title: microRNA counts from hindbrain (ENCLB296CTN)

description:
https://www.encodeproject.org/experiments/ENCSR722SLO/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR722SLO
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-27
lab: Ali Mortazavi, UCI
library encode accession: ENCLB296CTN
size range: <30

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

value: Hindbrain from 51 embryonic 10.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS723QMZ at ENCODE; https://www.encodeproject.org/ENCBS723QMZ/


title: microRNA counts from limb (ENCLB551SAF)

status: Public on Dec 08 2022

type: RNA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR664WGP/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse limb
experiment encode accession: ENCSR664WGP
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB551SAF
size range: <30

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

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

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (15.5 days)

label_protocol: Nanostring protocol

value: limb

value: tissue

tag: description

value: Limb from 78 embryonic 15.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

tag: link

value: ENCBS735QNY at ENCODE; https://www.encodeproject.org/ENCBS735QNY/

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


title: microRNA counts from skeletal muscle tissue (ENCLB416FLR)

description:
https://www.encodeproject.org/experiments/ENCSR753HJF/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse skeletal muscle
experiment encode accession: ENCSR753HJF
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB416FLR
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl skeletal muscle tissue postnatal (0 days)

value: skeletal muscle tissue

value: single organ portion from 1 pup

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS482FSQ at ENCODE; https://www.encodeproject.org/ENCBS482FSQ/


title: microRNA counts from neural tube (ENCLB182PGX)

description:
https://www.encodeproject.org/experiments/ENCSR702DUC/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR702DUC
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB182PGX
size range: <30

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (15.5 days)

value: neural tube

value: Neural tube from 62 embryonic 15.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS206NRE at ENCODE; https://www.encodeproject.org/ENCBS206NRE/


title: microRNA counts from stomach (ENCLB326MBV)

description:
https://www.encodeproject.org/experiments/ENCSR805WTW/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR805WTW
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB326MBV
size range: <30

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (14.5 days)

value: stomach

value: tissue

value: single stomach from pup 1 pregnant 2 collected 7/17/2014

value: ENCBS987ARB at ENCODE; https://www.encodeproject.org/ENCBS987ARB/


title: microRNA counts from forebrain (ENCLB516AHA)

description:
https://www.encodeproject.org/experiments/ENCSR669EWD/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse forebrain
experiment encode accession: ENCSR669EWD
assay title: microRNA counts
assembly: mm10
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB516AHA
size range: <30

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (11.5 days)

value: forebrain

value: Forebrain from 88 embyronic 11.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS720JOH at ENCODE; https://www.encodeproject.org/ENCBS720JOH/


title: microRNA counts from hindbrain (ENCLB639WYE)

description:
https://www.encodeproject.org/experiments/ENCSR722SLO/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR722SLO
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-27
lab: Ali Mortazavi, UCI
library encode accession: ENCLB639WYE
size range: <30

value: hindbrain

value: Hindbrain from 69 embryonic 10.5 day mice

value: ENCBS626UIA at ENCODE; https://www.encodeproject.org/ENCBS626UIA/

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


title: microRNA counts from skeletal muscle tissue (ENCLB586OZP)

description:
https://www.encodeproject.org/experiments/ENCSR753HJF/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse skeletal muscle
experiment encode accession: ENCSR753HJF
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB586OZP
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: skeletal muscle tissue

value: single organ portion from 1 pup

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS015TUQ at ENCODE; https://www.encodeproject.org/ENCBS015TUQ/


title: microRNA counts from forebrain (ENCLB898CNP)

description:
https://www.encodeproject.org/experiments/ENCSR669EWD/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse forebrain
experiment encode accession: ENCSR669EWD
assay title: microRNA counts
assembly: mm10
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB898CNP
size range: <30

value: forebrain

value: tissue

value: Forebrain from 109 embyronic 11.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS745VOM at ENCODE; https://www.encodeproject.org/ENCBS745VOM/


title: microRNA counts from limb (ENCLB776UBX)

description:
https://www.encodeproject.org/experiments/ENCSR664WGP/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse limb
experiment encode accession: ENCSR664WGP
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB776UBX
size range: <30

value: limb

value: Limb from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS696JKV at ENCODE; https://www.encodeproject.org/ENCBS696JKV/


title: microRNA counts from heart (ENCLB342XIY)

description:
https://www.encodeproject.org/experiments/ENCSR652IDV/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse heart
experiment encode accession: ENCSR652IDV
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB342XIY
size range: <30

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (13.5 days)

value: heart

value: Heart from embryonic 13.5 day mice

value: ENCBS490ZWZ at ENCODE; https://www.encodeproject.org/ENCBS490ZWZ/

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


title: microRNA counts from neural tube (ENCLB935FZU)

description:
https://www.encodeproject.org/experiments/ENCSR702DUC/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR702DUC
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB935FZU
size range: <30

value: neural tube

value: Neural tube from 78 embryonic 15.5 day mice

value: ENCBS944KEZ at ENCODE; https://www.encodeproject.org/ENCBS944KEZ/


title: microRNA counts from forebrain (ENCLB893WGE)

description:
https://www.encodeproject.org/experiments/ENCSR743UOB/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR743UOB
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB893WGE
size range: <30

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (15.5 days)

value: forebrain

value: tissue

value: Forebrain from 62 embryonic 15.5 day mice

value: ENCBS841GER at ENCODE; https://www.encodeproject.org/ENCBS841GER/


title: TJ016-WYF

status: Public on Dec 09 2022

type: SRA

city: Wuhan

first: Yingying

last: Dong

address: 1095 Jie Fang Avenue

department: Department of Dermatology

country: China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

library_source: transcriptomic

data_processing:
The raw reads were manufactured by removing containing adapter, poly‘N’, low quality and <17nt reads using FASTQC to acquire clean reads.
Mapping reads were got by mapping clean reads to reference genome of BWA
The miRDeep2 was used to recognize known mature miRNAs according to miRBase21 (www.miRBase.org) and to predict novel miRNAs.
The miRNA expression were counted by Reads Per Million (RPM) values
Differential expression between two sets of specimens was counted by edgeR algorithm based on two criteria of |log2（Fold Change）|≥1 and P-value < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: text files include all detected miRNAs

organism: Homo sapiens

source_name: Exosome

extract_protocol:
Plasma exosomes and exosomal RNA of 20 samples were extracted and purified by exoRNeasy Maxi Kit.
Appropriately 50ng exosomal RNA of each samples was used to establish small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina

tag: age(years)

tag: gender

value: Female

tag: disease

value: Health person


title: microRNA counts from limb (ENCLB081AWE)

description:
https://www.encodeproject.org/experiments/ENCSR685QWR/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR685QWR
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB081AWE
size range: <30

