description:
https://www.encodeproject.org/experiments/ENCSR107BQR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-85-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR107BQR
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR545DXH
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB441ODB
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP539 (unc-119(tm4063) III; wgIs539) hermaphrodite L1 larva 6 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans nhr-85

value: whole organisms

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to NHR-85

tag: Sex

value: hermaphrodite

tag: dev stage

value: L1 larva

value: Valerie Reinke, Yale

value: Valerie Reinke

value: L1 larva starved after bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS989DRZ at ENCODE; https://www.encodeproject.org/ENCBS989DRZ/


title: Hs-0 infected by S. sclerotiorum rep 1

source_name: Leaves of 5-week old plants

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB169AGL)

description:
https://www.encodeproject.org/experiments/ENCSR107BQR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing NHR-85-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR107BQR
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR545DXH
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB169AGL
fragmentation methods: sonication (generic microtip)

value: whole organism

value: not applicable

tag: age

value: unknown

tag: lab

tag: source

tag: worm synchronization stage

value: ENCBS219LUD at ENCODE; https://www.encodeproject.org/ENCBS219LUD/


title: Es-0 infected by S. sclerotiorum rep 1

tag: tissue

tag: genotype

tag: treatment


title: Control ChIP-seq from whole organism (ENCLB373WUO)

description:
https://www.encodeproject.org/experiments/ENCSR007JPR/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing REC-8-eGFP fusion proteins.
experiment encode accession: ENCSR007JPR
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB373WUO
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain YL581 hermaphrodite young adult 50 hours post synchronization at L1 larva starved after bleaching stage insertion targeting C. elegans rec-8

tag: biosample encode accession

tag: collection date

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to REC-8

value: young adult

tag: link

value: ENCBS888SNS at ENCODE; https://www.encodeproject.org/ENCBS888SNS/


title: Vikl-077_non-SVR_pre

city: Kanazawa

first: Kazunori

last: Kawaguchi

address: 13-1 Takara-Machi

department: Gastroenterology

country: Japan

institute: Kanazawa University

data_processing:
Flow cell specified by manufacture were used for sequencing. Read length was 151bp (valid read length was 150bp).
transcribed region was obtained.
Assembly: human NCBI build37.2
Supplementary files format and content: GTF format: transcribed region was included for each sample.

source_name: peripheral blood mononuclear cells

extract_protocol:
total RNA was isolated from PBMCs, 1.2x10^7 to 2.8x10^ per sample,  collected in PAXgene (Becton Dickinson) using a PAXgene Blood RNA Kit (QIAGEN, Valencia, CA).
RNA libraries for RNA-seq were prepared using TruSeq Standard mRNA Library Prep kit (illumina) following manufacture's protocols. Library length was 310~387bp.

tag: cell type

value: peripheral blood mononuclear cells

tag: group


title: Vikl-046_non-SVR_post

value: ombitasvir/paritaprevir/ritonavir


title: Control human CD8+ T cells, donor 3

source_name: Human blood

value: Human blood

value: CD8+ T cells

value: WT


title: Vikl-077_non-SVR_post


title: Control ChIP-seq from whole organism (ENCLB590CXV)

description:
https://www.encodeproject.org/experiments/ENCSR032KWU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG4328-eGFP fusion proteins.
experiment encode accession: ENCSR032KWU
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB590CXV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG4328-GFP mixed sex embryo (8-24 hours) insertion targeting D. melanogaster CG4328

value: whole organisms

tag: geographic location

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG4328

tag: Sex

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: Kevin White

value: ENCBS262OKU at ENCODE; https://www.encodeproject.org/ENCBS262OKU/


title: Vikl-046_non-SVR_pre


title: Control ChIP-seq from whole organism (ENCLB150PRU)

description:
https://www.encodeproject.org/experiments/ENCSR213QMS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing kni-eGFP fusion proteins.
experiment encode accession: ENCSR213QMS
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB150PRU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain kni-GFP mixed sex embryo (0-14 hours) insertion targeting D. melanogaster kni

value: whole organism

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to kni

tag: dev stage

value: 0-14 hour

value: ENCBS371TAF at ENCODE; https://www.encodeproject.org/ENCBS371TAF/


title: Control ChIP-seq from whole organism (ENCLB853XRV)

description:
https://www.encodeproject.org/experiments/ENCSR187HHD/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing ETS-4-eGFP fusion proteins.
experiment encode accession: ENCSR187HHD
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB853XRV
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain OP509 (unc-119(tm4063) III; wgIs509) hermaphrodite late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans ets-4

