title: TF ChIP-seq from HCT116 (ENCLB577ZMM)

description:
https://www.encodeproject.org/experiments/ENCSR160GVO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR160GVO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR862XXV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB577ZMM
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: CTCF

tag: line

value: cell line

value: Erez Aiden

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS088IDX at ENCODE; https://www.encodeproject.org/ENCBS088IDX/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: P2_ROI8_TV_Vimentin

status: Public on Apr 30 2023

type: SRA

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

description:
rawdata.csv
normdata.csv

library_source: transcriptomic

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
Supplementary files format and content: Processed data files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: rawdata: raw count data, normdata: normalized count data
Library strategy: GeoMx Seq

molecule: total RNA

organism: Homo sapiens

source_name: Placenta

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: tissue

value: Placenta

tag: idontma

tag: fetalgender

value: Male

tag: covidstatus

tag: roilabel

tag: structure

value: TerminalVilli

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: Histone ChIP-seq from heart left ventricle (ENCLB519HNH)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR704JQF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR704JQF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB519HNH
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

source_name: Homo sapiens male adult (69 years) heart left ventricle tissue

tag: antibody

value: heart left ventricle

value: tissue

tag: biosample encode accession

tag: age

value: 69 year

tag: Sex

value: male

tag: health state

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

tag: dev stage

value: adult

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Shin Lin

tag: link

value: ENCBS987PRB at ENCODE; https://www.encodeproject.org/ENCBS987PRB/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: P2_ROI7_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

value: AnchoringVillus

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey


title: P2_ROI7_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: TF ChIP-seq from HCT116 (ENCLB600DTX)

description:
https://www.encodeproject.org/experiments/ENCSR160GVO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR160GVO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR862XXV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB600DTX
size range: 200-600

tag: antibody

value: CTCF

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

tag: health state

value: colorectal carcinoma

tag: dev stage

tag: age

value: 48 year

tag: lab

tag: source

value: Erez Aiden

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link


title: intestinal tumors 0Gy_Stype

type: genomic

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 24 hours at 67°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 in an ozone-depleted hood.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
Normalized log2 ratio (Cy3/Cy5) in table

organism: Mus musculus

source_name: Non-irradiated intestinal tumors

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Mice were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 3°C) and humidity (50 ± 10%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet and sterilized water ad libitum.

extract_protocol: Genomic DNA of intestinal tumors  and  normal livers were extarcted by PAXgene Tissue DNA Kit.

treatment_protocol: Mice were left untreated or were subjected to whole-body irradiated with X-rays (2 Gy)  at 2 weeks of age.

tag: tissue

value: intestinal tumors

tag: gender

value: Male

tag: strain

value: C3B6F1 ApcMin/+

source_name: Normal liver

value: liver


title: P2_ROI6_TV_PanCK

description:
rawdata.csv
normdata.csv

value: Placenta

tag: idontma

tag: fetalgender

value: Female

tag: covidstatus

tag: roilabel

tag: structure

value: TerminalVilli

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: P2_ROI6_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: sequencingsaturation

tag: area


title: Control ChIP-seq from HCT116 (ENCLB178KBQ)

description:
https://www.encodeproject.org/experiments/ENCSR147MKT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR147MKT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB178KBQ
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

tag: dev stage

value: adult

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

tag: treatments

tag: link

value: ENCBS984YEY at ENCODE; https://www.encodeproject.org/ENCBS984YEY/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Control ChIP-seq from HCT116 (ENCLB596JIT)

description:
https://www.encodeproject.org/experiments/ENCSR147MKT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR147MKT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB596JIT
size range: 200-600

value: cell line


title: P2_ROI5_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

value: AnchoringVillus

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: Histone ChIP-seq from heart left ventricle (ENCLB354AJD)

description:
https://www.encodeproject.org/experiments/ENCSR704JQF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR704JQF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB354AJD
size range: 200-600

tag: antibody

value: heart left ventricle

value: tissue

tag: biosample encode accession

value: 69 year

tag: Sex

tag: health state

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

tag: dev stage

value: Shin Lin

value: ENCBS987PRB at ENCODE; https://www.encodeproject.org/ENCBS987PRB/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: Control ChIP-seq from HCT116 (ENCLB600FML)

description:
https://www.encodeproject.org/experiments/ENCSR147CEU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR147CEU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB600FML
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

value: colorectal carcinoma

tag: age

value: 48 year

tag: lab

tag: source

value: Erez Aiden

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS216VOD at ENCODE; https://www.encodeproject.org/ENCBS216VOD/


title: P2_ROI5_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

value: Placenta

tag: idontma

tag: fetalgender

value: Female

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: P2_ROI4_TV_PanCK

description:
rawdata.csv
normdata.csv

value: Male

value: TerminalVilli

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: TF ChIP-seq from heart right ventricle (ENCLB249MVY)

description:
https://www.encodeproject.org/experiments/ENCSR138FTN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR138FTN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB249MVY
size range: 200-600

source_name: Homo sapiens male adult (54 years) heart right ventricle tissue

tag: antibody

value: CTCF

value: heart right ventricle

tag: biosample encode accession

tag: age

value: 54 year

tag: Sex

value: male

tag: health state

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

tag: dev stage

value: adult

tag: lab

value: Bradley Bernstein, Broad

tag: source

tag: link

value: ENCBS310DXQ at ENCODE; https://www.encodeproject.org/ENCBS310DXQ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: Control ChIP-seq from HCT116 (ENCLB065QEQ)

description:
https://www.encodeproject.org/experiments/ENCSR147CEU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR147CEU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB065QEQ
size range: 200-600

tag: line

value: cell line

value: colorectal carcinoma

value: 48 year

tag: treatments

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: P2_ROI3_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

value: Placenta

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

value: AnchoringVillus

tag: aoisurfacearea

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: TF ChIP-seq from heart right ventricle (ENCLB283HTX)

description:
https://www.encodeproject.org/experiments/ENCSR138FTN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR138FTN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB283HTX
size range: 200-600

tag: antibody

value: tissue

tag: biosample encode accession

tag: age

tag: Sex

tag: health state

tag: dev stage

tag: lab

value: Shin Lin


title: Histone ChIP-seq from heart left ventricle (ENCLB551XTP)

description:
https://www.encodeproject.org/experiments/ENCSR678RFS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR678RFS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB551XTP
size range: 200-600

value: heart left ventricle

value: 69 year

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

tag: source

tag: link

value: ENCBS987PRB at ENCODE; https://www.encodeproject.org/ENCBS987PRB/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: P2_ROI3_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

value: Male

tag: covidstatus

tag: roilabel

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: P2_ROI4_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: structure

value: TerminalVilli

tag: aoisurfacearea

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: Single cell RNAseq of FACS sorted VitA- Col1a1-cells from DEN+WAD mouse liver.

city: Los Angeles

first: Hidekazu

last: Tsukamoto

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

description: samples were processed through 10x Genomics Single Cell 3' v3.1 following manufacturer protocol. Sequencing data was package using 10x Genomics CellRanger.

