title: microRNA-seq from forebrain (ENCLB654HPT)

description:
https://www.encodeproject.org/experiments/ENCSR509NLH/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR509NLH
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB654HPT
size range: <30

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (10.5 days)

value: forebrain

value: tissue

value: Forebrain from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS152ONW at ENCODE; https://www.encodeproject.org/ENCBS152ONW/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA-seq from forebrain (ENCLB379IHE)

status: Public on Oct 23 2017

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/ENCSR509NLH/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR509NLH
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB379IHE
size range: <30

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

extract_protocol: not provided

tag: description

value: Forebrain from 51 embryonic 10.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

tag: Sex

tag: health state

tag: lab

tag: link

value: ENCBS790BBA at ENCODE; https://www.encodeproject.org/ENCBS790BBA/


title: microRNA-seq from midbrain (ENCLB935KTR)

description:
https://www.encodeproject.org/experiments/ENCSR591SJC/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse midbrain
experiment encode accession: ENCSR591SJC
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB935KTR
size range: <30

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (12.5 days)

value: midbrain

value: Midbrain from 120 embryonic 12.5 day mice

value: ENCBS309WCU at ENCODE; https://www.encodeproject.org/ENCBS309WCU/


title: ChIP-seq from breast epithelium (ENCLB101GUR)

description:
https://www.encodeproject.org/experiments/ENCSR501LEH/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on mammary gland
experiment encode accession: ENCSR501LEH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR226SNN
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB101GUR

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens breast epithelium tissue male adult (54 years)

extract_protocol: extraction method: see document

tag: antibody

value: breast epithelium

value: male

value: Richard Myers, HAIB

value: 54 year

value: adult

value: ENCBS173VHR at ENCODE; https://www.encodeproject.org/ENCBS173VHR/

value: derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/3a8c7636-3c0d-4a8c-b793-17502ed1acc2/@@download/attachment/82375.svs


title: microRNA-seq from liver (ENCLB588RJB)

description:
https://www.encodeproject.org/experiments/ENCSR453ESQ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse liver
experiment encode accession: ENCSR453ESQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB588RJB
size range: <30

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (12.5 days)

value: liver

value: tissue

value: Liver from 88 embryonic 12.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS479VPX at ENCODE; https://www.encodeproject.org/ENCBS479VPX/


title: USC-TI-3

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
cells were cultured for 24 h prior to analysis
counts.raw.csv.gz
counts.norm.csv.gz

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
HTSeq package was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: uterus of progesterone-treated, non-pregnant mouse

growth_protocol: Cells were cultured for a total of 24 h prior to analysis.

extract_protocol:
RNeasy Mini Plus reagents (Qiagen) and QIAshredder columns (Qiagen).
Poly(A)+ RNA was enriched using magnetic oligo(dT) containing beads (Invitrogen). cDNA was prepared and strand-specific libraries were constructed using the dUTP method.

treatment_protocol: When indicated, cells were treated with cytokines for the last 6 hours of the 24 culture period.

tag: strain

tag: tissue/cell

value: purified stromal cells from entire undecidualized uterus

tag: embryonic day

tag: treatment

value: TNF-alpha plus IFN-gamma


title: microRNA-seq from limb (ENCLB785EQF)

description:
https://www.encodeproject.org/experiments/ENCSR618GKP/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse limb
experiment encode accession: ENCSR618GKP
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB785EQF
size range: <30

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (12.5 days)

value: limb

value: Limb from 88 embryonic 12.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS731DGJ at ENCODE; https://www.encodeproject.org/ENCBS731DGJ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from HepG2 (ENCLB971FYE)

description:
https://www.encodeproject.org/experiments/ENCSR382PVA/
***************
biological replicate number: 2
technical replicate number: 1
description: GTF2F1 ChIP-seq in HepG2
experiment encode accession: ENCSR382PVA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB971FYE
size range: 200-400

source_name: Homo sapiens HepG2 immortalized cell line

tag: line

value: immortalized cell line

value: GTF2F1 ChIP-seq in HepG2

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS989AFC at ENCODE; https://www.encodeproject.org/ENCBS989AFC/

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


title: USC-3

value: untreated


title: USC-TI-2

value: purified stromal cells from entire undecidualized uterus


title: microRNA-seq from embryonic facial prominence (ENCLB392SJR)

description:
https://www.encodeproject.org/experiments/ENCSR549EOE/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR549EOE
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB392SJR
size range: <30

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (10.5 days)

value: embryonic facial prominence

value: tissue

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/


title: RT112-R4 BGJ_7days [lab: Hammerman-DFCI]

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using bowtie2 v2.2.1 and quantified using RSEM v1.2.12.
hg19 prepared using RSEM with bowtie2 and transcript annotations from Gencode release12.
Genome_build: hg19
Supplementary_files_format_and_content: matrix file with expression counts for each sample

source_name: Urinary bladder carcinoma

growth_protocol: Cells were cultured in RPMI media, supplemented with 10% FBS, and penicillin/streptomycin/L-glutamine. Cells were cultured at 37 °C in a humidified chamber in the presence of 5% CO2.

extract_protocol:
RNA was isolated using the RNeasy micro kit (Qiagen). cDNA libraries were prepared using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. Library integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent).
RNeasy micro kit (Qiagen)

treatment_protocol: Cells were treated with BGJ (1 uM) for 7D prior to harvesting

tag: cell line

tag: tissue

value: bladder

tag: drug

tag: concentration

value: 1 uM

tag: treatment duration


title: RT112-T4 THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (100nM) for 48h prior to harvesting


title: RT112-T3 THZ1 [lab: Hammerman-DFCI]


title: microRNA-seq from limb (ENCLB919MMW)

description:
https://www.encodeproject.org/experiments/ENCSR618GKP/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 12.5 day mouse limb
experiment encode accession: ENCSR618GKP
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-08-15
lab: Ali Mortazavi, UCI
library encode accession: ENCLB919MMW
size range: <30

value: limb

tag: description

value: Limb from 68 embryonic 12.5 day mice

tag: biosample encode accession

tag: age

value: Len Pennacchio, LBNL

value: ENCBS313XRY at ENCODE; https://www.encodeproject.org/ENCBS313XRY/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from HepG2 (ENCLB799DHF)

description:
https://www.encodeproject.org/experiments/ENCSR514EOE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR514EOE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR055XHN
encode release date: 2017-08-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB799DHF
size range: 200-600
nucleic acid starting quantity: 1.32
nucleic acid starting quantity units: ng

value: immortalized cell line

value: Hep G2 (Hepatocellular carcinoma, human) Hep G2 is a perpetual cell line which was derived from the liver tissue of a 15-year-old Caucasian American male with a well-differentiated hepatocellular carcinoma. These cells are epithelial in morphology, have a model chromosome number of 55, and are not tumorigenic in nude mice.

tag: dev stage

value: child

tag: Sex

value: male

value: 15 year

tag: health state

value: hepatocellular carcinoma

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS467HWM at ENCODE; https://www.encodeproject.org/ENCBS467HWM/

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


title: ChIP-seq from K562 (ENCLB743KTG)

description:
https://www.encodeproject.org/experiments/ENCSR594BNR/
***************
biological replicate number: 1
technical replicate number: 1
description: HNRNPL ChIP-seq in K562
experiment encode accession: ENCSR594BNR
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR436OZQ
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB743KTG
size range: 200-400

source_name: Homo sapiens K562 immortalized cell line

tag: antibody

value: HNRNPL

value: HNRNPL ChIP-seq in K562

value: female

tag: lab

value: Xiang-Dong Fu, UCSD

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

tag: link

value: ENCBS779EKH at ENCODE; https://www.encodeproject.org/ENCBS779EKH/

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


title: USC-2

tag: strain

tag: tissue/cell

value: purified stromal cells from entire undecidualized uterus

tag: embryonic day

tag: treatment

value: untreated


title: RT112-R3 BGJ_7days [lab: Hammerman-DFCI]

tag: cell line

tag: tissue

value: bladder

tag: drug

value: 1 uM


title: USC-1


title: ChIP-seq from HepG2 (ENCLB464NZY)

description:
https://www.encodeproject.org/experiments/ENCSR356ECR/
***************
biological replicate number: 2
technical replicate number: 1
description: RBM22 ChIP-seq in HepG2
experiment encode accession: ENCSR356ECR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867VPL
encode release date: 2017-08-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB464NZY
size range: 200-400

tag: line

value: immortalized cell line

tag: description

value: RBM22 ChIP-seq in HepG2

value: male

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS018BAD at ENCODE; https://www.encodeproject.org/ENCBS018BAD/

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


title: E7-MSC-TI-3

source_name: pregnant uterus, myometrium

value: purified myometrial stromal cells from implantation sites

value: TNF-alpha plus IFN-gamma


title: RT112-R1 BGJ_7days [lab: Hammerman-DFCI]

tag: concentration

tag: treatment duration


title: ChIP-seq from K562 (ENCLB217ZXW)

description:
https://www.encodeproject.org/experiments/ENCSR440VKE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ADNP ChIP-seq on human K562
experiment encode accession: ENCSR440VKE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR845MXF
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB217ZXW
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ADNP fusion protein

value: eGFP-ADNP

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

tag: biosample encode accession

tag: Sex

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

tag: age

value: 53 year

tag: dev stage

value: adult

value: ENCBS037KCN at ENCODE; https://www.encodeproject.org/ENCBS037KCN/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ75; http://web.expasy.org/cellosaurus/CVCL_GZ75


title: E7-MSC-3

value: untreated


title: RT112-T2 THZ1 [lab: Hammerman-DFCI]

value: bladder


title: ChIP-seq from right atrium auricular region (ENCLB602MDC)

description:
https://www.encodeproject.org/experiments/ENCSR368ORV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR368ORV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR195BZZ
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB602MDC
size range: 200-600

source_name: Homo sapiens right atrium auricular region tissue female adult (53 years)

tag: antibody

value: right atrium auricular region

value: tissue

value: EnTEX:Heart - Atrial Appendage

tag: lab

value: Bradley Bernstein, Broad

value: ENCBS493WOF at ENCODE; https://www.encodeproject.org/ENCBS493WOF/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: E15-MSC-3

tag: strain

value: purified myometrial stromal cells from implantation sites


title: ChIP-seq from HepG2 (ENCLB047HAW)

description:
https://www.encodeproject.org/experiments/ENCSR514EOE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR514EOE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR055XHN
encode release date: 2017-08-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB047HAW
size range: 200-600
nucleic acid starting quantity: 16.02
nucleic acid starting quantity units: ng

value: immortalized cell line

value: Hep G2 (Hepatocellular carcinoma, human) Hep G2 is a perpetual cell line which was derived from the liver tissue of a 15-year-old Caucasian American male with a well-differentiated hepatocellular carcinoma. These cells are epithelial in morphology, have a model chromosome number of 55, and are not tumorigenic in nude mice.

