title: TF ChIP-seq from gastrocnemius (ENCLB063RFS)

description:
https://www.encodeproject.org/experiments/ENCSR798CCX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR798CCX
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR820CZJ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB063RFS
size range: 200-600

value: CTCF

value: Bernstein pool E of 2 gastrocnemius biosamples

value: adult

value: ENCBS707VDM at ENCODE; https://www.encodeproject.org/ENCBS707VDM/


title: TF ChIP-seq from gastrocnemius (ENCLB368TYB)

status: Public on Apr 30 2023

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR798CCX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR798CCX
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR820CZJ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB368TYB
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) gastrocnemius tissue

tag: antibody

value: gastrocnemius

value: tissue

tag: biosample encode accession

tag: note

value: Bernstein pool F of 2 gastrocnemius biosamples

tag: Sex

value: female

tag: dev stage

tag: age

value: 2 month

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS703UIG at ENCODE; https://www.encodeproject.org/ENCBS703UIG/

value: derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: TF ChIP-seq from gastrocnemius (ENCLB312IYW)

description:
https://www.encodeproject.org/experiments/ENCSR798CCX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR798CCX
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR820CZJ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB312IYW
size range: 200-600


title: Control ChIP-seq from gastrocnemius (ENCLB548AKB)

description:
https://www.encodeproject.org/experiments/ENCSR820CZJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR820CZJ
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB548AKB
size range: 200-600


title: Control ChIP-seq from gastrocnemius (ENCLB761LGA)

description:
https://www.encodeproject.org/experiments/ENCSR820CZJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR820CZJ
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB761LGA
size range: 200-600


title: Histone ChIP-seq from heart (ENCLB210TFM)

description:
https://www.encodeproject.org/experiments/ENCSR349EHZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR349EHZ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR477YXE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB210TFM
size range: 200-600

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) heart tissue

value: heart

value: Bernstein pool H of 2 heart biosamples

value: ENCBS509WQM at ENCODE; https://www.encodeproject.org/ENCBS509WQM/


title: Histone ChIP-seq from heart (ENCLB490DLW)

description:
https://www.encodeproject.org/experiments/ENCSR349EHZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR349EHZ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR477YXE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB490DLW
size range: 200-600

value: Bernstein pool G of 2 heart biosamples

value: ENCBS786IOZ at ENCODE; https://www.encodeproject.org/ENCBS786IOZ/


title: Histone ChIP-seq from heart (ENCLB282NJM)

description:
https://www.encodeproject.org/experiments/ENCSR349EHZ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR349EHZ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR477YXE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB282NJM
size range: 200-600


title: Histone ChIP-seq from gastrocnemius (ENCLB314OPU)

description:
https://www.encodeproject.org/experiments/ENCSR283HPZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR283HPZ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR820CZJ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB314OPU
size range: 200-600

value: Bernstein pool E of 2 gastrocnemius biosamples


title: Histone ChIP-seq from gastrocnemius (ENCLB332ISI)

description:
https://www.encodeproject.org/experiments/ENCSR283HPZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR283HPZ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR820CZJ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB332ISI
size range: 200-600

value: adult


title: Histone ChIP-seq from gastrocnemius (ENCLB898XDH)

description:
https://www.encodeproject.org/experiments/ENCSR283HPZ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR283HPZ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR820CZJ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB898XDH
size range: 200-600


title: TF ChIP-seq from left cerebral cortex (ENCLB361HMF)

description:
https://www.encodeproject.org/experiments/ENCSR644VYX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR644VYX
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR513BAE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB361HMF
size range: 200-600

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) left cerebral cortex tissue

value: CTCF

value: left cerebral cortex

value: Bernstein pool I of 4 left cerebral cortex biosamples

value: ENCBS593FWT at ENCODE; https://www.encodeproject.org/ENCBS593FWT/


title: TF ChIP-seq from heart (ENCLB067NOL)

description:
https://www.encodeproject.org/experiments/ENCSR024KGB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR024KGB
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR477YXE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB067NOL
size range: 200-600

value: tissue

value: female


title: TF ChIP-seq from heart (ENCLB815EDT)

description:
https://www.encodeproject.org/experiments/ENCSR024KGB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR024KGB
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR477YXE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB815EDT
size range: 200-600

value: 2 month

value: Barbara Wold, Caltech


title: TF ChIP-seq from heart (ENCLB484UAT)

description:
https://www.encodeproject.org/experiments/ENCSR024KGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR024KGB
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR477YXE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB484UAT
size range: 200-600

value: The Jackson Laboratory


title: TF ChIP-seq from left cerebral cortex (ENCLB763PGY)

description:
https://www.encodeproject.org/experiments/ENCSR644VYX/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR644VYX
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR513BAE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB763PGY
size range: 200-600

value: Bernstein pool J of 4 left cerebral cortex biosamples

value: ENCBS590UIC at ENCODE; https://www.encodeproject.org/ENCBS590UIC/

value: derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Histone ChIP-seq from gastrocnemius (ENCLB605ROF)

description:
https://www.encodeproject.org/experiments/ENCSR283HPZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR283HPZ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR820CZJ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB605ROF
size range: 200-600

value: gastrocnemius

value: Bernstein pool F of 2 gastrocnemius biosamples

value: ENCBS703UIG at ENCODE; https://www.encodeproject.org/ENCBS703UIG/


title: Histone ChIP-seq from heart (ENCLB693VBZ)

description:
https://www.encodeproject.org/experiments/ENCSR349EHZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR349EHZ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR477YXE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB693VBZ
size range: 200-600

value: heart

value: Bernstein pool H of 2 heart biosamples

value: ENCBS509WQM at ENCODE; https://www.encodeproject.org/ENCBS509WQM/


title: 2AS_sy_ost_D1

type: RNA

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: mesenchymal stem cells

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: Angeln Saddleback

tag: sorts of synovial membrane

value: adipose synovium

tag: time point

value: Osteocyte at day 1


title: 2DL_sy_Ko_D7

value: German Landrace

value: fibrous synovium

value: control un-differentiaed cells at day 7


title: 2DL_sy_ost_D1


title: 2DL_fp_Ko_D1

value: control un-differentiaed cells at day 1


title: 2DL_fp_ost_D1


title: 2DL_fp_ost_D7

value: Osteocyte at day 7


title: 2AS_fp_ost_D1


title: TF ChIP-seq from heart (ENCLB978GLZ)

description:
https://www.encodeproject.org/experiments/ENCSR024KGB/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR024KGB
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR477YXE
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB978GLZ
size range: 200-600

value: CTCF

value: tissue

value: Bernstein pool G of 2 heart biosamples

value: female

value: adult

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS786IOZ at ENCODE; https://www.encodeproject.org/ENCBS786IOZ/


title: 2AS_fp_Ko_D1

value: Angeln Saddleback


title: 2AS_sy_Ko_D1


title: 2DL_fp_Ko_D7

value: adipose synovium


title: 2DL_sy_ost_D7


title: 2_DL_sy_ost_D14

value: Osteocyte at day 14


title: 2_DL_sy_Ko_D14

value: German Landrace

value: control un-differentiaed cells at day 14


title: 2_DL_sy_ost_D21

value: fibrous synovium

value: Osteocyte at day 21


title: 2_DL_fp_ost_D14


title: 2_DL_sy_Ko_D21

value: control un-differentiaed cells at day 21


title: 2_DL_fp_Ko_D14


title: 2_DL_fp_D0

value: control un-differentiaed cells at day 0


title: 2_AS_sy_ost_D21


title: 2_AS_sy_Ko_D7

value: control un-differentiaed cells at day 7


title: 2_DL_fp_ost_D21


title: 2_AS_sy_ost_D7

value: Osteocyte at day 7


title: 2_AS_sy_Ko_D21


title: 2_AS_sy_ost_D14


title: 2_DL_sy_D0


title: 2_AS_sy_Ko_D14


title: 2DL_sy_Ko_D1

value: control un-differentiated cells at day 1


title: 2_DL_fp_Ko_D21


title: 2_AS_fp_ost_D21


title: 2_AS_fp_Ko_D7

value: control un-differentiaed cells at day7


title: 1_DL_sy_ost_D1

value: Osteocyte at day 1


title: 1_DL_sy_Ko_D21


title: 2_AS_fp_Ko_D21


title: 1_DL_sy_D0


title: 1_DL_fp_ost_D7


title: Control ChIP-seq from HepG2 (ENCLB192DHE)

