title: ATAC-seq from foreskin keratinocyte (ENCLB189VFV)

description:
https://www.encodeproject.org/experiments/ENCSR798IJQ/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB189VFV

value: newborn


title: ATAC-seq from foreskin keratinocyte (ENCLB120SNK)

status: Public on Apr 22 2021

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/ENCSR798IJQ/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB120SNK

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 5.5 days

value: foreskin keratinocyte

value: primary cell

tag: description

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

tag: age

value: 2-4 day

tag: lab

value: Paul Khavari, Stanford

tag: source

value: Paul Khavari

tag: treatments

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

tag: health state

value: Healthy

tag: passage number

tag: link

value: ENCBS389AUD at ENCODE; https://www.encodeproject.org/ENCBS389AUD/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB981GVD)

description:
https://www.encodeproject.org/experiments/ENCSR798IJQ/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB981GVD

value: ENCBS135YLX at ENCODE; https://www.encodeproject.org/ENCBS135YLX/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB112FTD)

description:
https://www.encodeproject.org/experiments/ENCSR798IJQ/
***************
biological replicate number: 1
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB112FTD


title: ATAC-seq from foreskin keratinocyte (ENCLB674WWG)

description:
https://www.encodeproject.org/experiments/ENCSR798IJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB674WWG


title: ATAC-seq from foreskin keratinocyte (ENCLB662WCS)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB662WCS

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 0.5 days

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 1.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:0.5; duration_units:day;

value: ENCBS821VLO at ENCODE; https://www.encodeproject.org/ENCBS821VLO/


title: ATAC-seq from foreskin keratinocyte (ENCLB193BUE)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB193BUE

value: newborn

value: ENCBS982NWD at ENCODE; https://www.encodeproject.org/ENCBS982NWD/


title: ATAC-seq from foreskin keratinocyte (ENCLB907LKG)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB907LKG

value: foreskin keratinocyte

value: primary cell


title: ATAC-seq from foreskin keratinocyte (ENCLB597NRR)

description:
https://www.encodeproject.org/experiments/ENCSR572UDP/
***************
biological replicate number: 2
technical replicate number: 6
description: ATAC-seq on primary keratinocytes in day 2.0 of differentiation
experiment encode accession: ENCSR572UDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB597NRR

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 1.5 days

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 2.0

value: male

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:1.5; duration_units:day;

value: ENCBS242GKJ at ENCODE; https://www.encodeproject.org/ENCBS242GKJ/


title: ATAC-seq from foreskin keratinocyte (ENCLB994SZO)

description:
https://www.encodeproject.org/experiments/ENCSR572UDP/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 2.0 of differentiation
experiment encode accession: ENCSR572UDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB994SZO

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari


title: ATAC-seq from foreskin keratinocyte (ENCLB249ZCE)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB249ZCE

value: Healthy


title: ATAC-seq from foreskin keratinocyte (ENCLB891LFO)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB891LFO


title: ATAC-seq from foreskin keratinocyte (ENCLB765OIZ)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB765OIZ


title: ATAC-seq from foreskin keratinocyte (ENCLB376XLB)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB376XLB


title: ATAC-seq from foreskin keratinocyte (ENCLB915ZDP)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB915ZDP

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB029WIY)

description:
https://www.encodeproject.org/experiments/ENCSR521RAL/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 4.0 of differentiation
experiment encode accession: ENCSR521RAL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB029WIY

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 3.5 days

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 4.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:3.5; duration_units:day;

value: ENCBS081FMT at ENCODE; https://www.encodeproject.org/ENCBS081FMT/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB118KNG)

description:
https://www.encodeproject.org/experiments/ENCSR521RAL/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 4.0 of differentiation
experiment encode accession: ENCSR521RAL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB118KNG

value: newborn


title: ATAC-seq from foreskin keratinocyte (ENCLB293BPT)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 1
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB293BPT

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 1.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:0.5; duration_units:day;

value: ENCBS982NWD at ENCODE; https://www.encodeproject.org/ENCBS982NWD/


title: ATAC-seq from foreskin keratinocyte (ENCLB788BWY)

description:
https://www.encodeproject.org/experiments/ENCSR521RAL/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 4.0 of differentiation
experiment encode accession: ENCSR521RAL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB788BWY

value: foreskin keratinocyte

value: primary cell

value: ENCBS870NXI at ENCODE; https://www.encodeproject.org/ENCBS870NXI/


title: ATAC-seq from foreskin keratinocyte (ENCLB316GSQ)

description:
https://www.encodeproject.org/experiments/ENCSR521RAL/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 4.0 of differentiation
experiment encode accession: ENCSR521RAL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB316GSQ

value: male


title: ATAC-seq from foreskin keratinocyte (ENCLB490ZOG)

description:
https://www.encodeproject.org/experiments/ENCSR521RAL/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 4.0 of differentiation
experiment encode accession: ENCSR521RAL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB490ZOG

value: 2-4 day


title: ATAC-seq from foreskin keratinocyte (ENCLB414PDL)

description:
https://www.encodeproject.org/experiments/ENCSR521RAL/
***************
biological replicate number: 1
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 4.0 of differentiation
experiment encode accession: ENCSR521RAL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB414PDL

value: Paul Khavari, Stanford


title: ATAC-seq from foreskin keratinocyte (ENCLB406MWM)

description:
https://www.encodeproject.org/experiments/ENCSR521RAL/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 4.0 of differentiation
experiment encode accession: ENCSR521RAL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB406MWM

value: Paul Khavari


title: ATAC-seq from foreskin keratinocyte (ENCLB204YKK)

description:
https://www.encodeproject.org/experiments/ENCSR521RAL/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 4.0 of differentiation
experiment encode accession: ENCSR521RAL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB204YKK

value: Healthy


title: ATAC-seq from foreskin keratinocyte (ENCLB081PBN)

description:
https://www.encodeproject.org/experiments/ENCSR521RAL/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 4.0 of differentiation
experiment encode accession: ENCSR521RAL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB081PBN

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: Islets_DP248_IGT

status: Public on Apr 13 2021

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

library_source: transcriptomic

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8)
Reads were filtered for low complexity with reaper (v. 15-065)
Reads were aligned against Homo sapiens GRCh38.92 genome using STAR (v. 2.5.3a)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1) using Homo sapiens GRCh38.92 gene annotation.
Genome_build: Homo sapiens GRCh38.92
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read counts
Supplementary_files_format_and_content: Matrix table of gene-level read counts for each gene and each sample. Row names were simplied to Ensembl IDs without version information. Genes from pseudoautosomal regions (PAR), which all had 0 counts in all samples, were removed in order to avoid ambiguity in Ensembl IDs.

molecule: total RNA

source_name: Pancreatic islets (living donor, in situ)

extract_protocol:
Pancreatic tissue was sectioned in a cryostat and mounted on UV pre-treated Zeiss MembraneSlide 1.0 PEN slides. Laser capture microdissection (LCM) was done with a Zeiss Palm MicroBeam system using autofluorescence to identify islets, as previously described30. RNA was isolated from approximately 20x6µm3 of islet tissue using the Arcturus PicoPure RNA Isolation Kit.
Sequencing libraries were prepared from bulk RNA using the Illumina SmartSeq protocol.

tag: diabetes status

value: IGT

value: TRUE


title: Islets_DP235_IGT


title: Islets_DP237_IGT


title: Islets_DP209_IGT


title: Islets_DP224_IGT


title: Islets_DP216_IGT


title: Islets_DP208_T3cD


title: ATAC-seq from foreskin keratinocyte (ENCLB834WOD)

description:
https://www.encodeproject.org/experiments/ENCSR290YMN/
***************
biological replicate number: 1
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 1.0 of differentiation
experiment encode accession: ENCSR290YMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB834WOD


