title: Control ChIP-seq from whole organism (ENCLB926YEG)

description:
https://www.encodeproject.org/experiments/ENCSR286EOA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing mirr-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR286EOA
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB926YEG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain mirr-GFP mixed sex embryo (4-20 hours) insertion targeting D. melanogaster mirr

value: whole organism

value: whole organisms

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

tag: lab

tag: source

tag: link

value: ENCBS051FFA at ENCODE; https://www.encodeproject.org/ENCBS051FFA/


title: ChIPseq NGN2 24h AroPERFECT Rep 1

status: Public on Feb 27 2024

type: SRA

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: ChIP-seq

library_source: genomic

data_processing:
Reads were mapped to genome using BWA and samtools was used for SAM to BAM conversion, sorting and indexing. Genome Analysis Toolkit v4 was used to remove duplicated reads. Peak calling was then performed using MACS3 v3.0.0 b1 using the input of the respective sample
genome_build: hg38

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Cells were detached with Accutase solution (Sigma), washed twice in PBS and fixed in rotation with 1% formaldehyde for 10 minutes at room temperature. Subsequently, the reaction was quenched by addition of glycine leading to a final concentration of 125 mM. Per replicate, three million cells were used as starting material. In brief, we followed the ChIPmentation protocol version 3 for histone marks and transcription factors (Schmidl et al., 2015).  Cells were lysed in lysis buffer 3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% N-laurosylsarcosine) supplemented with 1x cOmplete protease inhibitor cocktail. Afterwards, chromatin was sonicated for 10 minutes using a Covaris E220evolution focused-ultrasonicator with 2% duty cycles, 105 W peak incident power and 200 cycles per burst. Lysates were clarified by centrifugation for 10 minutes at 20,000g. 10% of the clarified lysate was put aside as input control. The remaining lysate was mixed with 50 µL of equilibrated anti-FLAG antibody (Merck, F1804, 1 µg total) coupled to DynabeadsTM Protein G magnetic beads (Invitrogen) and incubated on a 3D-shaker over night at 4oC. The next day, samples were washed twice in TF-wash buffer I (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% sodium dodecyl sulfate, 1% Triton-X-100 and 2 mM EDTA pH 8.0) followed by two washes in TF-wash buffer III (10mM Tris-HCl pH 8.0, 250 mM LiCl, 1% Triton-X-100, 0.7% sodium deoxycholate and 1 mM EDTA pH 8.0) and a final wash with 10 mM Tris-HCl pH 8.0
All samples were tagmented for 5 minutes at 37oC using the Illumina Tagment DNA kit and immediately put on ice. Tagmented chromatin was washed in ice-cold wash buffer I and TET buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA pH 8.0, 0.2% Tween-20) twice each, and reverse-crosslinked for 1h at 55oC and 9h at 65oC in the presence of 300 mM NaCl and proteinase K (Ambion). Subsequently, DNA was purified using AMPureXP beads. Sequencing libraries were amplified using the Kapa HiFi HotStart Ready Mix (Roche) and Nextera custom primers (Illumina) (Buenrostro et al., 2013) for a total of 12 cycles
Paired-end 100 with 50 million fragments per library

tag: cell type

tag: age

tag: chip antibody

value: anti-FLAG antibody Merck, F1804


title: ChIPseq NGN2 24h AroPERFECT Rep 2

description: ChIP-seq


title: ZT61 Mature bio rep 1

city: Melbourne

first: Christopher

middle: Robert

last: Buckley

state: VIC

address: School of BioSciences, Level 3, Building 184, The University of Melbourne

country: Australia

institute: University of Melbourne

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT61_M_R1

library_source: transcriptomic

data_processing:
bcl2fastq 2.17. Raw data was filtered as follows: (1) Discard pair-end reads with adapter; (2) Discard pair-end reads when the content of N bases is more than 10% in either read; (3) Discard pair-end reads when the ration of bases of low quality (Q<20) is more than 0.5 in either read.
STAR. Filtered reads were mapped to the T. aestivum cv. Mace (PGSBv2.1) genome sequence and annotation using STAR with default parameters
Cufflinks. Mapped reads were quantified and normalised using the cuffquant and cuffnorm modules of Cufflinks with default parameters
Assembly: Triticum aestivum cv. Mace. Genbank assembly ID:  GCA_903994175.1
Supplementary files format and content: tab-delimited text file includes raw counts for mature samples
Supplementary files format and content: tab-delimited text file includes raw counts for senescent samples
Supplementary files format and content: tab-delimited text file includes fpkm for mature samples
Supplementary files format and content: tab-delimited text file includes fpkm for senescent samples

molecule: total RNA

organism: Triticum aestivum

source_name: whole flag leaf

growth_protocol: Seeds were chilled at 4°C for 48 h and sown in a mix of sterilised potting soil with 4.5 g/L Osmocote 6-9 month slow-release fertiliser. Growth room was set to 12 h light (200-280 µmol m-2 s-1, 20ºC), 12 h dark (15ºC) prior to switch to continuous conditions.

extract_protocol:
Frozen leaf tissue was ground to a fine powder in liquid nitrogen-cooled mortar and pestles. Lysate buffer was added to the tissue (350 µL per 100 mg of tissue) and the mixture was vortexed immediately. RNA was extracted using ISOLATE II RNA Plant Kit (Meridian Bioscience). RNA from two individual leaf samples was equally pooled to provide two replicates for sequencing.
Library preparation and RNA-sequencing was performed by a commercial provider (Azenta). Library preparations were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs; NEB).

treatment_protocol: When plants had concurrently reached the mature and senescent developmental stages, at dawn (Zeitgeber Time 0; ZT0), the growth room was set to continuous light and temperature (20ºC) and whole flag leaves from the primary tiller of four plants were collected every 2 h from ZT45 to ZT91 (48 h).

tag: tissue

value: whole flag leaf

tag: cultivar

value: Mace

tag: treatment

value: Mature leaf

tag: time


title: Uninfected Col-0 rep 9

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

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: Leaves of 5-week old plants

tag: genotype

value: Uninfected (LNI)

value: 24 hours


title: Uninfected Col-0 rep 8


title: ZT59 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT59_S_R2

value: Senescent leaf


title: ChIPseq NGN2 24h AroLITE Rep 2

description: ChIP-seq


title: TF ChIP-seq from whole organism (ENCLB868LEK)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR120ICM/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Dp-eGFP fusion proteins.
experiment encode accession: ENCSR120ICM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR333ZYI
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB868LEK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

organism: Drosophila melanogaster

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

tag: antibody

value: Dp

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: note

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

tag: Sex

value: pooled male and female

tag: dev stage

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS735YJU at ENCODE; https://www.encodeproject.org/ENCBS735YJU/


title: Uninfected Col-0 rep 7


title: ZT59 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT59_S_R1


title: Uninfected Col-0 rep 6


title: ZT59 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT59_M_R2


title: TF ChIP-seq from whole organism (ENCLB259GSS)

description:
https://www.encodeproject.org/experiments/ENCSR119OUI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing twi-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR119OUI
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR981YAA
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB259GSS
size range: 200-800

source_name: Drosophila melanogaster strain twi mixed sex embryo (2-12 hours) insertion targeting D. melanogaster twi

value: twi

value: whole organism

value: whole organisms

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

tag: lab

tag: source

tag: link

value: ENCBS940YOE at ENCODE; https://www.encodeproject.org/ENCBS940YOE/


title: TF ChIP-seq from whole organism (ENCLB792MRQ)

description:
https://www.encodeproject.org/experiments/ENCSR120ICM/
***************
biological replicate number: 3
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Dp-eGFP fusion proteins.
experiment encode accession: ENCSR120ICM
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR333ZYI
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB792MRQ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: age

value: ENCBS092CMA at ENCODE; https://www.encodeproject.org/ENCBS092CMA/


title: Uninfected Col-0 rep 5

tag: tissue

value: Leaves of 5-week old plants

value: Uninfected (LNI)

value: 24 hours


title: ChIPseq NGN2 24h AroLITE Rep 1

description: ChIP-seq

tag: cell type

tag: chip antibody

value: anti-FLAG antibody Merck, F1804


title: TF ChIP-seq from whole organism (ENCLB894LBC)

description:
https://www.encodeproject.org/experiments/ENCSR119OUI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing twi-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR119OUI
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR981YAA
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB894LBC
size range: 200-800

value: not applicable

value: ENCBS445LDK at ENCODE; https://www.encodeproject.org/ENCBS445LDK/


title: Uninfected Col-0 rep 4

tag: treatment

tag: time


title: Bulk RNAseq NGN2 AroPERFECT Rep 2

description: Bulk RNA-seq

data_processing:
Reads were mapped to a genome using STAR aligner. Count read tables were generated by the same program
genome_build: hg38

molecule: polyA RNA

extract_protocol:
ZIP13K2 induced neurons were harvested following the Direct-zolTM RNA MicroPrep Kit (Zymo Research) standard protocol
1 μg of RNA of each sample was used as input for library preparation using the KAPA Stranded mRNA-Seq Kit (Roche) following the manufacturer’s instructions. Unique Dual-Indexed Set-B (UDI; KAPA biosystems) adapters were ligated and the library was amplified for 8 cycles
Paired-end 100 with 50 million fragments per library


title: ZT59 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT59_M_R1

value: whole flag leaf

tag: cultivar

value: Mace

value: Mature leaf


title: Control ChIP-seq from whole organism (ENCLB356SVC)

description:
https://www.encodeproject.org/experiments/ENCSR119OOH/
***************
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: ENCSR119OOH
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-05-16
lab: Kevin White, UChicago
library encode accession: ENCLB356SVC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: biosample encode accession

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

value: pooled male and female

value: embryonic

value: 0-12 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS098ZBC at ENCODE; https://www.encodeproject.org/ENCBS098ZBC/


title: ZT57 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT57_S_R2

value: Senescent leaf


title: Uninfected Co-1 rep 3

value: Leaves of 5-week old plants

tag: genotype


title: Uninfected Co-1 rep 2

value: Uninfected (LNI)


title: Bulk RNAseq NGN2 AroPERFECT Rep 1

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB275QSZ)

description:
https://www.encodeproject.org/experiments/ENCSR118TAH/
***************
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: ENCSR118TAH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR188ZKB
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB275QSZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG17806 pupa (24 hours) insertion targeting D. melanogaster CG17806

tag: antibody

value: whole organism

value: whole organisms

tag: collection date

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG17806

value: not collected

value: pupa

value: 24 hour

value: ENCBS112MWA at ENCODE; https://www.encodeproject.org/ENCBS112MWA/


title: Bulk RNAseq NGN2 AroLITE Rep 3

description: Bulk RNA-seq


title: ZT57 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT57_M_R2

value: whole flag leaf

value: Mace

value: Mature leaf


title: TF ChIP-seq from whole organism (ENCLB155WSM)

description:
https://www.encodeproject.org/experiments/ENCSR118TAH/
***************
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: ENCSR118TAH
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR188ZKB
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB155WSM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: not applicable

tag: encode accession

tag: note

tag: Sex

value: ENCBS147PQR at ENCODE; https://www.encodeproject.org/ENCBS147PQR/


title: Uninfected Co-1 rep 1

value: 24 hours


title: Bulk RNAseq NGN2 AroLITE Rep 2

description: Bulk RNA-seq


title: ZT57 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT57_M_R1


title: Control ChIP-seq from whole organism (ENCLB955CXV)

description:
https://www.encodeproject.org/experiments/ENCSR010TXY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing ash1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR010TXY
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB955CXV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Ash1-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster ash1