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to ETS-4

value: hermaphrodite

value: late embryonic

tag: age

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

value: egg bleaching

tag: post synchronization time

tag: post synchronization time units

value: hour

value: ENCBS604ICW at ENCODE; https://www.encodeproject.org/ENCBS604ICW/


title: Ei-2 infected by S. sclerotiorum rep 2

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: TF ChIP-seq from whole organism (ENCLB084GNM)

description:
https://www.encodeproject.org/experiments/ENCSR132XDY/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6654-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR132XDY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR693BJZ
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB084GNM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG6654-GFP mixed sex embryo (0-12 hours) insertion targeting D. melanogaster CG6654

tag: antibody

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG6654

value: pooled male and female

value: embryonic

value: 0-12 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS232GGB at ENCODE; https://www.encodeproject.org/ENCBS232GGB/


title: Vikl-050_non-SVR_post

value: peripheral blood mononuclear cells

tag: treatment

value: ombitasvir/paritaprevir/ritonavir


title: TF ChIP-seq from whole organism (ENCLB434OMF)

description:
https://www.encodeproject.org/experiments/ENCSR132XDY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG6654-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR132XDY
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR693BJZ
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB434OMF
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: biosample encode accession

tag: collection date

value: not applicable

value: ENCBS242UET at ENCODE; https://www.encodeproject.org/ENCBS242UET/


title: Pilot8 Soil Community DNA Seqeunces from Indian University

city: Bundoora

first: Anya

last: Shindler

state: VIC

address: 1 Kingsbury Drive

country: Australia

institute: La Trobe University

description: 16S seqeuncing was conducted on DNA extracted from soil obtained from eight plots. Four from around a hospital and four from a university, both located in India

data_processing:
Fastq files obtained from the Miseq machine were processed using QIIME2 2021.11
Excel files were the end product from the QIIME2 processing
Assembly: N/A
Supplementary files format and content: Processed files are in excel .csv format.  The POTU contains the OTUs obtained, the Ptax.csv files contains the Taxonomy identified during the QIIME2 processing, and PSamples.csv contains the metadata for the other two .csv files.
Library strategy: 16S Metagenomic

organism: Bacteria

extract_protocol:
Qiagen DNeasy® PowerSoil® Kits
Illumina 16S Metagenomic Sequencing Library Preparation

tag: location

value: University

tag: cell line

tag: cell type

tag: genotype


title: Control ChIP-seq from whole organism (ENCLB177MOZ)

description:
https://www.encodeproject.org/experiments/ENCSR101VVI/
***************
biological replicate number: 1
technical replicate number: 1
description: This is the ChIP-seq control of transgenic worms expressing SMA-3-eGFP fusion proteins.
experiment encode accession: ENCSR101VVI
assay title: Control ChIP-seq
assembly: ce11, ce10
encode release date: 2016-05-10
lab: Valerie Reinke, Yale
library encode accession: ENCLB177MOZ
fragmentation methods: sonication (generic microtip)

source_name: Caenorhabditis elegans strain CS152 (sma-3(wk30);qcIs[gfp::sma-3+rol-6]) hermaphrodite L2 larva 24 hours post synchronization at L1 larva starved after bleaching stage whole organism genetically modified (insertion) using microinjection targeting C. ...