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

value: limb

value: Limb from 51 embryonic 10.5 day mice

value: embryonic

value: Len Pennacchio, LBNL

value: ENCBS892NXC at ENCODE; https://www.encodeproject.org/ENCBS892NXC/


title: microRNA counts from kidney (ENCLB433XOF)

description:
https://www.encodeproject.org/experiments/ENCSR672TMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR672TMZ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB433XOF
size range: <30

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (15.5 days)

value: kidney

value: Kidney from 78 embryonic 15.5 day mice

value: pooled male and female

value: healthy

value: ENCBS899UOK at ENCODE; https://www.encodeproject.org/ENCBS899UOK/


title: microRNA counts from kidney (ENCLB960LHC)

description:
https://www.encodeproject.org/experiments/ENCSR672TMZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR672TMZ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB960LHC
size range: <30

value: Kidney from 62 embryonic 15.5 day mice

value: ENCBS924ZKF at ENCODE; https://www.encodeproject.org/ENCBS924ZKF/

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


title: microRNA counts from limb (ENCLB253VSY)

description:
https://www.encodeproject.org/experiments/ENCSR685QWR/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR685QWR
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB253VSY
size range: <30

value: tissue

value: Limb from 69 embryonic 10.5 day mice

value: ENCBS844FSC at ENCODE; https://www.encodeproject.org/ENCBS844FSC/


title: microRNA counts from heart (ENCLB564RBB)

description:
https://www.encodeproject.org/experiments/ENCSR652IDV/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse heart
experiment encode accession: ENCSR652IDV
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB564RBB
size range: <30

value: heart

value: Heart from embryonic 13.5 day mice

value: ENCBS814PLT at ENCODE; https://www.encodeproject.org/ENCBS814PLT/


title: microRNA counts from limb (ENCLB596IQI)

description:
https://www.encodeproject.org/experiments/ENCSR608HDW/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse limb
experiment encode accession: ENCSR608HDW
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB596IQI
size range: <30

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (13.5 days)

value: limb

value: Limb from embryonic 13.5 day mice

value: embryonic

value: ENCBS896ZED at ENCODE; https://www.encodeproject.org/ENCBS896ZED/


title: microRNA counts from limb (ENCLB689JCG)

description:
https://www.encodeproject.org/experiments/ENCSR608HDW/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse limb
experiment encode accession: ENCSR608HDW
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB689JCG
size range: <30

value: Len Pennacchio, LBNL

value: ENCBS176PGP at ENCODE; https://www.encodeproject.org/ENCBS176PGP/


title: Alb-Cre;UBR7fl/fl #3

city: Guangxi

first: Bo

last: Tang

address: 6 Shuangyong Road

institute: Guangxi Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRCh38.91 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include normalized Conut values and raw fragment counts for each Sample

source_name: Mouse liver primary cells

growth_protocol: The conditionally immortalized mouse liver primary cells were cultured under growth permissive conditions at 37 °C in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: Wild-type and Alb-Cre;UBR7fl/fl mouse liver primary cells

tag: tissue

value: Mouse liver primary cells

tag: genotype/variation


title: microRNA counts from limb (ENCLB931SIA)

description:
https://www.encodeproject.org/experiments/ENCSR606IHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse limb
experiment encode accession: ENCSR606IHZ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB931SIA
size range: <30

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (11.5 days)

value: Limb from 109 embyronic 11.5 day mice

value: pooled male and female

value: healthy

value: ENCBS066IEL at ENCODE; https://www.encodeproject.org/ENCBS066IEL/


title: microRNA counts from hindbrain (ENCLB568INI)

description:
https://www.encodeproject.org/experiments/ENCSR598WZW/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse hindbrain
experiment encode accession: ENCSR598WZW
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB568INI
size range: <30

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (13.5 days)

value: hindbrain

value: tissue

value: Hindbrain from embryonic 13.5 day mice

value: ENCBS052EWC at ENCODE; https://www.encodeproject.org/ENCBS052EWC/

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


title: microRNA counts from hindbrain (ENCLB032NXA)

description:
https://www.encodeproject.org/experiments/ENCSR598WZW/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse hindbrain
experiment encode accession: ENCSR598WZW
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB032NXA
size range: <30

value: ENCBS296PIR at ENCODE; https://www.encodeproject.org/ENCBS296PIR/


title: microRNA counts from limb (ENCLB599BTA)

description:
https://www.encodeproject.org/experiments/ENCSR606IHZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse limb
experiment encode accession: ENCSR606IHZ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB599BTA
size range: <30

value: limb

value: Limb from 88 embyronic 11.5 day mice

value: ENCBS681XPR at ENCODE; https://www.encodeproject.org/ENCBS681XPR/


title: microRNA counts from heart (ENCLB997CGA)

description:
https://www.encodeproject.org/experiments/ENCSR590PHU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse heart
experiment encode accession: ENCSR590PHU
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB997CGA
size range: <30

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (11.5 days)

value: heart

value: Heart from 109 embyronic 11.5 day mice

value: embryonic

value: ENCBS225RIF at ENCODE; https://www.encodeproject.org/ENCBS225RIF/


title: microRNA counts from heart (ENCLB418BVI)

description:
https://www.encodeproject.org/experiments/ENCSR594ZQX/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse heart
experiment encode accession: ENCSR594ZQX
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB418BVI
size range: <30

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

value: Len Pennacchio, LBNL

value: ENCBS004ZLN at ENCODE; https://www.encodeproject.org/ENCBS004ZLN/


title: Islets, del1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina NovaSeq6000 platform in a 100 base paired-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: Isolated islets

extract_protocol:
Total RNA was extracted Qiagen MiRNeasy kit
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

tag: strain

tag: genotype

value: Cdh13 exon2 deleted

tag: diet

value: high-fat diet 6wks

value: 14 weeks old


title: microRNA counts from embryonic facial prominence (ENCLB101XJB)

description:
https://www.encodeproject.org/experiments/ENCSR506JCY/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR506JCY
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB101XJB
size range: <30

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (14.5 days)

value: embryonic facial prominence

value: tissue

value: single cranioface from pup 1 pregnant 2 collected 7/30/2014

value: pooled male and female

value: Barbara Wold, Caltech

value: ENCBS903HZW at ENCODE; https://www.encodeproject.org/ENCBS903HZW/


title: microRNA counts from limb (ENCLB642XQX)

description:
https://www.encodeproject.org/experiments/ENCSR552NEH/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse limb
experiment encode accession: ENCSR552NEH
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB642XQX
size range: <30