library_source: transcriptomic single cell

data_processing:
The samples were sequenced using a 2x150 Paired End configuration on the Illumina HiSeq
Raw sequencing data were converted to fastq files and de-multiplexed using the 10x Genomics’ Cell Ranger software version 3.1.0.
UMI and cell barcode de-convolution and mapping to the mm10 reference genome were performed with the software to generate the final digital gene expression matrices and cloupe files using the Cell Ranger count command with default parameters.
The cells which passed the quality assessment by a barcode rank graph, were subjected to sequencing and the data analysis was performed with 10X Genomics’ Loupe Browser software.
Assembly: mm10
Supplementary files format and content: Cell Ranger h5 matrix file

source_name: Liver

extract_protocol:
Liver non-parenhcymal cells were isoalted by in-situ liver perfusion with pronase and collagenase and vitamin A+ (VitA+) and VitA- Col1a1-expressing cells were collected via FACS on ARIA IIu (Becton Dickinson) with solid state laser excited at 488nm and measured with 510/20BP emission mirrors for GFP and excited at 355nm and measured with 450/50BP mirrors for VitA and data were analyzed by FlowJo 10.8.1 version.  The cells were immediately bar-coded for scRNA-seq.
The library was prepared immediately after cell sorting with the target cell number of 10,000 and validated on the Agilent TapeStation (Agilent Technologies) and quantified by using Qubit 2.0 Fluorometer (Invitrogen) and qPCR (KAPA Biosystems) according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and  sample index were added.

treatment_protocol: Male Rosa26mTmG; Col1a1-Cre (mTmG;CC) mice on C57BL/6J background were  injected with diethyl nitrosamine (DEN, 10mg/kg) or saline at 2-wk old and fed for 5 months from 6-wk old  liquid Western alcohol diet (WAD) containing ethanol (3.5%v/v) or chow.

tag: tissue

value: Liver

tag: cell line

value: Disease state

tag: cell type

value: Hepatic stellate cell

tag: genotype

tag: treatment

value: diethyl nitrosamine (i.p)+ Western alcohol diet (fed)


title: Single cell RNAseq of FACS sorted VitA+ Col1a1+ cells from chow fed control mouse liver.

value: Control

value: Saline (i.p)+ Chaw fed


title: Single cell RNAseq of FACS sorted VitA- Col1a1+ cells from chow fed control mouse liver.


title: P2_ROI2_TV_PanCK

description:
rawdata.csv
normdata.csv

value: Placenta

tag: idontma

tag: fetalgender

value: Female

tag: covidstatus

tag: roilabel

tag: aoinucleicount


title: Histone ChIP-seq from heart left ventricle (ENCLB895JMN)

description:
https://www.encodeproject.org/experiments/ENCSR678RFS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR678RFS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB895JMN
size range: 200-600

tag: antibody

value: tissue

tag: biosample encode accession

tag: age

tag: Sex

value: male

tag: health state

tag: dev stage

value: adult

tag: lab

value: Bradley Bernstein, Broad

tag: source

tag: link


title: P2_ROI2_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: structure

tag: aoisurfacearea

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: Histone ChIP-seq from heart right ventricle (ENCLB957FIS)

description:
https://www.encodeproject.org/experiments/ENCSR678IYC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR678IYC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB957FIS
size range: 200-600

tag: antibody

value: heart right ventricle

tag: biosample encode accession

tag: age

value: 54 year

tag: Sex

tag: health state

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: Shin Lin

value: ENCBS310DXQ at ENCODE; https://www.encodeproject.org/ENCBS310DXQ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: P2_ROI1_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

value: AnchoringVillus

tag: aoinucleicount


title: P1_ROI21_TV_PanCK

description:
rawdata.csv
normdata.csv

tag: structure

value: TerminalVilli

tag: aoisurfacearea

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: Control ChIP-seq from HCT116 (ENCLB071WSH)

description:
https://www.encodeproject.org/experiments/ENCSR862XXV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR862XXV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB071WSH
size range: 200-600

tag: line

value: cell line

value: colorectal carcinoma

tag: dev stage

value: 48 year

tag: lab

tag: source

value: Erez Aiden

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS088IDX at ENCODE; https://www.encodeproject.org/ENCBS088IDX/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Single cell RNAseq of FACS sorted VitA+ Col1a1+ cells from DEN+WAD mouse liver.

tag: tissue

value: Liver

tag: cell line

value: Disease state

tag: cell type

value: Hepatic stellate cell

tag: genotype

tag: treatment

value: diethyl nitrosamine (i.p)+ Western alcohol diet (fed)


title: Single cell RNAseq of FACS sorted VitA- Col1a1+  cells from DEN+WAD mouse liver.


title: Histone ChIP-seq from heart right ventricle (ENCLB664NRU)

description:
https://www.encodeproject.org/experiments/ENCSR678IYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR678IYC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB664NRU
size range: 200-600

tag: antibody

value: heart right ventricle

value: tissue

tag: biosample encode accession

tag: age

value: 54 year

tag: Sex

value: male

tag: health state

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: adult

value: Bradley Bernstein, Broad


title: P2_ROI1_AV_Vimentin

description:
rawdata.csv
normdata.csv

value: Placenta

tag: idontma

tag: fetalgender

value: Female

tag: covidstatus

tag: roilabel

tag: structure

value: AnchoringVillus

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: TF ChIP-seq from HCT116 (ENCLB032MQG)

description:
https://www.encodeproject.org/experiments/ENCSR385CDF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR385CDF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR317ZOF
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB032MQG
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4

tag: antibody

value: CTCF

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

tag: health state

value: colorectal carcinoma

tag: dev stage

tag: age

value: 48 year

tag: lab

tag: source

value: Erez Aiden

tag: link

value: ENCBS981HND at ENCODE; https://www.encodeproject.org/ENCBS981HND/


title: P1_ROI21_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

value: TerminalVilli

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: P1_ROI20_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: MCF-7, Input

city: Beijing

first: Yanan

last: Zhang

address: Taipin Rd 27

country: China

institute: Beijing institute of biotechnology

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19, GRCh37
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 50 bp single-end reads or 150 bp paired-end reads was generated.

tag: cell line

tag: cell type

value: breast cancer epithelial cells

tag: chip antibody


title: Control ChIP-seq from HCT116 (ENCLB707FXZ)

description:
https://www.encodeproject.org/experiments/ENCSR862XXV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR862XXV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB707FXZ
size range: 200-600

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS088IDX at ENCODE; https://www.encodeproject.org/ENCBS088IDX/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: MCF-7, HOMEZ, rep2

value: HOMEZ (Ptoteintech, 23965-1-AP)


title: MCF-7, HOMEZ, rep1


title: TF ChIP-seq from HCT116 (ENCLB707IVN)

description:
https://www.encodeproject.org/experiments/ENCSR385CDF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR385CDF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR317ZOF
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB707IVN
size range: 200-600

tag: antibody

value: male

value: adult


title: P1_ROI20_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

value: Placenta

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: P1_ROI19_TV_PanCK

description:
rawdata.csv
normdata.csv

value: Male

tag: sequencingsaturation

tag: area


title: Control ChIP-seq from HCT116 (ENCLB577TOV)

description:
https://www.encodeproject.org/experiments/ENCSR858IFL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR858IFL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB577TOV
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

tag: treatments

tag: link

value: ENCBS086NCD at ENCODE; https://www.encodeproject.org/ENCBS086NCD/


title: Control ChIP-seq from HCT116 (ENCLB396VOR)

description:
https://www.encodeproject.org/experiments/ENCSR858IFL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR858IFL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB396VOR
size range: 200-600

value: cell line


title: JM109 cells selected for ciprofloxacin resistance

city: Rende

first: Dina

last: Bellizzi

state: Cosenza

address: Ponte P. Bucci Cubo 4C

department: Biology, Ecology and Earth Science

country: Italy

institute: University of Calabria

description: 385275_R1_Ciprofloxacin-resistant cells

data_processing:
alignment of paired-end reads was done with hisat2 version 2.1.0
construction of the count table with featureCounts (Version 1.6.0) considering only the fragments in which both reads are correctly mapped
Assembly: E.coli K12 assembly ASM80076v1
Supplementary files format and content: Tab-delimited text files include counts for each gene