title: Islets_DP204_IGT


title: Islets_DP206_IGT


title: Islets_DP197_T2D


title: Islets_DP194_T2D

value: FALSE


title: Islets_DP190_IGT


title: Islets_DP195_IGT


title: Islets_DP185_T2D


title: Islets_DP192_T2D


title: Islets_DP181_ND

value: ND


title: Islets_DP184_IGT


title: Islets_DP193_T2D


title: Islets_DP180_T3cD


title: Islets_DP186_IGT


title: Islets_DP187_T2D


title: Islets_DP179_T2D


title: Islets_DP176_T3cD


title: Islets_DP229_IGT


title: Islets_DP177_T2D


title: Islets_DP170_T3cD


title: Islets_DP167_T3cD


title: Islets_DP173_ND


title: Islets_DP169_T3cD


title: Islets_DP166_T2D


title: Islets_DP207_IGT


title: Islets_DP163_T2D


title: Islets_DP161_T2D


title: Islets_DP160_T3cD


title: Islets_DP152_T3cD


title: Islets_DP157_T2D


title: Islets_DP151_IFG

value: IFG


title: Islets_DP145_IGT


title: Islets_DP147_ND


title: Islets_DP143_T2D


title: Islets_DP144_IGT


title: Islets_DP174_T3cD


title: Islets_DP140_IGT


title: Islets_DP129_T2D


title: Islets_DP139_T2D


title: Islets_DP138_IGT


title: Islets_DP126_T2D


title: Islets_DP132_ND


title: Islets_DP137_IGT


title: Islets_DP123_IGT


title: Islets_DP125_ND


title: Islets_DP124_T2D


title: Islets_DP122_T2D


title: Islets_DP116_IFG


title: Islets_DP117_T3cD


title: Islets_DP162_T3cD


title: Islets_DP118_T2D


title: Islets_DP146_ND


title: Islets_DP114_T3cD


title: Islets_DP110_IGT


title: Islets_DP120_T3cD


title: Islets_DP108_IGT


title: Islets_DP109_T2D


title: Islets_DP150_T2D


title: Islets_DP103_T2D


title: Islets_DP111_T2D


title: Islets_DP105_T2D


title: Islets_DP095_ND


title: Islets_DP106_T3cD


title: Islets_DP089_T3cD


title: Islets_DP097_T2D


title: Islets_DP096_T3cD


title: Islets_DP104_T2D


title: Islets_DP093_IGT


title: Islets_DP112_T3cD


title: Islets_DP090_T3cD


title: Islets_DP086_ND


title: Islets_DP083_T2D


title: Islets_DP080_T3cD


title: Islets_DP087_T2D


title: Islets_DP081_IGT


title: Islets_DP102_T2D


title: Islets_DP079_ND


title: Islets_DP077_T3cD


title: Islets_DP107_T2D


title: Islets_DP075_T3cD


title: Islets_DP071_IGT


title: Islets_DP088_IGT


title: Islets_DP074_T3cD


title: Islets_DP099_T2D


title: Islets_DP068_IGT


title: Islets_DP065_T3cD


title: Islets_DP067_IFG


title: Islets_DP070_T2D


title: Islets_DP063_IGT


title: Islets_DP076_IGT


title: Islets_DP073_T3cD


title: Islets_DP053_T3cD


title: Islets_DP066_T3cD


title: Islets_DP054_ND


title: Islets_DP082_IGT


title: Islets_DP058_T2D


title: Islets_DP061_T3cD


title: Islets_DP052_ND


title: Islets_DP072_T3cD


title: Islets_DP043_T3cD


title: Islets_DP055_T2D


title: Islets_DP051_IGT


title: Islets_DP049_T2D


title: Islets_DP042_T2D


title: Islets_DP064_ND


title: Islets_DP048_IGT


title: Islets_DP069_ND


title: Islets_DP057_T3cD


title: Islets_DP059_IGT


title: Islets_DP039_T3cD


title: Islets_DP040_T3cD


title: Islets_DP034_T2D


title: Islets_DP025_IGT


title: Islets_DP017_T3cD


title: Islets_DP030_T2D


title: Islets_DP028_T3cD


title: Islets_DP010_ND


title: Islets_DP007_IGT


title: Islets_DP003_T2D


title: Islets_DP021_ND


title: Islets_DP005_IGT


title: milk genistein rep 3

status: Public on Mar 31 2021

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St. Slot 782

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to Ensembl 11.1
Unique reads were calculated with CLC Genomics Workbench v20 Qiagen
Mapping parameters ;  Mismatch cost = 2;  Insertion cost = 3;  Deletion cost = 3; Length fraction = 0.95;  Similarity fraction = 0.95
Genome_build: Ensembl 11.1
Supplementary_files_format_and_content: Matrix table with unique reads for every gene and every sample

organism: Sus scrofa

source_name: postnatal day 21 pig  testes

growth_protocol: Piglets were feed with sow for two days postnatally.  Piglets were assigned to one of five diet groups: sow, soy, cow milk, milk with 17beta estradiol added their food to read serum E2 concentratins between 15-30 pmol/L, and milkadded genistein to obtain serum concentrtion of 84 mg/L. At sacrifice (PND 21) testes were collected and fresh frozen in liquid nitrogen.

extract_protocol:
Total RNA was isolated from the rats testes using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed .
RNA libraries were prepared for sequencing using standard Illumina protocols for RNA-Seq

treatment_protocol: Testes were collected and fresh frozen in liquid nitrogen

tag: treatment

value: Milk + genistein

value: postnatal day 21

tag: tissue

value: testes


title: milk genistein rep 1


title: Islets_DP012_ND


title: milk  rep 3

value: Milk


title: Islets_DP011_ND


title: milk  rep 2


title: milk genistein rep 2


title: milk estradiol rep 3

value: Milk + 17-b estradiol


title: milk estradiol rep 1


title: soy rep 2

value: Soy protein isolate


title: Islets_DP008_IGT


title: Islets_DP002_T3cD


title: sow rep 3

value: Sow


title: milk  rep 1


title: sow rep 2


title: Islets_DP013_IGT


title: sow rep 1


title: soy rep 3


title: M16-106 RNASeq Sample 041

status: Public on Feb 17 2021

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

description:
650802240912_
M16-106_Merge_Batch1-2_Log2FPKM.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned using the OmicSoft aligner and gene expression quantified based on UCSC gene model.
FPKM values from 2 batches were calculated separately, log2 transformed, and combined with batch effect corrected using linear model within OmicSoft software.
Genome_build: B37
Supplementary_files_format_and_content: M16-106_Merge_Batch1-2_Log2FPKM.txt: Batch effect corrected log2FPKM value combining batch 1 and batch 2.

source_name: Bone Marrow

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA Micro Kit (QIAGEN 80284) following manufacturer's instructions.
Total stranded transcriptome sequencing was performed using the TruSeq Stranded Total RNA library preparation kit. The low input RNA library preparation kit (NuGen Ovation V2) was used for samples with limiting material.
RNAseq was done with 2x101 pair-end.

tag: subtype

value: T-ALL

tag: diagnosis

value: R/R acute lymphoblastic leukemia

value: Adult

value: Bone Marrow

tag: time point

value: Baseline

tag: batch


title: M16-106 RNASeq Sample 042

description:
650730676212_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: B-ALL


title: M16-106 RNASeq Sample 040

description:
650730667109_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: Pediatric


title: M16-106 RNASeq Sample 030

description:
650919677612_
M16-106_Merge_Batch1-2_Log2FPKM.txt

source_name: Peripheral Blood

value: Other, but was T-ALL

value: Peripheral Blood


title: Islets_DP019_ND

value: ND

value: TRUE


title: M16-106 RNASeq Sample 012

description:
650678180712_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 034

description:
650880825707_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 011

description:
650644279906_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: soy rep 1

value: postnatal day 21


title: M16-106 RNASeq Sample 010

description:
650553464816_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 036

description:
650940924703_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 035

description:
650938402909_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: LL-T


title: M16-106 RNASeq Sample 026

description:
650938470809_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 037

description:
650941134012_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 023

description:
650752390012_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 033

description:
650828812106_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: milk estradiol rep 2

value: testes


title: M16-106 RNASeq Sample 014

description:
650678178715_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 031

description:
650824451406_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 007

description:
650730676306_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 025

description:
660166118606_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: Common


title: M16-106 RNASeq Sample 013

description:
650553466612_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 039

description:
660134808518_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 009

description:
650620533628_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 027

description:
660170650712_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 032

description:
650701559809_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 006

description:
650702204016_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 008

description:
660134808412_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 028

description:
650781675915_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 038

description:
650730676406_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: LL-B


title: M16-106 RNASeq Sample 003

description:
650656580409_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 002

description:
650646279332_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 024

description:
650776228912_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 029

description:
650861951609_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 015

description:
650890333603_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 005

description:
650702205718_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: M16-106 RNASeq Sample 018

description:
650656281815_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: 75umCadmium.WGS.Rep2

status: Public on Feb 01 2021

city: Aurora

first: Joshua

middle: C

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

data_processing:
Library strategy: Rerep-seq
Fastq files were aligned to HG38 using BWA-mem
Sam files were transformed into bam files and blacklisted using samtools (v1.2, RRID:SCR_002105). Blacklists were the same as previously used for Rerep-seq analysis (Menzel et al., 2020). Bedtools (v2.26.0, RRID:SCR_006646) was used to generate bedGraphs
Bedgraphs were binned and normalized by RPM and mitochondrial reads using a custom R script
Replicates were then averaged
Genome_build: HG38
Supplementary_files_format_and_content: bedgraph

growth_protocol: MDA-MB-231 female breast cancer cell line and hTERT-RPE-1 female retinal pigment epithelial cell line (called RPE throughout) were maintained at 37°C in Dulbecco’s Modified Essential Medium (DMEM) with 10% FB essence (VWR), 1% penicillin/streptomycin, and L-glutamine.