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (14.5 days)

value: limb

value: 4 limbs from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS300NIO at ENCODE; https://www.encodeproject.org/ENCBS300NIO/

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


title: microRNA counts from kidney (ENCLB451CXY)

description:
https://www.encodeproject.org/experiments/ENCSR596MKU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse kidney
experiment encode accession: ENCSR596MKU
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB451CXY
size range: <30

source_name: Mus musculus strain B6NCrl kidney tissue postnatal (0 days)

value: kidney

value: 2 kidneys from pup1 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: ENCBS103FKB at ENCODE; https://www.encodeproject.org/ENCBS103FKB/


title: microRNA counts from thymus (ENCLB614CRU)

description:
https://www.encodeproject.org/experiments/ENCSR523DJZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse thymus
experiment encode accession: ENCSR523DJZ
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB614CRU
size range: <30

source_name: Mus musculus strain B6NCrl thymus tissue postnatal (0 days)

value: thymus

value: two thymus lobes from pup2 pregnant 1

value: ENCBS079WTJ at ENCODE; https://www.encodeproject.org/ENCBS079WTJ/


title: microRNA counts from kidney (ENCLB089CNT)

description:
https://www.encodeproject.org/experiments/ENCSR498PUG/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse kidney
experiment encode accession: ENCSR498PUG
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB089CNT
size range: <30

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (16.5 days)

value: tissue

value: Kidney from 41 embyonic 16.5 day mice

value: embryonic

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS529OHA at ENCODE; https://www.encodeproject.org/ENCBS529OHA/


title: microRNA counts from kidney (ENCLB339ZDF)

description:
https://www.encodeproject.org/experiments/ENCSR498PUG/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse kidney
experiment encode accession: ENCSR498PUG
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB339ZDF
size range: <30

value: Kidney pooled from embyonic 16.5 day mice

value: pooled male and female

value: ENCBS519MUD at ENCODE; https://www.encodeproject.org/ENCBS519MUD/


title: microRNA counts from liver (ENCLB700BQY)

description:
https://www.encodeproject.org/experiments/ENCSR495JDH/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR495JDH
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB700BQY
size range: <30

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (13.5 days)

value: liver

value: Liver from embryonic 13.5 day mice

value: ENCBS373XWZ at ENCODE; https://www.encodeproject.org/ENCBS373XWZ/

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


title: microRNA counts from thymus (ENCLB993FGD)

description:
https://www.encodeproject.org/experiments/ENCSR523DJZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse thymus
experiment encode accession: ENCSR523DJZ
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB993FGD
size range: <30

value: two thymus lobes from pup3 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS898VIJ at ENCODE; https://www.encodeproject.org/ENCBS898VIJ/


title: microRNA counts from embryonic facial prominence (ENCLB866WRN)

description:
https://www.encodeproject.org/experiments/ENCSR506JCY/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR506JCY
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB866WRN
size range: <30

value: embryonic facial prominence

value: tissue

value: single cranioface from pup 1 pregnant 2 collected 7/24/2014

value: embryonic

value: ENCBS776GWF at ENCODE; https://www.encodeproject.org/ENCBS776GWF/


title: microRNA counts from liver (ENCLB055JZZ)

description:
https://www.encodeproject.org/experiments/ENCSR495JDH/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR495JDH
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB055JZZ
size range: <30

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS146FGW at ENCODE; https://www.encodeproject.org/ENCBS146FGW/


title: microRNA counts from embryonic facial prominence (ENCLB713PAV)

description:
https://www.encodeproject.org/experiments/ENCSR489TWI/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR489TWI
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB713PAV
size range: <30

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (12.5 days)

value: Embryonic facial prominence from 120 embryonic 12.5 day mice

value: ENCBS047UII at ENCODE; https://www.encodeproject.org/ENCBS047UII/


title: microRNA counts from embryonic facial prominence (ENCLB356DKU)

description:
https://www.encodeproject.org/experiments/ENCSR489TWI/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR489TWI
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB356DKU
size range: <30

value: Embryonic facial prominence from 88 embryonic 12.5 day mice

value: ENCBS399GYO at ENCODE; https://www.encodeproject.org/ENCBS399GYO/

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


title: microRNA counts from neural tube (ENCLB484JZQ)

description:
https://www.encodeproject.org/experiments/ENCSR485BIK/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse neural tube
experiment encode accession: ENCSR485BIK
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB484JZQ
size range: <30

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

value: neural tube

value: Neural tube from 88 embryonic 12.5 day mice

value: ENCBS254TSW at ENCODE; https://www.encodeproject.org/ENCBS254TSW/


title: microRNA counts from hindbrain (ENCLB899OXA)

description:
https://www.encodeproject.org/experiments/ENCSR471YND/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse hindbrain
experiment encode accession: ENCSR471YND
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB899OXA
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl hindbrain tissue postnatal (0 days)

value: hindbrain

value: single hindbrain from pup 3

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS901BYV at ENCODE; https://www.encodeproject.org/ENCBS901BYV/


title: microRNA counts from neural tube (ENCLB228PTA)

description:
https://www.encodeproject.org/experiments/ENCSR485BIK/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse neural tube
experiment encode accession: ENCSR485BIK
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB228PTA
size range: <30

value: tissue

value: Neural tube from 120 embryonic 12.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS405OOH at ENCODE; https://www.encodeproject.org/ENCBS405OOH/


title: microRNA counts from kidney (ENCLB998ZJK)

description:
https://www.encodeproject.org/experiments/ENCSR596MKU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse kidney
experiment encode accession: ENCSR596MKU
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB998ZJK
size range: <30

value: kidney

value: 2 kidneys from pup2 pregnant 1

value: ENCBS540QNA at ENCODE; https://www.encodeproject.org/ENCBS540QNA/

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


title: microRNA counts from heart (ENCLB286HJK)

description:
https://www.encodeproject.org/experiments/ENCSR594ZQX/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse heart
experiment encode accession: ENCSR594ZQX
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB286HJK
size range: <30

value: heart

value: Heart from 12.5 day mice

value: ENCBS452TDN at ENCODE; https://www.encodeproject.org/ENCBS452TDN/


title: microRNA counts from heart (ENCLB431KMM)

description:
https://www.encodeproject.org/experiments/ENCSR590PHU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse heart
experiment encode accession: ENCSR590PHU
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB431KMM
size range: <30