organism: Escherichia coli

extract_protocol:
RNA samples were extracted by using RNeasy Micro Kit (Qiagen)
RNA libraries were prepared using Illumina's TruSeq stranded RNA protocol while rRNA removal was performed with Qiagen's FastSelect bacteria kit

tag: cell line

tag: cell type

value: Bacterial cells

tag: treatment

value: ciprofloxacin


title: JM109 cells selected for gentamicin resistance

description: 476822_R1_Gentamicin-resistant cells

value: gentamicin


title: JM109 control strain (untreated)

description: 385274_R1_JM109 parental strain

value: no treatment (control)


title: P1_ROI19_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

value: TerminalVilli

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: JM109 cells selected for ampicillin resistance

description: 385273_R1_Ampicillin-resistant cells

tag: cell line

value: ampicillin


title: Control ChIP-seq from HCT116 (ENCLB714WSV)

description:
https://www.encodeproject.org/experiments/ENCSR661KFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR661KFD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB714WSV
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

value: colorectal carcinoma

tag: dev stage

tag: age

value: 48 year

tag: lab

tag: source

value: Erez Aiden

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS026RHM at ENCODE; https://www.encodeproject.org/ENCBS026RHM/


title: TF ChIP-seq from HCT116 (ENCLB526UOI)

description:
https://www.encodeproject.org/experiments/ENCSR671ITY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR671ITY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR936ENS
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB526UOI
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: antibody

value: CTCF

value: male

value: adult

value: ENCBS628SFE at ENCODE; https://www.encodeproject.org/ENCBS628SFE/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: P1_ROI18_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

value: Placenta

tag: idontma

tag: fetalgender

value: Male

tag: covidstatus

tag: roilabel

tag: structure

value: AnchoringVillus

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: P1_ROI15_TV_PanCK

description:
rawdata.csv
normdata.csv

value: Female

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: Control ChIP-seq from HCT116 (ENCLB680MDT)

description:
https://www.encodeproject.org/experiments/ENCSR661KFD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR661KFD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB680MDT
size range: 200-600

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

tag: treatments

tag: link


title: P1_ROI14_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads


title: TF ChIP-seq from HCT116 (ENCLB848VBL)

description:
https://www.encodeproject.org/experiments/ENCSR107GWZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR107GWZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR147MKT
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB848VBL
size range: 200-600

tag: antibody

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

value: ENCBS984YEY at ENCODE; https://www.encodeproject.org/ENCBS984YEY/


title: P1_ROI15_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

value: TerminalVilli

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation

tag: area


title: TF ChIP-seq from HCT116 (ENCLB773XVE)

description:
https://www.encodeproject.org/experiments/ENCSR107GWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR107GWZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR147MKT
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB773XVE
size range: 200-600

value: colorectal carcinoma

tag: age

value: 48 year

tag: lab

tag: source

tag: treatments

tag: link


title: P1_ROI13_TV_PanCK

description:
rawdata.csv
normdata.csv

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads


title: P1_ROI14_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation


title: P1_ROI13_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: area


title: Control ChIP-seq from HCT116 (ENCLB147RUB)

description:
https://www.encodeproject.org/experiments/ENCSR365VOI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR365VOI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB147RUB
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

value: Erez Aiden

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS872CCI at ENCODE; https://www.encodeproject.org/ENCBS872CCI/


title: P1_ROI11_TV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads


title: Control ChIP-seq from HCT116 (ENCLB858CZM)

description:
https://www.encodeproject.org/experiments/ENCSR365VOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR365VOI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB858CZM
size range: 200-600

tag: line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

tag: dev stage


title: Histone ChIP-seq from heart left ventricle (ENCLB230TGU)

description:
https://www.encodeproject.org/experiments/ENCSR359HLC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR359HLC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB230TGU
size range: 200-600

tag: antibody

value: heart left ventricle

value: tissue

tag: age

value: 69 year

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: adult

tag: lab

tag: source

value: Shin Lin

tag: link

value: ENCBS987PRB at ENCODE; https://www.encodeproject.org/ENCBS987PRB/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: P1_ROI12_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

value: Placenta

tag: idontma

tag: fetalgender

value: Female

tag: covidstatus

tag: roilabel

value: AnchoringVillus

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation

tag: area


title: Histone ChIP-seq from heart right ventricle (ENCLB749OKY)

description:
https://www.encodeproject.org/experiments/ENCSR842TXG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR842TXG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB749OKY
size range: 200-600

value: heart right ventricle

tag: biosample encode accession

value: 54 year

tag: Sex

tag: health state

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

tag: dev stage

value: Bradley Bernstein, Broad

value: ENCBS310DXQ at ENCODE; https://www.encodeproject.org/ENCBS310DXQ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: Histone ChIP-seq from heart right ventricle (ENCLB532SHK)

description:
https://www.encodeproject.org/experiments/ENCSR842TXG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR842TXG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB532SHK
size range: 200-600

tag: antibody

tag: age

value: male

tag: lab

tag: source


title: P1_ROI12_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads


title: Histone ChIP-seq from heart left ventricle (ENCLB988KGO)

description:
https://www.encodeproject.org/experiments/ENCSR359HLC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR359HLC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB988KGO
size range: 200-600

value: heart left ventricle

value: tissue

tag: biosample encode accession

tag: link


title: P1_ROI11_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: covidstatus

tag: roilabel

value: TerminalVilli

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation

tag: area


title: P1_ROI18_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

value: Male


title: TF ChIP-seq from HCT116 (ENCLB757YGC)

description:
https://www.encodeproject.org/experiments/ENCSR352EIC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR352EIC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR557ZCZ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB757YGC
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5

tag: antibody

value: CTCF

tag: line

value: cell line

tag: Sex

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

tag: age

value: 48 year

tag: lab

tag: source

value: Erez Aiden

value: ENCBS889ZME at ENCODE; https://www.encodeproject.org/ENCBS889ZME/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: P1_ROI10_AV_Vimentin

description:
rawdata.csv
normdata.csv

value: Placenta

value: Female

tag: covidstatus

tag: roilabel

tag: structure

value: AnchoringVillus

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: stitchedreads


title: TF ChIP-seq from HCT116 (ENCLB704HCC)

description:
https://www.encodeproject.org/experiments/ENCSR671ITY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR671ITY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR936ENS
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB704HCC
size range: 200-600

tag: antibody

tag: biosample encode accession

value: Bradley Bernstein, Broad

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS628SFE at ENCODE; https://www.encodeproject.org/ENCBS628SFE/


title: P1_ROI10_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation

tag: area


title: P1_ROI4_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount


title: P1_ROI4_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: stitchedreads


title: Control ChIP-seq from HCT116 (ENCLB023HNW)

description:
https://www.encodeproject.org/experiments/ENCSR621MTI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR621MTI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB023HNW
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7

tag: line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: link

value: ENCBS385ZCY at ENCODE; https://www.encodeproject.org/ENCBS385ZCY/


title: P1_ROI3_TV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

value: TerminalVilli

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation

tag: area


title: P1_ROI3_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: stitchedreads


title: Histone ChIP-seq from heart left ventricle (ENCLB563ZOK)

description:
https://www.encodeproject.org/experiments/ENCSR072GNA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR072GNA
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB563ZOK
size range: 200-600

tag: antibody

value: heart left ventricle

value: tissue

tag: biosample encode accession

tag: age

value: 69 year

tag: Sex

tag: health state

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

tag: dev stage

tag: lab

tag: source

value: Shin Lin

tag: link

value: ENCBS987PRB at ENCODE; https://www.encodeproject.org/ENCBS987PRB/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: TF ChIP-seq from HCT116 (ENCLB088XOY)