description:
https://www.encodeproject.org/experiments/ENCSR542TKO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR542TKO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-09-26
lab: Richard Myers, HAIB
library encode accession: ENCLB192DHE
fragmentation methods: sonication (generic)

organism: Homo sapiens

source_name: Homo sapiens HepG2 cell line

tag: line

value: cell line

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS379SJR at ENCODE; https://www.encodeproject.org/ENCBS379SJR/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: 1_DL_fp_ost_D1

value: German Landrace

value: adipose synovium


title: 1_DL_sy_ost_D14

value: fibrous synovium

value: Osteocyte at day 14


title: 2_AS_sy_D0

value: Angeln Saddleback

value: control un-differentiaed cells at day 0


title: 1_DL_sy_ost_D21

value: Osteocyte at day 21


title: 1_DL_sy_Ko_D14

value: control un-differentiaed cells at day 14


title: 2_AS_fp_ost_D7

value: Osteocyte at day 7


title: 2_AS_fp_ost_D14


title: 2_AS_fp_Ko_D14


title: 1_DL_fp_ost_D21


title: 1_DL_sy_Ko_D7

value: control un-differentiaed cells at day 7


title: 1_DL_sy_ost_D7


title: 1_DL_sy_Ko_D1

value: control un-differentiaed cells at day 1


title: 1_DL_fp_Ko_D21

value: control un-differentiaed cells at day 21


title: 1_DL_fp_Ko_D1


title: 2_AS_fp_D0


title: 1_DL_fp_Ko_D7


title: 1_DL_fp_ost_D14


title: 1_DL_fp_Ko_D14


title: 1_AS_sy_ost_D21


title: 1_AS_sy_ost_D14


title: 1_AS_sy_ost_D7


title: 1_DL_fp_D0


title: Control ChIP-seq from HepG2 (ENCLB229ZMV)

description:
https://www.encodeproject.org/experiments/ENCSR533ASI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR533ASI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB229ZMV
fragmentation methods: sonication (generic)

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS153VJG at ENCODE; https://www.encodeproject.org/ENCBS153VJG/


title: MCF-7 cells, HOMEZ-Tet on, Day7

city: Beijing

first: Yanan

last: Zhang

address: Taipin Rd 27

country: China

institute: Beijing institute of biotechnology

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19, GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute equences to each sample.

tag: cell line

tag: cell type

value: breast cancer epithelial cells

tag: genotype

value: HOMEZ overexpression

tag: treatment

value: tetracycline treatment

tag: time

value: Day 7


title: MCF-7 cells, HOMEZ-Tet on, Day0

value: WT

value: Day 0


title: 1_AS_sy_ost_D1

value: Angeln Saddleback

value: fibrous synovium

value: Osteocyte at day 1


title: MCF-7 cells, HOMEZ-Tet on, Day21

value: Day 21


title: MCF-7 cells, HOMEZ-Tet on, Day14

value: Day 14


title: E16.5 retina, H3K9AC

city: Houston

first: Chai-An

last: Mao

state: Texas

address: 6431 Fannin Street, MSB7.242

department: Ophthalmology And Visual Scien

institute: University of Texas McGovern Medical School

data_processing:
Sequence reads were trimmed free of adaptor sequences and masked for low-complexity or low-quality sequences, then  mapped to the mouse mm10 reference genome using Bowtie2 (v2.4.5) software. Peak calling was performed by SEACR under relaxed mode. Two independent replicates using anti-Pou4f1 antibody and rabbit IgG respectively were analyzed using SEACR.
Library strategy: CUT&Tag

source_name: Retina

extract_protocol:
Four retinas isolated from wildtype mouse embryos at E16.5 were pooled, and then dissociated using papain dissociation system (#LK003150, Worthington Biochemical Corporation, Lakewood, NJ).
The CUT&Tag library was prepared using CUT&TAG-IT Assay Kit (#53160, Active Motif, Carlsbad, CA) following manufacturer's protocols.

tag: tissue

value: Retina

tag: antibody

value: rabbit anti-H3K9AC

tag: developmental stage


title: E16.5 retina, Pou4f1, rep1

value: rabbit anti-Pou4f1


title: 1_AS_sy_Ko_D1

value: control un-differentiaed cells at day 1


title: 1_AS_sy_Ko_D21

value: control un-differentiaed cells at day 21


title: 1_AS_sy_Ko_D7

value: control un-differentiaed cells at day 7


title: E16.5 retina, IgG control, rep2

value: rabbit IgG


title: 1_AS_fp_ost_D7

value: adipose synovium

value: Osteocyte at day 7


title: 1_AS_sy_Ko_D14

value: control un-differentiaed cells at day 14


title: 1_AS_sy_D0

value: control un-differentiaed cells at day 0


title: Control ChIP-seq from HepG2 (ENCLB249UAA)

description:
https://www.encodeproject.org/experiments/ENCSR720MOD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR720MOD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB249UAA
fragmentation methods: sonication (generic)

value: cell line

tag: biosample encode accession

tag: Sex

value: male

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS117UZV at ENCODE; https://www.encodeproject.org/ENCBS117UZV/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: Control ChIP-seq from WTC11 (ENCLB011FAS)

description:
https://www.encodeproject.org/experiments/ENCSR491BNK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR491BNK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB011FAS
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line

value: adult

value: 30 year

tag: lab

tag: source

tag: link

value: ENCBS595GKI at ENCODE; https://www.encodeproject.org/ENCBS595GKI/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: 1_AS_fp_ost_D21

tag: breed

value: Angeln Saddleback

tag: sorts of synovial membrane

value: adipose synovium

tag: time point

value: Osteocyte at day 21


title: Control ChIP-seq from HEK293 (ENCLB601IIY)

description:
https://www.encodeproject.org/experiments/ENCSR148MVL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HEK293
experiment encode accession: ENCSR148MVL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-08-31
lab: Richard Myers, HAIB
library encode accession: ENCLB601IIY
fragmentation methods: sonication (generic)

source_name: Homo sapiens HEK293 cell line

tag: line

value: female

tag: health state

value: unknown

value: embryonic

value: ENCBS435HZC at ENCODE; https://www.encodeproject.org/ENCBS435HZC/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: 1_AS_fp_ost_D1

value: Osteocyte at day 1


title: 1_AS_fp_ost_D14

value: Osteocyte at day 14


title: Control ChIP-seq from HEK293 (ENCLB921VAW)

description:
https://www.encodeproject.org/experiments/ENCSR151LCI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HEK293
experiment encode accession: ENCSR151LCI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-12-20
lab: Richard Myers, HAIB
library encode accession: ENCLB921VAW
fragmentation methods: sonication (generic)

value: cell line

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS350KVF at ENCODE; https://www.encodeproject.org/ENCBS350KVF/


title: 1_AS_fp_Ko_D7

value: control un-differentiaed cells at day 7


title: 1_AS_fp_D0

value: control un-differentiaed cells at day 0


title: 1_AS_fp_Ko_D14

value: control un-differentiaed cells at day 14


title: 1_AS_fp_Ko_D21

value: Angeln Saddleback

value: control un-differentiaed cells at day 21


title: Control ChIP-seq from WTC11 (ENCLB642IXH)

description:
https://www.encodeproject.org/experiments/ENCSR428BNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR428BNQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB642IXH
fragmentation methods: sonication (generic)

value: male

value: adult

value: 30 year

value: ENCBS081PLF at ENCODE; https://www.encodeproject.org/ENCBS081PLF/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: Control ChIP-seq from K562 (ENCLB960PHD)

description:
https://www.encodeproject.org/experiments/ENCSR188MIS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR188MIS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB960PHD
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS136UPE at ENCODE; https://www.encodeproject.org/ENCBS136UPE/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: 1_AS_fp_Ko_D1

value: adipose synovium

value: control un-differentiaed cells at day 1


title: Zebrafish embryos, cora 4, 96 hpf

city: St. Louis

first: Kory

last: Lavine

state: MO

address: 660 S Euclid Ave

department: Cardiology

institute: Washington University School of Medicine

data_processing:
Gene counts were derived from the number of uniquely aligned unambiguous readsby Subread:featureCount version 1.4.5
Transcript counts were produced by Sailfish version 0.6.3.
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
All gene-level and transcript counts were thenimported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust samples for differences in library size.
TMM size factors and the matrix of counts were then imported into R/Bioconductor package Limma and weighted likelihoods based on the observed mean-variance relationship of every gene/transcript and sample were then calculated for all samples with the voomWithQualityWeights function.
Assembly: Ensembl release 76 top-level assembly with STAR version 2.0.4b
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: Heart