value: Heart from embryonic 11.5 day mice

value: ENCBS046IMM at ENCODE; https://www.encodeproject.org/ENCBS046IMM/


title: microRNA counts from hindbrain (ENCLB922PMO)

description:
https://www.encodeproject.org/experiments/ENCSR471YND/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse hindbrain
experiment encode accession: ENCSR471YND
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB922PMO
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: hindbrain

value: single hindbrain from pup 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS489BYD at ENCODE; https://www.encodeproject.org/ENCBS489BYD/


title: microRNA counts from limb (ENCLB135TDG)

description:
https://www.encodeproject.org/experiments/ENCSR552NEH/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse limb
experiment encode accession: ENCSR552NEH
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB135TDG
size range: <30

value: limb

value: tissue

value: 4 limbs from pup 1 pregnant 2 collected 7/17/2014

value: embryonic

value: pooled male and female

value: ENCBS471PIU at ENCODE; https://www.encodeproject.org/ENCBS471PIU/


title: microRNA counts from hindbrain (ENCLB545PZF)

description:
https://www.encodeproject.org/experiments/ENCSR392BBU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse hindbrain
experiment encode accession: ENCSR392BBU
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB545PZF
size range: <30

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (11.5 days)

value: Hindbrain from 109 embyronic 11.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS199NDR at ENCODE; https://www.encodeproject.org/ENCBS199NDR/

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


title: microRNA counts from hindbrain (ENCLB169RQJ)

description:
https://www.encodeproject.org/experiments/ENCSR392BBU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse hindbrain
experiment encode accession: ENCSR392BBU
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB169RQJ
size range: <30

value: hindbrain

value: Hindbrain from 88 embyronic 11.5 day mice

value: ENCBS976DPO at ENCODE; https://www.encodeproject.org/ENCBS976DPO/


title: microRNA counts from forebrain (ENCLB339YXT)

description:
https://www.encodeproject.org/experiments/ENCSR392AII/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse forebrain
experiment encode accession: ENCSR392AII
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB339YXT
size range: <30

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (14.5 days)

value: forebrain

value: single forebrain from pup1 pregnant 2 collected 7/24/2014

value: ENCBS567ABO at ENCODE; https://www.encodeproject.org/ENCBS567ABO/


title: microRNA counts from midbrain (ENCLB168TNP)

description:
https://www.encodeproject.org/experiments/ENCSR347QCM/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse midbrain
experiment encode accession: ENCSR347QCM
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB168TNP
size range: <30

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (16.5 days)

value: midbrain

value: Midbrain pooled from embyonic 16.5 day mice

value: ENCBS684MLE at ENCODE; https://www.encodeproject.org/ENCBS684MLE/


title: microRNA counts from neural tube (ENCLB939YWM)

description:
https://www.encodeproject.org/experiments/ENCSR369ZII/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse neural tube
experiment encode accession: ENCSR369ZII
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB939YWM
size range: <30

source_name: Mus musculus strain B6NCrl neural tube tissue postnatal (0 days)

value: neural tube

value: tissue

value: single neural tube from pup 2 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS897LGY at ENCODE; https://www.encodeproject.org/ENCBS897LGY/


title: microRNA counts from midbrain (ENCLB850YGH)

description:
https://www.encodeproject.org/experiments/ENCSR340CTF/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR340CTF
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB850YGH
size range: <30

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

value: Midbrain from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS491CAX at ENCODE; https://www.encodeproject.org/ENCBS491CAX/

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


title: microRNA counts from midbrain (ENCLB121YVA)

description:
https://www.encodeproject.org/experiments/ENCSR347QCM/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse midbrain
experiment encode accession: ENCSR347QCM
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB121YVA
size range: <30

value: midbrain

value: Midbrain from 37 embryonic 16.5 day mice

value: ENCBS463JSE at ENCODE; https://www.encodeproject.org/ENCBS463JSE/


title: microRNA counts from midbrain (ENCLB241DIY)

description:
https://www.encodeproject.org/experiments/ENCSR378DMT/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse midbrain
experiment encode accession: ENCSR378DMT
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB241DIY
size range: <30

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (11.5 days)

value: tissue

value: Midbrain of 109 embyronic 11.5 day mice

value: ENCBS228OBS at ENCODE; https://www.encodeproject.org/ENCBS228OBS/


title: microRNA counts from midbrain (ENCLB485FUS)

description:
https://www.encodeproject.org/experiments/ENCSR378DMT/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse midbrain
experiment encode accession: ENCSR378DMT
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB485FUS
size range: <30

value: Midbrain from 88 embyronic 11.5 day mice

value: ENCBS802FTI at ENCODE; https://www.encodeproject.org/ENCBS802FTI/


title: microRNA counts from neural tube (ENCLB997UNK)

description:
https://www.encodeproject.org/experiments/ENCSR369ZII/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse neural tube
experiment encode accession: ENCSR369ZII
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB997UNK
size range: <30

value: neural tube

value: single neural tube from pup 1 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS310ESD at ENCODE; https://www.encodeproject.org/ENCBS310ESD/


title: microRNA counts from spleen (ENCLB833EKC)

description:
https://www.encodeproject.org/experiments/ENCSR332XWL/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse spleen
experiment encode accession: ENCSR332XWL
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB833EKC
size range: <30

source_name: Mus musculus strain B6NCrl spleen tissue postnatal (0 days)

value: spleen

value: 1 spleen from pup1 pregnant 1

value: ENCBS051QLA at ENCODE; https://www.encodeproject.org/ENCBS051QLA/


title: microRNA counts from liver (ENCLB186OFU)

description:
https://www.encodeproject.org/experiments/ENCSR327VOK/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse liver
experiment encode accession: ENCSR327VOK
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB186OFU
size range: <30

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (16.5 days)

value: liver

value: Liver from 41 embyonic 16.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS279BWR at ENCODE; https://www.encodeproject.org/ENCBS279BWR/