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to Ash1

value: pooled male and female

tag: dev stage

value: embryonic

value: 0-24 hour

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

value: ENCBS629UGI at ENCODE; https://www.encodeproject.org/ENCBS629UGI/


title: Bulk RNAseq NGN2 AroLITE Rep 1

description: Bulk RNA-seq

tag: age


title: Uninfected Bor-1 rep 3

tag: tissue

value: Leaves of 5-week old plants

value: Uninfected (LNI)


title: Bulk RNAseq NGN2 AroPERFECT Rep 3

description: Bulk RNA-seq

tag: cell type


title: Control ChIP-seq from whole organism (ENCLB401KXL)

description:
https://www.encodeproject.org/experiments/ENCSR116ZCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing REPTOR-eGFP fusion proteins.
experiment encode accession: ENCSR116ZCQ
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-01-11
lab: Kevin White, UChicago
library encode accession: ENCLB401KXL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG18619-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster REPTOR-BP

value: whole organism

value: whole organisms

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

tag: link

value: ENCBS540WPL at ENCODE; https://www.encodeproject.org/ENCBS540WPL/


title: ZT55 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT55_S_R2

value: whole flag leaf

value: Mace

tag: treatment

value: Senescent leaf

tag: time


title: Bulk RNAseq NGN2 WT Rep 3

description: Bulk RNA-seq


title: Uninfected Bor-1 rep 1

value: 24 hours


title: ZT55 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT55_S_R1

tag: cultivar


title: ZT55 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT55_M_R2

value: Mature leaf


title: Bulk RNAseq NGN2 WT Rep 1

description: Bulk RNA-seq


title: Control ChIP-seq from whole organism (ENCLB619VQY)

description:
https://www.encodeproject.org/experiments/ENCSR111RAO/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing trem-eGFP fusion proteins.
experiment encode accession: ENCSR111RAO
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB619VQY
size range: 200-800

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

tag: biosample encode accession

value: not applicable

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

value: pooled male and female

value: 0-14 hour

value: ENCBS175VJX at ENCODE; https://www.encodeproject.org/ENCBS175VJX/


title: Bulk RNAseq NGN2 WT Rep 2

description: Bulk RNA-seq


title: Uninfected Bor-1 rep 2

tag: genotype


title: TF ChIP-seq from whole organism (ENCLB154PEM)

description:
https://www.encodeproject.org/experiments/ENCSR110JFN/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing schlank-eGFP fusion proteins.
experiment encode accession: ENCSR110JFN
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR231WZH
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB154PEM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

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

tag: antibody

value: schlank

tag: collection date

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

value: embryonic

value: 0-24 hour

value: Kevin White, UChicago

value: Kevin White

value: ENCBS432UUY at ENCODE; https://www.encodeproject.org/ENCBS432UUY/


title: Bulk RNAseq ZIP13K2 WT Rep 3

description: Bulk RNA-seq


title: Uninfected Bla-1 rep 3

value: Leaves of 5-week old plants

value: Uninfected (LNI)


title: ZT57 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT57_S_R1

value: whole flag leaf

value: Mace

value: Senescent leaf


title: ZT53 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT53_S_R2


title: Bulk RNAseq ZIP13K2 WT Rep 2

description: Bulk RNA-seq


title: Uninfected Bla-1 rep 1

value: 24 hours


title: Uninfected Bla-1 rep 2


title: Bulk RNAseq ZIP13K2 WT Rep 1

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB440JMZ)

description:
https://www.encodeproject.org/experiments/ENCSR110JFN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing schlank-eGFP fusion proteins.
experiment encode accession: ENCSR110JFN
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR231WZH
encode release date: 2018-06-12
lab: Kevin White, UChicago
library encode accession: ENCLB440JMZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

tag: geographic location

tag: encode accession

value: ENCBS852ZLW at ENCODE; https://www.encodeproject.org/ENCBS852ZLW/


title: TF ChIP-seq from whole organism (ENCLB804MLF)

description:
https://www.encodeproject.org/experiments/ENCSR008NYP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing sug-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR008NYP
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR544ESS
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB804MLF
size range: 200-800

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

value: sug

tag: note

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

tag: Sex

value: pooled male and female

value: ENCBS003VKM at ENCODE; https://www.encodeproject.org/ENCBS003VKM/


title: TF ChIP-seq from whole organism (ENCLB028PEJ)

description:
https://www.encodeproject.org/experiments/ENCSR008NYP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing sug-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR008NYP
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR544ESS
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB028PEJ
size range: 200-800

tag: dev stage

value: embryonic

tag: lab

value: Kevin White, UChicago

value: ENCBS979DZK at ENCODE; https://www.encodeproject.org/ENCBS979DZK/


title: ZT53 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT53_M_R2

value: Mature leaf


title: Bulk RNAseq HAP1 HOXD4 KO Rep 3

description: Bulk RNA-seq

extract_protocol:
HAP1 cells were seeded with a density of 1x105 cells per 6-well and cultured for 3 days until 80% confluency was reached. RNA was extracted using the Direct-zolTM RNA MicroPrep Kit (Zymo Research) following the manufacturer’s instructions.
1 μg of RNA of each sample was used as input for library preparation using the KAPA Stranded mRNA-Seq Kit (Roche) following the manufacturer’s instructions. Unique Dual-Indexed Set-B (UDI; KAPA biosystems) adapters were ligated and the library was amplified for 8 cycles
Paired-end 100 with 50 million fragments per library

tag: age


title: Uninfected Ang-0 rep 3

tag: tissue

value: Leaves of 5-week old plants

value: Uninfected (LNI)


title: ZT53 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT53_S_R1

value: whole flag leaf

value: Mace


title: ZT53 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT53_M_R1


title: TF ChIP-seq from whole organism (ENCLB704QJS)

description:
https://www.encodeproject.org/experiments/ENCSR109RMR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing tap-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR109RMR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR250MXW
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB704QJS
size range: 200-800

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

value: tap

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

tag: source

value: Kevin White

value: ENCBS326LUR at ENCODE; https://www.encodeproject.org/ENCBS326LUR/


title: Uninfected Ang-0 rep 2

value: 24 hours


title: Control ChIP-seq from whole organism (ENCLB124LIP)

description:
https://www.encodeproject.org/experiments/ENCSR114LFX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG4707-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR114LFX
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB124LIP
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

value: not applicable

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

value: 0-14 hour

tag: link

value: ENCBS615JXT at ENCODE; https://www.encodeproject.org/ENCBS615JXT/


title: Uninfected Ang-0 rep 1

tag: treatment


title: ZT51 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT51_S_R2

value: Senescent leaf

tag: time


title: TF ChIP-seq from whole organism (ENCLB774CGF)

description:
https://www.encodeproject.org/experiments/ENCSR109RMR/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing tap-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR109RMR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR250MXW
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB774CGF
size range: 200-800

value: pooled male and female

value: embryonic

value: Kevin White, UChicago

value: ENCBS140SHA at ENCODE; https://www.encodeproject.org/ENCBS140SHA/


title: Bulk RNAseq HAP1 HOXD4 KO Rep 1

description: Bulk RNA-seq

tag: cell type


title: ZT55 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT55_M_R1

value: whole flag leaf

tag: cultivar

value: Mace

value: Mature leaf


title: TF ChIP-seq from whole organism (ENCLB486QYJ)

description:
https://www.encodeproject.org/experiments/ENCSR109RMR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing tap-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR109RMR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR250MXW
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB486QYJ
size range: 200-800

value: tap

tag: biosample encode accession

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

value: Kevin White

value: ENCBS070LSN at ENCODE; https://www.encodeproject.org/ENCBS070LSN/


title: Bulk RNAseq HAP1 HOXD4 AroPLUS GFP Rep 3

description: Bulk RNA-seq


title: ZT51 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT51_S_R1


title: Stroke_VEGF_r2

city: New Haven

first: Jean-Leon

last: Thomas

state: CT

address: 800 Howard Ave

institute: Yale University

data_processing:
Transcripts were quantified with Salmon v1.4.062 against Gencode vM24 mm10/GRCm38
Expression normalization was performed in R using DESeq2 v1.30.1 rlog function
Assembly: mm10
Supplementary files format and content: rlog normalized expresion values per sample, using default rlog normalization in DESeq2, Ensembl IDs and MGI gene symbol identifiers are provided

organism: Mus musculus

source_name: MACS beads purified CD11b+ microglia/macrophages from mice brains

extract_protocol:
RNA isolation was performed on frozen cell pellets on DNA/RNA Shield (Zymo research) using Direct-zol RNA Miniprep kit (Zymo Research). RNA concentration was measured by NanoDrop 1000 (Thermo Fisher Scientific) and RNA integrity was determined using Bioanalyzer (Agilent)
Library construction of 300 ng total RNA for each sample was made using KAPA Stranded mRNA-Seq Kit (Illumina Platforms; Kapa Biosystems) using 10 cycles of PCR amplification. Libraries were purified using AxyPrep Mag PCR Clean-up kit (AxygenTM). Each library was quantified using a Qubit fluorometer (Life Technologies) and the size distribution assessed using the 2,100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

value: VEGFc AAV + tMCAO


title: ZT51 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT51_M_R2


title: Bulk RNAseq HAP1 HOXD4 AroPLUS GFP Rep 2

description: Bulk RNA-seq


title: Stroke_VEGF_r1

value: MACS beads purified CD11b+ microglia/macrophages from mice brains


title: ZT51 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT51_M_R1


title: Control ChIP-seq from whole organism (ENCLB965CYO)

description:
https://www.encodeproject.org/experiments/ENCSR188ZKB/
***************
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: ENCSR188ZKB
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-09-26
lab: Kevin White, UChicago
library encode accession: ENCLB965CYO
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG17806

value: not collected

value: pupa

value: 24 hour

value: ENCBS027QDW at ENCODE; https://www.encodeproject.org/ENCBS027QDW/


title: Bulk RNAseq HAP1 HOXD4 AroPLUS GFP Rep 1

description: Bulk RNA-seq


title: Control ChIP-seq from whole organism (ENCLB882QPW)

description:
https://www.encodeproject.org/experiments/ENCSR283MGP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG10669-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR283MGP
assay title: Control ChIP-seq
assembly: dm6
encode release date: 2018-02-05
lab: Kevin White, UChicago
library encode accession: ENCLB882QPW
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG10669-GFP mixed sex prepupa (24 days) insertion targeting D. melanogaster CG10669