value: child

value: male

value: 15 year

tag: health state

value: hepatocellular carcinoma

tag: passage number

tag: link

value: ENCBS777VZC at ENCODE; https://www.encodeproject.org/ENCBS777VZC/

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


title: E7-MSC-TI-2

tag: tissue/cell

tag: embryonic day

tag: treatment

value: TNF-alpha plus IFN-gamma


title: RT112-D2 DMSO [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO (0.1%) for 48h prior to harvesting

tag: cell line

tag: tissue

value: bladder

tag: drug

value: DMSO


title: ChIP-seq from K562 (ENCLB779JJT)

description:
https://www.encodeproject.org/experiments/ENCSR440VKE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ADNP ChIP-seq on human K562
experiment encode accession: ENCSR440VKE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR845MXF
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB779JJT
size range: 200-800

value: eGFP-ADNP

tag: line

tag: description

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

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS995QNX at ENCODE; https://www.encodeproject.org/ENCBS995QNX/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ75; http://web.expasy.org/cellosaurus/CVCL_GZ75


title: E15-MSC-2

value: purified myometrial stromal cells from implantation sites

value: untreated


title: ChIP-seq from K562 (ENCLB753FQL)

description:
https://www.encodeproject.org/experiments/ENCSR436OZQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR436OZQ
assay title: ChIP-seq
encode release date: 2017-02-13
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB753FQL
size range: 200-400

value: Control

value: immortalized cell line

value: Control ChIP-seq on K562 cells

tag: biosample encode accession

tag: Sex

value: Xiang-Dong Fu, UCSD

value: ENCBS354IWX at ENCODE; https://www.encodeproject.org/ENCBS354IWX/


title: E7-MSC-TI-1

value: TNF-alpha plus IFN-gamma


title: ChIP-seq from K562 (ENCLB704EMG)

description:
https://www.encodeproject.org/experiments/ENCSR436OZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR436OZQ
assay title: ChIP-seq
encode release date: 2017-02-13
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB704EMG
size range: 200-400

tag: age

tag: dev stage

value: ENCBS612SGW at ENCODE; https://www.encodeproject.org/ENCBS612SGW/


title: RT112-D1 DMSO [lab: Hammerman-DFCI]

value: bladder

value: DMSO

tag: concentration

tag: treatment duration


title: E7-MSC-1

tag: strain


title: USC-TI-1

value: purified stromal cells from entire undecidualized uterus


title: E15-MSC-1


title: RT112-C3 Combo_THZ1_BGJ [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 / BGJ (100nM / 1 uM) for 48h prior to harvesting

value: THZ1 / BGJ398


title: RT112-C2 Combo_THZ1_BGJ [lab: Hammerman-DFCI]


title: ChIP-seq from K562 (ENCLB013LPN)

description:
https://www.encodeproject.org/experiments/ENCSR641BSL/
***************
biological replicate number: 1
technical replicate number: 1
description: AGO1 ChIP-seq in K562
experiment encode accession: ENCSR641BSL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR932KYH
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB013LPN
size range: 200-400

tag: antibody

value: AGO1 ChIP-seq in K562

value: female

tag: lab

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS190WBQ at ENCODE; https://www.encodeproject.org/ENCBS190WBQ/


title: Hi-C from LNCaP clone FGC (ENCLB191OGC)

description:
https://www.encodeproject.org/experiments/ENCSR346DCU/
***************
biological replicate number: 1
technical replicate number: 1
description: HiC experiment done on LNCaP clone FGC
experiment encode accession: ENCSR346DCU
assay title: Hi-C
assembly: hg19
encode release date: 2016-05-13
lab: Job Dekker, UMass
library encode accession: ENCLB191OGC
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens LNCaP clone FGC immortalized cell line

value: LNCaP clone FGC

value: prostate adenocarcinoma, LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma. - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.)

value: male

value: John Stamatoyannopoulos, UW

value: prostate adenocarcinoma

value: 50 year

tag: link

value: ENCBS235TSM at ENCODE; https://www.encodeproject.org/ENCBS235TSM/

value: derived from ENCODE donor ENCDO000ACX; https://www.encodeproject.org/ENCDO000ACX/

value: ENCODE dbxrefs Cellosaurus CVCL_1379; http://web.expasy.org/cellosaurus/CVCL_1379

value: ENCODE dbxrefs LNCaP; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=LNCaP


title: E15-DSC-3

source_name: pregnant uterus, decidua

tag: tissue/cell

value: purified decidual stromal cells from implantation sites

tag: embryonic day

tag: treatment

value: untreated


title: E7-DSC-3


title: E7-DSC-TI-2

value: TNF-alpha plus IFN-gamma


title: RT112-C1 Combo_THZ1_BGJ [lab: Hammerman-DFCI]

tag: cell line

tag: tissue

value: bladder

tag: drug

value: THZ1 / BGJ398


title: E7-DSC-2


title: RT112-D3 DMSO [lab: Hammerman-DFCI]

value: DMSO


title: Hi-C from LNCaP clone FGC (ENCLB473XWD)

description:
https://www.encodeproject.org/experiments/ENCSR346DCU/
***************
biological replicate number: 2
technical replicate number: 1
description: HiC experiment done on LNCaP clone FGC
experiment encode accession: ENCSR346DCU
assay title: Hi-C
assembly: hg19
encode release date: 2016-05-13
lab: Job Dekker, UMass
library encode accession: ENCLB473XWD

tag: line

value: immortalized cell line

tag: description

tag: biosample encode accession

value: adult

value: ENCBS418ENC at ENCODE; https://www.encodeproject.org/ENCBS418ENC/


title: RT112-B4 BGJ [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with BGJ (1 uM) for 48h prior to harvesting

value: 1 uM


title: E7-DSC-TI-1

description:
cells were cultured for 24 h prior to analysis
counts.raw.csv.gz
counts.norm.csv.gz


title: E15-DSC-2


title: E7-DSC-1


title: E15-DSC-1


title: E7-MSC-2

value: purified myometrial stromal cells from implantation sites


title: E7-DSC-TI-3


title: E7-myo-1-input

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Reads were aligned to the mouse genome (build mm10/GRCm38) with Bowtie 2 using local alignment.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
MACS was utilized to generate pileup signal file and perform peak calling for each replicate.
Genome_build: mm10

extract_protocol:
Histone-DNA complexes were immuoprecipitated from sonicated nuclei.
Libraries were prepared using the Illumina TruSeq system and PCR amplification.

value: whole myometrium from implantation sites

tag: ChIP

value: input


title: RT112-B2 BGJ [lab: Hammerman-DFCI]

tag: concentration


title: PC9-T4 THZ1 [lab: Hammerman-DFCI]

source_name: Lung Adenocarcinoma

value: Lung

tag: treatment duration


title: ChIP-seq from HepG2 (ENCLB801TCQ)

description:
https://www.encodeproject.org/experiments/ENCSR315JJE/
***************
biological replicate number: 2
technical replicate number: 1
description: HNRNPL ChIP-seq in HepG2
experiment encode accession: ENCSR315JJE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB801TCQ
size range: 200-400

value: HNRNPL

value: HNRNPL ChIP-seq in HepG2

tag: Sex

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

tag: age

value: 15 year

tag: dev stage

value: child

value: ENCBS269MQV at ENCODE; https://www.encodeproject.org/ENCBS269MQV/

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


title: ChIP-seq from GM12878 (ENCLB674CRX)

description:
https://www.encodeproject.org/experiments/ENCSR330OEO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR330OEO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2017-08-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB674CRX
size range: 200-600
nucleic acid starting quantity: 22.2
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

tag: antibody

value: immortalized cell line

tag: passage number

tag: lab

value: Bradley Bernstein, Broad

value: unknown

tag: health state

value: female

value: ENCBS155GIM at ENCODE; https://www.encodeproject.org/ENCBS155GIM/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: ChIP-seq from K562 (ENCLB406WJW)

description:
https://www.encodeproject.org/experiments/ENCSR641BSL/
***************
biological replicate number: 2
technical replicate number: 1
description: AGO1 ChIP-seq in K562
experiment encode accession: ENCSR641BSL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR932KYH
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB406WJW
size range: 200-400

value: AGO1 ChIP-seq in K562

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

tag: link

value: ENCBS542KXR at ENCODE; https://www.encodeproject.org/ENCBS542KXR/

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


title: RT112-B1 BGJ [lab: Hammerman-DFCI]

tag: cell line

value: bladder

value: 1 uM


title: E7-myo-1-H3K27me3

tag: strain

tag: tissue/cell

value: whole myometrium from implantation sites

tag: embryonic day


title: E7-MSC-3-input

description: cells were cultured for 24 h prior to analysis

source_name: artificially decidualized uterus, myometrium

value: purified myometrial stromal cells

value: input


title: ChIP-seq from GM12878 (ENCLB774RSM)

description:
https://www.encodeproject.org/experiments/ENCSR330OEO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR330OEO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2017-08-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB774RSM
size range: 200-600
nucleic acid starting quantity: 6.4
nucleic acid starting quantity units: ng

tag: line

value: immortalized cell line

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/


title: E7-myo-2-input


title: PC9-T3 THZ1 [lab: Hammerman-DFCI]

tag: tissue

value: Lung

tag: drug


title: ChIP-seq from K562 (ENCLB483DXU)

description:
https://www.encodeproject.org/experiments/ENCSR311ULL/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-GABPA tagged K562 cell line.
experiment encode accession: ENCSR311ULL
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB483DXU
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-GABPA fusion protein

value: Control

tag: description

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

tag: biosample encode accession

value: female

value: Kevin White, UChicago

value: ENCBS164UBJ at ENCODE; https://www.encodeproject.org/ENCBS164UBJ/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ86; http://web.expasy.org/cellosaurus/CVCL_GZ86


title: E7-MSC-1-input

tag: ChIP


title: E7-MSC-2-input


title: PC9-T2 THZ1 [lab: Hammerman-DFCI]

tag: concentration

tag: treatment duration


title: E7-MSC-3-H3K27me3


title: ChIP-seq from K562 (ENCLB361LGY)

description:
https://www.encodeproject.org/experiments/ENCSR414HEF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF83 tagged K562 cell line.
experiment encode accession: ENCSR414HEF
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB361LGY
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZNF83 fusion protein

tag: antibody

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF83

tag: Sex

value: chronic myelogenous leukemia (CML)

tag: age

value: 53 year

tag: dev stage

value: adult

value: ENCBS285PHZ at ENCODE; https://www.encodeproject.org/ENCBS285PHZ/

value: ENCODE dbxrefs Cellosaurus CVCL_HA10; http://web.expasy.org/cellosaurus/CVCL_HA10


title: ChIP-seq from HepG2 (ENCLB978JFA)

description:
https://www.encodeproject.org/experiments/ENCSR315JJE/
***************
biological replicate number: 1
technical replicate number: 1
description: HNRNPL ChIP-seq in HepG2
experiment encode accession: ENCSR315JJE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB978JFA
size range: 200-400

value: HNRNPL

value: HNRNPL ChIP-seq in HepG2

value: male

tag: lab

value: Xiang-Dong Fu, UCSD

tag: health state

value: hepatocellular carcinoma

value: 15 year

value: child

tag: link

value: ENCBS619EOB at ENCODE; https://www.encodeproject.org/ENCBS619EOB/

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


title: E7-MSC-2-H3K27me3

tag: strain

tag: tissue/cell

value: purified myometrial stromal cells


title: PC9-P4 Erlo_7days [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Erlotinib (1 uM) for 7D prior to harvesting

tag: cell line

value: Lung

value: Erlotinib

value: 1 uM


title: 26_RT112 RTKi_7d_input [lab: Hammerman-DFCI]