extract_protocol:
Rerep-seq was performed as described in . Briefly, In an 8 strip PCR tube 1 – 5 ug high molecular weight genomic DNA was mixed with 2.5uL 10X Hoechst 33258 (0.1mg/ml) and 2.5uL 10X NEB 4 (50 mM Potassium Acetate, 20 mM Tris-acetate , 10 mM Magnesium Acetate, 1 mM DTT pH 7.9@25°C) to a final volume of 24uL; open tubes placed upright in PCR tube rack, covered with a glass plate (3" x 3" glass plate from VWR Vertical Gel Electrophoresis Systems), exposed to 7.5 minutes of glass plate filtered (UVA only) from Stratalinker followed by addition of 0.5uL UDG (5 units of Uracil-DNA Glycosylase), 0.5uL APE1 (10 units of human apurinic/apyrimidinic endonuclease 1) for 2 hours at 37°C. The digested DNA was repaired with NEB’s FFPE DNA Repair Mix for 30 minutes; mixed with 10X loading dye then run on 0.8% agarose gel for 15 minutes. The fragmented DNA ranging from 0.1Kb to 3Kb was gel extracted with Wizard® SV Gel and PCR Clean-Up System with the purified DNA eluted in 50uL nuclease free water.
Sequencing libraries were constructed using the Illumina Nextera DNA Flex Library Prep Kit (catalog number 20018704) following the manufacturers’ protocol and using 14 cycles of amplification for final library construction. Libraries were constructed using dual index barcodes from the Nextera DNA CD Indexes (catalog number 20018707).

treatment_protocol: Cadmium-resistant cell (MDA-MB-231cadR) cell lines were selected by passage in medium containing CdSO4. The CdSO4 concentration was increased by increments of 5-25 μM after 10 passages at the current concentration and when cell count increased at least 1.8 times average daily over at least four passages consistently. Cells used in this study were adapted to CdSO4 containing medium for 7 months up to 75 μM CdSO4.

tag: cell line

value: 75uM cadmium resistance

tag: input or rerep

value: input


title: M16-106 RNASeq Sample 022

description:
650752389612_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: T-ALL

value: R/R acute lymphoblastic leukemia


title: M16-106 RNASeq Sample 021

description:
650857177512_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: Adult

value: Bone Marrow


title: M16-106 RNASeq Sample 019

description:
650715056509_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: Baseline


title: noCopperWGS_rep2

data_processing:
Library strategy: Rerep-seq
Fastq files were aligned to SacCer3 using BWA-mem
Sam files were transformed into bam files and blacklisted using samtools (v1.2, RRID:SCR_002105). Blacklists were the same as previously used for Rerep-seq analysis (Menzel et al., 2020). Bedtools (v2.26.0, RRID:SCR_006646) was used to generate bedGraphs
Bedgraphs were binned and normalized by RPM and mitochondrial reads using a custom R script
Replicates were then averaged
The CUP1 gene is exactly duplicated in the yeast genome, so we replaced the CUP1.1 gene copy with ambiguous nucleotides “N” to force alignment to CUP1.2 rather than allow for random alignment between the two copies.
Genome_build: SacCer3, with cup 1.1 removed
Supplementary_files_format_and_content: bedgraph

organism: Saccharomyces cerevisiae

source_name: noCopperInput

growth_protocol: Yeast strains and plasmids used in this study are listed in Table 1 and were grown according to standard procedures in YPD (yeast extract, peptone, and 2% dextrose) at 30°C for all experiments unless otherwise stated. To accommodate S. cerevisiae’s lack of the thymidine salvage pathway, yeast strains in this paper are all stably transformed with NheI linearized p403–BrdU–Inc HIS3, a reconstituted thymidine salvage pathway cassette, consisting of Herpes simplex virus thymidine kinase (HSV–TK) and human equilibrative nucleoside transporter (hENT1), that enables efficient cellular uptake and incorporation of the thymidine analogue BrdU into DNA . Inserts were confirmed by spot assays for sensitivity to 75 µg/ml FUDR and susceptibility to BrdU uptake and genomic fragmentation via Rerep-seq.

treatment_protocol: We developed a copper-resistant yeast strain by culturing cells in the presence of 6 mM copper for approximately 30 generations. Controls were cultured under normal conditions.

value: untreated


title: M16-106 RNASeq Sample 001

description:
650642042812_
M16-106_Merge_Batch1-2_Log2FPKM.txt


title: copperTreatedWGS_rep2

source_name: copperTreatedInput

value: copper treated


title: copperTreatedWGS_rep1


title: flag-eIF4E HeLa cells; rapamycin treatment; biological replicate #2

status: Public on Dec 31 2020

city: Adelaide

first: Kirk

middle: B

last: Jensen

state: South Australia

address: North Terrace

department: Lifelong Health

country: Australia

institute: South Australian Health & Medical Research Institute

description:
4E1-rapa-02
Modified CLIP-seq (capCLIP-seq)
eIF4E protein & crosslinked RNA fragments (by anti-flag mAb immunoprecipitation)

data_processing:
Library strategy: capCLIP-seq
Raw sequencing data was adaptor trimmed and filtered for short sequences during basecalling with bcl2fastq2 (--find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35).
FASTQ files were analysed and quality checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc) and Picard (broadinstitute.github.io/picard).
Filtered reads were mapped against the human reference genome (hg19) using the STAR alignment algorithm (39) (version 2.5.3a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts).
UMItools was used to deduplicate reads in each sample using unique molecular identifiers (UMI’s) (default settings with --method adjacency --edit-distance-threshold).
Peak calling was performed with MACS2 (version 2.1.1.20160309) using default parameters and reporting only peaks with an FDR cut-off (-q) < 0.05.
Differential binding analysis was performed using R (version 3.4.3) and the DiffBind package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Peak data (merged.narrowPeak) was generated with MACS2; bed and tsv data were generated from DiffBind and MACS2 peak calling data.

source_name: HeLa cells

growth_protocol: flag-eIF4E HeLa cells were grown to ~90% confluency in DMEM + 10% FBS in 150 mm plates.

extract_protocol:
Cells were immediately harvested in 1X PXL buffer; and the lysate collected and stored @ -80 ˚C.
Single read - Illumina.

treatment_protocol: Cells were either treated with 100 nM rapamycin for 2 hours @ 37˚C, or with DMSO carrier (solvent) only for the same time period. Following treatment, all plates were placed atop an ice-water slurry and irradiated in a short-wavelength (~254 nm) Stratalinker to 350 mJ/cm2.

value: HeLa cells with N-terminal 3X-flag tag on endogenous eIF4E protein

tag: drug treatment

value: 100 nM rapamycin (in DMSO)

tag: uv irradiation

tag: antibody

value: anti-flag mAb


title: Control transfection Replicate 1

status: Public on Jan 18 2021

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

description:
RNA-seq of Control GFP+ cells Rep1
Control pCIG plasmid
Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the HoxB8 mix : Hoxb8-pCIG 1 µg/µl + pCIG 1µg/µl . Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.

data_processing:
Basecalls performed using RTA (Illumina)
RNA-seq reads were aligned to the galgal4 genome assembly using subread-align
Gene exon counts were made using featureCounts
RNA-Seq differentially expressed genes were called using DESeq2 using a false discovery rate (FDR;padj) cut-off of 0.01
Genome_build: gg4
Supplementary_files_format_and_content: DGE files show the DESeq output of differentially expressed genes (Log2Fold Change, p-value, p-adjusted) of Hoxb8 vs Control

organism: Gallus gallus

source_name: Control transfection, GFP positive cells

extract_protocol:
RNA was extracted (RNeasy Mini Kit) and reverse transcribed and cDNA was amplified using a linear amplification system and used for sequencing library building
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Control GFP expressing cells


title: flag-eIF4E HeLa cells; DMSO only; biological replicate #1

description:
4E1-ctrl-01
Modified CLIP-seq (capCLIP-seq)
eIF4E protein & crosslinked RNA fragments (by anti-flag mAb immunoprecipitation)

value: None; DMSO carrier only


title: M16-106 RNASeq Sample 016

description:
650936027113_
M16-106_Merge_Batch1-2_Log2FPKM.txt

tag: age


title: EP_H3K4me3_ChIPSeq Rep 2

status: Public on Oct 23 2020

city: Bar Harbor

first: Natalie

middle: R

last: Powers

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
Sample 2
H3K4me3 ChIP-seq, B6.Prdm9EP/EP Rep2
EPHom_H3K4me3_ChIP_merge_mm10_RPM.bedgraph
EPHom_H3K4me3_merge_K4Peaks.bed
EPHom_H3K4me3_merge_K4peaks_Hotspots.bed