description:
https://www.encodeproject.org/experiments/ENCSR341OQG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR341OQG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR858IFL
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB088XOY
size range: 200-600

value: CTCF

tag: line

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden

tag: treatments

value: ENCBS086NCD at ENCODE; https://www.encodeproject.org/ENCBS086NCD/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: P1_ROI2_TV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

value: Placenta

tag: idontma

tag: fetalgender

value: Male

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation

tag: area


title: P1_ROI2_TV_Vimentin

description:
rawdata.csv
normdata.csv

value: TerminalVilli

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: stitchedreads


title: Histone ChIP-seq from heart left ventricle (ENCLB311AHQ)

description:
https://www.encodeproject.org/experiments/ENCSR072GNA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR072GNA
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB311AHQ
size range: 200-600

tag: antibody

value: heart left ventricle

value: tissue

tag: biosample encode accession

tag: age

tag: Sex

value: male

tag: health state

tag: dev stage

tag: lab

value: Bradley Bernstein, Broad

tag: source

tag: link


title: TF ChIP-seq from HCT116 (ENCLB897YQD)

description:
https://www.encodeproject.org/experiments/ENCSR341OQG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR341OQG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR858IFL
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB897YQD
size range: 200-600

tag: line

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;


title: P1_ROI1_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

value: AnchoringVillus

tag: aoisurfacearea

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation

tag: area


title: TF ChIP-seq from HCT116 (ENCLB734EWH)

description:
https://www.encodeproject.org/experiments/ENCSR597TGH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR597TGH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR990OHC
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB734EWH
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14

tag: antibody

value: CTCF

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

value: ENCBS658CIB at ENCODE; https://www.encodeproject.org/ENCBS658CIB/


title: human PBMC 3x loading

city: Paris

first: Stuart

last: EDELSTEIN

state: Île-de-France

address: 29 rue du Faubourg Saint Jacques, Pépinière Paris Santé Cochin

country: France

institute: Scipio bioscience

description: Scipio bioscience. All provided R1 and R2 FASTQ files are already demultiplexed by sample index.

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed using Cytonaut v6.7.0 (https://cytonaut-scipio.bio) from raw FASTQ files to quality controls and count matrices.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools based on the first 25 millions input raw reads of the R1 FASTQ file of the sample "10Ka-XT" (human PBMC control sample) and based on the first 37,5 millions input raw reads of the R1 FASTQ file of the sample "30Ka-opt-XT" (human PBMC 3x loading).
Raw read downsampling was perfomed for each sample by randomly subsampling raw reads from the FASTQ files such that the mean number of raw reads belonging to cell-associated barcodes was 20,000.
The provided processed data is composed of one count matrix per sample, computed after raw read downsampling, such that for each sample the same sequencing depth is simulated at 20,000 mean number of raw reads per cell.
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38).  Unique Genome Name in Cytonaut v6.7.0: Human_Scipio_2022_A;  Species: Homo_sapiens;  Genome Source: ensembl;  Genome Version: GRCh38;  Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/;  Annotation Source: ensembl;  Annotation Version: 99;  Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/
Supplementary files format and content: Tab Separated Values (TSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

molecule: polyA RNA

source_name: blood

extract_protocol:
For human PBMC control, scRNA was extracted from 10,000 human PBMCs, according to the RevGel-Seq protocol instructions. Briefly, barcode beads and cells are attached via a bifunctional chemical linker. These tandems are dispersed in an hydrogel in the liquid state and immobilized upon gelation. Following cell lysis, polyA+ RNA molecules are captured on the barcoded beads via polyA-polyT interactions. Barcoded beads (and associated RNA molecules) are recovered following degelation, and reverse transcription and subsequent second strand synthesis with random primer are performed. Each sample is then split in 8 subfractions and PCR-amplified.  For the human PBMC 3x loading sample, following modifications were brought to the human PBMC control sample prep: the number of input cells is 30 000, all reagents quantity were doubled, PCR was made in 16 split tubes.
For each sample, barcoded cDNA of 2 PCR tubes were pooled then purified with 0.6X SPRIselect to remove short fragments. Sequencing libraries were prepared with illumina's Nextera XT kit for the purified pooled barcoded cDNA according to manufacturer's instructions with the following adaptations: 600pg of the cDNA was subjected to tagmentation reaction. The tagmented DNA was amplified by 12 cycles PCR. During this PCR, DNA fragments with cell barcode sequence at one end are selectively amplified by using a primer pair of custom P5-read1 primer to the original barcode end and Nextera N7xx P7 index primer to the tagmented end. Paired end sequencing was done.

tag: cell type

value: PBMC isolated from fresh blood

tag: tissue

value: blood

value: anonymous blood donor


title: TF ChIP-seq from HCT116 (ENCLB130YAC)

description:
https://www.encodeproject.org/experiments/ENCSR597TGH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR597TGH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR990OHC
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB130YAC
size range: 200-600

tag: line

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

tag: source

value: Erez Aiden

tag: link


title: TF ChIP-seq from HCT116 (ENCLB158IJT)

description:
https://www.encodeproject.org/experiments/ENCSR059BCO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR059BCO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR229ZIR
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB158IJT
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF

value: ENCBS814XCI at ENCODE; https://www.encodeproject.org/ENCBS814XCI/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Control ChIP-seq from HCT116 (ENCLB535TIV)

description:
https://www.encodeproject.org/experiments/ENCSR317ZOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR317ZOF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB535TIV
size range: 200-600

value: ENCBS981HND at ENCODE; https://www.encodeproject.org/ENCBS981HND/


title: Control ChIP-seq from HCT116 (ENCLB292QTA)

description:
https://www.encodeproject.org/experiments/ENCSR317ZOF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR317ZOF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB292QTA
size range: 200-600

value: male


title: human PBMC control


title: TF ChIP-seq from HCT116 (ENCLB785JEZ)

description:
https://www.encodeproject.org/experiments/ENCSR059BCO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR059BCO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR229ZIR
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB785JEZ
size range: 200-600

value: Bradley Bernstein, Broad


title: Control ChIP-seq from HCT116 (ENCLB127TEV)

description:
https://www.encodeproject.org/experiments/ENCSR313EED/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR313EED
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB127TEV
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

value: ENCBS154UAS at ENCODE; https://www.encodeproject.org/ENCBS154UAS/


title: Control ChIP-seq from HCT116 (ENCLB805PBX)

description:
https://www.encodeproject.org/experiments/ENCSR313EED/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR313EED
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB805PBX
size range: 200-600


title: TF ChIP-seq from HCT116 (ENCLB774CJU)

description:
https://www.encodeproject.org/experiments/ENCSR048RGR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR048RGR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR147CEU
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB774CJU
size range: 200-600

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS216VOD at ENCODE; https://www.encodeproject.org/ENCBS216VOD/


title: Control ChIP-seq from HCT116 (ENCLB955PMU)

description:
https://www.encodeproject.org/experiments/ENCSR621MTI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR621MTI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB955PMU
size range: 200-600

value: ENCBS385ZCY at ENCODE; https://www.encodeproject.org/ENCBS385ZCY/


title: TF ChIP-seq from HCT116 (ENCLB886KMN)

description:
https://www.encodeproject.org/experiments/ENCSR048RGR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR048RGR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR147CEU
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB886KMN
size range: 200-600

value: CTCF


title: Apc SI, replicate 2, scRNAseq

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing and gene counting were performed using Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: proximal small intestine

extract_protocol:
Samples were homogenised and digested using a McIlwain Tissue CHopper and the GentleMACS Octo Dissociator in combination with the Mouse tumour dissociation kit (Miltenyi Biotec). Debris was removed, and then cells were sorted using a FACSAria sorter (BD Biosciences) and DAPI to remove dead cells.
Cells were loaded into a Chromium Chip G using a 10x Chromium Single-Cell 3’ v3 Gel Bead kit and Library (10x Genomics), then libraries were analysed using the Bioanalyzer High Sensitivity DNA kit (Agilent technologies). Sequencing was performed on an Illumina NovaSeq 6000 with paired-end 150-base reads.