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

growth_protocol: Cells were grown in RPMI Medium, 10%FBS, 1% penn/strep at 37 degrees and 5% CO2.  Cells were maintained between 40-90% confluency.

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

treatment_protocol: Cells were treated with DMSO for 7 days prior to cross linking with formaldehyde.

tag: chip antibody

tag: tissue

value: bladder

value: BGJ

tag: cell number

value: 50 million


title: E7-iis-3-input

source_name: pregnant uterus, inter-implantation sites

value: whole tissue from inter-implantation sites

tag: embryonic day

value: input


title: E7-MSC-1-H3K27me3

tag: ChIP


title: PC9-P3 Erlo_7days [lab: Hammerman-DFCI]

tag: drug

tag: concentration


title: E7-myo-2-H3K27me3

value: whole myometrium from implantation sites


title: E7-iis-3-H3K27me3


title: 25_RT112 DMSO_7d_input [lab: Hammerman-DFCI]

value: DMSO

tag: treatment duration

value: 48h, but comparison is 7D


title: E7-iis-2-input


title: PC9-E4 Erlo [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Erlotinib (1 uM) for 48h prior to harvesting


title: 24_PC9 RTKi_7d_input [lab: Hammerman-DFCI]

source_name: Adenocarcinoma

growth_protocol: PC9 cells were cultured in RPMI media, supplemented with 10% FBS, and penicillin/streptomycin/L-glutamine. Cells were cultured at 37 ÃÂ°C in a humidified chamber in the presence of 5% CO2.


title: PC9-P2 Erlo_7days [lab: Hammerman-DFCI]


title: 23_PC9 DMSO_7d_input [lab: Hammerman-DFCI]


title: E7-iis-1-input


title: E7-iis-2-H3K27me3


title: PC9-E3 Erlo [lab: Hammerman-DFCI]


title: 32_N87 RTKi_7d_input [lab: Hammerman-DFCI]

source_name: Gastric Cancer

growth_protocol: Cells were grown in RPMI Medium, 10%FBS, 1% penn/strep at 37 degrees and 5% CO2. Cells were maintained between 40-90% confluency.

treatment_protocol: Cells were treated with Lapatinib (100 nM) for 7 days prior to cross linking with formaldehyde.

value: Stomach

value: Lapatinib


title: E7-iis-1-H3K27me3


title: E15-MSC-3-input

value: purified myometrial stromal cells from implantation sites


title: E15-MSC-2-input


title: PC9-E2 Erlo [lab: Hammerman-DFCI]


title: E15-MSC-3-H3K27me3


title: E15-MSC-1-input


title: PC9-D4 DMSO [lab: Hammerman-DFCI]


title: E15-MSC-2-H3K27me3


title: PC9-D3 DMSO [lab: Hammerman-DFCI]


title: 27_H3122 DMSO_7d_input [lab: Hammerman-DFCI]


title: E15-DSC-3-input

value: purified decidual stromal cells from implantation sites


title: 31_N87 DMSO_7d_input [lab: Hammerman-DFCI]


title: E15-MSC-1-H3K27me3


title: E15-DSC-3-H3K27me3


title: E15-DSC-2-input


title: 28_H3122 RTKi_7d_input [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Crizotinib (250 nM) for 7 days prior to cross linking with formaldehyde.

value: Crizotinib


title: PC9-D2 DMSO [lab: Hammerman-DFCI]


title: 29_A549 DMSO_7d_input [lab: Hammerman-DFCI]


title: E15-DSC-1-input


title: E15-DSC-2-H3K27me3


title: PC9-C3 Combo_THZ1_Erlo [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Erlotinib / THZ1 (1 uM / 100nM) for 48h prior to harvesting

value: Erlotinib / THZ1


title: 30_A549 RTKi_7d_input [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated 200 nM GSK1120212 for 7 days prior to cross linking with formaldehyde.

value: Lung


title: E7-DSC-3-input

source_name: artificially decidualized uterus, decidua

value: purified decidual stromal cells


title: E7-DSC-1-input


title: E15-DSC-1-H3K27me3


title: PC9-C2 Combo_THZ1_Erlo [lab: Hammerman-DFCI]


title: 22_A375 RTKi_7d_input [lab: Hammerman-DFCI]

source_name: Melanoma

growth_protocol: A375 cells were grown in DMEM, 10% FBS, PSG at 37 degrees and 5% CO2. Cells were maintained between 40-90% confluency.

treatment_protocol: Cells were treated with Vemurafenib for 7 days prior to cross linking with formaldehyde.

value: Skin

value: Vemurafenib

value: 1 uM


title: E7-DSC-2-input


title: 21_A375 DMSO_7d_input [lab: Hammerman-DFCI]

value: 50 million


title: PC9-C1 Combo_THZ1_Erlo [lab: Hammerman-DFCI]


title: E7-dec-2-input

value: whole decidua from implantation sites


title: E7-DSC-3-H3K27me3


title: N87-T4 THZ1 [lab: Hammerman-DFCI]

source_name: Gastric Carcinoma

treatment_protocol: Cells were treated with THZ1 (25 nM) for 48h prior to harvesting

value: 25 nM


title: N87-T3 THZ1 [lab: Hammerman-DFCI]


title: E7-DSC-2-H3K27me3


title: 10_RT112 RTKi_H3K27Ac [lab: Hammerman-DFCI]

source_name: Urinary bladder carcinoma

growth_protocol: Cells were grown in RPMI, 10% FBS,1% PSG at 37 degrees and 5% CO2.  Cells were maintained between 40-90% confluency.

treatment_protocol: Cells were treated with 1 uM BGJ398 for 7 days and then cells were cross linked.

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

value: bladder

value: BGJ


title: E7-dec-3-input

value: input


title: N87-T2 THZ1 [lab: Hammerman-DFCI]

value: Stomach


title: E7-dec-3-H3K27me3


title: E7-dec-2-H3K27me3


title: E7-dec-1-input


title: E7-dec-1-H3K27me3


title: 12_H3122 RTKi_H3K27Ac [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Crizotinib (250 nM)  for 7 days prior to cross linking with formaldehyde.


title: SC1_6h

city: xi'an

first: Zhiying

last: Ai

state: shannxi

address: No.3 Taicheng Road, Yangling

country: China

institute: Northwest A&F University (NWAFU)

description: Small RNA sequencing

data_processing:
Basecalls performed using Perl package developed by BGI
We will get rid of some contaminant reads from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
The data is processed by the following steps: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using …; Scores represent …

source_name: J1 mESC, SC1, 6h

growth_protocol: The J1 mouse embryonic stem cell line purchased from ATCC (Manassas, VA, USA) was gelatin adapted and grown on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF (ESGRO, Millipore, USA).

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: J1 mESCs maintained in medium containing 1000 U/mL LIF and treated by 1 μΜ SC1 for 6h, cells treated with equal volume of DMSO were used as control.

tag: cell type

value: Embryonic stem cell


title: 14_A549 RTKi_H3K27Ac [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with GSK1120212 (200 nM) for 7 days prior to cross linking with formaldehyde.


title: N87-L3-7 Lap_7days [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Lapatinib (100nM) for 7D prior to harvesting

value: Lapatinib


title: 16_N87 RTKi_H3K27Ac [lab: Hammerman-DFCI]


title: N87-L3 Lap [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Lapatinib (100nM) for 48h prior to harvesting


title: DMSO - control

description: Small RNA sequencing

source_name: J1 mESC, DMSO, 6h


title: 6_A375 RTKi_H3K27Ac [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with 1 uM Vemurafenib for 7 days prior to cross linking with formaldehyde.


title: bulkRNAseq 72h (PDGFRA-/ CD24 T1)

city: Leiden

first: Stefan

last: Semrau

state: Zuid-Holland

address: Einsteinweg 55

department: Physics

country: Netherlands

institute: Leiden University

description: column name in processed data file: 72h PDGFRA-/CD24 T1

data_processing:
SCRB-seq and bulk RNA-seq read alignment: All second sequence reads were aligned to a reference database consisting of all mouse RefSeq mRNA sequences (obtained from the UCSC Genome Browser mm10 reference set: http://genome.ucsc.edu/), the mouse mm10 mitochondrial reference sequence and the ERCC RNA spike-in reference sequences using bwa version 0.7.4 4 with non-default parameter “-l 24”. Read pairs for which the second read aligned to a mouse RefSeq gene were kept for further analysis if 1) the initial six bases of the first read all had quality scores of at least 10 and corresponded exactly to a designed well-barcode and 2) the next ten bases of the first read (the UMI) all had quality scores of at least 30. Digital gene expression (DGE) profiles were then generated by counting, for each microplate well and RefSeq gene, the number of unique UMIs associated with that gene in that well. Python scripts implementing the alignment and DGE derivation are available from the authors upon request.
SMART-seq read alignment: Alignment of the reads and calculation of gene expression was done through the Tuxedo pipeline (Tophat, Cuffquand, Cuffnorm). Gene expression was expressed as reads per kilobase exon model per million mapped reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: "scrbseq" data files: each row is a gene, each column is a single cell. Expression values are given as unnormalized UMIs (unique molecular identifiers). "smartseq" data files: each row is a gene, each column is a single cell. Expression values are given as unnormalized RPKM. "bulkRNAseq.txt" : each row is a gene, each column is a different experimental condition. Expression values are given as unnormalized UMIs (unique molecular identifiers).