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Heart

tag: cell line

tag: cell type

value: All

tag: genotype

value: KO

tag: treatment


title: Zebrafish embryos, cora 3, 96 hpf

tag: tissue


title: Control ChIP-seq from K562 (ENCLB482EKJ)

description:
https://www.encodeproject.org/experiments/ENCSR144DXT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR144DXT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-08-31
lab: Richard Myers, HAIB
library encode accession: ENCLB482EKJ
fragmentation methods: sonication (generic)

value: cell line

tag: biosample encode accession

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS042RRJ at ENCODE; https://www.encodeproject.org/ENCBS042RRJ/


title: Zebrafish embryos, cora 2, 96 hpf


title: Zebrafish embryos, cora 1, 96 hpf


title: E16.5 retina, Pou4f1, rep2

value: Retina

tag: antibody

value: rabbit anti-Pou4f1

tag: developmental stage

value: WT


title: Zebrafish embryos, control , 96 hpf


title: Zebrafish embryos, control 1, 96 hpf


title: Zebrafish embryos, control 3, 96 hpf


title: Control ChIP-seq from HepG2 (ENCLB289SPD)

description:
https://www.encodeproject.org/experiments/ENCSR396WYG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR396WYG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB289SPD
fragmentation methods: sonication (generic)

tag: Sex

value: male

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

value: ENCBS884RPN at ENCODE; https://www.encodeproject.org/ENCBS884RPN/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: Control ChIP-seq from WTC11 (ENCLB485ZIT)

description:
https://www.encodeproject.org/experiments/ENCSR678WJT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR678WJT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB485ZIT
fragmentation methods: sonication (generic)

value: adult

value: 30 year

tag: lab

tag: source

tag: link

value: ENCBS558AHG at ENCODE; https://www.encodeproject.org/ENCBS558AHG/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: Control ChIP-seq from K562 (ENCLB012AEY)

description:
https://www.encodeproject.org/experiments/ENCSR385DOV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR385DOV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-09-26
lab: Richard Myers, HAIB
library encode accession: ENCLB012AEY
fragmentation methods: sonication (generic)

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS814BBK at ENCODE; https://www.encodeproject.org/ENCBS814BBK/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Engineered lung d7 - Tri-culture_d7

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

molecule: polyA RNA

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: Mixed lung cells


title: Control ChIP-seq from HepG2 (ENCLB087EKF)

description:
https://www.encodeproject.org/experiments/ENCSR123ESD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR123ESD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-12-20
lab: Richard Myers, HAIB
library encode accession: ENCLB087EKF
fragmentation methods: sonication (generic)

tag: line

value: male

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS483OXY at ENCODE; https://www.encodeproject.org/ENCBS483OXY/


title: E16.5 retina, IgG control, rep1

value: Retina

value: rabbit IgG

value: WT


title: Engineered lung d7 - AEC2_FB_d7

description: 10x Genomics


title: Control ChIP-seq from K562 (ENCLB921QGX)

description:
https://www.encodeproject.org/experiments/ENCSR722TKK/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ATF4 fusion protein.
experiment encode accession: ENCSR722TKK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB921QGX
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ATF4

value: cell line

tag: note

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ATF4.

value: female

tag: health state

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS421UWC at ENCODE; https://www.encodeproject.org/ENCBS421UWC/


title: Control ChIP-seq from K562 (ENCLB443OCF)

description:
https://www.encodeproject.org/experiments/ENCSR085CJF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR085CJF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB443OCF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS946ZTK at ENCODE; https://www.encodeproject.org/ENCBS946ZTK/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: PSC72B-RNA

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

description: 10x multiome

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: filtered_contig_annotations.csv, countTable

source_name: Lamina propria

extract_protocol:
Colonic epithelial cells and lymphocytes were isolated via mechanical disruption and enzymatic digestion. Briefly, colonic biopsies were twice shaken at 250 revolutions per minute (rpm) for 30 minutes at 37°C in 7mL RPMI 1640 (Fisher Scientific) supplemented with 1% dialyzed fetal bovine serum (Biowest), 2mM EDTA (Corning), and 1.5 mM MgCl2 (Thermo Fisher Scientific). Cells were filtered through a 40mM filter (Fisher Scientific), centrifuged, and pooled for subsequent analysis. This fraction was considered the epithelial fraction. Subsequently, the remaining tissue was digested in two sequential shakes at 250rpm at 37°C for 30 minutes in 15mL RPMI 1640 supplemented with 20% fetal bovine serum and 1mg/mL collagenase type IV, from Clostridium histolyticum (Sigma-Aldrich). After each digestion, the solution was filtered, centrifuged, and then combined for downstream experimentation. This fraction was considered the lamina propria fraction.x
Cells were centrifuged and resuspended to a final concentration in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin, and the suspensions were loaded into a Chromium Controller (10x Genomics, Inc.) under conditions to generate an anticipated yield of 1,000-10,000, depending on yield of cells from the tissue. Single-cell 5’ RNA-seq libraries, as well as V(D)J libraries, were generated for each sample according to the manufacturer’s instructions (Chromium Single Cell 5’ Library Construction Kit V1 Chemistry, Single Cell V(D)J Enrichment Kit for Human T-cells, and Single Cell V(D)J Enrichment Kit for Human B-cells, all from 10x Genomics Inc). 5’ libraries were sequenced to a minimum depth of 50,000 reads per cell for 5’ gene expression libraries, or 5,000 reads per cell for V(D)J libraries

tag: disease state

value: PSC

tag: cell type

value: Lamina propria lymphocyte

value: Lamina propria


title: PSC94-RNA

description: 10x multiome


title: Control ChIP-seq from MCF-7 (ENCLB323DRB)

description:
https://www.encodeproject.org/experiments/ENCSR301NCS/
***************
biological replicate number: 1
technical replicate number: 1
description: MCF7 immortalized cell line stably expressing C-terminal eGFP-TSC22D1 fusion protein.
experiment encode accession: ENCSR301NCS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB323DRB
size range: 450-650

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TSC22D1

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to TSC22D1.