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


title: microRNA counts from spleen (ENCLB511EOA)

description:
https://www.encodeproject.org/experiments/ENCSR332XWL/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse spleen
experiment encode accession: ENCSR332XWL
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB511EOA
size range: <30

value: tissue

value: 1 spleen from pup2 pregnant 1

value: ENCBS173QYQ at ENCODE; https://www.encodeproject.org/ENCBS173QYQ/


title: microRNA counts from stomach (ENCLB557DKF)

description:
https://www.encodeproject.org/experiments/ENCSR323GNP/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse stomach
experiment encode accession: ENCSR323GNP
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB557DKF
size range: <30

source_name: Mus musculus strain B6NCrl stomach tissue postnatal (0 days)

value: stomach

value: 1 stomach from pup2 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: ENCBS796AGC at ENCODE; https://www.encodeproject.org/ENCBS796AGC/


title: microRNA counts from liver (ENCLB770QJO)

description:
https://www.encodeproject.org/experiments/ENCSR327VOK/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse liver
experiment encode accession: ENCSR327VOK
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB770QJO
size range: <30

value: liver

value: Liver pooled from embyonic 16.5 day mice

value: ENCBS236CDJ at ENCODE; https://www.encodeproject.org/ENCBS236CDJ/


title: microRNA counts from stomach (ENCLB892EEJ)

description:
https://www.encodeproject.org/experiments/ENCSR323GNP/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse stomach
experiment encode accession: ENCSR323GNP
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB892EEJ
size range: <30

value: 1 stomach from pup1 pregnant 1

value: Barbara Wold, Caltech

value: ENCBS762UVC at ENCODE; https://www.encodeproject.org/ENCBS762UVC/


title: microRNA counts from heart (ENCLB512FUI)

description:
https://www.encodeproject.org/experiments/ENCSR301FQU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse heart
experiment encode accession: ENCSR301FQU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB512FUI
size range: <30

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (15.5 days)

value: heart

value: Heart from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS909LOF at ENCODE; https://www.encodeproject.org/ENCBS909LOF/


title: microRNA counts from heart (ENCLB388XGI)

description:
https://www.encodeproject.org/experiments/ENCSR301FQU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse heart
experiment encode accession: ENCSR301FQU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB388XGI
size range: <30

value: tissue

value: Heart from 78 embryonic 15.5 day mice

value: ENCBS595EMK at ENCODE; https://www.encodeproject.org/ENCBS595EMK/

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


title: microRNA counts from liver (ENCLB814QOM)

description:
https://www.encodeproject.org/experiments/ENCSR283GCF/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR283GCF
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB814QOM
size range: <30

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (14.5 days)

value: liver

value: single liver from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS237YNZ at ENCODE; https://www.encodeproject.org/ENCBS237YNZ/


title: microRNA counts from forebrain (ENCLB699KIA)

description:
https://www.encodeproject.org/experiments/ENCSR392AII/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse forebrain
experiment encode accession: ENCSR392AII
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB699KIA
size range: <30

value: forebrain

value: single forebrain from pup1 pregnant 2 collected 7/30/2014

value: ENCBS295MUN at ENCODE; https://www.encodeproject.org/ENCBS295MUN/


title: microRNA counts from intestine (ENCLB729WSB)

description:
https://www.encodeproject.org/experiments/ENCSR262WRN/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse intestine
experiment encode accession: ENCSR262WRN
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB729WSB
size range: <30

source_name: Mus musculus strain B6NCrl intestine tissue mixed sex embryo (15.5 days)

value: intestine

value: Intestine from 78 embryonic 15.5 day mice

value: ENCBS401LLS at ENCODE; https://www.encodeproject.org/ENCBS401LLS/


title: microRNA counts from hindbrain (ENCLB432LWM)

description:
https://www.encodeproject.org/experiments/ENCSR269WSU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR269WSU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB432LWM
size range: <30

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (16.5 days)

value: hindbrain

value: Hindbrain pooled from embyonic 16.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS436LSH at ENCODE; https://www.encodeproject.org/ENCBS436LSH/


title: microRNA counts from lung (ENCLB145FJW)

description:
https://www.encodeproject.org/experiments/ENCSR277GWK/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR277GWK
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB145FJW
size range: <30

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (15.5 days)

value: lung

value: tissue

value: Lung from 78 embryonic 15.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS467HSM at ENCODE; https://www.encodeproject.org/ENCBS467HSM/


title: microRNA counts from intestine (ENCLB469QXC)

description:
https://www.encodeproject.org/experiments/ENCSR262WRN/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse intestine
experiment encode accession: ENCSR262WRN
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB469QXC
size range: <30

value: Intestine from 62 embryonic 15.5 day mice

value: ENCBS836WEU at ENCODE; https://www.encodeproject.org/ENCBS836WEU/

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


title: microRNA counts from liver (ENCLB224HBC)

description:
https://www.encodeproject.org/experiments/ENCSR283GCF/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR283GCF
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB224HBC
size range: <30

value: liver

value: single liver from pup 1 pregnant 2 collected 7/17/2014

value: Barbara Wold, Caltech

value: ENCBS314UPI at ENCODE; https://www.encodeproject.org/ENCBS314UPI/


title: microRNA counts from hindbrain (ENCLB050IQD)

description:
https://www.encodeproject.org/experiments/ENCSR269WSU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR269WSU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB050IQD
size range: <30

value: hindbrain

value: Hindbrain from 37 embryonic 16.5 day mice

value: ENCBS281ZLI at ENCODE; https://www.encodeproject.org/ENCBS281ZLI/


title: microRNA counts from lung (ENCLB325MXZ)

description:
https://www.encodeproject.org/experiments/ENCSR277GWK/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR277GWK
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB325MXZ
size range: <30

value: Lung from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS217WPC at ENCODE; https://www.encodeproject.org/ENCBS217WPC/


title: microRNA counts from midbrain (ENCLB172YLV)

description:
https://www.encodeproject.org/experiments/ENCSR340CTF/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR340CTF
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB172YLV
size range: <30

value: midbrain

value: tissue

value: Midbrain from 51 embryonic 10.5 day mice

value: healthy

value: ENCBS613YYL at ENCODE; https://www.encodeproject.org/ENCBS613YYL/


title: microRNA counts from midbrain (ENCLB538NNI)

description:
https://www.encodeproject.org/experiments/ENCSR247SSE/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR247SSE
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB538NNI
size range: <30

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (15.5 days)

value: Midbrain from 62 embryonic 15.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS381PEJ at ENCODE; https://www.encodeproject.org/ENCBS381PEJ/

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


title: microRNA counts from midbrain (ENCLB114TXZ)

description:
https://www.encodeproject.org/experiments/ENCSR257PBL/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse midbrain
experiment encode accession: ENCSR257PBL
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB114TXZ
size range: <30