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG10669

value: pooled male and female

value: prepupa

value: 24 day

value: Kevin White, UChicago

value: ENCBS819FJI at ENCODE; https://www.encodeproject.org/ENCBS819FJI/


title: Bulk RNAseq HAP1 HOXD4 AroPERFECT GFP Rep 3

description: Bulk RNA-seq


title: ZT49 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT49_S_R2

value: whole flag leaf

value: Mace

value: Senescent leaf


title: Stroke_Ctrl_r3

value: MACS beads purified CD11b+ microglia/macrophages from mice brains

value: CTRL AAV + tMCAO


title: Bulk RNAseq HAP1 HOXD4 KO Rep 2

description: Bulk RNA-seq


title: Stroke_Ctrl_r2


title: TF ChIP-seq from whole organism (ENCLB255NLV)

description:
https://www.encodeproject.org/experiments/ENCSR187IVR/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG14711-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR187IVR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR730QLJ
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB255NLV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster female adult insertion targeting D. melanogaster CG14711

tag: antibody

value: whole organism

value: whole organisms

value: not applicable

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG14711

value: female

value: adult

value: unknown

value: Kevin White

value: ENCBS924LMR at ENCODE; https://www.encodeproject.org/ENCBS924LMR/


title: ZT49 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT49_S_R1


title: Stroke_Ctrl_r1


title: ZT49 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT49_M_R2

value: Mature leaf


title: Bulk RNAseq HAP1 HOXD4 AroPERFECT GFP Rep 2

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB048WMM)

description:
https://www.encodeproject.org/experiments/ENCSR187IVR/
***************
biological replicate number: 4
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing CG14711-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR187IVR
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR730QLJ
encode release date: 2018-12-21
lab: Kevin White, UChicago
library encode accession: ENCLB048WMM
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: collection date

value: Kevin White, UChicago

value: ENCBS374DVJ at ENCODE; https://www.encodeproject.org/ENCBS374DVJ/


title: Bulk RNAseq HAP1 HOXD4 AroPERFECT GFP Rep 1

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB845PRU)

description:
https://www.encodeproject.org/experiments/ENCSR186ZKW/
***************
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: ENCSR186ZKW
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR505NGD
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB845PRU
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain CG15696 mixed sex embryo (2-8 hours) insertion targeting D. melanogaster CG15696

tag: geographic location

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG15696

value: pooled male and female

value: embryonic

value: ENCBS975IUM at ENCODE; https://www.encodeproject.org/ENCBS975IUM/


title: ZT49 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT49_M_R1

source_name: whole flag leaf

value: whole flag leaf

value: Mace


title: Stroke_VEGF_r3

value: MACS beads purified CD11b+ microglia/macrophages from mice brains

value: VEGFc AAV + tMCAO


title: VEGF_r3

source_name: MACS beads purified CD11b+ microglia from mice brains

value: VEGFc AAV


title: Control ChIP-seq from whole organism (ENCLB886BRP)

description:
https://www.encodeproject.org/experiments/ENCSR105HNS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing fd59A-eGFP fusion proteins.
experiment encode accession: ENCSR105HNS
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB886BRP
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain fd59A-GFP mixed sex prepupa (24 days) insertion targeting D. melanogaster fd59A

value: whole organism

value: whole organisms

value: not applicable

tag: encode accession

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to fd59A

value: prepupa

value: 24 day

value: ENCBS938WWB at ENCODE; https://www.encodeproject.org/ENCBS938WWB/


title: VEGF_r2

value: MACS beads purified CD11b+ microglia from mice brains


title: TF ChIP-seq from whole organism (ENCLB948OYG)

description:
https://www.encodeproject.org/experiments/ENCSR186ZKW/
***************
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: ENCSR186ZKW
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR505NGD
encode release date: 2019-05-23
lab: Kevin White, UChicago
library encode accession: ENCLB948OYG
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

tag: note

value: Transgenic D. mel line, stably expressing a C-terminal GFP fused to CG15696

value: Kevin White, UChicago

value: Kevin White

value: ENCBS054WPM at ENCODE; https://www.encodeproject.org/ENCBS054WPM/


title: Bulk RNAseq HAP1 HOXD4 WT GFP Rep 2

description: Bulk RNA-seq


title: VEGF_r1


title: ZT47 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT47_S_R2

value: whole flag leaf

value: Senescent leaf


title: ZT47 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT47_S_R1

value: Mace


title: Bulk RNAseq HAP1 HOXD4 WT GFP Rep 1

description: Bulk RNA-seq


title: ZT47 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT47_M_R2

value: Mature leaf


title: Ctrl_r3

value: CTRL AAV


title: TF ChIP-seq from whole organism (ENCLB771TBM)

description:
https://www.encodeproject.org/experiments/ENCSR104XOO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing trem-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR104XOO
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR111RAO
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB771TBM
size range: 200-800

value: trem

value: whole organism

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

tag: Sex

value: pooled male and female

value: embryonic

value: 0-14 hour

value: ENCBS098KJN at ENCODE; https://www.encodeproject.org/ENCBS098KJN/


title: Bulk RNAseq HAP1 Parental WT Rep 3

description: Bulk RNA-seq


title: TF ChIP-seq from whole organism (ENCLB726NFO)

description:
https://www.encodeproject.org/experiments/ENCSR104XOO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing trem-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR104XOO
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR111RAO
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB726NFO
size range: 200-800

value: whole organisms

value: not applicable

tag: dev stage

value: ENCBS200IZB at ENCODE; https://www.encodeproject.org/ENCBS200IZB/


title: ZT47 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT47_M_R1


title: Ctrl_r1

value: MACS beads purified CD11b+ microglia from mice brains


title: Bulk RNAseq HAP1 Parental WT Rep 2

description: Bulk RNA-seq


title: ZT45 Senescent bio rep 2

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT45_S_R2


title: Bulk RNAseq HAP1 Parental WT Rep 1

description: Bulk RNA-seq


title: Ctrl_r2


title: Embryo, siSPENH0335-rep2

city: Hangzhou

first: Hua

last: Yu

address: No.18 Shilongshan Road

country: China

institute: Westlake University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were trimmed and quality-filtered the sequencing reads using Trim Galore (V0.6.5) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the following parameters “-q 20 --phred33 --stringency 3 --trim-n”.
The high-quality reads were aligned to the mouse mm10 reference genome by HISAT2 (v2.1.0) with -dta parameter (83). PCR duplicate reads were removed using Picard tools (https://broadinstitute.github.io/picard/) (v2.18.2). Considering the multi-mapping of reads derived from repeat sequences, we used all mapped reads for subsequent analysis.
Assembly: mm10
Supplementary files format and content: csv file representing gene expression level (counts)

source_name: Embryo

growth_protocol: Zygotes were harvested from oviduct and culture in KSOM

extract_protocol:
The embryo were lysed with 0.2% Triton X-100
Sequencing libraries were constructed from 1 ng of pre-amplified cDNA using DNA library preparation kit

treatment_protocol: Zygotes were injected with 20μM siNC or siRNA of SPENH0335

tag: strain

tag: developmental stage

value: embryos of 2-cell stage

value: whole embryo


title: 770_tim3_pos

city: Suwon-si

first: Se Jin

last: Im

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu

department: Department of Immunology

country: South Korea

institute: Sungkyunkwan University School of Medicine

description: Exhausted (Tim-3+ PD-1+) CD8 TILs

data_processing:
Raw data (CEL files) were normalized by RMA using Affy R package.
Sequence data was aligned using HiSat2, and differential gene expression was determined using DeSeq2.
Assembly: Hg38
Supplementary files format and content: CSV file with normalized counts from the RNAseq for all samples.

source_name: Primary and metastatic tumors in lung tissues (NSCLC Tumor)

extract_protocol:
Tumors were harvested in cold L-15 Leibovitz media (Hyclone), cut into small pieces and digested for 1hour with an enzyme cocktail of Collagenase I (125mg/L), Collagenase II (125mg/L), Collagenase IV (125mg/L), DNase I (50mg/L), and Elastase (50mg/L) (Worthington) at 37ºC with shaking. Lymphocytes were isolated by 44%/67% Percoll gradient centrifugation. Peripheral blood mononuclear cells were isolated according to standard protocol.
RNA libraries for RNA-seq were prepared using the Illumnia Nextera kit following manufacturer's protocols.

tag: tissue

value: CD8 Tumor-infiltrating lymphocytes (TILs)

tag: tumor stage

value: stage I-IV disease


title: ZT45 Senescent bio rep 1

description:
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT45_S_R1

value: whole flag leaf

value: Mace

value: Senescent leaf


title: Bulk RNAseq HAP1 HOXD4 WT GFP Rep 3

description: Bulk RNA-seq

tag: age


title: Control ChIP-seq from whole organism (ENCLB886MAT)

description:
https://www.encodeproject.org/experiments/ENCSR102QDH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control for ChIP-seq on transgenic flies expressing Hand-eGFP fusion proteins.
experiment encode accession: ENCSR102QDH
assay title: Control ChIP-seq
assembly: dm6, dm3
encode release date: 2017-11-22
lab: Kevin White, UChicago
library encode accession: ENCLB886MAT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Drosophila melanogaster strain Hand-GFP mixed sex embryo (6-24 hours) insertion targeting D. melanogaster Hand

value: whole organism

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

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: link

value: ENCBS971BDG at ENCODE; https://www.encodeproject.org/ENCBS971BDG/


title: Embryo, siSPENH0335-rep1

tag: treatment


title: 770_cd28pos

description: Stem-like (Tim-3-CD28+ PD-1+) CD8 TILs

value: Primary and metastatic tumors in lung tissues (NSCLC Tumor)

tag: cell type


title: ZT45 Mature bio rep 2

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT45_M_R2

tag: cultivar

value: Mature leaf

tag: time


title: Single-cell RNA-Sequencing b-cells expressing CEBPa AroPerfect IS15

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The single-cell RNA-seq datasets were processed with 10x Genomics' Cell Ranger pipeline version 3.1.0 (Zheng et al., 2017) and mapped to a custom human genome hg38 including meGFP and codon-optimized C/EBPα wild type, C/EBPα AroPERFECT IS15, and C/EBPα AroPERFECT IS10 sequences.
Assembly: hg38

source_name: RCH-rtTA

growth_protocol: RCH-rtTA cells were derived from the RCH-ACV lymphoblastic leukemia cell line (Jack et al., 1986). RCH-rtTA cells and derivates were cultured in RPMI (Gibco) containing 10% FBS, supplemented with 1% glutamine (Gibco),1% penicillin/streptomycin (Thermo) and 550 µM β-mercaptoethanol (Gibco). Cells were maintained at a density of 0.1-6x106 cells/ml. Cells were checked for mycoplasma contamination every month and tested negative.