tag: geographic location

tag: encode accession

tag: note

value: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to SMA-3

value: hermaphrodite

value: L2 larva

value: unknown

value: Valerie Reinke, Yale

value: Valerie Reinke

tag: worm synchronization stage

value: L1 larva starved after bleaching

value: hour

tag: link

value: ENCBS723SCX at ENCODE; https://www.encodeproject.org/ENCBS723SCX/


title: Ei-2 infected by S. sclerotiorum rep 1

tag: tissue

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: Eds-1 infected by S. sclerotiorum rep 5

tag: time


title: Pilot7 Soil Community DNA Seqeunces from Indian University


title: TF ChIP-seq from whole organism (ENCLB840RZK)

description:
https://www.encodeproject.org/experiments/ENCSR032DLA/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Usf-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR032DLA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR481GXM
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB840RZK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Usf-GFP mixed sex embryo (0-16 hours) insertion targeting D. melanogaster Usf

tag: antibody

value: Usf

value: whole organism

value: whole organisms

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Usf

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

tag: age

value: 0-16 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS373NZW at ENCODE; https://www.encodeproject.org/ENCBS373NZW/


title: Eds-1 infected by S. sclerotiorum rep 4

tag: treatment


title: Pilot6 Soil Community DNA Seqeunces from Indian Hospital

value: Hospital


title: Vikl-055_non-SVR_pre

value: peripheral blood mononuclear cells

tag: group


title: Eds-1 infected by S. sclerotiorum rep 3


title: Vikl-055_non-SVR_post

value: ombitasvir/paritaprevir/ritonavir


title: TF ChIP-seq from whole organism (ENCLB258XGN)

description:
https://www.encodeproject.org/experiments/ENCSR132VFF/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR132VFF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR074DEG
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB258XGN
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG9948 pupa (24 hours) insertion targeting D. melanogaster CG9948

tag: biosample encode accession

tag: collection date

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG9948

value: not collected

value: pupa

value: 24 hour

tag: lab

tag: source

value: ENCBS818LLH at ENCODE; https://www.encodeproject.org/ENCBS818LLH/


title: TF ChIP-seq from whole organism (ENCLB212DGB)

description:
https://www.encodeproject.org/experiments/ENCSR032DLA/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Usf-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR032DLA
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR481GXM
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB212DGB
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: Usf

value: whole organism

value: whole organisms

tag: geographic location

value: ENCBS698ZSQ at ENCODE; https://www.encodeproject.org/ENCBS698ZSQ/


title: Pilot5 Soil Community DNA Seqeunces from Indian Hospital

tag: location

tag: cell line

tag: cell type

tag: genotype


title: Vikl-021_SVR_post


title: Pilot4 Soil Community DNA Seqeunces from Indian University

value: University


title: Eds-1 infected by S. sclerotiorum rep 2

tag: tissue

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: Vikl-021_SVR_pre


title: Eds-1 infected by S. sclerotiorum rep 1

tag: time


title: Ei-2 infected by S. sclerotiorum rep 3


title: TF ChIP-seq from whole organism (ENCLB879HKC)

description:
https://www.encodeproject.org/experiments/ENCSR132VFF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing -eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR132VFF
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR074DEG
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB879HKC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

tag: encode accession

tag: note

value: Kevin White, UChicago

value: Kevin White

tag: link

value: ENCBS492CIE at ENCODE; https://www.encodeproject.org/ENCBS492CIE/


title: Control ChIP-seq from whole organism (ENCLB527MHQ)

description:
https://www.encodeproject.org/experiments/ENCSR306EEX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing salr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR306EEX
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB527MHQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain salr-GFP mixed sex prepupa (24 hours) insertion targeting D. melanogaster salr

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to salr

tag: Sex

value: pooled male and female

tag: dev stage

value: prepupa

tag: age

value: ENCBS067LKA at ENCODE; https://www.encodeproject.org/ENCBS067LKA/


title: Vikl-047_SVR_post

value: peripheral blood mononuclear cells

tag: treatment

value: ombitasvir/paritaprevir/ritonavir

tag: group


title: Pilot3 Soil Community DNA Seqeunces from Indian University


title: Ct-1 infected by S. sclerotiorum rep 4


title: Pilot2 Soil Community DNA Seqeunces from Indian Hospital

value: Hospital


title: Vikl-047_SVR_pre


title: Ct-1 infected by S. sclerotiorum rep 3


title: Pilot1 Soil Community DNA Seqeunces from Indian Hospital


title: Vikl-020_SVR_post


title: Ct-1 infected by S. sclerotiorum rep 2


title: TF ChIP-seq from whole organism (ENCLB157RIW)