source_name: mouse ES cells

growth_protocol: E14 mouse embryonic stem cells were grown in modified 2i medium: DMEM/F12 (Life technologies) supplemented with 0.5x N2 supplement, 0.5x B27 supplement, 4mM L-glutamine (Gibco), 20 µg/ml human insulin (Sigma-Aldrich), 1x 100U/ml penicillin/streptomycin (Gibco), 1x MEM Non-Essential Amino Acids (Gibco), 7 µl 2-Mercaptoethanol (Sigma-Aldrich), 1 µM MEK inhibitor (PD0325901,Stemgent), 3 µM GSK3 inhibitor (CHIR99021, Stemgent), 1000 U/ml mouse LIF (ESGRO). Cells were passaged every other day with Accutase (Life technologies) and replated on gelatin coated tissue culture plates (Cellstar, Greiner bio-one).

extract_protocol:
SCRB-seq: For each differentiation time point cells were harvested and medium removed by spinning for 5 min at 1000 rpm. RNA was stabilized by immediately resuspending the pelleted cells in RNAprotect Cell Reagent (Qiagen) and RNaseOUT Recombinant Ribonuclease Inhibitor (Life Technologies) at a 1:1000 dilution. Just prior to fluorescence-actived cell sorting (FACS), the cells were diluted in PBS and stained for viability using Hoechst 33342 (Life Technologies). 384-well SBS capture plates were filled with 5μl of a 1:500 dilution of Phusion HF buffer (New England Biolabs) in water and individual cells were then sorted into each well using a FACSAria II flow cytometer (BD Biosciences) based on Hoechst DNA staining. After sorting, the plates were immediately sealed, spun down, cooled on dry ice and then stored at -80°C. SMART-seq: The single-cell SMART-seq2 libraries were prepared according to the SMART-seq2 protocol with some modifications. Briefly, total RNA from single cells sorted in lysis buffer was purified using RNA-SPRI beads. Bulk RNA-seq: Populations of sorted cells were collected in RNAprotect, lysed in QIAzol (Qiagen) and total RNA was extracted and purified using Direct-zol RNA MiniPrep (Zymo Research).
SCRB-seq: Frozen cells were thawed for 5 minutes at room temperature and cell lysis was enhanced by a treatment with proteinase K (200 μg/mL;Ambion) followed by RNA desiccation to inactivate the proteinase K and simultaneously reduce the reaction volume (50 °C for 15 min in sealed plate, then 95 °C for 10 min with seal removed ).   To start, diluted ERCC RNA Spike-In Mix (1 μl of 1:10^7; Life Technologies) was added to each well and the template switching reverse transcription reaction was carried out using Maxima H Minus Reverse Transcriptase (Thermo Scientific), our universal adapter E5V6NEXT (1 pmol, Eurogentec): 5’-iCiGiCACACTCTTTCCCTACACGACGCrGrGrG-3’ where iC: iso-dC, iG: iso-dG, rG: RNA G, and our barcoded adapter E3V6NEXT (1 pmol, Integrated DNA Technologies):5'/5Biosg/ACACTCTTTCCCTACACGACGCTCTTCCGATCT[BC6]N10T30VN-3' where 5Biosg = 5’ biotin, [BC6] = 6bp barcode specific to each cell/well, N10 = Unique Molecular Identifiers. Following the template switching reaction, cDNA from 384 wells was pooled together, and then purified and concentrated using a single DNA Clean & Concentrator-5 column (Zymo Research). Pooled cDNAs were treated with Exonuclease I (New England Biolabs) and then amplified by single primer PCR using the Advantage 2 Polymerase Mix (Clontech) and our SINGV6 primer (10 pmol, Integrated DNA Technologies): 5’-/5Biosg/ACACTCTTTCCCTACACGACGC-3’ Full length cDNAs were purified with Agencourt AMPure XP magnetic beads (0.6x, Beckman Coulter) and quantified on the Qubit 2.0 Flurometer using the dsDNA HS Assay (Life Technologies). Full-length cDNA was then used as input to the Nextera XT library preparation kit (Illumina) according to the manufacturer’s protocol, with the exception that the i5 primer was replaced by our P5NEXTPT5 primer (5μM, Integrated DNA Technologies): 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T*-3’ where * = phosphorothioate bonds. The resulting sequencing library was purified with Agencourt AMPure XP magnetic beads (0.6x, Beckman Coulter), size selected (300-800bp) on a E-Gel EX Gel, 2% (Life Technologies), purified using the QIAquick Gel Extraction Kit (Qiagen) and quantified on the Qubit 2.0 Flurometer using the dsDNA HS Assay (Life Technologies). Libraries were sequenced on Illumina Hiseq paired-end flow cells with 17 cycles on the first read to decode the well barcode and UMI, an 9 cycle index read to decode the i7 Nextera barcode and finally a 46 cycle second read to sequence the cDNA. SMART-seq: The single-cell SMART-seq2 libraries were prepared according to the SMART-seq2 protocol with some modifications 29. Briefly, total RNA from single cells sorted in lysis buffer was purified using RNA-SPRI beads. Poly(A)+ mRNA from each single cell was converted to cDNA which was then amplified. cDNA was subjected to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each single cell. Barcoded cDNA fragments were then pooled prior to sequencing. Sequencing was carried out as paired-end 2x25bp with 8 additional cycles for each index. Bulk RNA-seq: DGE libraries were prepared from 10 ng of extracted total RNA, using the protocol previously described for SCRB-seq with the exception of using more concentrated E3V6NEXT and E5V6NEXT (10 pmol).  SCRB-seq: Frozen cells were thawed for 5 minutes at room temperature and cell lysis was enhanced by a treatment with proteinase K (200 μg/mL;Ambion) followed by RNA desiccation to inactivate the proteinase K and simultaneously reduce the reaction volume (50 °C for 15 min in sealed plate, then 95 °C for 10 min with seal removed ).   To start, diluted ERCC RNA Spike-In Mix (1 μl of 1:107; Life Technologies) was added to each well and the template switching reverse transcription reaction was carried out using Maxima H Minus Reverse Transcriptase (Thermo Scientific), our universal adapter E5V6NEXT (1 pmol, Eurogentec):  5’-iCiGiCACACTCTTTCCCTACACGACGCrGrGrG-3’  where iC: iso-dC, iG: iso-dG, rG: RNA G, and our barcoded adapter E3V6NEXT (1 pmol, Integrated DNA Technologies):  5'-/5Biosg/ACACTCTTTCCCTACACGACGCTCTTCCGATCT[BC6]N10T30VN-3'  where 5Biosg = 5’ biotin, [BC6] = 6bp barcode specific to each cell/well, N10 = Unique Molecular Identifiers. Following the template switching reaction, cDNA from 384 wells was pooled together, and then purified and concentrated using a single DNA Clean & Concentrator-5 column (Zymo Research). Pooled cDNAs were treated with Exonuclease I (New England Biolabs) and then amplified by single primer PCR using the Advantage 2 Polymerase Mix (Clontech) and our SINGV6 primer (10 pmol, Integrated DNA Technologies):  5’-/5Biosg/ACACTCTTTCCCTACACGACGC-3’  Full length cDNAs were purified with Agencourt AMPure XP magnetic beads (0.6x, Beckman Coulter) and quantified on the Qubit 2.0 Flurometer using the dsDNA HS Assay (Life Technologies). Full-length cDNA was then used as input to the Nextera XT library preparation kit (Illumina) according to the manufacturer’s protocol, with the exception that the i5 primer was replaced by our P5NEXTPT5 primer (5μM, Integrated DNA Technologies):  5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T*-3’  where * = phosphorothioate bonds.  The resulting sequencing library was purified with Agencourt AMPure XP magnetic beads (0.6x, Beckman Coulter), size selected (300-800bp) on a E-Gel EX Gel, 2% (Life Technologies), purified using the QIAquick Gel Extraction Kit (Qiagen) and quantified on the Qubit 2.0 Flurometer using the dsDNA HS Assay (Life Technologies). Libraries were sequenced on Illumina Hiseq paired-end flow cells with 17 cycles on the first read to decode the well barcode and UMI, an 9 cycle index read to decode the i7 Nextera barcode and finally a 46 cycle second read to sequence the cDNA.

treatment_protocol: Cells were differentiated with RA for 72 h and then sorted on PDGFRA and CD24: PDGFRA negative , CD24 first tercile


title: 9_RT112 DMSO_H3K27Ac [lab: Hammerman-DFCI]

value: DMSO

value: 48h, but comparison is 7D


title: bulkRNAseq 72h (PDGFRA+/ CD24-)

description: column name in processed data file: 72h PDGFRA+/CD24-

treatment_protocol: Cells were differentiated with RA for 72 h and then sorted on PDGFRA and CD24: PDGFRA positive , CD24 negative


title: bulkRNAseq 72h (PDGFRA-/ CD24 T2)

description: column name in processed data file: 72h PDGFRA-/CD24 T2

treatment_protocol: Cells were differentiated with RA for 72 h and then sorted on PDGFRA and CD24: PDGFRA negative , CD24 second tercile


title: 7_PC9 DMSO_H3K27Ac [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO for 7 days prior to cross linking with formaldehyde.

value: Lung


title: N87-L2 Lap [lab: Hammerman-DFCI]


title: N87-L1-7 Lap_7days [lab: Hammerman-DFCI]


title: bulkRNAseq 72h (PDGFRA-/ CD24 T3)

description: column name in processed data file: 72h PDGFRA-/CD24 T3

treatment_protocol: Cells were differentiated with RA for 72 h and then sorted on PDGFRA and CD24: PDGFRA negative , CD24 third tercile


title: E7-DSC-1-H3K27me3

value: purified decidual stromal cells


title: bulkRNAseq 48h (PDGFRA-/ CD24 Q1)

description: column name in processed data file: 48h PDGFRA-/CD24 Q1

treatment_protocol: Cells were differentiated with RA for 48 h and then sorted on PDGFRA and CD24: PDGFRA negative , CD24 first quartile


title: bulkRNAseq 48h (PDGFRA-/ CD24 Q3)

description: column name in processed data file: 48h PDGFRA-/CD24 Q3

treatment_protocol: Cells were differentiated with RA for 48 h and then sorted on PDGFRA and CD24: PDGFRA negative , CD24 third quartile


title: bulkRNAseq 48h (PDGFRA-/ CD24 Q2)

description: column name in processed data file: 48h PDGFRA-/CD24 Q2

treatment_protocol: Cells were differentiated with RA for 48 h and then sorted on PDGFRA and CD24: PDGFRA negative , CD24 second quartile


title: bulkRNAseq 48h (PDGFRA-/ CD24 Q4)

description: column name in processed data file: 48h PDGFRA-/CD24 Q4

treatment_protocol: Cells were differentiated with RA for 48 h and then sorted on PDGFRA and CD24: PDGFRA negative , CD24 fourth quartile


title: N87-D4 DMSO [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO (0.1%) for 48h prior to harvesting


title: 11_H3122 DMSO_H3K27Ac [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Crizotinib (250 nM) for 7 days prior to cross linking with formaldehyde.