data_processing:
(Samples 1 and 2) Single-end ChIP-Seq reads were trimmed with Trimmomatic and aligned to the mm10 genome assembly using BWA v0.7.9a
(Samples 1 and 2) ChIP-Seq reads were filtered to remove duplicates and to keep only uniquely mapped reads
(Samples 1 and 2) ChIP-Seq peaks were called using MACS v1.4
(Samples 3 and 4) Paired-end ChIP-Seq reads were trimmed with Trimmomatic and aligned to the mm10 genome assembly using BWA v0.5.10-tpx
(Samples 3 and 4) Bam files were parsed for detection of single-ended reads indicative of single-stranded fragments, using the micro-homologous region
(Samples 3 and 4) Fastq files containing only the selected reads were generated
(Samples 3 and 4) Fastq files containing only the selected reads were aligned to the mm10 genome using BWA v0.7.9a
(Samples 3 and 4) ChIP-seq peaks were called using MACS v2.1.0.20151222
Genome_build: mm10

organism: Mus musculus

source_name: spermatocytes

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Nuclei were fixed with 1% formaldehyde, and chromatin was fragmented by Mnase digestion. Cross-links were reversed and chromatin eluted by incubation at 68 degrees Celsius. After high-speed spin soluble chromatin was removed and used for ChIP with anti-H3K4me3.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: spermatocytes

value: 14 days post-partum

tag: strain

tag: chip antibody


title: parentalOf75umCadmium.ReRep.Rep2

value: Untreated control

value: rerep


title: noCopperWGS_rep1

value: input


title: parentalOf75umCadmium.WGS.Rep2


title: parentalOf75umCadmium.ReRep.Rep1


title: parentalOf75umCadmium.WGS.Rep1


title: M16-106 RNASeq Sample 020

description:
660177072406_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: B-ALL

value: Pediatric


title: flag-eIF4E HeLa cells; rapamycin treatment; biological replicate #1

description:
4E1-rapa-01
Modified CLIP-seq (capCLIP-seq)
eIF4E protein & crosslinked RNA fragments (by anti-flag mAb immunoprecipitation)


title: M16-106 RNASeq Sample 017

description:
660134808318_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: T-ALL

value: R/R acute lymphoblastic leukemia

value: Adult

value: Peripheral Blood


title: Control transfection Replicate 2

description:
RNA-seq of Control GFP+ cells Rep2
Control pCIG plasmid
Neural tube in ovo electroporations were performed at HH11. Eggs were windowed, and the DNA solution (1 to 2µg/µl) was injected in neural tube lumen. Needle L-shape platinum electrodes were place on both sides of the embryo at trunk level (5 mm apart), with the cathode always at its right. Five 50 ms pulses of 25 volts were given bilateral at 50 ms intervals with an electroporator NEPA21 (Nepagene). Plasmids DNA concentrations were for the control mix: pCIG 2µg/µl and for the HoxB8 mix : Hoxb8-pCIG 1 µg/µl + pCIG 1µg/µl . Part of the neural tube expressing the GFP were dissected 18 hours after electroporation and dissociated (Trypsin-EDTA 0,25%). A highly enriched population of GFP-expressing cells was isolated by FACS with the use of a dead cell exclusion (DCE)/discrimination dye (DAPI) to eliminate dying cells.


title: EP_H3K4me3_ChIPSeq Rep 1

description:
Sample 1
H3K4me3 ChIP-seq, B6.Prdm9EP/EP Rep1
EPHom_H3K4me3_ChIP_merge_mm10_RPM.bedgraph
EPHom_H3K4me3_merge_K4Peaks.bed
EPHom_H3K4me3_merge_K4peaks_Hotspots.bed


title: M16-106 RNASeq Sample 004

description:
650701559903_
M16-106_Merge_Batch1-2_Log2FPKM.txt

value: Bone Marrow

value: Baseline


title: DR_ZT16_Rep2: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT16_Replicate-2

status: Public on Sep 22 2020

type: RNA

city: MILL VALLEY

first: Brian

middle: A

last: Hodge

address: 338 EDGEWOOD AVE, A

institute: Buck Institute

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.

hyb_protocol: Samples were hybridized to the 12-plex Gene Expression array platform according to the manufacturers' protocol. NimbleGen's Sample Tracking Controls (05223512001), Hybridization Kit reagents (05583683001) and Wash Buffers (05584507001) were used. Each 12-plex array was sealed with a H12 mixer, provided with the Gene Expression array. 4µg of each Cy3 labeled sample was loaded onto an array on the 12-plex chip, using a Gilson M100 pipette. Hybridization was completed overnight on a NimbleGen Hybridization System 4 unit, at 42℃ for 16hrs.

scan_protocol: After the 12-plex chip was washed and dried, the chip was scanned on a GenePix 4200A scanner at 300PMT, 100POW. Arrays were then quantitated using NimbleGen's NimbleScan2 software.

data_processing: Arrays were normalized using LIMMA (Smyth & Speed 2003)

organism: Drosophila melanogaster

source_name: 35 female Canton-S flies reared on DR-diet for seven days

label_protocol: For each experimental sample, approximately 150ng of total RNA was amplified with Sigma's TransPlex Complete Whole Transcriptome Amplification Kit (WTA2). Qiagen's QIAquick PCR Purification Kit (28104) was used to purify the amplified samples. Following purification, the samples were further processed on the QIAcube according to the manufacturers' protocol: QIAquick PCR Purification-Standard. For each biological sample the NimbleGen (Roche) One-Color DNA Labeling kit (05223555011) was used to label dscDNA with Cy3 according to the manufacturers' protocol.

extract_protocol: Total RNA was extracted from whole fly lystates of approximately 35 flies (4 biological replicates per diet and time-point) with Qiagen's Rneasy Lipid Tissue Mini Kit (74804). Samples were then lysed in Qiagen's Qiazol lysis buffer with Qiagen's TissueLyser (pulverized for approximately nine minutes). Qiagen's QIAcube robot was used to futher proccess the samples utilizing a modified version of Qiagen's QIAcube protocol: RNeasy Lipid Tissue Mini-Animal Tissues-Aqueous Phase.

treatment_protocol: Four-day old mated female flies (Canton-S and Tim01) were sorted on either Ad libitum (5.0% yeast-extract) or Dietary Restriction (0.5% yeast-extract) and reared in a 12:12hr light-dark cycle for seven days. On the seventh day flies were collected every four hours for 20 hours (6 timepoints) starting at ZT 0 (lights on).

value: Canton-S

tag: Sex

value: Female

value: Whole fly lysate

tag: time of collection

tag: diet

value: Dietary restriction (0.5% yeast-extract)


title: DR_ZT16_Rep1: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT16_Replicate-1

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.

tag: tissue


title: DR_ZT20_Rep3: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT20_Replicate-3

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: 75umCadmium.WGS.Rep1

tag: treatment

value: 75uM cadmium resistance


title: DR_ZT8_Rep2: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT8_Replicate-2

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: flag-eIF4E HeLa cells; DMSO only; biological replicate #2

description:
4E1-ctrl-02
Modified CLIP-seq (capCLIP-seq)
eIF4E protein & crosslinked RNA fragments (by anti-flag mAb immunoprecipitation)

value: HeLa cells with N-terminal 3X-flag tag on endogenous eIF4E protein

value: None; DMSO carrier only

value: anti-flag mAb


title: DR_ZT8_Rep3: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT8_Replicate-3

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: DR_ZT12_Rep2: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT12_Replicate-2

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.

value: ZT 12 (8:00pm, lights off)


title: DR_ZT20_Rep4: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT20_Replicate-4

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: DR_ZT20_Rep2: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT20_Replicate-2

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: DR_ZT16_Rep3: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT16_Replicate-3

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: DR_ZT20_Rep1: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT20_Replicate-1

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: DR_ZT16_Rep4: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT16_Replicate-4

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: DR_ZT8_Rep4: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT8_Replicate-4

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: DR_ZT12_Rep1: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT12_Replicate-1

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: DR_ZT0_Rep4: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT0_Replicate-4

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.

value: ZT 0 (8:00am, lights on)


title: AL_ZT20_Rep3: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT20_Replicate-3

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.

source_name: 35 female Canton-S flies reared on AL-diet for seven days

value: Ad libitum (5% yeast-extract)


title: AL_ZT20_Rep4: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT20_Replicate-4

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: AL_ZT16_Rep3: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT16_Replicate-3

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: AL_ZT16_Rep2: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT16_Replicate-2

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: DR_ZT0_Rep2: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT0_Replicate-2

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: DR_ZT8_Rep1: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT8_Replicate-1

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: AL_ZT12_Rep3: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT12_Replicate-3

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: DR_ZT4_Rep4: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT4_Replicate-4

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: DR_ZT0_Rep3: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT0_Replicate-3

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: AL_ZT12_Rep2: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT12_Replicate-2