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS390JIM at ENCODE; https://www.encodeproject.org/ENCBS390JIM/

value: derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: Native control - P7

description: 10x Genomics

value: Lung

value: Sprague Dawley

value: Mixed lung cells

value: 7 days


title: PSC59C-RNA

description: 10x multiome


title: PSC70C-RNA

description: 10x multiome


title: PSC70D-RNA

description: 10x multiome


title: PSC50B-RNA

description: 10x multiome


title: PSC4E-RNA

description: 10x multiome


title: PSC28D-RNA

description: 10x multiome


title: PSC2F-RNA

description: 10x multiome


title: PSC51B-RNA

description: 10x multiome


title: PSC40C-RNA

description: 10x multiome


title: Primary cell population - EC

description: 10x Genomics

growth_protocol: Fibroblasts (FB) were cultured 72 hrs on uncoated tissue-culture plastic in DMEM + 10% FBS + 1% Pen/Strep. Endothelial cells (ECs) were cultured to passage 5 on fibronectin-coated tissue-culture plastic in MCDB-131 Complete medium with serum (VEC Technologies)

value: Microvascular endothelial cells

value: 4-6 weeks


title: PSC40D-RNA

description: 10x multiome


title: PSC19D-RNA

description: 10x multiome


title: PSC70D-scTCR

description: 10x multiome

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: filtered_contig_annotations.csv, countTable
Library strategy: sc-TCR


title: PSC79-scBCR

description: 10x multiome

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: filtered_contig_annotations.csv, countTable
Library strategy: sc-BCR


title: PSC94-scTCR

description: 10x multiome


title: PSC72B-scBCR

description: 10x multiome


title: PSC15E-RNA

description: 10x multiome


title: PSC84C-scBCR

description: 10x multiome


title: PSC50B-scBCR

description: 10x multiome


title: PSC51B-scBCR

description: 10x multiome


title: PSC40C-scBCR

description: 10x multiome


title: Control ChIP-seq from WTC11 (ENCLB209JGE)

description:
https://www.encodeproject.org/experiments/ENCSR828IIG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR828IIG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-08-31
lab: Richard Myers, HAIB
library encode accession: ENCLB209JGE
fragmentation methods: sonication (generic)

value: cell line

value: male

value: adult

value: 30 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS609TOR at ENCODE; https://www.encodeproject.org/ENCBS609TOR/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: PSC84C-RNA

description: 10x multiome

value: PSC

value: Lamina propria lymphocyte

value: Lamina propria


title: PSC19D-scBCR

description: 10x multiome


title: PSC15E-scBCR

description: 10x multiome


title: PSC,3

city: Lanzhou

first: John

last: Ohiolei

state: Gansu

address: 1 Xujiapin Road, Yanchang Bu, Chengguan District

institute: Lanzhou Veterinary Research Institute

data_processing:
Data trimming
Data mapping
RIP-QC
Peak Calling
Diiferential, functional anotation, and Motif analysis
Assembly: https://parasite.wormbase.org/Echinococcus_granulosus_prjeb121/Info/Index
Supplementary files format and content: bigWig

organism: Echinococcus granulosus

source_name: Protoscoleces

extract_protocol:
TRIzol and Chloroform extraction protocol
Illumina TrueSeq Stranded mRNA
MeRIP-seq

value: Protoscoleces

tag: genotype

tag: location

value: China

tag: hosts

value: Sheep


title: PSC28D-scBCR

description: 10x multiome

tag: tissue


title: PSC,1


title: Control ChIP-seq from K562 (ENCLB846KYH)

description:
https://www.encodeproject.org/experiments/ENCSR615INN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR615INN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-08-16
lab: Richard Myers, HAIB
library encode accession: ENCLB846KYH
fragmentation methods: sonication (generic)

tag: biosample encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS862HUB at ENCODE; https://www.encodeproject.org/ENCBS862HUB/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: PSC,2


title: Adult,2

source_name: Whole adult worms

value: Whole adult worms


title: Adult,3


title: PSC50B-scTCR

description: 10x multiome


title: 4448-2 resistant clinical isolate

city: Birmingham

first: Keonte

middle: Jamel

last: Graves

state: AL

address: 1900 University Blvd, THT 230

department: Medicine-Infectious Diseases

institute: The University of Alabama at Birmingham

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Trichomonas_vaginalis reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: txid5722
Supplementary files format and content: Tab-delimited text files include raw read counts, gene id, chromosome location, gene length, and strand position for each sample

organism: Trichomonas vaginalis

source_name: protozoan

growth_protocol: All T. vaginalis isolates were grown under anaerobic conditions using Diamond’s Trypticase-Yeast-Maltose (TYM) media.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s instructions.
Pre-made library -- no library preparation performed

tag: sample type

value: resistant clinical isolate

value: protozoan


title: 4448-1 resistant clinical isolate


title: 4266-3 resistant clinical isolate


title: 1073-3 resistant clinical isolate


title: 4266-1 resistant clinical isolate


title: 4266-2 resistant clinical isolate


title: 1073-1 resistant clinical isolate


title: 1021-2 sensitive clinical isolate

value: sensitive clinical isolate


title: 1021-1 sensitive clinical isolate


title: 1012-2 sensitive clinical isolate


title: 1012-3 sensitive clinical isolate


title: 1021-3 sensitive clinical isolate


title: 1003-3 sensitive clinical isolate


title: 1003-2 sensitive clinical isolate


title: 1012-1 sensitive clinical isolate


title: 1003-1 sensitive clinical isolate


title: 904-2 sensitive CDC control

value: sensitive CDC control


title: 904-3 sensitive CDC control


title: 904-1 sensitive CDC control


title: 4448-3 resistant clinical isolate


title: Control ChIP-seq from K562 (ENCLB452EDA)

description:
https://www.encodeproject.org/experiments/ENCSR802WKU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR802WKU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB452EDA
fragmentation methods: sonication (generic)

value: cell line

tag: Sex

tag: dev stage

value: adult

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS792LDH at ENCODE; https://www.encodeproject.org/ENCBS792LDH/


title: 252-1 resistant CDC control

value: resistant CDC control


title: Adult,1

value: China

value: Sheep


title: 252-3 resistant CDC control


title: 1073-2 resistant clinical isolate


title: 20220502_YE#16_IGS 220310 22-014 RNA H0 EPI _02

city: besancon

first: irène

last: gallais sérézal

address: boulevard stalingrad

country: France

institute: CHU Besançon

description: SAMPLE 91

hyb_protocol: NOT PROVIDED

scan_protocol: NOT PROVIDED

data_processing: Nsolver software was used to perform the analysis, normalization and calculation of the folc changes used in the publication. Normalized data are presented (G6PD, GUSB, HPRT1, SF3A3, ZC3H14). Housekeeping genes are in bold. Sample 46 was not included in the data analysis as the normalization failed (too low RNA load)

label: not provided

source_name: Healthy skin

label_protocol: LBMMS du CHU de Lyon performed the nanostring quantification according to Manufacturer's protocol

growth_protocol: Skin was collected as well from 13 patients with psoriasis undergoing treatment with biologics, in complete remission for over one year. Sampling included tape-stripping for lipid analysis, and a 4mm biopsy was taken on both resolved and non-lesional skin. Skin was collected as well from 13 patients with psoriasis undergoing treatment with biologics, in complete remission for over one year. Sampling included tape-stripping for lipid analysis, and a 4mm biopsy was taken on both resolved and non-lesional skin. RTL buffer and DTT 4% (43816, Merck) were added to the frozen epidermis and lysing matrix. Homogenization used a FastPrep (MP Biomedicals TM FastPrep-24TM-Classic): 20 seconds three times (6m/s-30s cooling between each cycle).

extract_protocol: RNAEasy qiagen for RNA purification

treatment_protocol: Then, RNeasy kits were used for RNA purification following the manufacturer’s protocol (Qiagen). RNA was eluded in 30µL of RNAse-free water and stored at -80°C after quality check using Nanodrop. The Nanostring technologies® analysis was performed by the Nanostring platform at Hospices Civils de Lyon, France. The Custom CodeSet-panel included 116 genes, 5 housekeeping genes (Supplementary Table 1). Normalized copy count were generated with nSolver® software.