description:
https://www.encodeproject.org/experiments/ENCSR302AQS/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG4707-eGFP fusion proteins.
experiment encode accession: ENCSR302AQS
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR114LFX
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB157RIW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG4707-GFP mixed sex embryo (0-14 hours) insertion targeting D. melanogaster CG4707

value: whole organism

value: whole organisms

tag: biosample encode accession

tag: collection date

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG4707

value: embryonic

value: 0-14 hour

tag: lab

tag: source

value: ENCBS129IZC at ENCODE; https://www.encodeproject.org/ENCBS129IZC/


title: TF ChIP-seq from whole organism (ENCLB177GCT)

description:
https://www.encodeproject.org/experiments/ENCSR302AQS/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG4707-eGFP fusion proteins.
experiment encode accession: ENCSR302AQS
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR114LFX
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB177GCT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: geographic location

value: Kevin White, UChicago

value: ENCBS842IXI at ENCODE; https://www.encodeproject.org/ENCBS842IXI/


title: Ct-1 infected by S. sclerotiorum rep 1

value: Leaves of 5-week old plants

tag: genotype

value: infected by S. sclerotiorum (FRT)

value: 24 hours


title: Vikl-020_SVR_pre

tag: cell type


title: Col-0 infected by S. sclerotiorum rep 5

tag: tissue

tag: time


title: Vikl-034_SVR_post


title: Vikl-034_SVR_pre


title: Control ChIP-seq from whole organism (ENCLB936QPH)

description:
https://www.encodeproject.org/experiments/ENCSR300JHR/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing l(3)neo38-eGFP fusion proteins.
experiment encode accession: ENCSR300JHR
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB936QPH
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain l(3)neo38-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster l(3)neo38

value: not applicable

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to l(3)neo38

value: pooled male and female

value: 0-24 hour

value: Kevin White

value: ENCBS852FMX at ENCODE; https://www.encodeproject.org/ENCBS852FMX/


title: Col-0 infected by S. sclerotiorum rep 4


title: Vikl-001_SVR_post

value: peripheral blood mononuclear cells

value: ombitasvir/paritaprevir/ritonavir


title: Vikl-050_non-SVR_pre


title: Col-0 infected by S. sclerotiorum rep 3


title: TF ChIP-seq from whole organism (ENCLB645EZR)

description:
https://www.encodeproject.org/experiments/ENCSR296MRL/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG17385-eGFP fusion proteins.
experiment encode accession: ENCSR296MRL
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR174KFQ
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB645EZR
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG17385-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG17385

tag: antibody

value: whole organism

value: whole organisms

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG17385

value: ENCBS567QVP at ENCODE; https://www.encodeproject.org/ENCBS567QVP/


title: SSL rep3

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina Casava1.7 software used for basecalling.
The genome of Lactuca sativa (version: Lsativa_467_v5) from JGI (Joint Genome Institute, Berkeley, USA) was used as the reference genome for RNA-seq analysis. The cleaned reads of each sample were mapped individually to the reference sequences using the STAR package
The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2) (Anders et al., 2015), samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates, choose and count uniquely mapped reads for gene expression analysis
The counted reads of each gene were analyzed by a DESeq2-based R pipeline. Differentially expressed (DE) genes were analyzed in a pairwise comparison between genotypes 60814 and ‘Okeechobee’ samples. Transcripts per million (TPM) counts were averaged across biological replicates and genes were filtered for moderate expression (TPM ≥ 100) in at least one genotype.
Assembly: Arabidopsis thaliana , version: Lsativa_467_v5
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

organism: Lactuca sativa

source_name: leaf

growth_protocol: Lettuce plants were grown in 4-inch pots in a growth chamber maintained with a 16 h day light cycle at 22 ºC.