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: DR_ZT12_Rep3: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT12_Replicate-3

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: AL_ZT8_Rep2: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT8_Replicate-2

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: DR_ZT4_Rep2: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT4_Replicate-2

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: AL_ZT12_Rep4: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT12_Replicate-4

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: AL_ZT20_Rep1: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT20_Replicate-1

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 20 RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: DR_ZT4_Rep1: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT4_Replicate-1

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: DR_ZT0_Rep1: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT0_Replicate-1

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: DR_ZT12_Rep4: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT12_Replicate-4

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 12. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: AL_ZT12_Rep1: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT12_Replicate-1

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 12 RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: AL_ZT16_Rep4: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT16_Replicate-4

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 16. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: AL_ZT8_Rep3: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT8_Replicate-3

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: AL_ZT20_Rep2: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT20_Replicate-2

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 20. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: AL_ZT16_Rep1: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT16_Replicate-1

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 16 RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: DR_ZT4_Rep3: D.Melanogaster_female_whole-fly-lysate_DR-diet_ZT4_Replicate-3

description: This sample is from mated Canton-S females reared on DR (0.5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: AL_ZT8_Rep4: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT8_Replicate-4

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 8. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: sperm long RNA dex rep1

status: Public on Jul 15 2020

city: Cambridge

first: Eric

last: Miska

state: Cambridgeshire

address: Gurdon Institute, Tennis Court Rd

department: Cambridge University

country: United Kingdom

institute: Cambridge University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using Star.
Reads matching Ensemble annotations and backsplice junctions were quantified using feature counts.
Circular RNAs were quantified using Circexplorer2
Countmatrix obtained was normalized using EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: comma separated text file with EdgeR normalized readcounts

source_name: sperm cells

growth_protocol: Alife mice

extract_protocol:
Mature sperm was extracted from cauda epididymis and placed in M2 medium. Sperm was subjected to somatic lysis and 2 washes. RNA was extracted Trizol.
Ilumina truseq stranded Total RNA library preparation using Ribozero treatment, starting amount: 200ng RNA. .Adapter dilution 1:3.

treatment_protocol: intraperitoneal injection of Dexamethasone 2mg/kg in 10% DMSO and saline.

value: Sperm

value: 10 weeks

value: wild type

value: treated


title: sperm long RNA dex rep4


title: AL_ZT4_Rep4: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT4_Replicate-4

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: AL_ZT0_Rep4: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT0_Replicate-4

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the fourth of four replicates.


title: sperm long RNA veh rep3

value: vehicle


title: AL_ZT4_Rep2: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT4_Replicate-2

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.


title: AL_ZT4_Rep1: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT4_Replicate-1

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: AL_ZT8_Rep1: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT8_Replicate-1

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 8 RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: AL_ZT4_Rep3: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT4_Replicate-3

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 4. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: sperm long RNA dex rep3


title: sperm long RNA dex rep2


title: AL_ZT0_Rep3: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT0_Replicate-3

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.


title: Sample 20_nCoV 11 scRNA-seq [SW122]

status: Public on Jul 06 2020

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Fastq files were generated using cellranger mkfastq (v3.0.2)
From Sample 1 to Sample 20, they have the barcode sequence which end with '-1' to '-20', respectively;
Sample 1 : AAACCCAAGGGCAATC-1 ~ TTTGTTGTCGCCAATA-1
…
Sample 20 : AAACCCACACAGTCGC-20 ~ TTTGTTGTCTGCTTAT-20
The sequenced reads were aligned using cellranger count (v3.0.2; --r1-length 28 --r2-length 91) to cellranger reference GRCh38 (v 3.0.0).
Aligned files were aggregated with cellranger aggr (v3.0.2; --normalize=mapped)
Genome_build: GRCh38
Supplementary_files_format_and_content: gene expression matrix, cell barcode information, and gene name list

extract_protocol:
The library was constructed using the Chromium Single Cell 3' Library & Gel Bead Kit v3.
The experimental process was conducted according to manufacturer's instruction without modification. The final libraries were sequenced on Nextseq 550.

tag: subject group

value: COVID-19 patient

tag: subject status

value: Asymptomatic case of COVID-19 patient

tag: gender

value: F

value: PBMC


title: AL_ZT0_Rep2: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT0_Replicate-2

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the second of four replicates.

value: Canton-S

value: Female

value: Whole fly lysate


title: Sample 16_nCoV 8 scRNA-seq [SW118]

value: severe COVID-19 patient


title: sperm long RNA veh rep4


title: Sample 19_Normal 4 scRNA-seq [SW121]

value: healthy control

value: M


title: Sample 18_nCoV 10 scRNA-seq [SW120]

value: mild COVID-19 patient


title: Sample 11_nCoV 5 scRNA-seq [SW113]


title: AL_ZT0_Rep1: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT0_Replicate-1

description: This sample is from mated Canton-S females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.

value: ZT 0 (8:00am, lights on)

value: Ad libitum (5% yeast-extract)


title: Sample 13_Normal 2 scRNA-seq [SW115]


title: Sample 9_nCoV 3 scRNA-seq [SW111]


title: Sample 14_Normal 3 scRNA-seq [SW116]


title: Sample 15_nCoV 7 scRNA-seq [SW117]


title: sperm long RNA veh rep2

value: Sperm

value: 10 weeks


title: Sample 12_nCoV 6 scRNA-seq [SW114]


title: Sample 2_nCoV 2 scRNA-seq [SW104]


title: sperm long RNA veh rep1

value: wild type


title: Sample 5_Normal 1 scRNA-seq [SW107]


title: Sample 7_Flu 4 scRNA-seq [SW109]

value: Influenza patient


title: Sample 4_Flu 2 scRNA-seq [SW106]


title: Non-Human Primate Lung epithelial cells, Healthy4

status: Public on Apr 23 2020

first: Alex

last: Shalek

state: MA

address: 45 Carleton Street

department: Chemistry

institute: MIT

description:
Non-human primate lung tissue from healthy donor, Healthy4
NHP_lung_epithelial_raw_expression_counts.csv.gz

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
Data was normalized, scaled, and clustered using the Seurat R package v2.3.4 (https://github.com/satija.lab/seurat). Clusters were annotated based on the identification of highly expressed genes and cells identified as epithelial were included in these matrices.
M. mulatta genome assembly 8.0.1 annotation version 102
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

molecule: polyA RNA

organism: Macaca mulatta

source_name: Lung epithelial cells

extract_protocol: Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well method (Gierahn et al Nature Methods 2017)

value: Lung epithelial cells


title: Non-Human Primate Ileum Small Intestine Enterocytes, SHIV-infected donor, SHIV3

description:
Non-human primate ileum tissue from SHIV-infected donor, SHIV3
NHP_ileum_epithelial_raw_expression_counts.csv.gz

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
Data was normalized, scaled, and clustered using the Seurat R package v2.3.4 (https://github.com/satija.lab/seurat). Clusters were annotated based on the identification of highly expressed genes and cells identified as enterocytes were included in these matrices.
M. mulatta genome assembly 8.0.1 annotation version 102
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: Ileum Enterocytes

tag: agent

value: SHIV

value: Ileum Enterocytes


title: Sample 1_nCoV 1 scRNA-seq [SW103]

value: COVID-19 patient

value: PBMC


title: ChIP-seq 293 Pol II NM 15 minutes

status: Public on Jun 03 2020

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt v1.9.1
Mapping to the hg19 genome was performed with Bowtie2 v2.2.5 (ChIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq)
Bigwig files were generated with the Deeptools2 bamCoverage tool
Genome_build: hg38 (except HEK293 CDK12as Pol II, Ser2P, and Ser5P ChIP-seq which are mapped on the hg19)
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: ChIP-seq 293 Pol II NM 15 minutes

growth_protocol: HEK293 cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
DNA were purified from chromatin IP products.
For ChIP-seq, libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions.

treatment_protocol: Cells were treated with 1-NM-PP1 for 15 minutes.

tag: cell line

value: sc-899 X, Santa Cruz Biotechnology (discontinuited antibody)

value: NM 15 minutes


title: Sample 10_nCoV 4 scRNA-seq [SW112]

value: severe COVID-19 patient

value: F


title: Sample 8_Flu 5 scRNA-seq [SW110]

value: M


title: Non-human primate mTB infected granulomas and uninvolved lungs [30518_Array5]

description:
Samples of several granulomas and uninvolved lung lobes from 10 mTB-infected monkeys
NHP_TB_Grans_and_Lung_dge.txt