value: H0 EPI

value: Healthy skin

tag: treatment/time point

value: Baseline


title: 20220502_YE#15_IGS 220310 22-012 RNA H0 EPI _10

description: SAMPLE 89


title: 20220502_YE#16_IGS 220310 22-015 RNA H0 EPI _04

description: SAMPLE 92


title: Control ChIP-seq from HepG2 (ENCLB429MXZ)

description:
https://www.encodeproject.org/experiments/ENCSR315QCW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR315QCW
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-08-16
lab: Richard Myers, HAIB
library encode accession: ENCLB429MXZ
fragmentation methods: sonication (generic)

value: male

value: hepatocellular carcinoma

value: child

tag: age

value: 15 year

tag: lab

tag: source

value: ENCBS466IJE at ENCODE; https://www.encodeproject.org/ENCBS466IJE/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: Control ChIP-seq from HepG2 (ENCLB515TAM)

description:
https://www.encodeproject.org/experiments/ENCSR800SRA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR800SRA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB515TAM
fragmentation methods: sonication (generic)

tag: line

value: cell line

tag: link

value: ENCBS778RZT at ENCODE; https://www.encodeproject.org/ENCBS778RZT/


title: 20220502_YE#15_IGS 220310 22-013 RNA H0 EPI _12

description: SAMPLE 90


title: 252-2 resistant CDC control

value: protozoan


title: 20220502_YE#15_IGS 220310 22-010 RNA H0 EPI _06

description: SAMPLE 87


title: 20220502_YE#15_IGS 220310 22-008 RNA H0 EPI _02

description: SAMPLE 85


title: 20220502_YE#14_IGS 220311 22-006 RNA H0 EPI _10

description: SAMPLE 83


title: 20220502_YE#14_IGS 220311 22-005 RNA H0 EPI _08

description: SAMPLE 82


title: 20220502_YE#14_IGS 220311 22-003 RNA H0 EPI _04

description: SAMPLE 80


title: 20220502_YE#15_IGS 220310 22-011 RNA H0 EPI _08

description: SAMPLE 88


title: 20220502_YE#14_IGS 220311 22-004 RNA H0 EPI _06

description: SAMPLE 81


title: 20220428_YE#13_IGS 220310 2020-534-13 RNA H16 OKT EPI RES_05

description: SAMPLE 78

source_name: Psoriasis resolved

value: H16 OKT EPI

value: Psoriasis resolved

value: OKT3 treated


title: 20220502_YE#14_IGS 220311 22-002 RNA H0 EPI _02

description: SAMPLE 79


title: 20220428_YE#13_IGS 220310 2020-534-13 RNA H16 OKT EPI NL_02

description: SAMPLE 77

source_name: Psoriasis non lesional

value: Psoriasis non lesional


title: 20220428_YE#13_IGS 220310 2020-534-13 RNA H16 IGG EPI RES_04

description: SAMPLE 76

value: H16 IGG EPI

value: IgG treated


title: 20220428_YE#13_IGS 220310 2020-534-13 RNA H0 EPI RES_03

description: SAMPLE 74

value: H0 EPI


title: 20220428_YE#13_IGS 220310 2020-534-13 RNA H16 IGG EPI NL_01

description: SAMPLE 75


title: 20220427_YE#12_IGS 220310 2020-534-13 RNA H0 EPI NL_12

description: SAMPLE 73

value: Baseline


title: 20220502_YE#14_IGS 220311 22-007 RNA H0 EPI _12

description: SAMPLE 84

value: Healthy skin


title: Young hamster lung number 2

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

institute: Inserm 1052

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After fragmentation 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent GE Whole Human Genome Oligo Microarrays (Agilent-026652) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried briefly in acetonitrile.

scan_protocol: Microarrays were scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).Fluorescent signals were extracted and normalized with the Feature Extraction software version 10.5.1.1 (Agilent Technologies),

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mesocricetus auratus

source_name: lung tissue

label_protocol: cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommandations, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Golden Hamster of 2 and 22 months were used

extract_protocol: Total RNA was extracted from frozen lungs after using Nucleospin RNA kit (Macherey Nagel)

treatment_protocol: No specific treatment - generation of young and old cohorts

value: 2 months old

value: lung


title: Young hamster lung number 4


title: Aged hamster lung number 3

value: 22 months old


title: Aged hamster lung number 2


title: 20220427_YE#12_IGS 220309 2020-534-12 RNA H16 OKT EPI NL_02

description: SAMPLE 71


title: 20220427_YE#12_IGS 220309 2020-534-12 RNA H16 IGG EPI RES_04

description: SAMPLE 70


title: Young hamster lung number 3


title: 20220427_YE#12_IGS 220309 2020-534-12 RNA H0 EPI RES_03

description: SAMPLE 68


title: 20220426_YE#11_IGS 220311 2020-534-11 RNA H16 OKT EPI RES_05

description: SAMPLE 67


title: 20220427_YE#12_IGS 220309 2020-534-12 RNA H16 IGG EPI NL_01

description: SAMPLE 69


title: 20220426_YE#11_IGS 220311 2020-534-11 RNA H0 EPI RES_03

description: SAMPLE 63


title: 20220426_YE#11_IGS 220311 2020-534-11 RNA H16 IGG EPI NL_01

description: SAMPLE 64


title: 20220426_YE#11_IGS 220309 2020-534-12 RNA H0 EPI NL_12

description: SAMPLE 62


title: 20220425_YE#10_IGS 220308 2020-534-10 RNA H16 OKT EPI NL_02

description: SAMPLE 59


title: 20220425_YE#10_IGS 220311 2020-534-11 RNA H0 EPI NL_12

description: SAMPLE 61


title: Young hamster lung number 1


title: Aged hamster lung number 1


title: 20220425_YE#10_IGS 220308 2020-534-10 RNA H0 EPI RES_03

description: SAMPLE 56


title: 20220426_YE#11_IGS 220311 2020-534-11 RNA H16 IGG EPI RES_04

description: SAMPLE 65


title: Control ChIP-seq from HepG2 (ENCLB360YED)

description:
https://www.encodeproject.org/experiments/ENCSR578XKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR578XKJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB360YED
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS119TMR at ENCODE; https://www.encodeproject.org/ENCBS119TMR/


title: Control ChIP-seq from WTC11 (ENCLB547CWG)

description:
https://www.encodeproject.org/experiments/ENCSR783VJL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR783VJL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-09-26
lab: Richard Myers, HAIB
library encode accession: ENCLB547CWG
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line

value: cell line

value: adult

value: 30 year

value: ENCBS101JAZ at ENCODE; https://www.encodeproject.org/ENCBS101JAZ/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: 20220421_YE#09_IGS 220307 2020-534-9 RNA H16 OKT EPI RES_05