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

value: Midbrain from 88 embryonic 12.5 day mice

value: ENCBS280TPA at ENCODE; https://www.encodeproject.org/ENCBS280TPA/


title: microRNA counts from midbrain (ENCLB246SCB)

description:
https://www.encodeproject.org/experiments/ENCSR247SSE/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR247SSE
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB246SCB
size range: <30

value: Midbrain from 78 embryonic 15.5 day mice

value: ENCBS190ETJ at ENCODE; https://www.encodeproject.org/ENCBS190ETJ/


title: microRNA counts from intestine (ENCLB317QOX)

description:
https://www.encodeproject.org/experiments/ENCSR232JFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse intestine
experiment encode accession: ENCSR232JFQ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB317QOX
size range: <30

source_name: Mus musculus strain B6NCrl intestine tissue postnatal (0 days)

value: intestine

value: 1 intestine from pup1 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS182YRY at ENCODE; https://www.encodeproject.org/ENCBS182YRY/


title: microRNA counts from intestine (ENCLB114LNC)

description:
https://www.encodeproject.org/experiments/ENCSR232JFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse intestine
experiment encode accession: ENCSR232JFQ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB114LNC
size range: <30

value: tissue

value: 1 intestine from pup2 pregnant 1

value: ENCBS623WQD at ENCODE; https://www.encodeproject.org/ENCBS623WQD/


title: microRNA counts from stomach (ENCLB371IIJ)

description:
https://www.encodeproject.org/experiments/ENCSR213NEM/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR213NEM
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB371IIJ
size range: <30

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (16.5 days)

value: stomach

value: Stomach pooled from embyonic 16.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS243DCE at ENCODE; https://www.encodeproject.org/ENCBS243DCE/


title: microRNA counts from embryonic facial prominence (ENCLB057RQJ)

description:
https://www.encodeproject.org/experiments/ENCSR201KHF/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse embryonic facial prominence
experiment encode accession: ENCSR201KHF
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB057RQJ
size range: <30

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (11.5 days)

value: embryonic facial prominence

value: Craniofacial prominence from 88 embyronic 11.5 day mice

value: ENCBS468NAL at ENCODE; https://www.encodeproject.org/ENCBS468NAL/

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


title: microRNA counts from embryonic facial prominence (ENCLB724HWR)

description:
https://www.encodeproject.org/experiments/ENCSR207NKU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR207NKU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB724HWR
size range: <30

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (13.5 days)

value: Embryonic facial prominence from embryonic 13.5 day mice

value: ENCBS847MIW at ENCODE; https://www.encodeproject.org/ENCBS847MIW/


title: microRNA counts from embryonic facial prominence (ENCLB834URQ)

description:
https://www.encodeproject.org/experiments/ENCSR201KHF/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse embryonic facial prominence
experiment encode accession: ENCSR201KHF
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB834URQ
size range: <30

value: Craniofacial prominence from 109 embyronic 11.5 day mice

value: ENCBS141GPQ at ENCODE; https://www.encodeproject.org/ENCBS141GPQ/


title: microRNA counts from neural tube (ENCLB929ALO)

description:
https://www.encodeproject.org/experiments/ENCSR184JSL/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse neural tube
experiment encode accession: ENCSR184JSL
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB929ALO
size range: <30

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (14.5 days)

value: neural tube

value: tissue

value: single neural tube from pup 1 pregnant 2 collected 7/29/2014

value: Barbara Wold, Caltech

value: ENCBS883PNF at ENCODE; https://www.encodeproject.org/ENCBS883PNF/


title: microRNA counts from stomach (ENCLB931GXB)

description:
https://www.encodeproject.org/experiments/ENCSR213NEM/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR213NEM
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB931GXB
size range: <30

value: stomach

value: Stomach from 41 embyonic 16.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS793TEW at ENCODE; https://www.encodeproject.org/ENCBS793TEW/


title: microRNA counts from forebrain (ENCLB382NTE)

description:
https://www.encodeproject.org/experiments/ENCSR184PQQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR184PQQ
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB382NTE
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl forebrain tissue postnatal (0 days)

value: forebrain

value: single forebrain from pup 1

value: 0 day

value: postnatal

value: not collected

value: ENCBS033OJJ at ENCODE; https://www.encodeproject.org/ENCBS033OJJ/


title: microRNA counts from lung (ENCLB836SMV)

description:
https://www.encodeproject.org/experiments/ENCSR137ZTO/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse lung
experiment encode accession: ENCSR137ZTO
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB836SMV
size range: <30

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (16.5 days)

value: lung

value: Lung from 41 embyonic 16.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS833ZFI at ENCODE; https://www.encodeproject.org/ENCBS833ZFI/

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


title: microRNA counts from neural tube (ENCLB391WPZ)

description:
https://www.encodeproject.org/experiments/ENCSR132FJG/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR132FJG
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB391WPZ
size range: <30

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (13.5 days)

value: neural tube

value: tissue

value: Neural tube from embryonic 13.5 day mice

value: ENCBS549OYR at ENCODE; https://www.encodeproject.org/ENCBS549OYR/


title: microRNA counts from midbrain (ENCLB692EWW)

description:
https://www.encodeproject.org/experiments/ENCSR215OAK/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR215OAK
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB692EWW
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl midbrain tissue postnatal (0 days)

value: midbrain

value: single midbrain from pup 1

value: Barbara Wold, Caltech

value: ENCBS169PZD at ENCODE; https://www.encodeproject.org/ENCBS169PZD/


title: microRNA counts from forebrain (ENCLB106YIE)

description:
https://www.encodeproject.org/experiments/ENCSR184PQQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR184PQQ
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB106YIE
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: forebrain

value: single forebrain from pup 3

value: 0 day

value: postnatal

value: ENCBS804WMS at ENCODE; https://www.encodeproject.org/ENCBS804WMS/


title: microRNA counts from midbrain (ENCLB262UQU)

description:
https://www.encodeproject.org/experiments/ENCSR215OAK/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR215OAK
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB262UQU
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: single midbrain from pup 3

value: not collected

value: ENCBS960FNV at ENCODE; https://www.encodeproject.org/ENCBS960FNV/


title: microRNA counts from midbrain (ENCLB568DQB)

description:
https://www.encodeproject.org/experiments/ENCSR257PBL/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse midbrain
experiment encode accession: ENCSR257PBL
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB568DQB
size range: <30

value: Midbrain from 120 embryonic 12.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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