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
Normalization, variable gene selection, and clustering were performed using Leiden clustering in the Scanpy v1.4.5.2 (scanpy.readthedocs.io) package (Wolf et al., 2018). Cell type labels were assigned using known marker genes and epithelial cell clusters are included in these matrices.
Macaca_fascicularis_5.0
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

organism: Macaca fascicularis

source_name: mTB granulomas and lung lobes

extract_protocol: Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well S^3 method (Hughes et al., BioRxiv 2019)

value: TB Granuloma and Adjacent Uninvolved Lung epithelial cells


title: Non-human primate mTB infected granulomas and uninvolved lungs [30518_Array3]


title: Sample 6_Flu 3 scRNA-seq [SW108]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30518_Array2]


title: Sample 3_Flu 1 scRNA-seq [SW105]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30518_Array1]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30418_Array8]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30418_Array10]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30418_Array7]


title: Non-Human Primate Ileum Small Intestine Enterocytes, SHIV-infected donor, SHIV2

description:
Non-human primate ileum tissue from SHIV-infected donor, SHIV2
NHP_ileum_epithelial_raw_expression_counts.csv.gz


title: Non-human primate mTB infected granulomas and uninvolved lungs [30218_Array9]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30418_Array9]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30218_Array10]


title: Non-Human Primate Lung epithelial cells, Healthy3

description:
Non-human primate lung tissue from healthy donor, Healthy3
NHP_lung_epithelial_raw_expression_counts.csv.gz


title: Non-human primate mTB infected granulomas and uninvolved lungs [29818_Array4]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29818_Array3]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30218_Array8]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29818_Array1]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30518_Array4]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29618_Array9]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29618_Array8]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29618_Array7]


title: Non-Human Primate Ileum Small Intestine Enterocytes, Healthy3

description:
Non-human primate ileum tissue from healthy donor, Healthy3
NHP_ileum_epithelial_raw_expression_counts.csv.gz


title: Non-human primate mTB infected granulomas and uninvolved lungs [30218_Array7]


title: Non-Human Primate Ileum Small Intestine Enterocytes, Healthy4

description:
Non-human primate ileum tissue from healthy donor, Healthy4
NHP_ileum_epithelial_raw_expression_counts.csv.gz


title: Non-human primate mTB infected granulomas and uninvolved lungs [29318_Array2]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29318_Array1]


title: Non-Human Primate Lung epithelial cells, SHIV-infected donor, SHIV4

description:
Non-human primate lung tissue from 1 SHIV-infected donor, SHIV4
NHP_lung_epithelial_raw_expression_counts.csv.gz


title: Non-human primate mTB infected granulomas and uninvolved lungs [29218_Array3]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29218_Array5]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29218_Array2]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29118_Array9]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29818_Array2]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29218_Array1]


title: Non-Human Primate Ileum Small Intestine Enterocytes, SHIV-infected donor, SHIV4

description:
Non-human primate ileum tissue from SHIV-infected donor, SHIV4
NHP_ileum_epithelial_raw_expression_counts.csv.gz


title: Non-human primate mTB infected granulomas and uninvolved lungs [29618_Array6]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30418_Array6]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29118_Array10]


title: Non-human primate mTB infected granulomas and uninvolved lungs [30218_Array6]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29318_Array3]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29618_Array10]


title: Non-human primate mTB infected granulomas and uninvolved lungs [28918_Array1]


title: Non-human primate mTB infected granulomas and uninvolved lungs [28918_Array3]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29818_Array5]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29318_Array4]


title: NS_19

status: Public on Mar 27 2020

city: Seoul

first: Hae-Ock

last: Lee

address: 222 Banpo-daero, Seocho-gu

department: Department of Microbiology

institute: College of Medicine, The Catholic University of Korea

description:
Single-cell RNA-seq
Lung_Cancer_raw_UMI_matrix.txt
Lung_Cancer_normalized_log2TPM_matrix.txt

data_processing:
Fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 2.1.0) with default parameters.
For each cell, we applied the three quality measures of mitochondrial genes (≤20%), and UMI and gene count (range from 100 to 150,000 and range from 200 to 10,000, respectively), which was applied to the raw gene-cell-barcode matrix.
UMI count for a gene in each cell was log-normalized to TPM-like values and then finally used in the scale of log2 (TPM+1), as previously described.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files representing: UMI counts (Lung_Cancer_raw_UMI_matrix.txt); normalized data as described above (Lung_Cancer_normalized_log2TPM_matrix.txt)

source_name: Metastatic brain

growth_protocol: Single-cell suspensions of the collected tissues were prepared by mechanical dissociation and enzymatic digestion within 16 hours after the surgery without any in vitro culture.

extract_protocol:
Single cell isolation was differently performed following each sample conditions. (1) Tumour and distant normal lung tissue dissociation was performed using tumor dissociation kit (Miltenyi Biotech, Germany) following the manufacturer’s instruction. Briefly, tissue was cut into 2-4 mm pieces and transferred to C tube containing the enzyme mix (Enzyme H, R, and A in RPMI1640 media). GentleMACS programs; h_tumor_01, 02, and 02 were run with two 30 min incubation in the MACSmix tube rotator at 37 oC. (2) Normal lymph node tissue and biopsy samples of metastatic lymph node and lung tumour tissue were dissociated using Collagenase/Hyaluronidase and DNase I. The tissue was chopped into 2-4 mm pieces with a sterile scissor in a 35 mm dish and incubated in an enzyme solution (Collagenase/Hyaluronidase (STEMCELL Technologies, Vancouver, Canada) and DNase I (QIAGEN, Hilden, Germany) in RPMI1640 media) at 37 oC for 1 hour. Tissue pieces are re-mixed by gentle pipetting at an interval of 20 min during incubation. (3) Metastatic brain tissue was chopped into 2-4 mm pieces with a sterile scissor in a 100 mm dish and incubated in an enzyme solution (Collagenase (Gibco, Waltham, MA, USA), DNase1 (Roche,  Basel, Switzerland), and Dispase1 (Gibco, Waltham, MA, USA) in DMEM media) at 37 oC within 1 hour. Tissue pieces are re-mixed by gentle pipetting at an interval of 15 min during incubation. (4) Pleural fluids were transferred to a 50 ml tube and spun down at 300g.  The cell suspension was transferred into a new 50 ml (or 15 ml; for biopsy samples) tube through 70um strainer. The volume in the tube was readjusted to 50 ml (or 15ml) with RPMI1640 media and spun down to remove enzymes. The supernatant was aspirated out and the cell pellet was resuspended in 4 ml of RPMI1640 media and dead cells were removed by Ficoll-Paque PLUS (GE Healthcare, Chicago, IL, USA) separation.
Each cell suspension was subjected to 3’ single-cell RNA sequencing using the GemCode system (10x genomics, Pleasanton, CA, USA) with cell recovery target at 5000, following the manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq2500.

tag: patient id

tag: tumor stage

value: IV

tag: tissue origin abbrevation

value: mBrain

tag: lung cancer subtype

value: lung adenocarcinoma


title: NS_17


title: Non-human primate mTB infected granulomas and uninvolved lungs [28918_Array10]

tag: cell type


title: Non-human primate mTB infected granulomas and uninvolved lungs [28818_Array6]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29218_Array4]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29318_Array5]


title: NS_16

value: III


title: Non-human primate mTB infected granulomas and uninvolved lungs [28918_Array5]


title: NS_13


title: Non-human primate mTB infected granulomas and uninvolved lungs [29118_Array8]


title: NS_07


title: NS_06


title: NS_02


title: Non-human primate mTB infected granulomas and uninvolved lungs [28818_Array9]


title: EFFUSION_12

source_name: Pleural effusion

value: PE


title: Non-human primate mTB infected granulomas and uninvolved lungs [28918_Array4]


title: LN_12

source_name: Normal lymph node

value: I

value: nLN


title: EFFUSION_11


title: Non-human primate mTB infected granulomas and uninvolved lungs [29118_Array6]


title: NS_12


title: LN_11


title: LN_04


title: Non-human primate mTB infected granulomas and uninvolved lungs [28818_Array8]


title: NS_04


title: EBUS_15

source_name: Metastatic lymph node

value: mLN


title: LN_01

value: II


title: EBUS_13


title: EFFUSION_13


title: NS_03


title: Non-human primate mTB infected granulomas and uninvolved lungs [28918_Array2]


title: Non-human primate mTB infected granulomas and uninvolved lungs [29118_Array7]


title: LN_03


title: LN_07


title: LN_05


title: LN_08


title: EBUS_51


title: EBUS_28

source_name: Tumour lung

value: tL/B


title: Non-human primate mTB infected granulomas and uninvolved lungs [28818_Array7]


title: LN_06


title: EBUS_19


title: EBUS_12


title: Liver-6

status: Public on Feb 22 2020

city: Rochester

first: Walter

last: Park

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Base-calling was performed using Illumina’s RTA version 2.7.3
Sequencing reads were aligned to hg19 genome using Tophat v2
Normalized counts per million (CPM) values were calculated based on edgeR package
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file containing normalized CPM values for each sample

source_name: Liver

growth_protocol: Cultures were maintained at 37°C, 5% CO2 in a humidified incubator.  Cells were allowed to proliferate for approximately 2 weeks before being passaged.  The confluency measurements were done daily using the IncuCyte Live Cell Zoom analysis tool.