description: SAMPLE 54

value: H16 OKT EPI

value: Psoriasis resolved

value: OKT3 treated


title: 20220427_YE#12_IGS 220309 2020-534-12 RNA H16 OKT EPI RES_05

description: SAMPLE 72


title: 20220425_YE#10_IGS 220308 2020-534-10 RNA H16 IGG EPI NL_01

description: SAMPLE 57

value: H16 IGG EPI

value: Psoriasis non lesional

value: IgG treated


title: 20220421_YE#09_IGS 220308 2020-534-10 RNA H0 EPI NL_12

description: SAMPLE 55

value: H0 EPI

value: Baseline


title: 20220426_YE#11_IGS 220311 2020-534-11 RNA H16 OKT EPI NL_02

description: SAMPLE 66


title: 20220421_YE#09_IGS 220307 2020-534-9 RNA H16 OKT EPI NL_02

description: SAMPLE 53


title: 20220421_YE#09_IGS 220307 2020-534-9 RNA H16 IGG EPI RES_04

description: SAMPLE 52


title: 20220421_YE#09_IGS 220307 2020-534-9 RNA H16 IGG EPI NL_01

description: SAMPLE 51


title: 20220425_YE#10_IGS 220308 2020-534-10 RNA H16 IGG EPI RES_04

description: SAMPLE 58


title: 20220425_YE#10_IGS 220308 2020-534-10 RNA H16 OKT EPI RES_05

description: SAMPLE 60


title: 20220419_YE#08_IGS 220307 2020-534-9 RNA H0 EPI NL_12

description: SAMPLE 49


title: 20220419_YE#08_IGS 220307 2020-534-8 RNA H16 OKT EPI RES_05

description: SAMPLE 48


title: 20220419_YE#08_IGS 220307 2020-534-8 RNA H16 IGG EPI RES_04

description: SAMPLE 46


title: 20220419_YE#08_IGS 220307 2020-534-8 RNA H16 IGG EPI NL_01

description: SAMPLE 45


title: 20220419_YE#08_IGS 220307 2020-534-8 RNA H0 EPI RES_03

description: SAMPLE 44


title: 20220419_YE#07_IGS 220307 2020-534-7 RNA H16 IGG EPI RES_04

description: SAMPLE 40


title: 20220419_YE#07_IGS 220307 2020-534-7 RNA H16 OKT EPI NL_02

description: SAMPLE 41


title: 20220419_YE#07_IGS 220307 2020-534-8 RNA H0 EPI NL_12

description: SAMPLE 43


title: 20220419_YE#07_IGS 220307 2020-534-7 RNA H16 OKT EPI RES_05

description: SAMPLE 42


title: 20220412_YE#06_IGS 220305 2020-534-6 RNA H16 OKT EPI RES_05

description: SAMPLE 36


title: 20220412_YE#06_IGS 220307 2020-534-7 RNA H0 EPI NL_12

description: SAMPLE 37


title: 20220411_YE#05_IGS 220305 2020-534-6 RNA H0 EPI NL_12

description: SAMPLE 31


title: 20220419_YE#07_IGS 220307 2020-534-7 RNA H16 IGG EPI NL_01

description: SAMPLE 39


title: 20220421_YE#09_IGS 220307 2020-534-9 RNA H0 EPI RES_03

description: SAMPLE 50


title: 20220412_YE#06_IGS 220305 2020-534-6 RNA H16 IGG EPI NL_01

description: SAMPLE 33


title: 20220419_YE#08_IGS 220307 2020-534-8 RNA H16 OKT EPI NL_02

description: SAMPLE 47


title: 20220412_YE#06_IGS 220305 2020-534-6 RNA H16 IGG EPI RES_04

description: SAMPLE 34


title: 20220412_YE#06_IGS 220305 2020-534-6 RNA H16 OKT EPI NL_02

description: SAMPLE 35


title: 20220412_YE#06_IGS 220305 2020-534-6 RNA H0 EPI RES_03

description: SAMPLE 32


title: 20220411_YE#05_IGS 220301 2020-534-5 RNA H16 OKT EPI NL_02

description: SAMPLE 29


title: 20220411_YE#05_IGS 220301 2020-534-5 RNA H16 IGG EPI RES_04

description: SAMPLE 28


title: 20220411_YE#05_IGS 220301 2020-534-5 RNA H16 IGG EPI NL_01

description: SAMPLE 27


title: 20220411_YE#05_IGS 220301 2020-534-5 RNA H16 OKT EPI RES_05

description: SAMPLE 30


title: 20220411_YE#04_IGS 220301 2020-534-5 RNA H0 EPI NL_12

description: SAMPLE 25


title: 20220419_YE#07_IGS 220307 2020-534-7 RNA H0 EPI RES_03

description: SAMPLE 38


title: 20220411_YE#05_IGS 220301 2020-534-5 RNA H0 EPI RES_03

description: SAMPLE 26


title: 20220411_YE#04_IGS 220228 2020-534-4 RNA H16 OKT EPI RES_05

description: SAMPLE 24


title: 20220411_YE#04_IGS 220228 2020-534-4 RNA H0 EPI RES_03

description: SAMPLE 20


title: 20220411_YE#04_IGS 220228 2020-534-4 RNA H16 OKT EPI NL_02

description: SAMPLE 23


title: 20220411_YE#04_IGS 220228 2020-534-4 RNA H16 IGG EPI RES_04

description: SAMPLE 22


title: 20220408_YE#03_IGS 220222 2020-534-3 RNA H16 OKT EPI NL_02

description: SAMPLE 17


title: 20220411_YE#04_IGS 220228 2020-534-4 RNA H16 IGG EPI NL_01

description: SAMPLE 21


title: 20220408_YE#03_IGS 220222 2020-534-3 RNA H16 OKT EPI RES_05

description: SAMPLE 18


title: 20220408_YE#03_IGS 220228 2020-534-4 RNA H0 EPI NL_12

description: SAMPLE 19


title: 20220408_YE#03_IGS 220222 2020-534-3 RNA H16 IGG EPI RES_04

description: SAMPLE 16


title: 20220502_YE#15_IGS 220310 22-009 RNA H0 EPI _04

description: SAMPLE 86

value: Healthy skin


title: 20220408_YE#03_IGS 220222 2020-534-3 RNA H0 EPI RES_03

description: SAMPLE 14


title: 20220408_YE#02_IGS 220221 2020-534-2 RNA H16 OKT EPI RES_05

description: SAMPLE 12


title: 20220408_YE#02_IGS 220222 2020-534-3 RNA H0 EPI NL_12

description: SAMPLE 13


title: 20220408_YE#02_IGS 220221 2020-534-2 RNA H16 OKT EPI NL_02

description: SAMPLE 11


title: 20220408_YE#02_IGS 220221 2020-534-2 RNA H16 IGG EPI RES_04

description: SAMPLE 10


title: 20220408_YE#02_IGS 220221 2020-534-2 RNA H16 IGG EPI NL_01

description: SAMPLE 9


title: 20220408_YE#02_IGS 220221 2020-534-2 RNA H0 EPI RES_03

description: SAMPLE 8


title: 20220408_YE#01_IGS 220221 2020-534-1 RNA H16 OKT EPI NL_03

description: SAMPLE 5


title: 20220408_YE#01_IGS 220221 2020-534-1 RNA H16 IGG EPI NL_02

description: SAMPLE 3


title: 20220408_YE#01_IGS 220221 2020-534-1 RNA H16 IGG EPI RES_05

description: SAMPLE 4


title: 20220408_YE#01_IGS 220221 2020-534-1 RNA H16 OKT EPI RES_06

description: SAMPLE 6


title: Control ChIP-seq from HepG2 (ENCLB623VDA)

description:
https://www.encodeproject.org/experiments/ENCSR005ZFP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR005ZFP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB623VDA
fragmentation methods: sonication (generic)

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: ENCBS738GXU at ENCODE; https://www.encodeproject.org/ENCBS738GXU/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: Control ChIP-seq from WTC11 (ENCLB511TPE)

description:
https://www.encodeproject.org/experiments/ENCSR730ATD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR730ATD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB511TPE
fragmentation methods: sonication (generic)

value: cell line

value: adult

value: 30 year

value: Richard Myers

value: ENCBS046WNC at ENCODE; https://www.encodeproject.org/ENCBS046WNC/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: 20220408_YE#01_IGS 220221 2020-534-2 RNA H0 EPI NL_12

description: SAMPLE 7

value: Psoriasis non lesional


title: Control ChIP-seq from HEK293 (ENCLB713FSY)

description:
https://www.encodeproject.org/experiments/ENCSR245JDY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HEK293
experiment encode accession: ENCSR245JDY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-25
lab: Richard Myers, HAIB
library encode accession: ENCLB713FSY
fragmentation methods: sonication (generic)

source_name: Homo sapiens HEK293 cell line

value: female

value: unknown

value: embryonic

value: ENCBS569ETH at ENCODE; https://www.encodeproject.org/ENCBS569ETH/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: 20220408_YE#01_IGS 220221 2020-534-1 RNA H0 EPI NL_01

description: SAMPLE 1

value: H0 EPI

value: Baseline


title: Control ChIP-seq from WTC11 (ENCLB151PLE)

description:
https://www.encodeproject.org/experiments/ENCSR549JGF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR549JGF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-09-26
lab: Richard Myers, HAIB
library encode accession: ENCLB151PLE
fragmentation methods: sonication (generic)

value: male

value: Richard Myers, HAIB

value: ENCBS295IAB at ENCODE; https://www.encodeproject.org/ENCBS295IAB/


title: MM_3 [CUTnRUN]

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

description: mock infected bio replicate3

data_processing:
library strategy: CUT&RUN
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Reads were trimmed from 3' end until the final base had a quality score > 30
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.
Peaks were called using SEACR keeping top 20% of peaks.  These are saved as .bed files
Assembly: hg38
Supplementary files format and content: SEACR bed files

growth_protocol: Immortalized primary hSAECs were obtained from commercial repository and grown in SAGM small airway epithelial cell growth medium (Lonza, Walkersville, MD, USA) in 5% CO2.