title: N87-L2-7 Lap_7days [lab: Hammerman-DFCI]


title: N87-D2 DMSO [lab: Hammerman-DFCI]


title: 8_PC9 RTKi_H3K27Ac [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Erlotinib for 7 days  prior to cross linking with formaldehyde.

value: Erlotinib


title: bulkRNAseq 2i rep2

description: column name in processed data file: 2i rep2

treatment_protocol: no treatment; mES growing in 2i media


title: 15_N87 DMSO_H3K27Ac [lab: Hammerman-DFCI]


title: Plantaris_6 hours of hypoxia #2

city: La Jolla

first: Andrew

middle: Douglas

last: McCulloch

address: 9500 Gilman Drive

department: Bioengineering

institute: UC San Diego

data_processing:
The quality of RNA-seq data was evaluated by FastQC and the FASTX-Toolkit. The inner distance between reads was estimated by an open-source script, getinsertsize.py, and SAMtools.The RNA-seq data was then aligned using TopHat2 and Bowtie2 with UCSC.mm9 as the reference genome. The accepted reads were then assembled and normalized by BEDTools and AltAnalyze. Genes with an insufficient copy number were excluded from further statistical analyses. Differentially expressed genes were determined using a one-way ANOVA analysis with P<0.01 after gene expression was normalized using RPKM in AltAnalyze.
Genome_build: mm9
Supplementary_files_format_and_content: quality control-alignment-normalization-differentially expressed analysis

source_name: in vivo plantaris muscle

extract_protocol:
Illumina ® TruSeq™ RNA Sample Preparation Kit
Libraries of extracted RNAs were built using the Illumina TruSeqTM RNA sample preparation kit, which yielded ~350 bp fragments. The prepared samples were then sequenced by Illumina HiSeq 2000 with paired-end 100-bp reads (Illumina, San Diego, CA, USA). Yield read numbers of each sample were in the range of 60-100 million reads, generating 100-160× coverage for each sample.

treatment_protocol: 3-month old male C57BL/6J mice were exposed to 8% oxygen for 0, 2, and 6 hours. After exposure, mice were immediately euthanized by cervical dislocation with the mouse covered by a mask filled with 8% O2. Plantaris muscles were dissected from the fresh hind limbs and stored in RNAlater solution (Ambion, Grand Island, NY, USA) at 4°C before further processing for RNA extraction. Plantaris muscles were homogenized using a Kontes Duall® 20 tissue grinder (Kimble Chase, Vineland, NJ, USA) in an ice bath. RNA was extracted using Qiagen RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s guidelines. All RNA samples showed a Agilent Bioanalyzer RIN score in the range of 9.5~10.0 and the A260/A280 ratio around 2.0 ~2.1.

value: Skeletal muscle

tag: condition

value: hypoxia

tag: time point

value: 6 hours


title: Plantaris_6 hours of hypoxia #1


title: Plantaris_6 hours of hypoxia #3


title: Plantaris_2 hours of hypoxia #3

value: 2 hours


title: N87-L1 Lap [lab: Hammerman-DFCI]


title: N87-D1 DMSO [lab: Hammerman-DFCI]


title: Plantaris_2 hours of hypoxia #1


title: 5_A375 DMSO_H3K27Ac [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO for 7 days to cross linking with formaldehyde.

value: Skin

value: 50 million


title: Plantaris_2 hours of hypoxia #2


title: N87-C3 Combo [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Lapatinib / THZ1 (100nM / 25 nM) for 48h prior to harvesting

value: Lapatinib / THZ1


title: Plantaris_control #3

value: Control

value: 0 hours


title: N87-C1 Combo [lab: Hammerman-DFCI]

value: Stomach


title: RT112_8 Input combo BGJ398 plus THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with BGJ398 (1 uM) and THZ1 (100 nM) for 48 hours prior to cross linking with formaldehyde.

value: bladder

value: THZ1 / BGJ


title: RT112_7 Input BGJ398 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with BGJ398 (1 uM) for 48 hours prior to cross linking with formaldehyde.

value: BGJ

value: 1 uM


title: N87-C2 Combo [lab: Hammerman-DFCI]


title: Plantaris_control #1


title: Plantaris_control #2


title: bulkRNAseq sort XEN (rep 1)

description:
column name in processed data file: sort XEN (rep 1), barcode: ATTATC
processed data in Series supplementary file

treatment_protocol: After 96h of retinoic acid exposure XEN-like cells (PDGFRA+/CD24-) were purified by FACS (biological replicate 1)


title: RT112_5 Input DMSO [lab: Hammerman-DFCI]

treatment_protocol: cells were treated with DMSO for 48 hours prior to cross linking with formaldehyde.

value: DMSO


title: bulkRNAseq XEN culture 3 w

description:
column name in processed data file: XEN culture 3 w, barcode: TATAAG
processed data in Series supplementary file

treatment_protocol: After sorting XEN-like cells were replated on poly-D-lysine and laminin coated tissue culture dishes in basal (N2B27) medium complemented with 20 ng/ml mouse EGF (E5160, Sigma-Aldrich) and 10 ng/ml mouse FGF2 (SRP4038-50UG, Sigma-Aldrich).   Floating aggregates of XEN-like cells were propagated in suspension in uncoated plastic petri dishes. Aggregates were not dissociated but the medium was refreshed roughly every 4 days. Cells in this sample had been cultured for 3 weeks.


title: bulkRNAseq sort XEN (rep 2)

description:
column name in processed data file: sort XEN (rep 2), barcode: AATATG
processed data in Series supplementary file

treatment_protocol: After 96h of retinoic acid exposure XEN-like cells (PDGFRA+/CD24-) were purified by FACS (biological replicate 2)


title: bulkRNAseq ecto culture P5

description:
column name in processed data file: ecto culture P5, barcode: TACAAA
processed data in Series supplementary file

treatment_protocol: After sorting ectoderm-like cells were replated on poly-D-lysine and laminin coated tissue culture dishes in basal (N2B27) medium complemented with 20 ng/ml mouse EGF (E5160, Sigma-Aldrich) and 10 ng/ml mouse FGF2 (SRP4038-50UG, Sigma-Aldrich). Ectoderm-like cells were propagated by dissociation with accutase (Life Technoliges) and replating under identical conditions every 3-4 days. Cells in this sample had been cultured for 5 passages


title: PC9_DMSO_input [lab: Hammerman-DFCI]

growth_protocol: PC9 cells were cultured in RPMI media, supplemented with 10% FBS, and penicillin/streptomycin/L-glutamine. Cells were cultured at 37 °C in a humidified chamber in the presence of 5% CO2.

treatment_protocol: Cells were treated with DMSO for 48 hours

value: Lung


title: H3122-T4 THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (50nM) for 48h prior to harvesting


title: 13_A549 DMSO_H3K27Ac [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO (0.1%) for 7 days followed by cross linking with formaldehyde.

value: Abcam

value: 48h, but comparison is 7D


title: H3122-T1 THZ1 [lab: Hammerman-DFCI]


title: bulkRNAseq_sort ecto (rep 1)

description:
column name in processed data file: sort ecto (rep 1), barcode: ATTGTT
processed data in Series supplementary file

treatment_protocol: After 96h of retinoic acid exposure ectoderm-like cells (PDGFRA-/CD24+) were purified by FACS (biological replicate 1)


title: bulkRNAseq_84h

description:
column name in processed data file: 84h, barcode: TTCATA
processed data in Series supplementary file

treatment_protocol: Prior to differentiation cells were grown in 2i medium for at least 2 passages. Cells were seeded at 2.5 × 10^5 per 10 cm dish and grown over night (12 h). Cells were then washed twice with PBS and subsequently differentiated in basal N2B27 medium (2i medium without the inhibitors, LIF and the additional insulin) supplemented with all-trans retinoic acid (RA, Sigma-Aldrich). RA concentration was 0.25 µM unless stated otherwise. Samples were taken at the time points indicated in the file names. For differentiation beyond 48 h spent medium was exchanged with fresh medium at 48 h.


title: bulkRNAseq_96h

description:
column name in processed data file: 96h, barcode: TTGTTA
processed data in Series supplementary file


title: H3122-T2 THZ1 [lab: Hammerman-DFCI]


title: PC9_8 Input combo Erlotinib plus THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (100 nM) and Erlotinib (1 uM) for 48 hours prior to cross linking with formaldehyde.

value: Erlotinib / THZ1


title: RT112_6 Input THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (100 nM) for 48 hours prior to cross linking with formaldehyde.


title: bulkRNAseq sort ecto (rep 2)

description:
column name in processed data file: sort ecto (rep 2), barcode: AATTTC
processed data in Series supplementary file

treatment_protocol: After 96h of retinoic acid exposure ectoderm-like cells (PDGFRA-/CD24+) were purified by FACS (biological replicate 2)


title: H3122-H4 Criz_7days [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Crizotinib (250nM) for 7D prior to harvesting

value: Crizotinib


title: PC9_ERL_input [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with 1 uM erlotinib for 48 hours.

value: Erlotinib


title: H3122-H3 Criz_7days [lab: Hammerman-DFCI]


title: PC9_5 Input DMSO [lab: Hammerman-DFCI]

growth_protocol: PC9 cells were cultured in RPMI media, supplemented with 10% FBS, and penicillin/streptomycin/L-glutamine. Cells were cultured at 37 Â°C in a humidified chamber in the presence of 5% CO2.

treatment_protocol: Cells were treated with DMSO for 48 hours prior to cross linking with formaldehyde.