extract_protocol:
RNA extraction was with the TRIzol reagent (Invitrogen) and cleaned using he Rneasy Mini Kit (Qiagen)
TruSeq  v2

value: Mesenchymal Stromal Cell

value: Liver


title: EFFUSION_06


title: BRONCHO_11


title: Marrow-3

source_name: Bone Marrow

value: Bone Marrow


title: Liver-5


title: EBUS_10


title: EFFUSION_64


title: Liver-4


title: Adipose-1

source_name: Adipose

value: Adipose


title: Adipose-2


title: LN_02


title: BRONCHO_58


title: EBUS_49


title: Liver-2


title: Marrow-1


title: Adipose-3


title: EBUS_06


title: Marrow-2


title: Liver-3


title: Liver-1


title: ECMO_41

status: Public on Dec 31 2019

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: SAMPLE 32

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw signal data were normalized using quantile normalized by GenoStudio v2011.1 software

label: biotin

source_name: PBMC

label_protocol: cRNA were prepared with TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: course

value: Acute myocarditis

tag: age

value: F

tag: outcome

value: Success


title: ECMO_42

description: SAMPLE 33

value: Congestive heart failure

value: M


title: ECMO_35

description: SAMPLE 26

value: Dilated cardiomyopathy, DCMP

value: Failure


title: ECMO_37

description: SAMPLE 28


title: ECMO_33

description: SAMPLE 24


title: ECMO_20

description: SAMPLE 11

value: Acute myocardial infarction


title: ECMO_29

description: SAMPLE 20

value: Aortic dissection

value: failure


title: ECMO_25

description: SAMPLE 16

value: Dilated cardiomyopathy


title: ECMO_34

description: SAMPLE 25


title: ECMO_16

description: SAMPLE 8


title: ECMO_24

description: SAMPLE 15


title: ECMO_31

description: SAMPLE 22

value: Arrhythmia


title: ECMO_32

description: SAMPLE 23


title: ECMO_10

description: SAMPLE 4


title: ECMO_38

description: SAMPLE 29


title: ECMO_36

description: SAMPLE 27


title: ECMO_40

description: SAMPLE 31


title: ECMO_21

description: SAMPLE 12


title: ECMO_39

description: SAMPLE 30


title: ECMO_22

description: SAMPLE 13


title: ECMO_28

description: SAMPLE 19


title: H18_input_ChIP_R1

status: Public on Nov 27 2019

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
Reads were mapped using STAR (v.2.4.2a) for RNA-seq to galGal5. Read counts were obtained using subread (v.1.4.5) FeatureCounts. For ChIP-seq, reads were mapped using bowtie to gg5 genome
Differential Expression analysis was performed using DESeq2 R package. Diffbind package was used for ChIP-seq experiment
Genome_build: galGal5

growth_protocol: Fertilised wild-type chicken eggs were obtained from Henry Stewart & Co (Norfolk), staged according to Hamburger and Hamilton (1951) (24). All experiments were performed on chicken embryos younger than 12 days of development, and as such were not regulated by the Animals (Scientific Procedures) Act 1986.

extract_protocol:
FAC-sorted cells were washed with PBS and stored at 80°C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (Cat.#AM1931, ThermoFisher Scientific), the integrity was checked using Bioanalyser, and only samples with RIN>6 were used for analysis.  Bioin ChIP-seq was carried out using previously described protocol following crosslinking, sonication and library preparation
RNA-seq libraries were prepared using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Cat.#634889, Takara Bio Clontech) and sequenced using 40bp paired-end reads on Illumina NextSeq500. Biotin ChIP-seq libraries were prepared using MicroPlex library preparation kit v2 (Diagnode) and sequenced using 40 bp paired-end reads on Illumina NextSeq500 with a 75 cycle kit.

treatment_protocol: Dissected vagal regions from electroporated embryos were dissociated with dispase (1.5mg/ml in DMEM/10mM Hepes pH 7.5) at 37°C for 15min with intermittent pipetting to achieve a single cell suspension and 0.05% Trypsin at 37°C for a final 3min. The reaction was stopped and cells were resuspended in an excess of Hanks buffer. Cells were centrifuged at 500g for 10min and resuspended in Hanks buffer, passed through a 0.22mm filter and centrifuged at 750g for 10min, pelleted cells were resuspended in 500µl Hanks buffer. Fluorescent positive cells were sorted and collected using BD FACS-Aria Fusion.

tag: genotype/variation

value: Wild-type

tag: development

value: Embryo

value: Neural crest (E2+ cells)

value: Dissociation and FACS

value: E2:citrine electroporation at HH8

tag: amplification

tag: assay

value: Biotin ChIP-seq


title: Adipose tissue-resident CD45+, Adult_KD

status: Public on Sep 10 2019

city: New Haven

first: Emily

middle: L

last: Goldberg

state: CT

address: 310 Cedar Street

institute: Yale

description: KD

data_processing:
Demultiplexing, barcode processing, single-cell 3' counting was performed with Cell Ranger Single-Cell Software Suite v2.1.1
Alignment was performed using Cell Ranger
See detailed methods in Goldberg et al., Nature Metabolism 2019
Genome_build: mm10-2.1.0
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.
Supplementary_files_format_and_content: keto_clustering_data.tsv includes the cell cluster labels/barcode mapping.

source_name: tissue resident CD45+ cells from adipose tissue

extract_protocol: Single-cell libraries were prepared using standard 10x Genomics protocols.

tag: strain

tag: genotype

value: wt

tag: treatment

value: ketogenic diet (KD)

tag: tissue

value: adipose

value: adipose tissue-resident CD45+ cells


title: H18_tfap2B_ChIP_R2

value: MicroPlex library preparation kit v2 (Diagnode)


title: ECMO_26

description: SAMPLE 17

tag: gender

value: M

value: Failure


title: ECMO_14

description: SAMPLE 7

value: Acute myocardial infarction

value: Success


title: ECMO_23

description: SAMPLE 14

value: Congestive heart failure

value: F


title: ECMO_27

description: SAMPLE 18

value: Arrhythmia


title: ECMO_17

description: SAMPLE 9


title: ECMO_11

description: SAMPLE 5

value: Acute myocarditis


title: H18_tfap2B_ChIP_R1

value: Wild-type

value: Embryo

value: Neural crest (E2+ cells)


title: cerebellum_oxbs_60

status: Public on Mar 05 2019

type: genomic

city: Exeter

first: Katie

last: Lunnon

address: RILD Level 4, Barrack Road

department: Medical Research

institute: University of Exeter Medical School

description: whole blood taken from sample 6092

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol with the exception that 7ul of treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the final report files generated by Genome Studio (Illumina) software. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions. Pfilter function removed 15 samples and 38737 probes where 5% of sites had a detection p-value > 0.05

label: Cy5 and Cy3

source_name: cerebellum

label_protocol: 1μg DNA from each sample was treated with sodium BS and OxBS in parallel using the true-methyl CEGX 96 kit (CEGX, Cambridge, UK) according to the manufacturer’s standard protocol

extract_protocol: Genomic DNA was extracted from frozen 100mg postmortem brain samples using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.

tag: post-mortem diagnosis

value: Control

tag: age at death

tag: braak stage

value: II

tag: post-mortem interval(min)


title: cerebellum_bs_60

description: whole blood taken from sample 6182


title: Adipose tissue-resident CD45+, Adult_Chow

description: Chow

value: wt

value: control

tag: cell type


title: ECMO_8

description: SAMPLE 3

tag: course


title: TA muscle Ly6Clow macrophage day 2 after CTX rep 3

status: Public on Feb 01 2019

city: Debrecen

first: Nikolaos

last: Giannakis

address: Egyetem ter 1

department: Department of Biochemistry and Molecular  Biology

country: Hungary

institute: University of Debrecen

description:
Muscle_macrophages_neutrophils_after_CTX_normalised_counts.txt
[Ly6C lo, Day 2, CTX](normalized)

data_processing:
Alignment was performed  with TopHat v2.0.7 using default parameters.
Data analysis was performed using Strand NGS software, Version 2.8, Build 230243. © Strand Life Sciences, Bangalore, India
Read counts were calculated based on manufacturer's default parameters.
Normalisation of the read counts was performed with the Deseq method. The normalized counts are logtransformed  and baselined.This method is based on the paper ‘Differential expression analysis for sequence count data’ by  Simon Anders and Wolfgang Huber.
Changes in genes in the pairwise comparisions with FC>1.5 and p-value<0.05 were considered to be statistically significant.
Genome_build: mm10
Supplementary_files_format_and_content: normalised counts based on abundance measurements

source_name: TA muscle

extract_protocol:
Total RNA was isolated with TRIZOL reagent according to the manufacturer’s recommendation. 20ug glycogen (Ambion) was added as carrier for RNA ethanol precipitation
cDNA library for RNA-Seq was generated from 100ng-400ng total RNA using TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. Briefly poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, and then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.