extract_protocol: Upon reaching maturity, RNA was extracted using the Nucleospin RNA Plant and Fungi kit (Machery-Nagel, Düren, Germany) with on-column DNase treatment, and initial quantification and quality was checked on a NanoDrop OneC spectrophotometer

treatment_protocol: Three romaine lettuces (Lactuca sativa var. Longifolia) grown in Belle Glade, FL were selected for leaf tissue histological analysis, including the commercial cultivars ‘Manatee’, and ‘Okeechobee’ and an experimental breeding line named 60184. These accessions were selected from a larger set of romaine accessions based on genotypic variability in their shelf life

value: leaf

tag: location

value: Belle Glade, FL

tag: tissue type

value: mature


title: Col-0 infected by S. sclerotiorum rep 2

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)


title: Control ChIP-seq from whole organism (ENCLB193XHY)

description:
https://www.encodeproject.org/experiments/ENCSR303ZWP/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing dac-eGFP fusion proteins.
experiment encode accession: ENCSR303ZWP
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-10
lab: Kevin White, UChicago
library encode accession: ENCLB193XHY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain dac-GFP mixed sex prepupa (48 days) insertion targeting D. melanogaster dac

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to dac

tag: Sex

tag: dev stage

value: prepupa

tag: age

value: 48 day

value: Kevin White, UChicago

tag: link

value: ENCBS568RMK at ENCODE; https://www.encodeproject.org/ENCBS568RMK/


title: SWAP_1511_1515_S288vsTAT12

type: RNA

city: Cuernavaca

first: Luis

last: Caspeta

state: Morelos

address: Av Universidad 2001

department: Ingeniería Celular y Biocatálisis

country: Mexico

institute: Instituto de Biotecnología - Universidad Nacional Autónoma de México

description:
Gene expression of TAT12 strain compared with S288C under optimal growth conditions
YOMWG_15_11.txt:  S288C (Alexa555), TAT12 (Alexa647)
YOMWG_15_15.txt:  TAT12 (Alexa555), S288C (Alexa647)

hyb_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647. Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using 10µm resolution. For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing: Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM ( http://www.ifc.unam.mx/genarise/ ). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes. In the Matrix array of processed data, each sample column represent two merged arrays- For example, Sample 1 column represent the merged results of array YOMWG_15_09 and dye-swap array YOMWG_15_10. Each sample column represents Z-scores, and the Ri log-ratio represent TAT12/S288 ratios.

label: Alexa555, Alexa647

organism: Saccharomyces cerevisiae

label_protocol: Yeast 50-mer oligo library from MWGBiotech Oligo Sets (http:/www.mwgbiotech.com) were resuspended to 40μM in Micro Spotting solution (Telechem International Inc.). SuperAmine coated slides 25x75 mm (TeleChem International INC) were printed in duplicate, and fixed at 80°C or 4 hours. For pre-hybridization the slides were re-hydrated with water vapor at 60°C, and fixed with two cycles of UV light (1200J). After boiling for two minutes at 92°C, slides were washed with 95% ethanol for one minute and prehybridzed in 5X SSC, 0.1% SDS and 1% BSA for one hour at 42°C .The slides were washed and dried for further hybridization.

growth_protocol: All the strains were growth in flasks containing defined media with 2% glucose, pH 5.0. Flasks were incubated at 30°C and 250 RPMs of agitation.

extract_protocol: The total RNA was extracted with the YeaStar RNA kit (Zymo Research, Irvine). The RNA was sent to the DNA Microarrays Unit of the Institute of Cellular Physiology, in the National Autonomous University of Mexico for cDNA synthesis, cDNA staining, and hybridization in DNA microarrays.

treatment_protocol: All the strains populations were sampled in the middle of exponential phase of growth

tag: strain

tag: phase of growth

value: exponential

label: Alexa647, Alexa555


title: Vikl-001_SVR_pre

value: peripheral blood mononuclear cells

tag: group


title: SWAP_1516_1517_TTY23vsTAT12

description:
Gene expression of TAT12 strain compared with TTY23 under optimal growth conditions
YOMWG_15_16.txt:  TTY23 (Alexa555), TAT12 (Alexa647)
YOMWG_15_17.txt:  TAT12 (Alexa555), TTY23 (Alexa647)

data_processing: Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM ( http://www.ifc.unam.mx/genarise/ ). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes. In the Matrix array of processed data, each sample column represent two merged arrays- For example, Sample 1 column represent the merged results of array YOMWG_15_09 and dye-swap array YOMWG_15_10. Each sample column represents Z-scores, and the Ri log-ratio represent TAT12/TTY23" ratios.