extract_protocol:
To induce C/EBPα mediated B-cell to macrophage transdifferentiation, infected RCH-rtTA cells were seeded at 0.3x106 cells/ml in RCH culture medium supplemented with 10 ng/ml of each, IL-2 (200-03, Preprotech) and CSF-1 (315-03B, Preprotech), as well as 2 µg/ml of Doxycycline. The macrophage transdifferentiation was monitored by flow cytometry.
One week after induction of C/EBPα mediated B-cell to macrophage transdifferentiation, cells were collected and washed twice in PBS to remove dead cells and debris. Cells were resuspended in solution at a density of 700 cells/µl. We used a Chromium Next GEM Single Cell 3’ technology for generating gene expression libraries from single cells. Briefly, gel beads-in-emulsion (GEMs) are generated by combination of barcoded Single Cell 3’ v3.1 Gel Beads, a Master Mix containing cells, and Partitioning Oil on a Chromium Next GEM Chip G. To achieve single cell resolution, cells are delivered at a limiting dilution, such that the majority (~90-99%) of generated GEMs contain no cell, while the remainder largely contain a single cell. Immediately following GEM generation, gel beads were dissolved, primers were released, and any co-partitioned cell was lysed. Primer (containing an Illumina TruSeq Read 1, 16 nt 10x Barcode, 12 nucleotide unique molecular identifier and 30 nucleotide poly-dT sequence) were mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents. Incubation of the GEMs produced barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken and pooled fractions were recovered. Silane magnetic beads were used to purify the first-strand cDNA from the post GEM-RT reaction mixture, which includes leftover biochemical reagents and primers. Barcoded, full-length cDNA was amplified via PCR to generate sufficient mass for library construction. cDNA was analyzed using Agilent Bioanalyzer assay (ref. 5067-4626, Agilent) to check size distribution profile and quantification. Only 25% of cDNA was used to 3’ Gene Expression Library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. TruSeq Read 1 (read 1 primer sequence) was added to the molecules during GEM incubation. P5, P7, a sample index, and TruSeq Read 2 (read 2 primer sequence) were added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. Final libraries were analyzed using Agilent Bioanalyzer assay to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification K

value: RCH-rtTA

tag: genotype

value: expressing CEBPa AroPerfect IS15

tag: time point


title: Single-cell RNA-Sequencing b-cells expressing CEBPa AroPerfect IS10

description: 10x Genomics

value: expressing CEBPa AroPerfect IS10


title: 672_tim3_pos

description: Exhausted (Tim-3+ PD-1+) CD8 TILs


title: Embryo, Control-rep2

value: embryos of 2-cell stage

value: siNC


title: TF ChIP-seq from whole organism (ENCLB839ZNC)

description:
https://www.encodeproject.org/experiments/ENCSR104XOO/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing trem-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR104XOO
assay title: TF ChIP-seq
assembly: dm6
possible controls: ENCSR111RAO
encode release date: 2019-07-02
lab: Kevin White, UChicago
library encode accession: ENCLB839ZNC
size range: 200-800

tag: antibody

value: trem

value: whole organisms

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: note

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

value: pooled male and female

value: embryonic

value: 0-14 hour

value: ENCBS146TTR at ENCODE; https://www.encodeproject.org/ENCBS146TTR/


title: Single-cell RNA-Sequencing b-cells expressing CEBPa Wild-type

description: 10x Genomics

value: expressing CEBPa Wild-type


title: ZT45 Mature bio rep 1

description:
processed data file:
mature_counts.tsv
mature_fpkm.tsv
ZT45_M_R1

tag: tissue

value: whole flag leaf

value: Mace


title: ESHJ_IL1B

status: Public on Feb 26 2024

city: Hatfield

first: Ross

middle: Eric

last: Beaumont

state: Hertfordshire

address: Hawkshead Ln

department: Clinical science and services

country: United Kingdom

institute: Royal Veterinary College

description: ESHJ IL1B

data_processing:
RNA sequencing was performed on a NovaSeq6000 (Illumina) by external providers (Oxford Genomics, Oxford, UK & Novagene, Cambridge, UK).
30.7 – 38 million reads of 150 base pair paired-end data were generated per sample.
Resulting FASTQ files generated were quality control (QC) checked using FASTQC and MultiQC (Babraham Bioinformatics, Cambridge, UK).
QC checked reads were then aligned to the Ensemble version v95 EquCab 3.0 transcriptome using the pseudoaligner Salmon in Quasi-mapping based mode with GC-bias correction (-gcBias).
The tximport package (v.1.24; Soneson et al 2015) was used to import the quantified gene-level abundance data into R (v.4.2.1) and differential expression analysis conducted using R/Bioconductor DESeq2 (v.1.36) as described in Love et al., 2014.
Assembly: Genes with adjusted pvalue of less than 0.05 and log2 fold change of ± 1 were considered as differentially expressed.
Supplementary files format and content: Ensemble version v95 EquCab 3.0
Supplementary files format and content: A text document (.txt) includes the raw counts for each of the three biological replicates under both experimental conditions.

organism: Equus caballus

source_name: Equine embryonic stem cell-derived tenocytes

growth_protocol: Embryonic stem cell-derived tenocytes were cultured in Dulbecco’s modified eagle medium (DMEM)/F-12 with high glucose (4.5 g/L), 15% fetal bovine serum, 2 mM L-glutamine, 1% none-essential amino acids, 1 mM sodium pyruvate, and 0.1 mM 2-mercaptoethanol (all from Invitrogen, Renfrewshire, UK) with mechanical passaging every 5-7 days.

extract_protocol:
RNA was extracted using Tri-reagent (Sigma), purified using an RNeasy mini Kit (Qiagen, Manchester, UK) and contaminating genomic DNA removed using Ambion DNA-free (Life Technologies, Paisley, UK). RNA concentration was measured using a Nanodrop (ThermoFisher, Loughborough, UK) and a Qubit (ThermoFisher). RNA integrity was confirmed on a Tapestation (Agilent, Milton Keynes, UK).
mRNA libraries were prepared using a TruSeq stranded mRNA kit (Illumina, Cambridge, UK)

treatment_protocol: Embryonic stem cell-derived tenocytes were seeded in type 1 collagen gels (bovine; Advanced Biomatrix, California, USA) to generate a three-dimensional matrix and stimulated with IL-1ß (1 nM) or control for 14 days, with fresh media changes every 3-4 days before harvesting at day 14.

value: WT

value: Interleukin 1 beta


title: ESHJ_Con

description: ESHJ control

value: Equine embryonic stem cell-derived tenocytes

value: Control


title: ESPW_IL1B

description: ESPW IL1B


title: ESIG_IL1B

description: ESIG IL1B


title: ESIG_Con

description: ESIG control


title: Patient 10, site 2, responder, baseline [WS4]

city: Cleveland

first: Thomas

middle: S

last: McCormick

state: OH

address: 2109 Adelbert Rd

department: Dermatology

institute: Case Western Reserve University

data_processing:
Raw fastq single-end read files were demultiplexed and aligned using the Rsubread aligner to the Homo sapiens GENCODE reference genome GRCh38.p13 and counted using featureCounts as part of the Rsubread package
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Blood

extract_protocol:
Qiagen RNeasy Mini kit in combination with the Qiagen QIAshredder kit per the manufacturer’s protocol
Nextera XT DNA Library Preparation Kit
Pooled at 2nM and sequenced using a single-end, 75 cycle, rapid run design on an Illumina HiSeq 2500

value: Blood

tag: subject id

value: Patient 10

value: Monocyte

value: Responder


title: Patient 8, site 2, responder, baseline [WS12]

value: Patient 8


title: Patient 9, site 2, responder, baseline [WS3]

value: Patient 9


title: Patient 11, site 2, responder, baseline [WS9]

value: Patient 11


title: Patient 6, site 1, responder, baseline [UH9]

value: Patient 6


title: Patient 2, site 1, non-responder, baseline [UH18]

value: Patient 2

value: Non-responder


title: Patient 1, site 1, non-responder, baseline [UH15]

value: Patient 1


title: Patient 5, site 1, responder, baseline [UH24]

value: Patient 5


title: Embryo, Control-rep1

tag: strain

tag: developmental stage

value: embryos of 2-cell stage

value: siNC

value: whole embryo


title: Patient 3, site 1, non-responder, baseline [UH19]

value: Patient 3


title: Patient 4, site 2, non-responder, baseline [UH23]

value: Patient 4


title: Patient 7, site 1, responder, baseline [WS10]

value: Blood

value: Patient 7


title: CardioPlate02_M21

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

data_processing:
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
Quality control steps with the following criteria were performed: 1) genes with fewer than 5 mean counts across the entire sample spacewere removed, 2) samples with mean expression across all genes lower than 25 were removed, 3) outliers in vehicle control samples were identified and removed using mean correlation at <0.85 as the criteria to ensure the stability of further transcriptomic dose-response and differential expression analyses, 4) in addition, principal component analysis (PCA) was conducted on vehicle control samples using raw counts to identify any remaining outliers.
Assembly: Whole transcriptome assay
Supplementary files format and content: iCM_normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: iCM_hash.csv file with meta data of the QC samples

source_name: Blank

extract_protocol:
The media and chemicals from the 384-well plates was fully aspirated and replaced with 10 μL/well of 2X lysis buffer. The plates were then shaken using an orbital plate shaker for 10 minutes. The plates were then checked to ensure that the cells were lysed, and if not placed back on the plate shaker for an additional five minutes. Once the cells were lysed, adhesive seals were placed on the plates and the lysates were frozen in the 384-well plates and stored at −80 °C until further processing.  The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022).
TempO-seq libraries were prepared using the human whole transcriptome panel consisting of 22,537 protein-coding transcripts.