treatment_protocol: Mice were induced with two intraperitoneal injections of 2mg tamoxifen 24 hours apart, and were then sampled 4 days after induction. Segments of small intestine were collected and processed immediately for single cell sequencing

value: all cells

value: proximal small intestine

tag: genotype

value: VilCreER Apc fl/fl

tag: timepoint

value: Day 4


title: Apc SI, replicate 1, scRNAseq

description: 10x Genomics


title: Control ChIP-seq from HCT116 (ENCLB513QVN)

description:
https://www.encodeproject.org/experiments/ENCSR307VBQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR307VBQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB513QVN
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: cell line

value: colorectal carcinoma

value: adult

value: ENCBS959RJO at ENCODE; https://www.encodeproject.org/ENCBS959RJO/


title: Histone ChIP-seq from heart right ventricle (ENCLB183NQM)

description:
https://www.encodeproject.org/experiments/ENCSR589EMG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR589EMG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB183NQM
size range: 200-600

value: heart right ventricle

value: tissue

value: 54 year

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: Shin Lin

value: ENCBS310DXQ at ENCODE; https://www.encodeproject.org/ENCBS310DXQ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: Control ChIP-seq from HCT116 (ENCLB815SLH)

description:
https://www.encodeproject.org/experiments/ENCSR307VBQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR307VBQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB815SLH
size range: 200-600

value: male

value: 48 year

value: Bradley Bernstein, Broad

value: Erez Aiden

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Histone ChIP-seq from heart right ventricle (ENCLB012UJT)

description:
https://www.encodeproject.org/experiments/ENCSR589EMG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR589EMG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB012UJT
size range: 200-600


title: P1_ROI1_AV_PanCK

description:
rawdata.csv
normdata.csv

source_name: Placenta

value: Placenta

tag: idontma

tag: fetalgender

value: Male

tag: covidstatus

tag: roilabel

tag: structure

value: AnchoringVillus

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: TF ChIP-seq from HCT116 (ENCLB884PHB)

description:
https://www.encodeproject.org/experiments/ENCSR288YJL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR288YJL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR001YXI
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB884PHB
size range: 200-600

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: antibody

value: CTCF

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

tag: age

tag: lab

tag: source

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS802HCI at ENCODE; https://www.encodeproject.org/ENCBS802HCI/


title: TF ChIP-seq from HCT116 (ENCLB167UVT)

description:
https://www.encodeproject.org/experiments/ENCSR288YJL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR288YJL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR001YXI
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB167UVT
size range: 200-600


title: Histone ChIP-seq from heart left ventricle (ENCLB873FTM)

description:
https://www.encodeproject.org/experiments/ENCSR748OJA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR748OJA
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB873FTM
size range: 200-600

source_name: Homo sapiens male adult (69 years) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: 69 year

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: Shin Lin

value: ENCBS987PRB at ENCODE; https://www.encodeproject.org/ENCBS987PRB/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: Histone ChIP-seq from heart left ventricle (ENCLB275XVM)

description:
https://www.encodeproject.org/experiments/ENCSR748OJA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR748OJA
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB275XVM
size range: 200-600

value: male

value: Bradley Bernstein, Broad


title: Control ChIP-seq from HCT116 (ENCLB053OJK)

description:
https://www.encodeproject.org/experiments/ENCSR557ZCZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR557ZCZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB053OJK
size range: 200-600

value: 48 year

value: Erez Aiden

value: ENCBS889ZME at ENCODE; https://www.encodeproject.org/ENCBS889ZME/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Control ChIP-seq from HCT116 (ENCLB771DPN)

description:
https://www.encodeproject.org/experiments/ENCSR557ZCZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR557ZCZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB771DPN
size range: 200-600

value: cell line

value: colorectal carcinoma


title: Control ChIP-seq from HCT116 (ENCLB893IVO)

description:
https://www.encodeproject.org/experiments/ENCSR001YXI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR001YXI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB893IVO
size range: 200-600

value: adult

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;


title: MousePlacentaUE1

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: Mouse Placenta UE 1

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v6.1.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tab separated values and matrix files.

molecule: nuclear RNA

source_name: placenta

extract_protocol:
Females were time-mated and on day 16 of gestation, pregnant females were killed by cervical dislocation and uteri removed. Each fetus and its corresponding placenta was identified and placentas were then dissected and the endocrine region of the placenta (junctional zone) immediately snap-frozen in liquid nitrogen.  Samples were stored at -80ºC until further analysis. Samples were pooled  to create 2 x control samples and 2 x UE samples (4 placenta per sample). Samples were thawed immediately before nucleus dissociation. Placenta were homogenized using a dounce homogenizer in ice cold homogenate buffer containing DRAQ5. These were then centrifuged at 900xg for 10 minutes and pellets were resuspended in 25% Optiprep solution. Suspensions were layered on top of 29% optiprep and centrifuged for 20 minutes at 13,500xg. Nuclei pellets were then removed from the optiprep and resuspended in wash buffer and passed through a 40um cell strainer prior to FACS sorting. Saples were FACS sorted with gating set according to size, grnaularity and DRAQ5+ events to capture singlets and remove debris. Each sample was sorted into their own tubes and sequencing libraries were generated from these samples.
Library construction was perfomed using 10X Genomics Chromium Single Cell 3’ Reagent kits (Version 3.1) according to the standardised protocol.
Single nucleus RNA sequencing

treatment_protocol: Reciprocal crosses between homozygousTpbpaCreand homozygousIgf2Floxmice were conducted to generate litters with deletion of the maternally-inherited and silentIgf2allele (control litters) and litters with deletion of the paternally-inheritedIgf2allele in the placental endocrine cells (under-expression [UE] litters).

tag: tissue

value: placenta

tag: gestational day

tag: genotype

value: FEMALE Igf2Cre/Cre X MALE TpbpaFlox/Flox


title: MousePlacentaUE2

description: Mouse Placenta UE2


title: MousePlacentaControl1

description: Mouse Placenta Control1

value: FEMALE Igf2Flox/Flox X MALE TpbpaCre/Cre


title: FOXD3-cKO-MULTISEQ-BC

city: San Francisco

first: Robert

last: Blelloch

address: 35 Medical Center Way

department: Urology

institute: UCSF

library_source: other

data_processing:
Nextflow/scrnaseq
deMULTIplex
The GEX fastq files need to be demultiplexed using the Multi Seq BC fastq files to allocated cells to EtOH or 4HT condition based on McGinnis et al. 2019.
Assembly: mm10
Supplementary files format and content: h5 filtered matrix and MULTI-seq barcode Cell barcode assignment Rdata object
Library strategy: MULTI-seq

molecule: protein

source_name: mESCs

growth_protocol: Mouse ESCs were seeded on a well of a 6well plate (170k cells) in L2i containing growth medium.

extract_protocol: 10x v3 and MULTI-seq

treatment_protocol: 1µM 4HT was added for 24h.