title: H3122-H1 Criz_7days [lab: Hammerman-DFCI]


title: PC9_6 Input THZ1 [lab: Hammerman-DFCI]


title: bulkRNAseq_6h

description:
column name in processed data file: 6h, barcode: TCAAAA
processed data in Series supplementary file


title: H3122-D4 DMSO [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO (0.1%) for 48h prior to harvesting


title: bulkRNAseq_2i

description:
column name in processed data file: 2i, barcode: TATTAC
processed data in Series supplementary file

treatment_protocol: no treatment; mES growing in 2i media


title: H3122-D3 DMSO [lab: Hammerman-DFCI]


title: bulkRNAseq_12h

description:
column name in processed data file: 12h, barcode: TCTAAT
processed data in Series supplementary file


title: bulkRNAseq_36h

description:
column name in processed data file: 36h, barcode: TGTATT
processed data in Series supplementary file


title: bulkRNAseq_48h

description:
column name in processed data file: 48h, barcode: TTAACT
processed data in Series supplementary file


title: PC9_7 Input Erlotinib [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Erlotinib (1 um) for 48 hours prior to cross linking with formaldehyde.


title: bulkRNAseq_24h

description:
column name in processed data file: 24h, barcode: TGAATA
processed data in Series supplementary file


title: bulkRNAseq_72h

description:
column name in processed data file: 72h, barcode: TTATCA
processed data in Series supplementary file


title: H3122-D2 DMSO [lab: Hammerman-DFCI]


title: smartseq_24h

treatment_protocol: Prior to differentiation cells were grown in 2i medium for at least 2 passages. Cells were seeded at 2.5 × 10^5 per 10 cm dish and grown over night (12 h). Cells were then washed twice with PBS and subsequently differentiated in basal N2B27 medium (2i medium without the inhibitors, LIF and the additional insulin) supplemented with all-trans retinoic acid (RA, Sigma-Aldrich). RA concentration was 0.25 µM unless stated otherwise. Samples were taken at the time points indicated in the file names.


title: smartseq_2i


title: N87_7 Input Lapatinib [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Lapatinib (100 nM) for 48 hours prior to cross linking with formaldehyde.

value: Lapatinib


title: smartseq_12h


title: H3122-Cr4 Criz [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Crizotinib (250nM) for 48h prior to harvesting


title: bulkRNAseq_60h

description:
column name in processed data file: 60h, barcode: TTACTA
processed data in Series supplementary file


title: scrbseq_96h


title: N87_8 Input combo Lapatinib plus THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Lapatinib (100 nM) and THZ1 (25 nM) for 48 hours prior to cross linking with formaldehyde.

value: 50 million


title: H3122-Cr3 Criz [lab: Hammerman-DFCI]


title: scrbseq_72h


title: scrbseq_60h


title: scrbseq_48h


title: N87_5 Input DMSO [lab: Hammerman-DFCI]


title: scrbseq_36h


title: smartseq_48h


title: scrbseq_24h


title: H3122-Co4 Combo [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 / Crizotinib (50nM / 250nM) for 48h prior to harvesting

value: THZ1 / Crizotinib


title: N87_6 Input THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (25 nM) for 48 hours prior to cross linking with formaldehyde.

value: 25 nM


title: scrbseq_6h


title: scrbseq_12h


title: H3122_6 Input THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with 50 nM THZ1 for 48 hours prior to cross linking with formaldehyde.


title: scrbseq_2i


title: H3122_5 Input DMSO [lab: Hammerman-DFCI]


title: H3122-Co1 Combo [lab: Hammerman-DFCI]


title: H3122-Co3 Combo [lab: Hammerman-DFCI]


title: A13_E2_mm

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

description: Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse/human transcriptome (UCSC annotation, genome build mm9/hg19) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: Murine pancreatic ductal adenocarcinoma-derived cell line

growth_protocol: Cell lines were cultured in DMEM supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol:
Total RNA was isolated using TRIzol from Life Technologies.
RNA libraries were prepared for sequencing with the Illumina TruSeq kit according to the manufacturer's instructions.

treatment_protocol: 8988T and A13 cells were infected with lentiviruses that express Cas9 and sgRNAs targeting KRAS and subcloned to isolate KRAS intact and knockout cells

tag: genotype

value: Kras G12D/G12D;Trp53 -/-


title: wtmm1319ye

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: P1-wr; mop1-1 young ear sample 1319 (P1-wr/P1-wr; mop1-1/mop1-1)

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: maize AGPv2 genome
Supplementary_files_format_and_content: tag count file

organism: Zea mays

source_name: maize 2-4 cm young ear

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012).

tag: genotype/variation

value: P1-wr; mop1-1 young ear sample 1319


title: A13_E1_mm


title: A549_8 Input combo GSK1120212 plus THZ1 [lab: Hammerman-DFCI]

treatment_protocol: cells were treated with GSK1120212 (200 nM) and THZ1 (150 nM) for 48 hours prior to cross linking with formaldehyde.


title: A13_K1_mm

description: Cell line derived from LSL-KrasG12D; p53flox/flox; Pdx1-CreER murine pancreatic tumor and subject to CRISPR-mediated Kras knockout


title: A549-T2 THZ1 [lab: Hammerman-DFCI]

source_name: Lung Adenocarcinoma

treatment_protocol: Cells were treated with THZ1 (150nM) for 48h prior to harvesting


title: A549_5 Input DMSO [lab: Hammerman-DFCI]


title: wtmm195ye

description: P1-wr; mop1-1 young ear sample 195 (P1-wr/P1-wr; mop1-1/mop1-1)

value: P1-wr; mop1-1 young ear sample 195


title: wtMm155ye

description: P1-wr; Mop1 young ear sample 155 (P1-wr/P1-wr; Mop1/mop1-1)

value: P1-wr; Mop1 young ear sample 155


title: H3122-Cr2 Criz [lab: Hammerman-DFCI]


title: A549-T4 THZ1 [lab: Hammerman-DFCI]


title: A549-T1 THZ1 [lab: Hammerman-DFCI]


title: H3122_8 Input combo Crizotinib plus THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Crizotinib (250 nM) and THZ1 (50 nM) for 48 hours prior to cross linking with formaldehyde.

value: Crizotinib / THZ1


title: A13_K2_mm


title: H3122_7 Input Crizotinib [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Crizotinib (250 nM) for 48 hours prior to cross linking with formaldehyde.


title: A549-G4 GSK [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with GSK1120212 (200 nM) for 48h prior to harvesting


title: wtMm153ye

description: P1-wr; Mop1 young ear sample 153 (P1-wr/P1-wr; Mop1/mop1-1)

value: wtMm153ye P1-wr; Mop1 young ear sample 153


title: A549_6 Input THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with 150 nM THZ1 for 48 hours prior to cross linking with formaldehyde.


title: A549_7 Input GSK1120212 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with GSK1120212 (200 nM) for 48 hours prior to cross linking with formaldehyde.


title: A549-G3 GSK [lab: Hammerman-DFCI]


title: 20_A375 combo_48h_input [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (50 nM) and Vemurafenib (1 uM)  for 48 hours prior to cross linking with formaldehyde.

value: Skin

value: THZ1 / Vemurafenib

value: 50nM / 1 uM


title: WT Heart [CM29]

city: Edinburgh

first: Martin

last: Taylor

state: Midlothian

address: Crewe Road

department: MRC Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

description: Differential centrifugation and single step sucrose gradient for mitochondrial DNA enirchment

data_processing:
Trimming of residual adaptor sequences. Code for all data processing steps is available at https://github.com/taylorLab/mito
Alignment to reference genome (masked for nuclear inserted mitochondrial sequences).
Alignment to reference genome masked for nuclear inserted mitochondrial sequences and containing additional circularisation junction for the mitochondrial genome.
Resolution of coordinates for circularisation junction mapping
Calculation of embeded ribonucleotide position – one nucleotide upstream and on the opposite strand to the read 5’ end.
Genome_build: mm9 with additional sequence corresponding to the circularisation junction of the mitochondrial genome
Supplementary_files_format_and_content: Bed format files showing the coordinates and strand of inferred ribonucleotide incorporation sites, counts per nucleotide of the reference genome at all sites with signal indicated by the 5’ end of at least one read.

source_name: WT Heart

growth_protocol: cultured cells were grown on 90% dulbecco's modified growth medium containing 25 mM glucose and 100 mM pyruvate supplemented with 10% fetal bovine serum

extract_protocol:
DNA was extracted by the phenol chloroform extraction after proteinase K digestion of cells or tissue in 0.25% SDS
EmRibo-seq libraries were prepared according to Ding et al 2015 - doi: 10.1038/nprot.2015.099

treatment_protocol: Cells and tissues were homogenized and in the case of heart DNA extracted immediately, for other samples mitochondria were prepared by differential centrifugation, and in most cases with additional purification on a single step sucrose gradient

tag: strain background

value: wild-type

tag: tissue/cell type

value: Heart

tag: tissue/cell subtype

value: Primary tissue

tag: molecule subtype

value: Total DNA from homogenized tissue


title: MEF WT prolif [CM25]

source_name: MEF WT prolif

value: Embryonic fibroblast

value: Proliferating ex vivo primary cells

value: Mitochondrially enriched genomic DNA


title: MPV17 KO Heart [CM30]

source_name: MPV17 KO Heart

tag: strain


title: A549-G3-7 GSK_7days [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with GSK1120212 (200 nM) for 7D prior to harvesting

tag: cell line

tag: tissue

value: Lung


title: WT Brain [CM37]

source_name: WT Brain

value: Brain


title: 19_A375 RTKi_48h_input [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with 1 uM Vemurafenib for 48 hours prior to cross linking with formaldehyde.

tag: chip antibody

tag: drug

value: Vemurafenib

value: 1 uM

tag: cell number

value: 50 million


title: KO Brain [CM38]

source_name: KO Brain


title: MPV17 KO Brain [CM21]

source_name: MPV17 KO Brain


title: wtMm156ye

description: P1-wr; Mop1 young ear sample 156 (P1-wr/P1-wr; Mop1/mop1-1)

value: P1-wr; Mop1 young ear sample 156


title: A549-G2-7 GSK_7days [lab: Hammerman-DFCI]

tag: concentration

tag: treatment duration


title: 18_A375 THZ1_48h_input [lab: Hammerman-DFCI]


title: MPV17 WT Brain [CM20]

source_name: MPV17 WT Brain


title: 17_A375 DMSO_48h_input [lab: Hammerman-DFCI]

source_name: Melanoma

treatment_protocol: Cells were treated with DMSO for 48 hours prior to cross linking with formaldehyde.

value: DMSO


title: A549-G1-7 GSK_7days [lab: Hammerman-DFCI]


title: MEF prolif [CM12]

source_name: MEF prolif


title: crudeBrain [CM16]

source_name: crudeBrain


title: A549-D4 DMSO [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO (0.1%) for 48h prior to harvesting


title: T- MEFs [CM10A]

source_name: T- MEFs


title: RT112_4 RT112 combo BGJ398 plus THZ1 [lab: Hammerman-DFCI]

source_name: Urinary bladder carcinoma

treatment_protocol: Cells were treated with THZ1 (100 nM) and BGJ398 (1 uM) for 48 hours prior to cross linking with formaldehyde.