tag: cell line

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: DMSO


title: CardioPlate02_M22

tag: treatment


title: CardioPlate02_M18

tag: cell type


title: CardioPlate02_M19


title: 672_cd28pos

description: Stem-like (Tim-3-CD28+ PD-1+) CD8 TILs

value: Primary and metastatic tumors in lung tissues (NSCLC Tumor)

value: CD8 Tumor-infiltrating lymphocytes (TILs)

tag: tumor stage

value: stage I-IV disease


title: CardioPlate02_M16


title: CardioPlate02_M20


title: ESPW_Con

description: ESPW control

value: Equine embryonic stem cell-derived tenocytes

value: WT

value: Control


title: CardioPlate02_L23

value: Perfluoroheptanoic acid


title: CardioPlate02_L22


title: CardioPlate02_L21

value: 3:3 Fluorotelomer carboxylic acid


title: CardioPlate02_M17


title: K562 cells transfected with siControl_1

type: RNA

city: Xinxiang

first: Hai-Chuan

state: Henan

address: No. 601 Jinsui Avenue

institute: Xinxiang Medical University

description: Gene expression data from K562 cells transfected with siControl

hyb_protocol: Followed fragmentation and biotin labeling, 10 ug of cRNA were hybridized for 16 hr at 45C on the microarray Affymetrix HTA2.0. The microarray hybridization and washing were performed based on the manufacturer’s standard protocols.

scan_protocol: After washing and staining, the arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version 1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded separately. The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: K562 cells transfected with siControl

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The human chronic myelogenous leukemia cell line K562 cells were cultured at 37 °C and 5% CO2 in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), 2 mM L-glutamine, 100 U/mL penicillin, and 100 mg/mL streptomycin (Invitrogen).

extract_protocol: Total RNA was extracted by using Trizol reagent (Invitrogen) following the manufacturer’s instructions and quantified by the NanoDrop ND-2000 (Thermo Fisher Scientific, Inc.). RNAs integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies, USA).

treatment_protocol: K562 cells were transfected with siNFIL3 or siControl under hypoxia, respectively.

tag: cell

value: Chronic Myeloid Leukemia


title: CardioPlate02_L20

value: Ammonium perfluorooctanoate


title: CardioPlate02_L19


title: K562 cells transfected with siNFIL3_1

description: Gene expression data from K562 cells transfected with siNFIL3

source_name: K562 cells transfected with siNFIL3


title: CardioPlate02_L14

value: Nonafluoropentanamide


title: CardioPlate02_L18

value: Perfluoro(4-methoxybutanoic) acid


title: K562 cells transfected with siControl_3

description: Gene expression data from K564 cells transfected with siControl

source_name: K564 cells transfected with siControl


title: K562 cells transfected with siNFIL3_3


title: CardioPlate02_L15

value: Perfluorohexanesulfonamide


title: CardioPlate02_K23


title: K562 cells transfected with siControl_2

description: Gene expression data from K563 cells transfected with siControl

source_name: K563 cells transfected with siControl


title: CardioPlate02_L13

value: Perfluorononanoic acid


title: CardioPlate02_K20

value: Blank


title: CardioPlate02_L16

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorooctanamidine


title: K562 cells transfected with siNFIL3_2


title: CardioPlate02_K22


title: CardioPlate02_K17

value: Perfluoro-3,6,9-trioxatridecanoic acid


title: CardioPlate02_K16


title: CardioPlate02_K15


title: CardioPlate02_K19


title: CardioPlate02_K14


title: CardioPlate02_K18


title: iMOP-derived neurons, p300, CUT&Tag

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Paired-end CUT&Tag reads were aligned to the mm10 genome assembly with bowtie2.
deepTools bamCoverage was used to remove duplicate reads  and generate normalized bigiwigs files into reads per kilobase per million (RPKM) from individual samples.
Replicate bigiwig files were merged to generate the averaged bigwig files using deepTools bigwigCompare.
Peaks were called using SEACR under stringent conditions using IgG sample as the empirical background
Assembly: mm10
Supplementary files format and content: bigwig, averaged bigwig signals from two replicates
Supplementary files format and content: SEACR peaks (except for IgG control), consensus SEACR peaks from two replicates
Library strategy: CUT&Tag

source_name: iMOPs

growth_protocol: Proliferating iMOPs: DMEM/F12, 1XB27, 25 µg/ml carbenicillin and 20 ng/ml bFGF. iMOP-derived neurons: Neurobasal media, 1XN21, 2 mM L-glutamine, and 1 µM K03861.

extract_protocol:
500,000 cells were used for each CUT&Tag library prepration. Cells were incubated with primary antibodies against CHD4, H3K4me3, p300 and IgG (control). DNA libraries were amplified using PCR and purified using SPRI beads. Libraries were sequenced on illumina Hiseq 3000 platform (2X150bp).
pA-Tn5-transposomes mediated tagmentation using CUT&Tag-IT Assay kit (Active Motif).

value: iMOPs

value: iMOP-derived neurons

tag: genotype

value: wild-type


title: CardioPlate02_K13


title: Proliferating iMOPs, IgG (Control), CUT&Tag

value: IgG

value: Poliferating iMOPs


title: iMOP-derived neurons, H3K4me3, CUT&Tag


title: CardioPlate02_L17


title: CardioPlate02_K21


title: Proliferating iMOPs, p300, CUT&Tag


title: iMOP-derived neurons, IgG (Control), CUT&Tag


title: CardioPlate02_J18


title: CardioPlate02_J22


title: EM-seq library derived from 200 ng of purified genomic DNA as starting material

city: Yokohama

first: Yuki

last: Tanaka

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

data_processing:
*library strategy: Enzymatic Methyl-seq (EM-seq)
Adapter trimming: cutadapt 3.2 with Python 3.9.2
Quality control: PRINSEQ++ with the following options, -trim_qual_left 30 -trim_qual_right 30 -ns_max_n 20 -min_len 50
Genome alignment: Bismark or bwameth
Methylation calling: methylKit
Assembly: hg38
Supplementary files format and content: Methylation call files

growth_protocol: 610B1 human iPSC cells (RIKEN BRC, HPS0331) were maintained on Corning Matrigel hESC-Quantified Matrix (Corning) in mTeSRTM Plus-cGMP medium (STEMCELL Technologies Inc.) and were passaged every 6-7 days using an enzyme-free reagent, ReLeSR (STEMCELL Technologies Inc.).

extract_protocol:
Crude cell lysate was obtained using QuickExtractTM DNA Extraction Solution (Lucigen). Purified genomic DNA was isolated using a NucleoSpin® Tissue XS Kit (Macherey-Nagel).
Methylome libraries were prepared with the NEBNext® Enzymatic Methyl-seq Kit and the Unique Dual Index Primer Pairs (New England BioLabs (NEB)) according to manufacturer’s instructions (NEB, #E7120S).

value: human induced pluripotent stem cell line


title: CardioPlate02_J20


title: EM-seq library derived from 50 ng of crude cell lysate as starting material


title: EM-seq library derived from 10 ng of purified genomic DNA as starting material


title: iMOP-derived neurons, CHD4, CUT&Tag


title: EM-seq library derived from 50 ng of purified genomic DNA as starting material


title: Proliferating iMOPs, CHD4, CUT&Tag


title: Proliferating iMOPs, H3K4me3, CUT&Tag


title: EM-seq library derived from 10 ng of crude cell lysate as starting material


title: CardioPlate02_J17


title: CardioPlate02_J16


title: CardioPlate02_J15


title: CardioPlate02_J13


title: CardioPlate02_J14


title: CardioPlate02_I23

value: Perfluorobutanesulfonic acid


title: FLI1-overexpressing CD34+CD45+ HPCs with RUNX1-Y287X heterozygous mutation, EM-seq

data_processing:
Adapter trimming: cutadapt 3.2 with Python 3.9.2
Quality control: PRINSEQ-lite 0.20.4 with the following options, -trim_qual_left 30 -trim_qual_right 30 -ns_max_n 20 -min_len 50
Genome alignment: Bismark
Methylation calling: methylKit
Assembly: hg38
Supplementary files format and content: Methylation call files
Library strategy: EM-seq

source_name: 610B1 human iPS cells

extract_protocol:
Genomic DNA was isolated using a NucleoSpin® Tissue XS Kit (Macherey-Nagel).
Methylome libraries were prepared with the NEBNext® Enzymatic Methyl-seq (EM-seq™) Kit and the Unique Dual Index Primer Pairs (New England BioLabs (NEB)) according to manufacturer’s instructions (NEB, #E7120S).

treatment_protocol: STEMdiff Hematopoietic Kit (STEMCELL Technologies Inc.) was used for in vitro hematopoietic differentiation.

value: 610B1 human iPS cells

value: hematopoietic progenitor cells

value: RUNX1-Y287X heterozygous mutation transfected with DOX-inducible FLI1 lentivirus vector (pCW57.1)

value: hematopoietic differentiation with doxycycline addition


title: CD34+CD45+ HPCs with RUNX1-Y287X heterozygous mutation as mock-control, EM-seq

value: RUNX1-Y287X heterozygous mutation transfected with mock-control lentivirus vector (pCW57.1)


title: CardioPlate02_I22

value: Perfluorodecanoic acid


title: CardioPlate02_I21

value: Blank

value: Perfluorotetradecanoic acid


title: CardioPlate02_J23

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluoroheptanoic acid


title: iPS cells with RUNX1-R201Q heterozygous mutation, WES

data_processing:
Adapter trimming: cutadapt 3.2 with Python 3.9.2
Quality control: PRINSEQ-lite 0.20.4 with the following options, -trim_qual_left 30 -trim_qual_right 30 -ns_max_n 20 -min_len 50
Genome alignment: BWA.
Oversequenced reads were marked as duplicate by Picard. The systematic and technical DNA sequencing base call errors were recalibrated by machine learning using GATK.
Variant calling: VarScan2, MuTect2, and Pindel
Assembly: hg38
Supplementary files format and content: VCF files with mutation calls
Library strategy: WES

extract_protocol:
Genomic DNA was isolated using a NucleoSpin® Tissue Kit (Macherey-Nagel).
Exome library preparations were performed at Azenta Life Science Co. Limited (Tokyo, Japan).

value: iPS cells

value: RUNX1-R201Q heterozygous mutation


title: iPS cells with RUNX1-Y287X heterozygous mutation, WES

value: RUNX1-Y287X heterozygous mutation


title: Wild-type iPS cells, WES

value: WT


title: CardioPlate02_I20

value: Perfluorooctanamide


title: CardioPlate02_J21

value: 3:3 Fluorotelomer carboxylic acid


title: EM-seq library derived from 200 ng of crude cell lysate as starting material

value: human induced pluripotent stem cell line

value: wild-type


title: CardioPlate02_I19

value: 6:2 Fluorotelomer sulfonic acid


title: CardioPlate02_I18

value: AFFF-7 (Tridol 6%)


title: DOX-inducible FLI1-overexpressing iPS cells, EM-seq

extract_protocol:
Genomic DNA was isolated using a NucleoSpin® Tissue Kit (Macherey-Nagel).
Methylome libraries were prepared with the NEBNext® Enzymatic Methyl-seq (EM-seq™) Kit and the Unique Dual Index Primer Pairs (New England BioLabs (NEB)) according to manufacturer’s instructions (NEB, #E7120S).