tag: cell type

value: mESCs

tag: culture conditions

value: FOXD3-iKO, control (mixed samples)

tag: treatment

value: FOXD3 loss was induced with 4HT for 24h (control was treated with EtOH)

tag: treatment time


title: Cell isolate - AEC2

city: New Haven

first: Katherine

middle: L

last: Leiby

state: CT

address: 10 Amistad St. Rm 314

department: Biomedical Engineering

institute: Yale University

description: 10x Genomics

data_processing:
FASTQs were aligned, filtered, and counted using the count function in Cell Ranger (v3.0.2, 10x Genomics)
Subsequent data processing was done in R v3.6.1 using Seurat v3.1.1. Initial filtering accepted cells having 500-10,000 genes and 500-100,000 UMI, and percentage mitochondrial reads as follows: >1% and <7% for AEC2; <5% for FB; <9% for EC; <28% for P7; <25% for AEC2_FB_d7; and >6% and <28% for Tri-culture_d7
In Seurat, expression matrices were normalized using the NormalizeData function and scaled with ScaleData, with regression on percentage mitochondrial reads, number of UMI counts, and cell cycle scoring.
As an additional filtration step, following clustering, objects were subclustered by lineage (Col3a1+ mesenchyme, Epcam+ epithelium, Cdh5+ endothelium, and Ptprc+ immune), if present, to identify and remove suspected doublets and low-information cells. The filtered subsets were merged to create the objects for downstream processing.
Assembly: Ensembl Rnor6.0 release 95
Supplementary files format and content: matrix.mtx: sparse matrix file of raw counts, from Cell Ranger output
Supplementary files format and content: genes.tsv: row indices (gene names) of the raw count matrix, from Cell Ranger output
Supplementary files format and content: barcodes.tsv: column indices (cell barcodes) of the raw count matrix, from Cell Ranger output
Supplementary files format and content: data.txt: matrix of raw counts for every gene and cell in the final filtered object; rows are genenames, columns are cell barcodes
Supplementary files format and content: idents.tsv: cluster IDs for cells in the final filtered object; row names match cell barcodes (columns) in data.txt file

organism: Rattus norvegicus

source_name: Lung

growth_protocol: Fibroblasts (FB) were cultured 72 hrs on uncoated tissue-culture plastic in DMEM + 10% FBS + 1% Pen/Strep

extract_protocol:
AEC2: processed from fresh isolate. FB: trypsinized to single-cell suspension. EC: trypsinized to single-cell suspension. Native and engineered tissues: inflated with enzyme solution containing collagenase/dispase, elastase, and DNase and incubated for 20min, then sequentially filtered. Following digestion all steps were performed on ice. Total time from tissue inflation to library preparation was <2hrs.
Single-cell libraries were prepared using standard 10x Genomics protocols for v2 assay (for AEC2s and FBs), v3 assay (for native and engineered lung tissue), or v3.1 assay (for ECs)

value: Lung

tag: strain

value: Sprague Dawley

value: Alveolar epithelial type 2 cells

value: 7 days


title: TF ChIP-seq from HCT116 (ENCLB796DQF)

description:
https://www.encodeproject.org/experiments/ENCSR352EIC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR352EIC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR557ZCZ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB796DQF
size range: 200-600

tag: antibody

value: CTCF

tag: line

tag: biosample encode accession

value: male

value: 48 year

value: Bradley Bernstein, Broad

value: Erez Aiden


title: tg, replicate 1, snRNAseq

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Nuclei from two replicates of TRF2DN-Tg mice and WT mice lungs were isolated with Nuclei EZ Lysis buffer (Sigma) supplemented with protease inhibitor (Roche) and RNase inhibitor (Promega, Life Technologies). Samples were cut into < 2-mm pieces and homogenized using a Dounce homogenizer in 2 mL of ice-cold Nuclei EZ Lysis buffer. The homogenate was filtered through 100 μm and  40 μm cell strainers (pluriSelect ) and then centrifuged at 500 × g for 5 min at 4°C. The pellet was resuspended in Nuclei Suspension Buffer (1x PBS, 1% bovine serum albumin, 0.2% RNase inhibitor), followed by filtration through a 5 μm cell strainer (pluriSelect).
Nuclei were counted on hemocytometers (InCYTO C-chip) and partitioned into each droplet with a barcoded gel bead using the 10× Chromium instrument (10× Genomics). Single nuclei were lysed, and RNAs were reverse-transcribed into complementary DNA (cDNA) within each droplet. After breaking the emulsion, cDNAs were amplified and fragmented, followed by the addition of Illumina adapters using Single Cell 3′ Library & Gel Bead Kit.

value: 8-9 weeks old


title: wt, replicate 2, snRNAseq

description: 10x Genomics


title: FOXD3-cKO-GEX


title: tg, replicate 2, snRNAseq

description: 10x Genomics


title: Control ChIP-seq from HCT116 (ENCLB919WUG)

description:
https://www.encodeproject.org/experiments/ENCSR001YXI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR001YXI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919WUG
size range: 200-600

value: cell line

tag: Sex

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS802HCI at ENCODE; https://www.encodeproject.org/ENCBS802HCI/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Histone ChIP-seq from heart right ventricle (ENCLB196ZGZ)

description:
https://www.encodeproject.org/experiments/ENCSR031SHV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR031SHV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB196ZGZ
size range: 200-600

source_name: Homo sapiens male adult (54 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

tag: age

value: 54 year

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

tag: lab

tag: source

value: Shin Lin

value: ENCBS310DXQ at ENCODE; https://www.encodeproject.org/ENCBS310DXQ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: Histone ChIP-seq from heart right ventricle (ENCLB122HAN)

description:
https://www.encodeproject.org/experiments/ENCSR031SHV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR031SHV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB122HAN
size range: 200-600

value: male

tag: link


title: MousePlacentaControl2

description: Mouse Placenta Control2

tag: tissue

value: placenta

tag: gestational day

value: FEMALE Igf2Flox/Flox X MALE TpbpaCre/Cre


title: wt, replicate 1, snRNAseq

description: 10x Genomics

value: Lung

value: 8-9 weeks old


title: Cell isolate - FB

description: 10x Genomics

value: Sprague Dawley

tag: cell type

value: Fibroblasts

value: 7 days


title: ChIPseq_ESC_Trim24adbkWT_IgG_Act_r2

status: Public on Apr 29 2023

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

institute: SAiGENCI

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10/hg19 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters, allowing only for uniquely mapping reads.
Assembly: mm10/hg19
Supplementary files format and content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and setting shift to 80. The scores in the wig file therefore represent the number of shifted alignments per 100bp window and per million reads in the library.