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog number

value: bladder

value: THZ1 / BGJ


title: RT112_2 BRD4 THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (100 nM) for 48 hours prior to cross linking with formaldehyde.


title: RT112_1 BRD4 DMSO [lab: Hammerman-DFCI]


title: MPV17 KO Liver [CM7]

source_name: MPV17 KO Liver

value: Liver


title: A549-D2 DMSO [lab: Hammerman-DFCI]


title: MPV17 WT Liver [CM6]

source_name: MPV17 WT Liver

value: wild-type


title: RT112_3 BRD4 BGJ398 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with BGJ398 (1 uM) for 48 hours prior to cross linking with formaldehyde.

value: BGJ


title: A549-C3 Combo [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 / GSK1120212 (150nM / 200 nM) for 48h prior to harvesting


title: PC9_ERL_BRD4 [lab: Hammerman-DFCI]

source_name: Adenocarcinoma

treatment_protocol: Cells were treated with 1 uM  Erlotinib for 48 hours.

value: Erlotinib


title: A549-C2 Combo [lab: Hammerman-DFCI]


title: MPV17 WT Liver [CM2]

value: Primary tissue


title: A549-C1 Combo [lab: Hammerman-DFCI]


title: PC9_DMSO_BRD4 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO for 48 hours.


title: A375-V4 Vem [lab: Hammerman-DFCI]

growth_protocol: A375 cells were cultured in DMEM media, supplemented with 10% FBS, and penicillin/streptomycin/L-glutamine. Cells were cultured at 37 °C in a humidified chamber in the presence of 5% CO2.

treatment_protocol: Cells were treated with Vemurafenib (1 uM) for 48h prior to harvesting


title: A549-G2 GSK [lab: Hammerman-DFCI]


title: A375-V3 Vem [lab: Hammerman-DFCI]

value: Skin


title: A375-V3-7 Vem_7days [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Vemurafenib (1 uM) for 7D prior to harvesting


title: A549-D3 DMSO [lab: Hammerman-DFCI]


title: PC9_1 BRD4 DMSO [lab: Hammerman-DFCI]


title: Nrdc KO, WT rescue rep1

city: kyoto

first: Yusuke

last: Morita

state: kyoto

address: kyoto

country: Japan

institute: kyoto university

description: mRNA was sequenced with the Ion Proton semiconducter sequencer.

data_processing:
Basecall was performed using Torrent Suite (Thermo Fischer Inc.)
The raw reads were aligned to the mouse reference genome (Ensemble, mm9) using STAR, then took any unmapped reads to Bowtie2 in local mode.
The raw read counts were calculated by featureCounts in the Subread R package.
Calculation of rpkm was performed by edgeR package with primary counts of 1 using GTF of Ensembl genes.
Genome_build: mm9
Supplementary_files_format_and_content: Rpkm values for each samples

source_name: mouse embryonic fibroblast

growth_protocol: The cells were cultured in low glucose (1.0mg/L) Dulbecco-modified eagle's medium (DMEM) (Sigma) supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol:
Total RNA was extracted using a combination of TRIzol® Reagent (Thermof Fischer Inc.) and RNeasy mini kit (QIAGEN) accrording to the manufacture’s protocol.
cDNA libraries were prepared from total RNA using Dynabeads mRNA Direct kit (Thermo Fischer Inc.) an Ion Xpress Plus Flagment Library Kit (Thermo Fischer Inc.). RNAseq libraries were assessed for concentration and length using Agilent High Sensitivity DNA kit (Agilent Biotechnology). Samples were sequenced with using Ion Proton semiconductors sequencers (Theremo Fischer Inc.) according to the manufacturer’s instructions.

treatment_protocol: Asynchronously growing cells were used for mRNA extraction.

value: Nrdc KO  infected with Nrdc-expressing virus

tag: cell type

value: MEF


title: A375-V2-7 Vem_7days [lab: Hammerman-DFCI]


title: Nrdc KO rep1

value: Nrdc KO


title: WT rep1

value: WT


title: Nrdc KO rep2


title: PC9_4 BRD4 combo Erlotinib plus THZ1[lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (100 nM) and Erlotinib (1 uM) for 48 hours prior to cross linking with formaldehyde.

value: Lung

value: Erlotinib / THZ1


title: N87_2 BRD4 THZ1 [lab: Hammerman-DFCI]

source_name: Gastric Cancer

treatment_protocol: Cells were treated with 25 nM THZ1 for 48 hours prior to cross linking with formaldehyde.

value: Stomach

value: 25 nM

value: 50 million


title: WT rep2


title: N87_3 BRD4 Lapatinib [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Lapatinib (100 nM) for 48 hours prior to cross linking with formaldehyde.

value: Bethyl

value: Lapatinib


title: PC9_3 BRD4 Erlotinib [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Erlotinib (1 uM) for 48 hours prior to cross linking with formaldehyde.

value: 1 uM


title: A375-V1-7 Vem_7days [lab: Hammerman-DFCI]

value: Vemurafenib


title: Nrdc KO, WT rescue H3K4me2 ChIP-seq-2

description:
ChIP DNA and input controls were sequenced with the Ion Proton semiconducter sequencer.
Nrdc_KO_WTrescue_H3K4me2.bw

data_processing:
Basecall was performed using Torrent Suite (Thermo Fischer Inc.)
Reads were aligned with mm9 genome using Bowtie2
The aligned reads with mapping quality score (MAPQ) >5 were used for peak detection.
Peak detection was performed with MACS v1.4.2 with default settings (p < 1*e-5).
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using MACS v1.4.2 with -w option.

extract_protocol:
Crosslinked samples were fragmented using Covaris S220, followed by immunoprecipitation with the specific antibodies.
ChIP DNA was subjected to library preparation with NEBNext Fast DNA Library Prep Set for Ion Torrent kit (New England Biolabs.). DNA was end-repaired, adapter-ligated, and size-selected with Agentcourt AMpure XP (Beckman Coulter Inc.) to median length of 300bp. Size-selected DNA was PCR amplified with Ion barcode adapter (Thermo Fischer Inc.) for 12 cycles, and purified with Agentcourt AMpure XP. High-throughput sequencing was performed using Ion Proton semiconductors sequencers (Thermo Fischer Inc.) according to the manufacturer’s instructions.

treatment_protocol: Asynchronously growing cells were used for ChIP-seq.

value: Nrdc KO infected with Nrdc-expressing virus

value: H3K4me2, 07-030 Millipore


title: N87_1 BRD4 DMSO [lab: Hammerman-DFCI]

value: DMSO


title: MPV17 KO Liver [CM3]

treatment_protocol: Cells and tissues were homogenized and in the case of heart DNA extracted immediately, for other samples mitochondria were prepared by differential centrifugation, and in most cases with additional purification on a single step sucrose gradient

value: Liver

value: Primary tissue

value: Mitochondrially enriched genomic DNA


title: PC9_2 BRD4 THZ1 [lab: Hammerman-DFCI]


title: A375-T4 THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (50nM) for 48h prior to harvesting

value: Skin


title: Nrdc KO, WT rescue H3K4me2 ChIP-seq-1

value: MEF


title: Nrdc KO, WT rescue rep2

value: Nrdc KO  infected with Nrdc-expressing virus


title: N87_4 BRD4 combo Lapatinib plus THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Lapatinib (100 nM) and THZ1 (25 nM) for 48 hours prior to cross linking with formaldehyde.

value: Lapatinib / THZ1


title: Nrdc KO H3K4me2 ChIP-seq-2

description:
ChIP DNA and input controls were sequenced with the Ion Proton semiconducter sequencer.
Nrdc_KO_H3K4me2.bw

value: Nrdc KO


title: A375-T2 THZ1 [lab: Hammerman-DFCI]


title: H3122_2 BRD4 THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (50 nM) for 48 hours prior to cross linking with formaldehyde.

value: Lung


title: A375-D4 DMSO [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO (0.1%) for 48h prior to harvesting


title: A375-V1 Vem [lab: Hammerman-DFCI]


title: A375-D3 DMSO [lab: Hammerman-DFCI]


title: H3122_1 BRD4 DMSO [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO for 48 hours prior to cross linking with formaldehyde.

value: 50 million


title: Nrdc KO H3K9ac ChIP-seq

description: ChIP DNA and input controls were sequenced with the Ion Proton semiconducter sequencer.

value: H3K9ac, 06-942 Millipore


title: WT H3K4me2 ChIPseq-2

description:
ChIP DNA and input controls were sequenced with the Ion Proton semiconducter sequencer.
WT_H3K4me2.bw

value: WT


title: A375-C3 Combo_THZ1_Vem [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Vemurafenib / THZ1 (1 uM / 50 nM) for 48h prior to harvesting

value: Vemurafenib / THZ1

value: 1 uM / 50 nM


title: A549_4 BRD4 combo GSK1120212 plus THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with THZ1 (150 nM) and GSK1120212 (200 nM) for 48 hours prior to cross linking with formaldehyde.

value: Bethyl


title: WT H3K4me2 ChIPseq-1

value: H3K4me2, 07-030 Millipore


title: A375-C2 Combo_THZ1_Vem [lab: Hammerman-DFCI]


title: H3122_4 BRD4 combo Crizotinib plus THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Crizotinib (250 nM) and THZ1 (50 nM) for 48 hours prior to cross linking with formaldehyde.

value: THZ1 / Crizotinib


title: A549_1 BRD4 DMSO [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with DMSO (0.1%) for 48 hours prior to cross linking with formaldehyde.

value: DMSO


title: WT H3K9ac ChIPseq


title: WT input ChIPseq


title: WT Nrdc ChIPseq

value: anti-Nrdc (purified monoclonal)


title: A375-C1 Combo_THZ1_Vem [lab: Hammerman-DFCI]


title: H3122_3 BRD4 Crizotinib [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Crizotinib (250 nM) for 48 hours prior to cross linking with formaldehyde.