treatment_protocol: The doxycycline (DOX)-inducible FLI1 lentivirus vectors were transduced to human 610B1 iPS cells. After selection of the successfully transduced cells by culturing with 2 μg/ml Puromycin (InvivoGen), FLI1 were overexpressed by adding DOX at the final concentration of 500 ng/ml.

value: 610B1 human iPS cells

value: transfected with DOX-inducible FLI1 lentivirus vector (pCW57.1)

value: puromycin and doxycycline addition


title: CardioPlate02_I15

value: Blank

value: Dodecafluoroheptanol


title: CardioPlate02_H23

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorobutanesulfonic acid


title: CD34+CD45+ HPCs with RUNX1-Y287X heterozygous mutation, rep2, EM-seq

value: hematopoietic progenitor cells

value: hematopoietic differentiation


title: CardioPlate02_I13

value: Perfluorooctanoic acid


title: CD34+CD45+ HPCs with RUNX1-R201Q heterozygous mutation, rep2, EM-seq

value: RUNX1-R201Q heterozygous mutation


title: CD34+CD45+ HPCs with RUNX1-Y287X heterozygous mutation, rep1, EM-seq

value: RUNX1-Y287X heterozygous mutation


title: Wild-type CD34+CD45+ HPCs, rep2, EM-seq

value: WT


title: CardioPlate02_H20

value: Perfluorooctanamide


title: CardioPlate02_H18


title: CardioPlate02_H16

value: Perfluorotridecanoic acid


title: DOX-minus iPS cells, EM-seq

value: iPS cells

value: only puromycin addition


title: MCF7-TAMR cells, shALDOA2, repeat1

city: yangzhou

first: Yu

last: Shiyi

state: Jiangsu

address: hanjiang district jiangyangzhonglu136, Hanjiang district, Jiangyangzhonglu 136

institute: yangzhou university

data_processing:
The sequencing data was filtered with SOAPnuke ( (v1.5.6))
The clean data were mapped to the GRCH38 whole genome using HISAT2 with default parameters.
The SAM files were processed with Samtools to generate BAM files.
The sorted BAM files were processed with featureCounts to calculate counts for each transcripts in GRCH38.
The differentially expressed genes were calculated by Deseq2.
Assembly: GRCH38
Supplementary files format and content: txt files with raw gene counts for every transcripts in each sample

growth_protocol: RPMI1640 medium, supplemented with 10% FBS and 1μM tamoxifen

extract_protocol:
RNA was extracted from cells using TRIzol reagent (Invitrogen)
DNBSEQ Eukaryotic Strand-specific mRNA library strategy was applied to establish libraries.

value: breast cancer cells

value: ALDOA knockdown


title: MCF7-TAMR cells, shALDOA1, repeat2


title: CardioPlate02_H19

value: 6:2 Fluorotelomer sulfonic acid


title: CardioPlate02_H15

value: Blank


title: MCF7-TAMR cells, shALDOA1, repeat1


title: MCF7-TAMR cells, shControl, repeat 2


title: CardioPlate02_H17

value: Perfluoro-3-methoxypropanoic acid


title: CardioPlate02_H21

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorotetradecanoic acid


title: CardioPlate02_H14

value: AFFF-4 (FireAde 6%)


title: MCF7-TAMR cells, shControl, repeat 1


title: CardioPlate02_H13


title: CardioPlate02_G22

value: Perfluorodecanoic acid


title: CardioPlate02_G21


title: gDNA_87_NAEH [GY270UU1]

type: genomic

city: Koto-ku

first: Osamu

last: Gotoh

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation For Cancer Research

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using iScan System using standard recommended Illumina scanner setting.

data_processing:
The minfi package in R/Bioconductor
The GA_illumina_methylation_EEA_Atypia_v1_processed.txt contains normalized Average Beta (background subtraction and control normalization)
The GA_illumina_methylation_EEA_Atypia_v1_signal_intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: NAEH

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Micro Kit (Qiagen), according to the manufacturer’s instructions.

tag: gender

value: Female

tag: anatomical site

value: Uterus

value: NAEH


title: gDNA_91_AEH [UB007TU2]

source_name: AEH

value: AEH


title: CardioPlate02_G20

value: Perfluorooctanamide


title: gDNA_89_NAEH [GY272UU1]


title: gDNA_88_NAEH [GY271UU1]


title: gDNA_90_NAEH [UB007TU1]


title: CD34+CD45+ HPCs with RUNX1-R201Q heterozygous mutation, rep1, EM-seq

value: 610B1 human iPS cells

value: hematopoietic progenitor cells

value: RUNX1-R201Q heterozygous mutation

value: hematopoietic differentiation


title: CardioPlate02_H22


title: gDNA_86_NAEH [GY269UU1]


title: Wild-type CD34+CD45+ HPCs, rep1, EM-seq

value: WT


title: MCF7-TAMR cells, shALDOA2, repeat2

value: breast cancer cells

value: ALDOA knockdown


title: CardioPlate02_G16

value: Blank

value: Perfluorotridecanoic acid


title: gDNA_84_NAEH [GY267UU1]


title: CardioPlate02_G15

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Dodecafluoroheptanol


title: CardioPlate02_G19

value: 6:2 Fluorotelomer sulfonic acid


title: CardioPlate02_G18

value: AFFF-7 (Tridol 6%)


title: gDNA_82_NAEH [GY266UU1]

value: Female

value: Uterus


title: gDNA_81_AEH [GY265UU2]

value: AEH


title: gDNA_80_NAEH [GY265UU1]

value: NAEH


title: CardioPlate02_F22

value: 4:2 Fluorotelomer alcohol


title: CardioPlate02_F23

value: AFFF-3 (Phos-Check)


title: gDNA_79_AEH [GY264UU4]


title: CardioPlate02_G13

value: Perfluorooctanoic acid


title: CardioPlate02_F21


title: CardioPlate02_F20

value: AFFF-5 (Solberg 6%)


title: CardioPlate02_G23

value: Perfluorobutanesulfonic acid


title: gDNA_78_NAEH [GY264UU3]


title: gDNA_77_AEH [GY264UU2]


title: gDNA_75_AEH [GY262UU2]


title: gDNA_76_NAEH [GY264UU1]


title: gDNA_74_NAEH [GY262UU1]


title: CardioPlate02_F18

value: Sodium perfluorodecanesulfonate


title: CardioPlate02_F17

value: Perfluoroundecanoic acid


title: gDNA_85_NAEH [GY268UU1]


title: CardioPlate02_F15

value: Blank

value: AFFF-1 (Foamtec 3%)


title: gDNA_83_AEH [GY266UU2]


title: CardioPlate02_F19

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: 8:2 Fluorotelomer alcohol


title: CardioPlate02_E23


title: gDNA_71_AEH [GY261UU2]


title: CardioPlate02_F14

value: AFFF-6 (FireStopper)


title: gDNA_69_AEH [GY260UU6]


title: CardioPlate02_E21


title: gDNA_73_AEH [GY261UU4]


title: gDNA_72_NAEH [GY261UU3]


title: CardioPlate02_E22


title: CardioPlate02_E20


title: gDNA_67_NAEH [GY260UU3]


title: CardioPlate02_E18


title: CardioPlate02_E17


title: gDNA_66_NAEH [GY260UU2]


title: gDNA_68_AEH [GY260UU5]


title: CardioPlate02_E16

value: AFFF-2 (Chemguard 6%)


title: gDNA_65_NAEH [GY260UU1]

value: Female


title: CardioPlate02_E15


title: gDNA_64_AEH [GY259UU3]

value: Uterus


title: gDNA_63_NAEH [GY259UU2]


title: CardioPlate02_E14


title: gDNA_61_AEH [GY258UU5]

value: AEH


title: CardioPlate02_E13

value: 8:2 Fluorotelomer sulfonic acid


title: CardioPlate02_D21


title: gDNA_62_AEH [GY259UU1]


title: gDNA_59_AEH [GY258UU3]


title: CardioPlate02_D22

value: 4:2 Fluorotelomer alcohol


title: gDNA_60_NAEH [GY258UU4]

value: NAEH


title: CardioPlate02_D23

value: AFFF-3 (Phos-Check)


title: CardioPlate02_E19


title: gDNA_58_NAEH [GY258UU2]


title: CardioPlate02_D20

value: AFFF-5 (Solberg 6%)


title: gDNA_57_NAEH [GY258UU1]


title: CardioPlate02_D17


title: gDNA_70_NAEH [GY261UU1]


title: CardioPlate02_D18


title: CardioPlate02_D16


title: gDNA_55_AEH [GY257UU4]


title: CardioPlate02_D19


title: gDNA_54_NAEH [GY257UU2]


title: CardioPlate02_D15


title: gDNA_52_AEH [GY256UU10]


title: gDNA_51_AEH [GY256UU9]


title: CardioPlate02_D13


title: CardioPlate01_M22

value: DMSO


title: gDNA_53_NAEH [GY257UU1]


title: CardioPlate01_M21


title: gDNA_50_AEH [GY256UU8]


title: CardioPlate01_M20


title: gDNA_49_NAEH [GY256UU7]


title: CardioPlate01_M19


title: gDNA_46_AEH [GY256UU4]


title: gDNA_47_AEH [GY256UU5]


title: gDNA_48_NAEH [GY256UU6]


title: gDNA_45_AEH [GY256UU3]


title: CardioPlate01_M18


title: gDNA_56_AEH [GY257UU5]


title: CardioPlate01_M16


title: CardioPlate01_L23

value: Perfluoroheptanoic acid


title: gDNA_43_AEH [GY256UU1]


title: gDNA_41_NAEH [GY255UU5]


title: gDNA_42_AEH [GY255UU3]


title: CardioPlate01_L21

value: 3:3 Fluorotelomer carboxylic acid


title: CardioPlate01_L20

value: Blank

value: Ammonium perfluorooctanoate


title: CardioPlate01_L22

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes


title: CardioPlate01_L19


title: gDNA_40_AEH [GY254UU3]


title: CardioPlate01_L17

value: Perfluoro-3,6,9-trioxatridecanoic acid


title: gDNA_39_NAEH [GY254UU2]


title: gDNA_38_NAEH [GY254UU1]


title: gDNA_37_AEH [GY253UU4]