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). The human primary cell line (HMEC) were cultured in Mammary Epithelial Cell Growth Medium (Gibco MEGM) supplemented with growth factors (Gibco MEGM-SingleQuots CC-4136) BPE, hydrocortisone, hEGF, insulin and gentamicin/amphotericin-B (37°C, 7% CO2).

extract_protocol:
DNA was purified by Phenol:Chloroform extraction.
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 12 PCR cycles.

treatment_protocol: Cells (1.5x10^7) were seeded into 15 cm plates the day before the experiment. Doxorubicin (1uM) or dTAG13 (500nM) compound were added to specific samples to activate p53 or degrade degron tagged alleles. Chromatin Immunoprecipitation (ChIP) was carried out as previously described (Lienert, F. et al. Nat. Genet., 2011) with following modifications: (1) chromatin was sonicated for 22 cycles of 20 sec. on and 40 sec. off using a Diagenode Bioruptor Pico, (2) 75ug of chromatin was used per IP, (3) protein A magnetic Dynabeads (Thermo Fisher Scientific) were used.

value: embryonic stem cells

tag: genotype

tag: treatment condition

value: activated p53

tag: chip antibody

value: Sigma Aldrich, IgG M7023


title: ChIPseq_ESC_Trim24adbkRINGmutant_Flag_Act_r1

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). The human primary cell line (HMEC) were cultured in Mammary Epithelial Cell Growth Medium (Gibco MEGM) supplemented with growth factors (Gibco MEGM-SingleQuots CC-4136) BPE, hydrocortisone, hEGF, insulin and gentamicin/amphotericin-B (37°C, 7% CO2). For neural differentiation, dishes were coated with sterile filtered (0.22μm) Poly-D-lysine hydrobromide (0.5mg/ml, Sigma, P-7886-100MG) diluted in Borate Buffer (50mM, pH 8.5) for 24 hours at 37oC, washed 3x with sterile water and coated for at least 2 hours with Laminin (6.65ug/ml, Sigma, L2020-1MG) in PBS at 37oC. To differentiate mouse ES cells they were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008), trypsinated and plated at a density of 7.5x10^6 per 15cm dish in proliferation medium (DMEM/F12 with Glutamax (LifeTech 31331-028), 1× B27 supplement without vitamin A (LifeTech 12587-010), 1× N2 supplement (LifeTech 17502-048)) supplemented with 1μg/ml Doxycycline for three days to generate neurons.

treatment_protocol: Cells (1.5x10^7) were seeded into 15 cm plates the day before the experiment. Neurons were generated by seeding cells into 6-well plates three days befor the experiment and treating with differentiation conditions. Doxorubicin (1uM) or dTAG13 (500nM) compound were added to specific samples to activate p53 or degrade degron tagged alleles. Chromatin Immunoprecipitation (ChIP) was carried out as previously described (Lienert, F. et al. Nat. Genet., 2011) with following modifications: (1) chromatin was sonicated for 22 cycles of 20 sec. on and 40 sec. off using a Diagenode Bioruptor Pico, (2) 75ug of chromatin was used per IP, (3) protein A magnetic Dynabeads (Thermo Fisher Scientific) were used.

tag: strain

value: Sigma-Aldrich, Flag F1804


title: Paternal obesity: eWAT CT, biological rep4

type: RNA

city: Barcelona

first: Carlos

last: Castaño

address: Rossello 153

country: Spain

institute: CIBER

description:
eWAT CT, biological rep4
Gene expression data from eWAT of offspring of CT male

hyb_protocol: Following fragmentation and terminal labeling,  ss-cDNA was hybridized for 17hr at 45ºC on Clariom™ S  HT, mouse array plate, using the automated GeneTitan System (Affymetrix), which includes the hybridization oven, Fluidic Station and Scanner

scan_protocol: Chips were scanned using the Scanner of the GeneTitan System

data_processing: Transcriptome Analysis Console 4.0 Software. Summarization Method: Gene Level-SST-RMA. Gene-Level Fold Change < -1,5 or > 1,5. Gene-Level P-Value < 0,05. Anova Method: ebayes

label: biotin

label_protocol: 150 ng of good quality RNA samples (RIN >8) with a Ratio 260/280 = 1.8-2 were used.  Fragmentation and Biotin labelling of ss-cDNA was prepared according to Affymetrix WT PLUS Reagent Kit user guide, using an automated system (Biomek FX System, Beckman Coulter)

growth_protocol: 14 weeks old male mice offspring from control or obese males and control females (named CT and F1, respectively) were analized. Prior to the crossing, 8 weeks old male mice were fed chow diet or a high-fat diet (45% lipids) for 12 weeks.

extract_protocol: Total RNA was extracted from frozen liver and eWAT with miRNeasy Mini Kit and treated with DNAse, following standard procedures

value: eWAT

tag: treatment

value: Offspring of CT male


title: ChIPseq_ESC_Trim24adbkRINGmutant_Flag_Act_r2


title: ChIPseq_ESC_Trim24adbkING1.PHDmutant_Flag_Act_r2


title: Paternal obesity: eWAT F1, biological rep4

description:
eWAT F1, biological rep4
Gene expression data from eWAT of offspring of HFD male

treatment_protocol: 14 weeks old male mice offspring from control or obese males and control females (named CT and F1, respectively) were analized. Prior to the crossing, 8 weeks old male mice were fed chow diet or a high-fat diet (45% lipids) for 12 weeks.

value: Offspring of HFD male


title: ChIPseq_ESC_Trim24adbkTaf3.PHDmutant_Flag_Act_r2


title: ChIPseq_ESC_Trim24adbkTaf3.PHDmutant_Flag_Act_r1


title: ChIPseq_ESC_Trim24adbkING1.PHDmutant_Flag_Act_r1


title: ChIPseq_ESC_Trim24adbkWT_IgG_Act_r1


title: Paternal obesity: Liver F1, biological rep3

description:
Liver F1, biological rep3
Gene expression data from liver of offspring of HFD male

value: Liver


title: Paternal obesity: eWAT F1, biological rep1

description:
eWAT F1, biological rep1
Gene expression data from eWAT of offspring of HFD male


title: Paternal obesity: eWAT CT, biological rep3

description:
eWAT CT, biological rep3
Gene expression data from eWAT of offspring of CT male


title: Paternal obesity: eWAT F1, biological rep3

description:
eWAT F1, biological rep3
Gene expression data from eWAT of offspring of HFD male


title: Paternal obesity: eWAT CT, biological rep2

description:
eWAT CT, biological rep2
Gene expression data from eWAT of offspring of CT male


title: Paternal obesity: Liver F1, biological rep4

description:
Liver F1, biological rep4
Gene expression data from liver of offspring of HFD male


title: Paternal obesity: Liver F1, biological rep1

description:
Liver F1, biological rep1
Gene expression data from liver of offspring of HFD male


title: ChIPseq_ESC_Trim24adbkPHDmutant_Flag_Act_r2


title: ChIPseq_ESC_Trim24adbkPHDmutant_Flag_Act_r1


title: Paternal obesity: eWAT F1, biological rep2

description:
eWAT F1, biological rep2
Gene expression data from eWAT of offspring of HFD male


title: Paternal obesity: Liver CT, biological rep4

description:
Liver CT, biological rep4
Gene expression data from liver of offspring of CT male


title: ChIPseq_ESC_Trim24adbkNdeletion_Flag_Act_r2


title: Paternal obesity: Liver CT, biological rep3

description:
Liver CT, biological rep3
Gene expression data from liver of offspring of CT male


title: Paternal obesity: eWAT CT, biological rep1

description:
eWAT CT, biological rep1
Gene expression data from eWAT of offspring of CT male


title: ChIPseq_ESC_Trim24adbkNterminal_Flag_Act_r2


title: Paternal obesity: Liver CT, biological rep2

description:
Liver CT, biological rep2
Gene expression data from liver of offspring of CT male


title: ChIPseq_ESC_Trim24adbkNdeletion_Flag_Act_r1


title: ChIPseq_ESC_Trim24adbkNterminal_Flag_Act_r1


title: Paternal obesity: Liver CT, biological rep1

description:
Liver CT, biological rep1
Gene expression data from liver of offspring of CT male


title: Paternal obesity: Liver F1, biological rep2

description:
Liver F1, biological rep2
Gene expression data from liver of offspring of HFD male