treatment_protocol:
Mice were anaesthetized with isoflurane (adjusted flow rate or concentration to 1.5%) and 50 µl of cardiotoxin (12x10-6 M in PBS) (Latoxan) was injected in the tibialis anterior (TA) muscle. Muscles were recovered for flow cytometry analysis at day 4 post-injury or for muscle histology and IHC-Fr at days 0, 1, 2, 4 and 8 post-injury. TA muscles from CTX-injured animals were isolated and fascia of the TA was removed. Muscles were dissociated in RPMI containing 0.2% collagenase B (Roche Diagnostics GmbH) at 37°C for 1 hour and filtered through a 100 µm and a 40 µm filter. CD45+ cells were isolated using magnetic sorting (Miltenyi Biotec). For FACS, macrophages were treated with Fcγ receptor blocking antibodies and with 10% normal rat serum: normal mouse serum 1:1 mix, then stained with a combination of PE-conjugated anti-Ly6C antibody (HK1.4, eBioscience), APC-conjugated F4/80 antibody (BM8, eBioscience) and FITC-conjugated Ly6G antibody (1A8, Biolegend). Ly6Chigh F4/80low macrophages, Ly6Clow F4/80high macrophages and Ly6Ghigh Ly6Cint F4/80- neutrophils were quantified.
For the bone marrow derived macrophages and only: Bone marrow was flushed from the tibiae and femurs of 8-10 week old male C57BL/6J mice using a 25 gauge needle and DMEM media (ATCC) containing 10% FBS, 20 mM HEPES and 1% penicillin/streptomycin. Once isolated, the bone marrow was plated in this medium supplemented with 10 ng/ml M-CSF (macrophage colony-stimulating factor; Sigma). On day four of differentiation, the media was replenished with fresh media (containing M-CSF). After seven days, the cells were liberated using a cell scraper centrifuged and re-plated in media lacking M-CSF. After 24 hours, cells were exposed to 10 nM RvD2 (Cayman Chemical) for four hours then collected in Buffer RLT (Qiagen) with 10 µl/ml 2-mercaptoethanol.

value: muscle

value: Ly6Clow macrophages

tag: time point

value: day 2

tag: agent

value: CTX

tag: age

value: adult 2-4 months old

tag: Sex

value: male


title: TA muscle Ly6Clow macrophage day 4 after CTX rep 1

description:
Muscle_macrophages_neutrophils_after_CTX_normalised_counts.txt
[Ly6C lo, Day 4, CTX](normalized)

value: day 4


title: ECMO_19

description: SAMPLE 10

value: Acute myocardial infarction

value: M

tag: outcome

value: Success


title: TA muscle Ly6Clow macrophage day 4 after CTX rep 3


title: ECMO_13

description: SAMPLE 6

value: Failure


title: ECMO_7

description: SAMPLE 2

value: Acute myocarditis


title: TA muscle Ly6Chigh macrophage day 2 after CTX rep 1

description:
Muscle_macrophages_neutrophils_after_CTX_normalised_counts.txt
[Ly6C hi, Day 2, CTX](normalized)

value: Ly6Chigh macrophages


title: TA muscle Ly6Chigh macrophage day 2 after CTX rep 2


title: TA muscle Ly6Chigh macrophage day 2 after CTX rep 3


title: TA muscle Ly6Clow macrophage day 2 after CTX rep 1


title: B6_H3K4me3_PRDM9-KO_ChIPSeq

status: Public on Mar 07 2019

first: Mary Ann

last: Handel

description: prdm9 mutant: It is a single amino acid substitution (Glu364Lys) that we induced via CRISPR/Cas9 gene editing. The mutant protein is has severely hypomorphic histone methyltransferase activity.

data_processing:
ChIP-Seq reads were aligned to the mm10 genome assembly using BWA v0.5.10
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v2.0 -> AllPeaks bed files
Bedtools Intersect was used to find the subset of peaks at Prdm9-dom2 recombination hotspots; options: -wb -f 0.20 -r; -> HotspotPeaks bed files
Genome_build: mm10
Supplementary_files_format_and_content: bed or bedGraph

source_name: spermatocytes

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Nuclei were fixed with 1% formaldehyde, and chromatin was fragmented by Mnase digestion. After high-speed spin soluble chromatin was removed and used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

value: spermatocytes

value: 14 days post-partum

value: prdm9 Glu364Lys mutant

tag: chip antibody

value: anti-H3K4me3; vendor:EMD Millipore; Cat# 07-473)


title: wt_GFPpos_72hpf_rep1

status: Public on Jan 10 2019

city: Warsaw

first: Michal

last: Pawlak

address: Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology

data_processing:
Illumina adapters removal was performed by using Trimmomatic (0.36) (Bolger et al. 2014)
Reads matching ribosomal RNA were removed by using rRNAdust (Hasegawa et al. 2014)
Reads quality filtering was performed by SAMtools (1.4) (Li et al. 2009) with parameters -b -h -f 3 -F 3340 -q 30
RNA-seq reads were aligned to zebrafish reference genome (GRCz10) using STAR (2.5) (Dobin et al. 2013)
Gene counts were calculated by using R (GenomicRanges Bioconductor package) and tranformed to regularized-logarithm (DESeq2 Bioconductor package)
Genome_build: GRCz10
Supplementary_files_format_and_content: RNAseq_rld_cardio_Pawlak_et_al_2018.csv: comma-separated file containing normalized read counts (rlog) of Ensembl-annotated genes organized in columns for each sample separately.
Supplementary_files_format_and_content: Pawlak_et_al_RNAseq_raw_counts.csv: comma-separated file containing raw counts.

organism: Danio rerio

source_name: FACS-sorted embryo cells

growth_protocol: Embryos were grown in embryo medium at 28°C, staged according to standard morphological criteria (Kimmel et al. 1995), and harvested at three different developmental stages: prim-5 (24 hpf), long-pec (48 hpf) and protruding-mouth (72 hpf).

extract_protocol:
Trizol-based Direct-Zol with DNAse treatment (Zymo Research)
Sequencing libraries were performed from total RNA by using SMARTer low input RNA Kit (Clontech), according to manufacturer protocol.

value: FACS-sorted embryo cells

tag: developmental stage

value: 72 hpf

tag: gfp status

value: GFP positive

tag: genetic background

value: wild type


title: tbx5_GFPpos_72hpf_rep2

tag: tissue


title: gata5_GFPpos_72hpf_rep2


title: tbx5_GFPpos_72hpf_rep1


title: gata5_GFPneg_72hpf_rep1

value: GFP negative


title: hand2_GFPpos_72hpf_rep2


title: TA muscle Ly6Clow macrophage day 2 after CTX rep 2

tag: strain

value: muscle

value: Ly6Clow macrophages

value: day 2

value: CTX

value: adult 2-4 months old

value: male


title: hand2_GFPneg_72hpf_rep1


title: wt_GFPpos_72hpf_rep2


title: tbx5_GFPneg_72hpf_rep1


title: gata5_GFPpos_72hpf_rep1


title: ECMO_6

description: SAMPLE 1

value: Acute myocarditis

tag: gender

value: F

value: Success


title: wt_GFPpos_48hpf_rep2

value: 48 hpf


title: wt_GFPpos_48hpf_rep1


title: hand2_GFPpos_72hpf_rep1


title: wt_GFPpos_24hpf_rep2

value: 24 hpf


title: wt_GFPneg_24hpf_rep1


title: wt_GFPpos_24hpf_rep1


title: wt_GFPneg_72hpf_rep1


title: wt_GFPneg_48hpf_rep1


title: Wild-type 4

status: Public on Apr 16 2018

city: Singapore

first: Hao

address: Science Drive 4

country: Singapore

institute: National University of Singapore

data_processing:
Alignment: TopHat v2.0.9 using default settings; expression levels: Cufflinks v2.1.1 using default settings
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Arabidopsis thaliana

source_name: Whole plant

growth_protocol: Arabidopsis thaliana plants were grown on MS plates in growth chambers under long day conditions (16 hr light/8 hr dark) at 23°C ± 2°C.

extract_protocol:
3-week-old wild-type  seedlings grown on MS plates were harvested and total RNA were extracted using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was removed by Ribo-zeroTM Rrna Removal Kit (Epicentre),
NEBNext® UltraTM Directional RNA Library Prep Kit for illumina® (NEB) was used to construct the library and sequencing was done on Illumina Hiseq 2500 platform.

tag: genotype/variation