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


title: microRNA counts from lung (ENCLB814SUE)

description:
https://www.encodeproject.org/experiments/ENCSR137ZTO/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse lung
experiment encode accession: ENCSR137ZTO
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB814SUE
size range: <30

value: lung

value: tissue

value: Lung pooled from embyonic 16.5 day mice

value: ENCBS377RBN at ENCODE; https://www.encodeproject.org/ENCBS377RBN/


title: microRNA counts from neural tube (ENCLB831MNE)

description:
https://www.encodeproject.org/experiments/ENCSR184JSL/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse neural tube
experiment encode accession: ENCSR184JSL
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB831MNE
size range: <30

value: neural tube

value: single neural tube from pup 1 pregnant 1 collected 7/29/2014

value: Barbara Wold, Caltech

value: ENCBS431CVS at ENCODE; https://www.encodeproject.org/ENCBS431CVS/


title: microRNA counts from neural tube (ENCLB252AJO)

description:
https://www.encodeproject.org/experiments/ENCSR132FJG/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR132FJG
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB252AJO
size range: <30

value: Neural tube from embryonic 13.5 day mice

value: ENCBS956BQY at ENCODE; https://www.encodeproject.org/ENCBS956BQY/


title: microRNA counts from midbrain (ENCLB841AMF)

description:
https://www.encodeproject.org/experiments/ENCSR130SVF/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse midbrain
experiment encode accession: ENCSR130SVF
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB841AMF
size range: <30

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (13.5 days)

value: midbrain

value: Midbrain from embryonic 13.5 day mice

value: ENCBS725LVX at ENCODE; https://www.encodeproject.org/ENCBS725LVX/


title: microRNA counts from urinary bladder (ENCLB405HRC)

description:
https://www.encodeproject.org/experiments/ENCSR108YYU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse bladder
experiment encode accession: ENCSR108YYU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB405HRC
size range: <30

source_name: Mus musculus strain B6NCrl bladder tissue postnatal (0 days)

value: urinary bladder

value: 1 bladder from pup1 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: ENCBS809DPZ at ENCODE; https://www.encodeproject.org/ENCBS809DPZ/


title: microRNA counts from urinary bladder (ENCLB676EVP)

description:
https://www.encodeproject.org/experiments/ENCSR108YYU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse bladder
experiment encode accession: ENCSR108YYU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB676EVP
size range: <30

value: tissue

value: 1 bladder from pup2 pregnant 1

value: ENCBS437LDX at ENCODE; https://www.encodeproject.org/ENCBS437LDX/

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


title: microRNA counts from midbrain (ENCLB611OOK)

description:
https://www.encodeproject.org/experiments/ENCSR130SVF/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse midbrain
experiment encode accession: ENCSR130SVF
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB611OOK
size range: <30

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS185VNZ at ENCODE; https://www.encodeproject.org/ENCBS185VNZ/


title: microRNA counts from hindbrain (ENCLB841ELL)

description:
https://www.encodeproject.org/experiments/ENCSR083USL/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse hindbrain
experiment encode accession: ENCSR083USL
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB841ELL
size range: <30

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (14.5 days)

value: hindbrain

value: single hindbrain from pup 1 pregnant 2 collected 7/24/2014

value: Barbara Wold, Caltech

value: ENCBS909QXI at ENCODE; https://www.encodeproject.org/ENCBS909QXI/


title: microRNA counts from lung (ENCLB403HJH)

description:
https://www.encodeproject.org/experiments/ENCSR100XAT/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse lung
experiment encode accession: ENCSR100XAT
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB403HJH
size range: <30

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (14.5 days)

value: lung

value: single lung from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS581DHV at ENCODE; https://www.encodeproject.org/ENCBS581DHV/


title: microRNA counts from lung (ENCLB692EFR)

description:
https://www.encodeproject.org/experiments/ENCSR100XAT/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse lung
experiment encode accession: ENCSR100XAT
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB692EFR
size range: <30

value: single lung from pup 1 pregnant 2 collected 7/17/2014

value: ENCBS133FDE at ENCODE; https://www.encodeproject.org/ENCBS133FDE/


title: microRNA counts from hindbrain (ENCLB203XBH)

description:
https://www.encodeproject.org/experiments/ENCSR083USL/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse hindbrain
experiment encode accession: ENCSR083USL
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB203XBH
size range: <30

value: tissue

value: single hindbrain from pup 1 pregnant 2 collected 7/30/2014

value: ENCBS233QWW at ENCODE; https://www.encodeproject.org/ENCBS233QWW/


title: microRNA counts from heart (ENCLB458BAT)

description:
https://www.encodeproject.org/experiments/ENCSR037NRU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR037NRU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB458BAT
size range: <30

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (16.5 days)

value: heart

value: Heart from 41 embyonic 16.5 day mice

value: embryonic

value: ENCBS217XWR at ENCODE; https://www.encodeproject.org/ENCBS217XWR/

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


title: microRNA counts from heart (ENCLB438RKU)

description:
https://www.encodeproject.org/experiments/ENCSR037NRU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR037NRU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB438RKU
size range: <30

value: Heart pooled from embyonic 16.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS955JPC at ENCODE; https://www.encodeproject.org/ENCBS955JPC/


title: microRNA counts from limb (ENCLB502NIK)

description:
https://www.encodeproject.org/experiments/ENCSR042BYK/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse limb
experiment encode accession: ENCSR042BYK
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB502NIK
size range: <30

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

value: limb

value: Limb from 68 embryonic 12.5 day mice

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


title: microRNA counts from limb (ENCLB752QIU)

description:
https://www.encodeproject.org/experiments/ENCSR042BYK/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse limb
experiment encode accession: ENCSR042BYK
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB752QIU
size range: <30

value: Limb from 88 embryonic 12.5 day mice

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


title: microRNA counts from embryonic facial prominence (ENCLB676VVG)

description:
https://www.encodeproject.org/experiments/ENCSR207NKU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR207NKU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB676VVG
size range: <30

value: embryonic facial prominence

value: tissue

value: Embryonic facial prominence from embryonic 13.5 day mice

value: ENCBS764ZZN at ENCODE; https://www.encodeproject.org/ENCBS764ZZN/


title: microRNA counts from liver (ENCLB543WYC)

description:
https://www.encodeproject.org/experiments/ENCSR035TGL/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse liver
experiment encode accession: ENCSR035TGL
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB543WYC
size range: <30

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (15.5 days)

value: liver

value: Liver from 62 embryonic 15.5 day mice

value: embryonic

value: ENCBS966PAM at ENCODE; https://www.encodeproject.org/ENCBS966PAM/


title: microRNA counts from liver (ENCLB599TLX)

description:
https://www.encodeproject.org/experiments/ENCSR035TGL/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse liver
experiment encode accession: ENCSR035TGL
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB599TLX
size range: <30

value: Liver from 78 embryonic 15.5 day mice

value: pooled male and female

value: ENCBS734ENZ at ENCODE; https://www.encodeproject.org/ENCBS734ENZ/

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


title: microRNA counts from heart (ENCLB177GPG)

description:
https://www.encodeproject.org/experiments/ENCSR023TWU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse heart
experiment encode accession: ENCSR023TWU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB177GPG
size range: <30