title: ChIPseq_ESC_Trim24adbkWT_Flag_Act_r2


title: ChIPseq_ESC_Trim24adbkWT_Flag_Act_r1


title: ChIPseq_ESC_dTrim24_p53_DegrAct_r2

value: degron-tagged Trim24

value: degraded Trim24; basal p53

value: Cell Signaling technologies, p53(1C12) mAb#2524


title: ChIPseq_ESC_dTrim24_IgG_Unt_r2

value: basal p53


title: ChIPseq_ESC_dp53_Trim24_Degr_r1

value: degron-tagged p53

value: degraded p53

value: Bethyl Laboratories, Trim24 A300-815A


title: ChIPseq_ESC_dTrim24_p53_Act_r2


title: ChIPseq_ESC_dTrim24_p53_DegrAct_r1


title: ChIPseq_ESC_DNMT.TKO_p53_r1

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-


title: ChIPseq_ESC_dTrim24_p53_Degr_r2


title: ChIPseq_ESC_parental_p53_r2

value: DNMT1+/+; DNMT3a+/+; DNMT3b+/+


title: ChIPseq_ESC_DNMT.TKO_p53_r2

value: embryonic stem cells


title: ChIPseq_ESC_dp53_Trim24_Degr_r2


title: ChIPseq_ESC_dTrim24_p53_Unt_r2


title: ChIPseq_ESC_dTrim24_p53_Degr_r1


title: ChIPseq_ESC_dTrim24_p53_Unt_r1


title: ChIPseq_ESC_wt_IgG_Unt_r1

value: wild type


title: ChIPseq_ESC_wt_IgG_Unt_r2

value: Sigma Aldrich, IgG M7023


title: ChIPseq_ESC_wt_H3K23ac_Unt_r1

value: Active motif, H3K23ac 39131


title: ChIPseq_ESC_wt_Trim24_Unt_r1


title: ChIPseq_ESC_wt_Trim24_Unt_r2


title: ChIPseq_ESC_dp53_Trim24_Unt_r2


title: ChIPseq_ESC_dTrim24_p53_Act_r1

value: activated p53


title: ChIPseq_ESC_wt_Trim24_Act_r1


title: ChIPseq_ESC_wt_Trim24_Act_r2


title: ChIPseq_ESC_wt_p53_Act_r1


title: ChIPseq_ESC_wt_p53_Unt_r2


title: ChIPseq_ESC_wt_H3K23ac_Unt_r2


title: ChIPseq_ESC_parental_p53_r1


title: ChIPseq_ESC_wt_p53_Unt_r1


title: ChIPseq_ESC_dTrim24_IgG_Unt_r1


title: ChIPseq_ESC_dp53_Trim24_Unt_r1


title: S7.2_108h

city: Basel

first: Nadim

last: Aizarani

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

data_processing:
Reference and Quantification: Genome sequence and transcript annotation was obtained from Gencode Mouse release M24 (GRCm38 primary assembly and annotation gtf file from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M24), and the coordinates of transcripts and introns were extracted using R (https://r-project.org, version 3.6) and the getFeatureRanges function from the eisaR package (version 0.9 available from https://github.com/fmicompbio/eisaR/tree/bbd8787d7e4b87d158a276af0787226530867b88) with arguments featureType = c("spliced", "intron"), intronType = "separate", flankLength = 0, joinOverlappingIntrons = FALSE. A transcript-to-gene map was created using the getTx2Gene function from eisaR, which links transcripts to genes, and introns to distinct genes for simultaneous quantification (see below). Sequences were extracted from the genome using extractTranscriptSeqs from the GenomicFeatures package (version 1.38.2, )94 and indexed with Salmon (version 1.1.095) with arguments -k 23 –gencode and using the genome as a decoy. Reads were then quantified using Salmon/Alevin (version 1.1.096) with parameters -l ISR --chromiumV3 and the transcript-to-gene map created above.
Quality control and filtering: Technical quality of single cell experiments, cell barcode identification and quantification were assessed using the Bioconductor package alevinQC (version 1.4.0, https://doi.org/doi:10.18129/B9.bioc.alevinQC). Salmon/Alevin counts from all twelve timepoints were imported into R (version 4.0.2) using the tximeta package (version 1.6.397) and stored in a SingleCellExperiment container for downstream analysis. The number of detected genes per cell and the fraction of counts in genes encoded on the mitochondrion (chrM) were calculated using the addPerCellQC function from the scater package (version 1.16.298), and cells with more than 1800 detected genes and less than 10% mitochondrial counts were retained. Gms, mitochondrial, and ribosomal protein genes (genes associated with the GeneOntology term "structural constituent of ribosome", GO:0003735, based on the org.Mm.eg.db package, version 3.11.4) were removed, resulting in a final analysis set of 27027 genes and 71005 cells.
Assembly: GRCm38 primary assembly

source_name: Gastruloids

growth_protocol: ESCs were grown in GMEM supplemented with 10% embryonic stem cell qualified FBS, GlutaMAX, sodium pyruvate, EmbryoMAX MEM NEAA, beta-mercaptoethanol, 0.1 µg/ml LIF, 3 µM CHIR99021, and 1 µM PD0305901. Gastruloids were generated from 300 cells and grown in 96-well ulta-low-attachment U-bottom plates in N2B27 medium (DMEM/F-12, Neurobasal medium, N2, B-27, GlutaMAX, HEPES, and beta-mercaptoethanol) and pulsed with 3 µM CHIR99021 from 48 to 72 hours.

extract_protocol:
0h ESC, gastruloids 12, 24, 36, 48, 52, 56, 60, 72, 84,96, and 120 hours were dissociated with Accutase and per sample 12,000 alive cells were sorted by FACS. Cellular supensions were loaded on a 10x Genomics Chromium Single Cell instrument.
Single cell RNAseq libraries were prepared using the 10x Genomics Single Cell 3’ Gel Bead and Library Kit according to CG000183 Single Cell 3' Reagent Kit v3 User Guide_RevA. GEMRT was performed in a Bio-Rad PTC-200 Thermal Cycler with 0.2ml PCR Tube Strips (Eppendorf P/N 0030 124.359): 53 °C for 45 minutes, 85 °C for 5 minutes; held at 4 °C. After RT, GEMs were broken and the single strand cDNA was cleaned up with DynaBeads® MyOneTM Silane Beads (Life Technologies P/N 37002D). cDNA was amplified using a Bio-Rad PTC-200 Thermal cycler with 0.2ml PCR Tube Strips (Eppendorf P/N 0030 124.359): 98 °C for 3 min; cycled 11x: 98 °C for 15 s, 63 °C for 20 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit (0.6X SPRI). Indexed sequencing libraries were constructed using the reagents in the Chromium Single Cell 3’ library kit V3 ( 10x Genomics P/N1000078), following these steps: 1) Fragmentation, End Repair and A-Tailing; 2) Post Fragmentation, End Repair & A-Tailing Double Sided Size Selection with SPRIselect Reagent Kit (0.6X SPRI and 0.8X SPRI); 3) adaptor ligation; 4) post-ligation cleanups with SPRIselect (0.8X SPRI); 5) sample index PCR using the Chromium Multiplex kit (10x Genomics P/N-120262); 6) Post Sample Index Double Sided Size Selection- with SPRIselect Reagent Kit (0.6X SPRI and 0.8X SPRI). The barcode sequencing libraries were quantified using a Qubit 2.0 with a Qubit TM dsDNA HS Assay Kit (Invitrogen P/N Q32854) and the quality of the libraries were performed on a 2100 Bioanalyzer from Agilent using an Agilent High Sensitivity DNA kit (Agilent P/N 5067-4626). Sequencing libraries were loaded at 1.6pM on an Illumina Nextseq500 with 75cycle kits using the following read length: 28 cycles Read1, 8 cycles i7 Index and 56 cycles Read2.

treatment_protocol: Gastruloids were not treated.

value: Gastruloids

tag: cell line

value: SBR (Sox1/Brachyury reporter)/CGR8


title: S8.2_120h