extract_protocol: 4 x 10^6 trypsinized cells were aliquoted and incubated on ice for 10 minutes in 1 ml of nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine), the released nuclei were pelleted at 600x g, 5 minutes at 4 oC. A basic wash buffer (WB) consisting of 20 mM HEPES, pH7.5, 150 mM NaCl, 0.05% Triton X-1000, 0.1% BSA, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine was used throughout. Between incubation steps, the nuclei were pelleted at 600x g, 3 minutes at 4 oC. Prior to antibody binding, the isolated nuclei were incubated with nutation at 4 oC for 5 minutes in WB containing 2 mM EDTA, followed by nutation at 4 oC for 25 minutes in WB. The nuclei were resuspended in antibody buffer produced by diluting 5 mg of FLAG-M2 in 500 ml of Triton X-100-free WB, and incubated with nutation overnight at 4 oC.  After washing three times in 500 ml of WB on ice (10 minutes each time), the nuclei were incubated at 4 oC for 1 h in 50 ml of WB containing 2.5 ml of EpiCypher pAG-MNase 20x stock (EpiCypher, NC). Washing as above, targeted chromatin cleavage was then conducted by incubating the nuclei on ice for 1 h in 150 ml of BSA-free WB containing 2 mM CaCl2. The cleavage was terminated by adding 150 ml of stop buffer (300 mM NaCl, 20 mM EDTA, 4 mM EGTA and 0.5 ng of E. coli Spike-in DNA (EpiCypher, NC) per 150 ml).  The samples were further incubated with nutation at 4 oC for 1 h, centrifuged at 16,000x g for 5 min at 4 oC and the supernatant was collected. Phenol-chloroform DNA precipitation with 80 mg of glycogen was performed and the Cut&Run-enriched DNA was dissolved in 20 ml of 0.1x TE buffer. Following DNA quantitation by a Qubit fluorometer, Cut&Run DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, MA) per the manufacturer’s instruction, with modification in SPRI bead clearance of adaptor ligation and library amplification reactions to retain small-sized DNA fragments (down to ~170 bp in post-library amplification size). The quality of the resultant DNA libraries was confirmed by Agilent TapeStation HS DNA assay (Agilend, CA), and paired-end Illumina NGS was carried out on NovaSeq 6000 with 5 million reads per sample.

treatment_protocol: Sucrose cushion purified RSV Long was prepared and tittered using methylcellulose plaque assay.  hSAECs were treated in triplicate replicates with or without RSV infection (MOI = 1.0, 24 h).

value: Lung

tag: cell line

value: hSAEC

value: lung epithelial

tag: treatment

value: mock infected


title: RM_3 [CUTnRUN]

description: RSV infected bioreplicate 3

tag: cell type

tag: genotype

value: RSV infected


title: RM_1 [CUTnRUN]

description: RSV infected bioreplicate 1


title: MM_1 [CUTnRUN]

description: mock infected bio replicate1


title: MM_2 [CUTnRUN]

description: mock infected bio replicate2


title: CON3 [CUTnRUN]

description: control bio replicate 3

value: control


title: 20220408_YE#03_IGS 220222 2020-534-3 RNA H16 IGG EPI NL_01

description: SAMPLE 15

value: H16 IGG EPI

value: Psoriasis non lesional

value: IgG treated


title: CON1 [CUTnRUN]

description: control bio replicate 1


title: blood_ctrl

city: Shanghai

first: Weijie

last: Chen

address: Furonghua Road 118

institute: Simcere Zaiming Pharmaceutical Co.

data_processing:
Raw fastaq files were input into Cell Ranger (v5.0.0) for demultiplexing of the reads, alignment to the modiﬁed turbot genome and generating gene expression matrix.
Assembly: ASM1334776v1
Supplementary files format and content: Expression matirx file

organism: Scophthalmus maximus

source_name: blood

extract_protocol:
Five turbots were randomly selected to collect blood for cell suspension preparation. Blood were added into anticoagulant (Solarbio) to inhibit coagulation. Cell suspensions were washed with 0.04% BSA/PBS and submitted to density gradient centrifugation at 400 × g, 30 min. Leukocytes were collected from the lower cell layer in the middle of discontinuous Percoll (1.057 g/mL and 1.077 g/mL) (BioDee) and washed with PBS twice at 600 × g.
Single-cell libraries were prepared using the Chromium 3’ v3 platform (10X Genomics). Briefly, blood leukocytes were diluted into 700 – 1200 cells/μl and combined with partitioning oil, and gel beads mix to generate gel beads in emulsion (GEM) on a microﬂuidic chip. After RNA reverse transcription and cDNA barcoding, GEMs were lysed and subjected to cDNA cleanup, cDNA ampliﬁcation, cDNA fragmentation, and library adaptor ligation.

value: blood

value: leukocytes


title: Human PBMCs,  before therapy,  scRNAseq

city: Nantong

first: Yao

last: Wang

address: Xinchengqiao Street

institute: Affiliated Hospital of Nantong University

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline
Assembly: GRCh38
Supplementary files format and content: raw data and matrix files

source_name: Peripheral blood

extract_protocol:
PBMCs were fractionated by density gradient centrifugation using Ficoll-Paque Plus medium (GE Healthcare, Chicago, IL, USA) and then rinsed in phosphate-buffered saline (PBS) without Ca2+ and Mg2+. Red blood cells were depleted by GEXSCOPE® red blood cell lysis buffer (Singleron) for 10 min at 25°C. After centrifugation at 500 ×g for 5 min and resuspension in PBS, the supernatant of the centrifuged blood samples was discarded after centrifugation at 400 ×g for 5 min at 4°C. The PBMCs were then centrifuged at 400 ×g for 10 min at 4°C and prepared without red blood cells. After discarding the supernatant, the PBMCs were resuspended in PBS to obtain single-cell suspensions. The final preparatory step was microscopic evaluation of cell viability using Trypan Blue staining.
Single cells were resuspended in PBS (2×105 cells/mL) and loaded onto a microchip using a Singleron Matrix® Single Cell Processing System. After collecting Barcoding Beads, the captured mRNA was reverse-transcribed and the resulting cDNA was amplified. The cDNA was then fragmented and processed for sequencing using the adapter ligation method. We prepared scRNA-seq libraries based on the GEXSCOPE Single Cell RNA Library Kit protocol (Singleron). Each library was diluted to 4 nM, pooled for sequencing, and pair‐ended reads with a length of 150 bp were generated using a NovaSeq 6000 system (Illumina, San Diego, CA, USA).

value: Peripheral blood

value: PBMCs

value: Before PD-1 inhibitor therapy


title: Human PBMCs,  after therapy,  scRNAseq

value: After PD-1 inhibitor therapy


title: TF ChIP-seq from HCT116 (ENCLB137JDC)

description:
https://www.encodeproject.org/experiments/ENCSR979ZEO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR979ZEO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR621MTI
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB137JDC
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: antibody

value: CTCF

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Bradley Bernstein, Broad

value: Erez Aiden

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

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


title: Histone ChIP-seq from heart right ventricle (ENCLB155BIA)

description:
https://www.encodeproject.org/experiments/ENCSR541TUX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR541TUX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB155BIA
size range: 200-600

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

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: TF ChIP-seq from HCT116 (ENCLB901ZOX)

description:
https://www.encodeproject.org/experiments/ENCSR979ZEO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR979ZEO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR621MTI
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB901ZOX
size range: 200-600

value: CTCF


title: 20220408_YE#01_IGS 220221 2020-534-1 RNA H0 EPI RES_04

description: SAMPLE 2

tag: tissue

value: H0 EPI

value: Psoriasis resolved

value: Baseline


title: Control ChIP-seq from HCT116 (ENCLB465LSK)

description:
https://www.encodeproject.org/experiments/ENCSR990OHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR990OHC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB465LSK
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

value: cell line

tag: biosample encode accession

value: male

value: colorectal carcinoma

value: adult

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


title: Control ChIP-seq from HCT116 (ENCLB329HYH)

description:
https://www.encodeproject.org/experiments/ENCSR990OHC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR990OHC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB329HYH
size range: 200-600