value: Crizotinib


title: A375-T3 THZ1 [lab: Hammerman-DFCI]

value: Skin


title: SK-MEL-5 BRD4_041112

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and grown to appr. 80% confluency.

tag: antibody manu.

tag: antibody catalog#


title: Nrdc KO, WT rescue H3K9ac ChIP-seq

tag: genotype/variation

value: Nrdc KO infected with Nrdc-expressing virus

value: MEF


title: A549_3 BRD4 GSK1120212 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with GSK1120212 200 nM for 48 hours prior to cross linking with formaldehyde.


title: 4_A375 combo_BRD4 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Vemurafenib (1 uM)  and THZ1 (50 nM) for 48 hours prior to cross linking with formaldehyde.

value: 1 uM / 50nM


title: SK-MEL-5 Input_041112


title: SK-MEL-5 BRD4_050212


title: Nrdc KO H3K4me2 ChIP-seq-1

value: Nrdc KO


title: 8988T_P3_hg

description: Cell line derived from liver metastasis and subject to CRISPR-mediate KRAS knockout

source_name: Human pancreatic ductal adenocarcinoma cell line (DSMZ ACC 162)

treatment_protocol: 8988T and A13 cells were infected with lentiviruses that express Cas9 and sgRNAs targeting KRAS and subcloned to isolate KRAS intact and knockout cells

tag: genotype


title: 2_A375 THZ1_BRD4 [lab: Hammerman-DFCI]


title: A375-D2 DMSO [lab: Hammerman-DFCI]


title: Adult_female_1

city: Barcelona

first: Guillem

last: Ylla

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37

country: Spain

institute: Institute of Evolutionary Biology

data_processing:
Quality control with FastQC
Read filtering and trimming with Trimmomatic
Reads mapping with Bowtie
miRNA counts with FeatureCounts
Genome_build: https://www.hgsc.bcm.edu/arthropods/german-cockroach-genome-project

organism: Blattella germanica

source_name: B. germanica  Adult female

growth_protocol: Blattella germanica specimens used for small RNA-seq  analysis were obtained from a population reared at the Institut de Biologia Evolutiva (CSIC-UPF). Conditions were 70% humidity at 30 ºC and a commercial dog food diet.

extract_protocol:
miRNeasy Mini Kit (Qiagen)
NEBNext® Small RNA Library Prep Set for Illumina®

treatment_protocol: We sequenced 22 small RNA-seq libraries, two replicates for each one of the 11 developmental stages selected according to Juvenil hormone and Ecdysone hormone patterns

tag: developmental stage

value: Adult female

value: Whole body


title: N6_2

source_name: B. germanica  Nymph 6

value: Nymph 6


title: 1_A375 DMSO_BRD4 [lab: Hammerman-DFCI]

value: 50 million


title: Adult_female_2


title: N5_2

source_name: B. germanica  Nymph 5

value: Nymph 5


title: A549_2 BRD4 THZ1 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with 150 nM THZ1 for 48 hours prior to cross linking with formaldehyde.

value: Lung


title: 8988T_P1_hg


title: N5_1


title: SK-MEL-5 THZ1 PolII

treatment_protocol: Cells were treated with 250 nM THZ1 for 6hrs and then cells were fixed with formaldehyde.

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz

tag: antibody lot#


title: 8988T_E5_hg

description: Cell line derived from liver metastasis


title: SK-MEL-5 H3K27Ac

treatment_protocol: Cells were treated with DMSO for 6 hrs and then formaldehyde fixed.

value: Abcam


title: 8988T_E4_hg

description: Cell line derived from liver metastasis


title: 8988T_E2_hg

description: Cell line derived from liver metastasis


title: 8988T_E1_hg

description: Cell line derived from liver metastasis


title: N3_1

source_name: B. germanica  Nymph 3

value: Nymph 3


title: 3_A375 RTKi_BRD4 [lab: Hammerman-DFCI]

treatment_protocol: Cells were treated with Vemurafenib (1 uM) for 48 hours prior to cross linking with formaldehyde.

value: Bethyl

value: Vemurafenib

value: 1 uM


title: N1_2

source_name: B. germanica  Nymph 1

value: Nymph 1


title: N1_1


title: 8FP3

city: Los Angeles

first: Eric

middle: Alva

last: Webb

address: 3616 Trousdale Parkway

institute: University of Southern California

description:
Cells were grown semi-continuously in Aquil medium with co-limiting iron (10 nM) and phosphorus (0.25 µM) in 750 µatm CO2. Samples were taken in the middle of the photoperiod (i.e. midday)
sampling protocol: Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.

data_processing:
Raw read files were downloaded from the UC San Diego Genomics Core server upon completion
Raw Fastq files were quality trimmed using Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) with the following settings: SE -threads 35 -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
Quality processed reads were mapped onto Trichodesmium IMS101 genes (per Integrated Microbial Genomes (JGI) annotation) using Bowtie2 v2.2.6 with default settings. Counts per gene were enumerated using the sam2counts.py script (https://github.com/vsbuffalo/sam2counts). Genes containing an average of less than 10 counts across libraries were removed.
Genome_build: Trichodesmium erythraeum IMS101 (https://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=637000329)
Supplementary_files_format_and_content: Tab-delimited file with raw counts per gene as rows and individual biological replicates as columns

organism: Trichodesmium erythraeum IMS101

source_name: cell population

growth_protocol: See description in the SAMPLES section

extract_protocol:
RNA was extracted using the Ambion MirVana miRNA Isolation Kit (Thermo Fisher Scientific) in an RNAse free environment according to the manufacturer’s instructions followed by Ambion’s Turbo DNA-free kit to degrade trace amounts of DNA.
Extracted RNA was sent to the UC San Diego IGM Genomics Center for library construction and Illumina sequencing. Briefly, rRNA was removed from total RNA using the Ribo-Zero rRNA Removal Kit (Illumina), and libraries were constructed with the TruSeq Stranded mRNA Library Prep Kit (Illumina) followed by 50 base pair, single end sequencing with the Illumina HiSeq4000.

tag: environment

value: cell culture

tag: co2 concentration

value: 750 µatm

tag: medium

value: Aquil medium w/o fixed nitrogen in co-limiting iron (10nM) and phosphorus (0.25 µM) concentrations

tag: location

value: University of Southern California, Los Angeles


title: 8FP1


title: ED13_2

source_name: B. germanica  embryo day 13

value: embryo day 13

tag: tissue

value: Whole body


title: 8988T_P2_hg

tag: cell line


title: ED13_1


title: N6_1

value: Nymph 6


title: 8P1

description:
Cells were grown semi-continuously in Aquil medium with limiting phosphorus (0.25 µM) in 750 µatm CO2. Samples were taken in the middle of the photoperiod (i.e. midday)
sampling protocol: Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.

value: Aquil medium w/o fixed nitrogen in limiting phosphorus concentrations (0.25 µM)


title: SK-MEL-5 DMSO PolII

source_name: Melanoma

treatment_protocol: Cells were treated with DMSO for 6 hrs and then fixed with formaldehyde.

tag: chip antibody

tag: drug

value: DMSO

tag: concentration


title: ED6_2

source_name: B. germanica  embryo day 6

value: embryo day 6


title: 3P2

description:
Cells were grown semi-continuously in Aquil medium with limiting phosphorus (0.25 µM) in 380 µatm CO2. Samples were taken in the middle of the photoperiod (i.e. midday)
sampling protocol: Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.

value: 380 µatm


title: ED6_1


title: ED2_2

source_name: B. germanica  embryo day 2

value: embryo day 2


title: 8P2


title: ED1_2

source_name: B. germanica  embryo day 1

value: embryo day 1


title: ED1_1


title: 8F1

description:
Cells were grown semi-continuously in Aquil medium with limiting iron (10nM) in 750 µatm CO2. Samples were taken in the middle of the photoperiod (i.e. midday)
sampling protocol: Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.

value: Aquil medium w/o fixed nitrogen in limiting iron concentrations (10 nM)


title: 3F2

description:
Cells were grown semi-continuously in Aquil medium with limiting iron (10nM) in 380 µatm CO2. Samples were taken in the middle of the photoperiod (i.e. midday)
sampling protocol: Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.


title: 3P1


title: N3_2

value: Nymph 3


title: 8F3


title: 3F1


title: 3FP2

description:
Cells were grown semi-continuously in Aquil medium with co-limiting iron (10 nM) and phosphorus (0.25 µM) in 380 µatm CO2. Samples were taken in the middle of the photoperiod (i.e. midday)
sampling protocol: Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.


title: ED0_2

source_name: B. germanica  embryo day 0

value: embryo day 0


title: 3FP1


title: ED0_1


title: 8R1

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2. Samples were taken in the middle of the photoperiod (i.e. midday)
sampling protocol: Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.

value: Aquil medium w/o fixed nitrogen in replete nutrients


title: 8R3

value: cell culture


title: WTZIAA

city: Wuhan

first: Bo

last: Wang

state: Hubei

address: No.1,Shizishan Street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

description: WTZIAA

data_processing:
Basecalls performed using bcl2fastq version 2.18
All reads were mapped to the B. napus Darmor-‘bzh’ genome v4.2 using hisat2 (v2.0.4)
Fragments per kilobase per million mapped reads (FPKM) were calculated using cufflinks (v2.2.1) to estimate gene expression levels.
Genome_build: B. napus Darmor-‘bzh’ genome v4.2
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample.

organism: Brassica napus

source_name: seedling

growth_protocol: Seeds of rapeseed were sterilized, rinsed three times in sterile water and sown on Murashige and Skoog (MS) culture medium with 1% agar. The seedlings were grown at 22℃ with 16h light/8h dark.

extract_protocol:
Each of ten seedlings for the both treatment were then pooled together. All materials were frozen in liquid nitrogen and subsequently stored at -80℃. Total RNA was extracted using the ultrapure total RNA isolation kit (BioTeke, Beijing).
The libraries were constructed according to TruSeq® RNA Sample Preparation v2 Guide (Illumina)

treatment_protocol: For the IAA treatment, two sets of 30-day-old seedlings were incubated in liquid MS medium with and without 1 μM IAA for three hours, respectively.

value: seedling

tag: development stage

tag: treatment

value: 1 μM IAA for 3 hours


title: 3R2

description:
Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2. Samples were taken in the middle of the photoperiod (i.e. midday)
sampling protocol: Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.

value: University of Southern California, Los Angeles


title: NFE_1

source_name: B. germanica non fecundated eggs

value: non fecundated eggs

value: eggs


title: NFE_2


title: WTFIAA

description: WTFIAA

value: ddH20 for 3 hours


title: 3R1


title: ED2_1

value: Whole body