title: CardioPlate01_L15

value: Perfluorohexanesulfonamide


title: CardioPlate01_L16

value: Perfluorooctanamidine


title: gDNA_36_NAEH [GY253UU3]

value: Female


title: CardioPlate01_L14

value: Nonafluoropentanamide


title: gDNA_35_AEH [GY253UU2]

value: Uterus

value: AEH


title: gDNA_34_NAEH [GY253UU1]


title: CardioPlate01_L13

value: Perfluorononanoic acid


title: CardioPlate01_K22


title: gDNA_33_AEH [GY252UU6]


title: gDNA_44_NAEH [GY256UU2]

value: NAEH


title: gDNA_32_NAEH [GY252UU5]


title: CardioPlate01_K20


title: CardioPlate01_K21


title: CardioPlate01_K23


title: gDNA_31_AEH [GY252UU4]


title: CardioPlate01_K19


title: gDNA_27_AEH [GY251UU2]


title: CardioPlate01_L18

value: Perfluoro(4-methoxybutanoic) acid


title: gDNA_29_NAEH [GY252UU2]


title: CardioPlate01_K18


title: CardioPlate01_K15


title: gDNA_28_NAEH [GY252UU1]


title: CardioPlate01_K13


title: gDNA_26_NAEH [GY251UU1]


title: CardioPlate01_K14


title: CardioPlate01_K17


title: gDNA_24_AEH [GY250UU4]


title: CardioPlate01_J22


title: CardioPlate01_J23


title: CardioPlate01_J21


title: gDNA_23_AEH [GY250UU3]


title: gDNA_22_AEH [GY250UU2]


title: CardioPlate01_J20


title: gDNA_20_AEH [GY249UU2]


title: gDNA_19_NAEH [GY249UU1]


title: gDNA_30_AEH [GY252UU3]


title: CardioPlate01_J18


title: gDNA_21_NAEH [GY250UU1]


title: gDNA_18_AEH [GY247UU2]


title: CardioPlate01_J17


title: gDNA_16_AEH [GY246UU5]


title: gDNA_17_NAEH [GY247UU1]


title: gDNA_15_NAEH [GY246UU4]


title: CardioPlate01_J14


title: CardioPlate01_J15


title: gDNA_14_AEH [GY246UU3]


title: gDNA_25_NAEH [GY250UU5]


title: CardioPlate01_J19


title: gDNA_12_NAEH [GY246UU1]


title: gDNA_13_NAEH [GY246UU2]


title: CardioPlate01_I23

value: Perfluorobutanesulfonic acid


title: gDNA_11_AEH [GY245UU2]


title: CardioPlate01_I22

value: Perfluorodecanoic acid


title: CardioPlate01_J13


title: gDNA_10_NAEH [GY245UU1]


title: CardioPlate01_I19

value: 6:2 Fluorotelomer sulfonic acid


title: CardioPlate01_I20

value: Perfluorooctanamide


title: gDNA_9_NAEH [GY244UU5]


title: CardioPlate01_I18

value: Blank

value: AFFF-7 (Tridol 6%)


title: gDNA_8_AEH [GY244UU4]


title: CardioPlate01_J16

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes


title: gDNA_7_NAEH [GY244UU3]


title: CardioPlate01_I17

value: Perfluoro-3-methoxypropanoic acid


title: CardioPlate01_I16

value: Perfluorotridecanoic acid


title: gDNA_6_AEH [GY244UU2]


title: CardioPlate01_I14

value: AFFF-4 (FireAde 6%)


title: CardioPlate01_I13

value: Perfluorooctanoic acid


title: gDNA_4_AEH [GY112TU2]

value: Female


title: CardioPlate01_H23


title: CardioPlate01_H21

value: Perfluorotetradecanoic acid


title: CardioPlate01_H22


title: CardioPlate01_I21


title: gDNA_1_NAEH [EN900TU1]

value: Uterus


title: gDNA_2_AEH [EN900TU2]

value: AEH


title: gDNA_3_NAEH [GY112TU1]

value: NAEH


title: CardioPlate01_H20


title: CardioPlate01_H18


title: CardioPlate01_H19


title: CardioPlate01_H17


title: CardioPlate01_H14


title: CardioPlate01_H13


title: gDNA_5_NAEH [GY244UU1]


title: CardioPlate01_G23


title: CardioPlate01_G21


title: CardioPlate01_G20


title: CardioPlate01_G18


title: CardioPlate01_G19


title: CardioPlate01_G22


title: CardioPlate01_H15

value: Dodecafluoroheptanol


title: CardioPlate01_G14


title: CardioPlate01_G15


title: jmj1-1_rep2

city: Shanghai

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

data_processing:
Cutadapt was used to trim the raw RNA-seq reads in order to remove the adapters and the bases with low sequencing quality.
The trimmed reads were aligned to the genome of Brachypodium distachyon (genome version is 3.0, download from http://plants.ensembl.org/) using Hisat2.
SAMtools was used to obtain high quality mapped reads.
FeatureCounts was used to calculate the number of reads for each gene.
Assembly: Brachypodium distachyon (genome version is 3.0, download from http://plants.ensembl.org/)
Supplementary files format and content: tab-delimited text files include featureCounts for each Sample

organism: Brachypodium distachyon

growth_protocol: The seedlings grown to the 4th leaf stage under 20h (20h light/4h dark) photoperiods, and the samples were harvested at ZT10.

extract_protocol:
RNA was extracted using RNAprep pure Plant Kit (Tiangen Biotech).
RNA-seq library construction was performed according to the instructions of KAPA stranded mRNA-seq Kit (Kapa Biosystems).

value: leaf

tag: time

value: Day 17


title: jmj1-1_rep1


title: CardioPlate01_F23

value: AFFF-3 (Phos-Check)


title: Embryo, wild-type, rep2

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description: Embryo, wild-type, rep2 WT_A014

data_processing:
STAR 2.5.0A was used to perform the alignment and gene level count with GRCm38/Ensembl 100
Assembly: GRCm38
Supplementary files format and content: raw gene level count in tab-delimited format

source_name: whole embryo

extract_protocol:
Qiagen Rneasy Mini Kit
Illumina TruSeq Stranded mRNA Kit

value: whole embryo

value: wild-type

tag: library


title: Embryo, wild-type, rep1

description: Embryo, wild-type, rep1 WT_A013


title: Embryo, 5C, rep2

description: Embryo, 5C, rep2 5c_A018


title: Embryo, 5C, rep3

description: Embryo, 5C, rep3 5c_A019


title: Embryo, 5C, rep1

description: Embryo, 5C, rep1 5c_A016


title: Bd21-3_rep2


title: CardioPlate01_F22

value: Blank

value: 4:2 Fluorotelomer alcohol


title: CardioPlate01_G16

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes


title: CardioPlate01_G17

value: Perfluoro-3-methoxypropanoic acid


title: Bd21-3_rep1


title: CardioPlate01_F21


title: CardioPlate01_F20

value: AFFF-5 (Solberg 6%)


title: Embryo, wild-type, rep3

description: Embryo, wild-type, rep3 WT_A015


title: jmj1-1_Input_rep1

data_processing:
Cutadapt was used to trim the raw ChIP-seq reads to obtain high sequencing qualiyt reads.
Bowtie2 was used to map cleaned reads to the genome of Brachypodium distachyon.
Using SAMtools to sort reads and remove duplicate reads.
MACS2 was utilized to find peaks, and MAnorm was used to find different peaks in mutant compared with WT.
Reads were normalized using the bamCoverage tool in deepTools and using heatmap to exhibit by plotHeatmap tool in deepTools.
Assembly: Brachypodium distachyon (genome version is 3.0, download from http://plants.ensembl.org/)
Supplementary files format and content: bigwig

extract_protocol:
Seedlings were harvested and fixed with the buffer containing 0.4 M sucrose, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 1% formaldehyde, and 1 mM PMSF.Chromatin was sonicated into DNA fragments around 200~500-bp in size using lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1% SDS, 0.1% Na deoxycholate, 1% Triton X-100 and Protease Inhibitor cocktail.
The ChIP-seq libraries were constructed by following the manufacturer’s instructions of VAHTSTM Universal DNA Library Prep Kit (Vazyme).

tag: chip antibody


title: CardioPlate01_F19

value: 8:2 Fluorotelomer alcohol


title: CardioPlate01_G13

value: Perfluorooctanoic acid


title: CardioPlate01_F18

value: Sodium perfluorodecanesulfonate


title: jmj1-1_H3_rep1


title: CardioPlate01_F15

value: AFFF-1 (Foamtec 3%)


title: CardioPlate01_F16

value: AFFF-2 (Chemguard 6%)


title: jmj1-1_H3K4me3_rep1


title: jmj1-1_H3K4me2_rep2


title: CardioPlate01_F13

value: 8:2 Fluorotelomer sulfonic acid


title: jmj1-1_Input_rep2


title: CardioPlate01_F17

value: Perfluoroundecanoic acid


title: jmj1-1_H3K4me3_rep2

value: leaf


title: CardioPlate01_E21


title: CardioPlate01_E23


title: jmj1-1_H3K4me1_rep1


title: CardioPlate01_E20


title: jmj1-1_H3_rep2


title: jmj1-1_H3K4me2_rep1


title: jmj1-1_H3K4me1_rep2


title: CardioPlate01_E22


title: Bd21-3_Input_rep2


title: Bd21-3_Input_rep1


title: CardioPlate01_E19


title: Bd21-3_H3_rep2


title: CardioPlate01_E18


title: CardioPlate01_E16


title: Bd21-3_H3K4me3_rep2


title: CardioPlate01_E15


title: Bd21-3_H3_rep1


title: CardioPlate01_D22


title: CardioPlate01_E13


title: Bd21-3_H3K4me3_rep1


title: Bd21-3_H3K4me1_rep2


title: Bd21-3_H3K4me2_rep1


title: Bd21-3_H3K4me1_rep1


title: CardioPlate01_E17


title: Bd21-3_H3K4me2_rep2


title: CardioPlate01_D23


title: CardioPlate01_D20


title: CardioPlate01_D18


title: CardioPlate01_D21


title: CardioPlate01_D19


title: CardioPlate01_D17


title: CardioPlate01_D13


title: CardioPlate01_D16


title: CardioPlate01_D15


title: HepaPlate02_L12

data_processing:
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
Quality control steps with the following criteria were performed: 1) genes with fewer than 5 mean counts across the entire sample spacewere removed, 2) samples with mean expression across all genes lower than 25 were removed, 3) outliers in vehicle control samples were identified and removed using mean correlation at <0.85 as the criteria to ensure the stability of further transcriptomic dose-response and differential expression analyses, 4) in addition, principal component analysis (PCA) was conducted on vehicle control samples using raw counts to identify any remaining outliers.
Assembly: Whole transcriptome assay
Supplementary files format and content: iHep_normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: iHep_hash.csv file with meta data of the QC samples

value: Perfluoroheptanoic acid


title: HepaPlate02_M09

value: DMSO


title: HepaPlate02_M07


title: HepaPlate02_M05


title: HepaPlate02_L10

value: 3:3 Fluorotelomer carboxylic acid


title: HepaPlate02_L09

value: Ammonium perfluorooctanoate


title: HepaPlate02_M03

value: Blank


title: HepaPlate02_M08


title: HepaPlate02_L07

value: Perfluoro(4-methoxybutanoic) acid


title: HepaPlate02_L08

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes


title: HepaPlate02_L06

value: Perfluoro-3,6,9-trioxatridecanoic acid


title: HepaPlate02_L11


title: HepaPlate02_L05

value: Perfluorooctanamidine


title: HepaPlate02_M04


title: HepaPlate02_L04

value: Perfluorohexanesulfonamide


title: HepaPlate02_M06


title: HepaPlate02_L03

value: Nonafluoropentanamide


title: HCT116_TAZ_2

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: Raw IDAT files for each sample were processed using the Bioconductor package “SeSAMe” (Version 1.8.2) for extraction of probe signal intensity values, normalization of probe signal intensity values, and calculation of β-values from the normalized probe signal intensity values. CpG probes with a detection p-value > 0.05 in any one sample were excluded from the analysis.