title: Control ChIP-seq from whole organism (ENCLB623HAO)

description:
https://www.encodeproject.org/experiments/ENCSR303RFP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG34376-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR303RFP
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB623HAO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG34376-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster CG34376

value: whole organism

tag: biosample encode accession

tag: collection date

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG34376

value: pooled male and female

value: embryonic

value: 0-24 hour

tag: lab

tag: source

value: Kevin White

value: ENCBS538EBB at ENCODE; https://www.encodeproject.org/ENCBS538EBB/


title: SSL rep2

tag: tissue

value: leaf

value: Belle Glade, FL

value: mature

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB192YIY)

description:
https://www.encodeproject.org/experiments/ENCSR296MRL/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing CG17385-eGFP fusion proteins.
experiment encode accession: ENCSR296MRL
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR174KFQ
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB192YIY
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: antibody

value: whole organisms

value: not applicable

tag: encode accession

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG17385

value: ENCBS242GJT at ENCODE; https://www.encodeproject.org/ENCBS242GJT/


title: Vikl-080_SVR_post

tag: cell type

tag: treatment

value: ombitasvir/paritaprevir/ritonavir


title: Col-0 infected by S. sclerotiorum rep 1

source_name: Leaves of 5-week old plants

value: Leaves of 5-week old plants

value: infected by S. sclerotiorum (FRT)

tag: time

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB547GSE)

description:
https://www.encodeproject.org/experiments/ENCSR203PPN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Oli-eGFP fusion proteins.
experiment encode accession: ENCSR203PPN
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB547GSE
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster mixed sex embryo (6-18 hours) insertion targeting D. melanogaster Oli

value: whole organism

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Oli

tag: Sex

tag: dev stage

tag: age

value: Kevin White, UChicago

tag: link

value: ENCBS134NDV at ENCODE; https://www.encodeproject.org/ENCBS134NDV/


title: SSL rep1

tag: location

tag: tissue type


title: SWAP_1518_1519_AT22vsTAT12

description:
Gene expression of TAT12 strain compared with AT22 under optimal growth conditions
YOMWG_15_18.txt:  AT22 (Alexa555), TAT12 (Alexa647)
YOMWG_15_19.txt:  TAT12 (Alexa555), AT22 (Alexa647)

data_processing: Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM ( http://www.ifc.unam.mx/genarise/ ). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes. In the Matrix array of processed data, each sample column represent two merged arrays- For example, Sample 1 column represent the merged results of array YOMWG_15_09 and dye-swap array YOMWG_15_10. Each sample column represents Z-scores, and the Ri log-ratio represent TAT12/AT22 ratios.

tag: strain

tag: phase of growth

value: exponential


title: SWAP_1509_1510_S288vsAT22

description:
Gene expression of AT22 strain compared with S288C under optimal growth conditions
YOMWG_15_09.txt:  S288C (Alexa555), AT22 (Alexa647)
YOMWG_15_10.txt:  AT22 (Alexa555), S288C (Alexa647)

data_processing: Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM ( http://www.ifc.unam.mx/genarise/ ). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes. In the Matrix array of processed data, each sample column represent two merged arrays- For example, Sample 1 column represent the merged results of array YOMWG_15_09 and dye-swap array YOMWG_15_10. Each sample column represents Z-scores, and the Ri log-ratio represent AT22/S288 ratios.


title: Vikl-080_SVR_pre

source_name: peripheral blood mononuclear cells

value: peripheral blood mononuclear cells

tag: group


title: Co-1 infected by S. sclerotiorum rep 3

tag: tissue


title: Vikl-043_SVR_post


title: Co-1 infected by S. sclerotiorum rep 2

tag: genotype