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 (ENCLB070ZQY)

description:
https://www.encodeproject.org/experiments/ENCSR528PVW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR528PVW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB070ZQY
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)


title: Histone ChIP-seq from heart right ventricle (ENCLB813OPD)

description:
https://www.encodeproject.org/experiments/ENCSR541TUX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541TUX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB813OPD
size range: 200-600

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 (ENCLB862HVW)

description:
https://www.encodeproject.org/experiments/ENCSR528PVW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR528PVW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR937OPV
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB862HVW
size range: 200-600


title: RM_2 [CUTnRUN]

description: RSV infected bioreplicate 2

source_name: Lung

value: Lung

value: hSAEC

value: lung epithelial

value: RSV infected


title: Control ChIP-seq from HCT116 (ENCLB651SFN)

description:
https://www.encodeproject.org/experiments/ENCSR229ZIR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR229ZIR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB651SFN
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: cell line

value: male

value: colorectal carcinoma

value: adult

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


title: Control ChIP-seq from HCT116 (ENCLB683FFA)

description:
https://www.encodeproject.org/experiments/ENCSR229ZIR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR229ZIR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB683FFA
size range: 200-600

value: 48 year

value: Bradley Bernstein, Broad

value: Erez Aiden

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


title: CON2 [CUTnRUN]

description: control bio replicate 2

value: control


title: P2_ROI19_TV_PanCK

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

description:
rawdata.csv
normdata.csv

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

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.

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: P2_ROI18_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

value: AnchoringVillus


title: P2_ROI18_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: idontma


title: P2_ROI17_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: fetalgender


title: TF ChIP-seq from HCT116 (ENCLB221XSX)

description:
https://www.encodeproject.org/experiments/ENCSR216SIK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR216SIK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313EED
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB221XSX
size range: 200-600

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

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

tag: antibody

value: CTCF

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: link

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


title: P2_ROI16_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: P2_ROI16_TV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: TF ChIP-seq from HCT116 (ENCLB353BZE)

description:
https://www.encodeproject.org/experiments/ENCSR954MUZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR954MUZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR307VBQ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB353BZE
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

tag: antibody

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: link

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


title: TF ChIP-seq from HCT116 (ENCLB143IDI)

description:
https://www.encodeproject.org/experiments/ENCSR216SIK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR216SIK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313EED
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB143IDI
size range: 200-600

value: cell line


title: P2_ROI14_TV_PanCK

description:
rawdata.csv
normdata.csv

value: Female

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: TF ChIP-seq from HCT116 (ENCLB227QDO)

description:
https://www.encodeproject.org/experiments/ENCSR954MUZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR954MUZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR307VBQ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB227QDO
size range: 200-600

tag: antibody

tag: line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: colorectal carcinoma


title: P2_ROI14_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: P2_ROI13_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex


title: Control ChIP-seq from HCT116 (ENCLB841RRX)

description:
https://www.encodeproject.org/experiments/ENCSR936ENS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR936ENS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB841RRX
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: 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: ENCBS628SFE at ENCODE; https://www.encodeproject.org/ENCBS628SFE/


title: P2_ROI13_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: Control ChIP-seq from HCT116 (ENCLB496BLL)

description:
https://www.encodeproject.org/experiments/ENCSR198TUZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR198TUZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB496BLL
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

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

value: 48 year

value: Bradley Bernstein, Broad

value: Erez Aiden

value: ENCBS338OSL at ENCODE; https://www.encodeproject.org/ENCBS338OSL/


title: P2_ROI12_TV_PanCK

description:
rawdata.csv
normdata.csv

value: Placenta

tag: fetalgender

value: Male

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: Control ChIP-seq from HCT116 (ENCLB306FLG)

description:
https://www.encodeproject.org/experiments/ENCSR198TUZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR198TUZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB306FLG
size range: 200-600

tag: dev stage

tag: age

tag: lab

tag: source

tag: link

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


title: P2_ROI19_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

value: TerminalVilli

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: P2_ROI12_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount


title: P2_ROI17_AV_PanCK

description:
rawdata.csv
normdata.csv

value: AnchoringVillus

tag: roicoordinatex

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: TF ChIP-seq from HCT116 (ENCLB600SSH)

description:
https://www.encodeproject.org/experiments/ENCSR450DXU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR450DXU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661KFD
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB600SSH
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: antibody

value: CTCF

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: treatments

tag: link

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


title: TF ChIP-seq from heart left ventricle (ENCLB820BHD)

description:
https://www.encodeproject.org/experiments/ENCSR461HOC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR461HOC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB820BHD
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: P2_ROI11_AV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: P2_ROI11_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: aoinucleicount

tag: roicoordinatex

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: TF ChIP-seq from HCT116 (ENCLB798IPZ)

description:
https://www.encodeproject.org/experiments/ENCSR450DXU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR450DXU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661KFD
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB798IPZ
size range: 200-600

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

tag: age

value: 48 year

tag: lab

value: Bradley Bernstein, Broad

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


title: P2_ROI10_TV_PanCK

description:
rawdata.csv
normdata.csv

tag: tissue

value: Placenta

tag: idontma

tag: fetalgender

value: Male

tag: covidstatus

tag: roilabel

tag: structure

value: TerminalVilli

tag: aoisurfacearea

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: P2_ROI9_AV_PanCK

description:
rawdata.csv
normdata.csv

value: AnchoringVillus

tag: aoinucleicount

tag: roicoordinatex

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: P2_ROI10_TV_Vimentin

description:
rawdata.csv
normdata.csv

tag: tissue


title: Control ChIP-seq from HCT116 (ENCLB355ZIT)

description:
https://www.encodeproject.org/experiments/ENCSR936ENS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR936ENS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB355ZIT
size range: 200-600

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

tag: link

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

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


title: TF ChIP-seq from HCT116 (ENCLB674LOP)

description:
https://www.encodeproject.org/experiments/ENCSR446FOM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR446FOM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR365VOI
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB674LOP
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: antibody

value: CTCF

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


title: P2_ROI9_AV_Vimentin

description:
rawdata.csv
normdata.csv

tag: idontma

tag: fetalgender

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: TF ChIP-seq from HCT116 (ENCLB124RNN)

description:
https://www.encodeproject.org/experiments/ENCSR908TBJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR908TBJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR198TUZ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB124RNN
size range: 200-600

tag: line

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

value: ENCBS338OSL at ENCODE; https://www.encodeproject.org/ENCBS338OSL/


title: TF ChIP-seq from HCT116 (ENCLB985HTA)

description:
https://www.encodeproject.org/experiments/ENCSR446FOM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR446FOM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR365VOI
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB985HTA
size range: 200-600

tag: antibody

value: cell line

tag: source

tag: treatments

tag: link


title: intestinal tumors 2Gy_Rtype2

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

source_name: intestinal tumors by the irradiation of X-rays at 2 weeks of age

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

tag: strain

value: C3B6F1 ApcMin/+

source_name: Normal liver

value: liver


title: intestinal tumors 2Gy_Rtype3


title: intestinal tumors 2Gy_Rtype1


title: intestinal tumors 2Gy_Stype


title: TF ChIP-seq from HCT116 (ENCLB531VTT)

description:
https://www.encodeproject.org/experiments/ENCSR908TBJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR908TBJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR198TUZ
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB531VTT
size range: 200-600

value: male

value: colorectal carcinoma

value: adult

value: 48 year


title: P2_ROI8_TV_PanCK

description:
rawdata.csv
normdata.csv

value: Placenta

tag: idontma

tag: fetalgender

value: Male

tag: covidstatus

tag: roilabel

tag: structure

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: TF ChIP-seq from heart left ventricle (ENCLB530JKS)

description:
https://www.encodeproject.org/experiments/ENCSR461HOC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR461HOC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-07-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB530JKS
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

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/