source_name: HCT116 Colorectal Carcinoma epithelial cells

label_protocol: Standard Illumina protocol

growth_protocol: HCT116 colon cancer cell lines was purchased from ATCC and maintained according to ATCC recommendations in McCoy's (Gibco 16600-082) media supplemented with 10% Fetal Bovine Serum (Millipore Sigma F0926) and 1% penicillin/streptomycin (Life Technologies, 15140-122) at 5% CO2 and 37C.

extract_protocol: DNA was extracted using Qiagen DNeasy Blood & Tissue Kit (cat no. 69504)

treatment_protocol: 5-aza-2’-deoxycytidine (DAC, Sigma A3656) was dissolved in DMSO:PBS at a ratio of 1:150 and stored at -80°C. Each drug or % vehicle equivalent was applied to attached cells for a period of 72 hours. Tazemetostat (TAZ or EPZ6438, Selleck Chemicals S7128 and Cayman Chemical 16174) was dissolved in DMSO and sotred at -20C. Cells were treated for 72 hours.

value: Tazemetostat (1 uM)

value: Wild type


title: HepaPlate02_K10


title: HepaPlate02_K08


title: HepaPlate02_K09


title: HCT116_TAZ_1


title: HepaPlate02_K06


title: HepaPlate02_K11


title: HepaPlate02_K04


title: HepaPlate02_K05


title: HepaPlate02_K03


title: HepaPlate02_K02

value: Perfluorononanoic acid


title: HepaPlate02_J12


title: HepaPlate02_J10


title: HepaPlate02_K07


title: HepaPlate02_J09


title: HepaPlate02_J08


title: HCT116_DMSO_1


title: HCT116_DAC300_2

value: 5'aza-2'deoxycytidine (300 nM)


title: HCT116_DMSO_2


title: HCT116_Combo_1

value: 5'aza-2'deoxycytidine (30 nM); Tazemetostat (1 uM)


title: HCT116_DAC30_2

value: 5'aza-2'deoxycytidine (30 nM)


title: HCT116_DAC30_1


title: HepaPlate02_J11


title: HepaPlate02_J06


title: HepaPlate02_J04


title: HepaPlate02_J07


title: HepaPlate02_K12

value: Perfluoroheptanoic acid


title: HepaPlate02_J02


title: HepaPlate02_I10

value: Perfluorotetradecanoic acid


title: HepaPlate02_I11

value: Perfluorodecanoic acid


title: HepaPlate02_I08

value: 6:2 Fluorotelomer sulfonic acid


title: HepaPlate02_I07

value: Blank

value: AFFF-7 (Tridol 6%)


title: HepaPlate02_I05

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorotridecanoic acid


title: HepaPlate02_J03


title: HepaPlate02_J05

value: Perfluorooctanamidine


title: HepaPlate02_I06

value: Perfluoro-3-methoxypropanoic acid


title: HepaPlate02_I12

value: Perfluorobutanesulfonic acid


title: HepaPlate02_I09

value: Perfluorooctanamide


title: HCT116_DAC300_1

value: Wild type


title: HepaPlate02_I04

value: Dodecafluoroheptanol


title: HepaPlate02_I03

value: AFFF-4 (FireAde 6%)


title: HepaPlate02_H12


title: HCT116_Combo_2

value: 5'aza-2'deoxycytidine (30 nM); Tazemetostat (1 uM)


title: HepaPlate02_I02

value: Perfluorooctanoic acid


title: HepaPlate02_H11


title: HepaPlate02_H08


title: HepaPlate02_H10


title: HepaPlate02_H07


title: HepaPlate02_H05


title: HepaPlate02_H06


title: HepaPlate02_H09


title: HepaPlate02_H04


title: HepaPlate02_H03


title: HepaPlate02_H02


title: HepaPlate02_G12


title: HepaPlate02_G09


title: HepaPlate02_G08


title: HepaPlate02_G11


title: Mtsoc1-4 triple mutant apex bio rep 2

city: Auckland

first: Joanna

last: Putterill

state: Auckland

address: 3A Symonds Street

department: School of Biological Sciences

country: New Zealand

institute: The University of Auckland

data_processing:
The quality of the sequenced raw reads (FASTQ files) was assessed and the trimming of the reads was done using Fastp (version 0.21) (Chen et al., 2018). Reads were trimmed from the 3′ end where quality dropped below a PHRED score of 20 and any remaining reads under 36 bp in length were also excluded.
The trimmed reads were mapped to the Mt4.0v2 transcriptome (Young et al., 2011; Tang et al., 2014) using Salmon (v0.8.2) (Patro et al., 2017). The resulting count tables, in which abundance is measured as Transcripts per Million (TPM), were then imported into R (R Core Team, 2018) using the tximport package (v1.12.0) (Soneson et al., 2015). Normalisation and differential expression analysis visualization were performed using DESeq2 (v1.24.0) (Love et al., 2014). Differentially expressed transcripts were filtered-out using a cut-off of adjusted p-value ≤ 0.05 and log2fold-change ≥ 1 or ≤-1.
Assembly: MedtrA17_4.0 (Mt4.0v2_GenesCDSSeq_20140818_1100.fasta)
Supplementary files format and content: Excel file including raw counts for each sample
Supplementary files format and content: excel file including normalised counts for each sample

organism: Medicago truncatula

source_name: apex

growth_protocol: Medicago seeds were first scarified in between two pieces of sandpaper, sterilized in chlorine solution  for 5-10 minutes and germinated overnight at 15°C in the dark. Germinated seeds were placed on moist filter paper and stored at 4°C in the dark for 3 weeks. Germinated seeds with or without vernalisation were planted in seed raising mix (Daltons Limited, NZ) and placed on sub-irrigated rockwool mats. Seedlings were transplanted after 11-14 days to 2L pots of soil mix consisting of potting mix,  vermiculite and number 2 sand. Plants were grown in controlled rooms in long day (LD, 16 hours light/8 hours dark) or short day (SD, 8 hours light/16 hours dark) photoperiods at 22°C.

extract_protocol:
Fully expanded trifoliate leaves (leaf) or shoot apices (apex) (15-100 mg), were harvested from plants grown under VLD conditions at Zeitgeber time 4 (4 h after dawn). Tissues were snap frozen with metal beads and homogenised using a Geno/Grinder (New Jersey, USA) into powder in liquid nitrogen. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Germany) following the manufacturer’s protocol. The quantity and quality of RNA were checked by Bioanalyzer 2100 (Agilent Technologies, USA).
The RNA of Mtsoc1a mutant and wild type R108 were constructed into 12 strand-specific mRNA libraries with polyA enrichment and were subjected to Illuminia NovaSeq 6000 paired-end 150 bp sequencing by Novogene. The RNA of triple Mtsoc1-4 mutant were constructed into three strand-specific mRNA libraries with polyA enrichment and sequenced on Illumina platform NovaSeq 6000, paired-end 150 bp by Novogene (Hong Kong).

treatment_protocol: Fully expanded trifoliate leaves (leaf) or shoot apices (apex) were harvested from 15 day old Mtsoc1a and WT. Two trifoliate leaves, one leaf taken from each of two plants, were pooled to make up one biological replicate; with three biological replicates harvested for each genotype. For the RNA-seq on the Mtsoc1-4 mutant, the upper portion of three primary stems with their shoot apex, from three plants, were pooled to make up one biological replicate, with three biological replicates harvested for each genotype.

value: apex

value: 83 days old

tag: genetic modification

value: CRISPR Cas9 targeting SOC1a, b, c


title: Mtsoc1a single mutant apex bio rep 3

value: 15 days old

value: SOC1a Tnt1 mutation


title: HepaPlate02_G10

value: Blank

value: Perfluorotetradecanoic acid


title: HepaPlate02_G07

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: AFFF-7 (Tridol 6%)


title: Mtsoc1-4 triple mutant apex bio rep 3


title: Mtsoc1-4 triple mutant apex bio rep 1


title: Mtsoc1a single mutant apex bio rep 1


title: HepaPlate02_G06

value: Perfluoro-3-methoxypropanoic acid


title: HepaPlate02_G04


title: Mtsoc1a single mutant leaf bio rep 3

source_name: leaf

value: leaf


title: Mtsoc1a single mutant apex bio rep 2


title: HepaPlate02_G03


title: HepaPlate02_G02


title: Mtsoc1a single mutant leaf bio rep 2


title: HepaPlate02_G05

value: Perfluorotridecanoic acid


title: WT apex bio bio rep 3

value: wild type


title: HepaPlate02_F10


title: WT apex bio bio rep 2


title: HepaPlate02_F12

value: AFFF-3 (Phos-Check)


title: HepaPlate02_F09

value: AFFF-5 (Solberg 6%)


title: CardioPlate01_D14

value: AFFF-6 (FireStopper)


title: WT apex bio bio rep 1


title: WT leaf bio bio rep 3


title: HepaPlate02_F06

value: Perfluoroundecanoic acid


title: WT leaf bio bio rep 2


title: HepaPlate02_F07

value: Sodium perfluorodecanesulfonate


title: HepaPlate02_F05

value: AFFF-2 (Chemguard 6%)


title: HepaPlate02_F04

value: AFFF-1 (Foamtec 3%)


title: HepaPlate02_F02

value: 8:2 Fluorotelomer sulfonic acid