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (14.5 days)

value: heart

value: single heart from pup 1 pregnant 2 collected 7/17/2014

value: Barbara Wold, Caltech

value: ENCBS925AWF at ENCODE; https://www.encodeproject.org/ENCBS925AWF/


title: microRNA counts from heart (ENCLB213XIG)

description:
https://www.encodeproject.org/experiments/ENCSR023TWU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse heart
experiment encode accession: ENCSR023TWU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB213XIG
size range: <30

value: single heart from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS824QSS at ENCODE; https://www.encodeproject.org/ENCBS824QSS/


title: microRNA counts from lung (ENCLB686PIK)

description:
https://www.encodeproject.org/experiments/ENCSR025YVG/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse lung
experiment encode accession: ENCSR025YVG
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB686PIK
size range: <30

source_name: Mus musculus strain B6NCrl lung tissue postnatal (0 days)

value: lung

value: tissue

value: 2 lungs from pup1 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: ENCBS747AFS at ENCODE; https://www.encodeproject.org/ENCBS747AFS/


title: microRNA counts from stomach (ENCLB550ZYX)

description:
https://www.encodeproject.org/experiments/ENCSR006GDO/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR006GDO
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB550ZYX
size range: <30

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (15.5 days)

value: stomach

value: Stomach from 78 embryonic 15.5 day mice

value: embryonic

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS915SZN at ENCODE; https://www.encodeproject.org/ENCBS915SZN/


title: microRNA counts from lung (ENCLB301BXL)

description:
https://www.encodeproject.org/experiments/ENCSR025YVG/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse lung
experiment encode accession: ENCSR025YVG
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB301BXL
size range: <30

value: 2 lungs from pup3 pregnant 1

value: Barbara Wold, Caltech

value: ENCBS438DQO at ENCODE; https://www.encodeproject.org/ENCBS438DQO/

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


title: microRNA counts from stomach (ENCLB260RDD)

description:
https://www.encodeproject.org/experiments/ENCSR006GDO/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR006GDO
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB260RDD
size range: <30

value: Stomach from 62 embryonic 15.5 day mice

value: pooled male and female

value: ENCBS355TAQ at ENCODE; https://www.encodeproject.org/ENCBS355TAQ/


title: microRNA counts from forebrain (ENCLB177YKT)

description:
https://www.encodeproject.org/experiments/ENCSR002TKA/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse forebrain
experiment encode accession: ENCSR002TKA
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB177YKT
size range: <30

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

value: forebrain

value: tissue

value: Forebrain from 68 embryonic 12.5 day mice

value: ENCBS617DPG at ENCODE; https://www.encodeproject.org/ENCBS617DPG/


title: Reindeer_3WD_Back__day_7 62167

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts.
Sequencing reads were mapped using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: Bos Taurus  transcriptome (NCBI: GCF_002263795.1_ARS-UCD1.2)
Supplementary_files_format_and_content: Collated rsem output into tab files, expected counts (ec) and transcripts per million (tpm's)

organism: Rangifer tarandus

extract_protocol:
Total RNA from cells were isolated with RNeasy Plus kit (QIAGEN).
Sequencing libraries were prepared following the LM-seq protocol (Hou et al., 2015).
Sequenced on Illumina HiSeq 2500 at a depth of 17 samples per lane.

value: Back

tag: days post wound

tag: control

value: FALSE


title: Reindeer__3WD_Antler__day_3 62164

value: Antler


title: Reindeer_3YD_Back__day_14_ 62170


title: Reindeer_3YD__Antler__day_14_Control 62169

value: TRUE


title: Reindeer_3WD__Antler__day_14 62168


title: Reindeer_3WD__Antler__day_7 62166


title: Reindeer_3WD__Back__day_3 62165


title: Reindeer_3YD__Antler__day_14_Control 62161


title: Reindeer_3YD__Antler__day_7 62159


title: Reindeer_3YD_Back__day_7 62160


title: Reindeer_3WD_Antler__day_0 62162


title: Reindeer_3WD__Back__day_0 62163


title: Reindeer_5XD__Antler__day_14_Control 62153


title: Reindeer_5XD__Antler__day_14 62152


title: Reindeer_3YD__Back__day_0 62156


title: Reindeer__3YD_Antler__day_3 62157


title: Reindeer_3YD__Back__day_3 62158


title: Reindeer_5XD_Back__day_7 62151


title: Reindeer_5XD__Back__day_3 62149


title: Reindeer_5XD__Back__day_0 62147


title: Reindeer_5XD__Antler__day_7 62150


title: Reindeer_1A__Antler__day_14_Control 62144


title: Reindeer_1A__Antler__day_7 62141


title: Reindeer_1A__Antler__day_14 62143


title: Reindeer_1A__Back__day_7 62142


title: Reindeer_1A__Back__day_3 62140


title: Reindeer_1A__Antler__day_3 62139


title: Reindeer__5XD_Antler__day_3 62148


title: Reindeer_5XD_Antler__day_0 62146


title: Reindeer_1A__Back__day_0 62138


title: Reindeer_5XD_Back__day_14_ 62154


title: Reindeer_3YD_Antler__day_0 62155


title: microRNA counts from forebrain (ENCLB164HME)

description:
https://www.encodeproject.org/experiments/ENCSR002TKA/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse forebrain
experiment encode accession: ENCSR002TKA
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB164HME
size range: <30

tag: description

value: Forebrain from 120 embryonic 12.5 day mice

tag: biosample encode accession

value: embryonic

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS974GPH at ENCODE; https://www.encodeproject.org/ENCBS974GPH/


title: Reindeer_1A__Back__day_14_ 62145


title: HepAD38 mRNA, B02 (20 uM), 7h, rep2 [s17]

city: Doylestown

first: Ju-Tao

last: Guo

state: PA

address: 3805 Old easton road

institute: Baruch S Blumberg Institute

data_processing:
The HiSeq Real Time Analysis software (RTA 1.18.64) was used for processing raw data files, the Illumina bcl2fastq2.17 was used to demultiplex and convert binary base calls and qualities to fastq format.
The sequencing reads were trimmed adapters and low quality bases using Cutadapt ( (version 1.18).
The trimmed reads were mapped to human reference genome (hg38) and GENCODE annotation v24  using  STAR aligner (version 2.6.1) with two-pass alignment option.
RSEM (version 1.3.1) was used for gene and transcript quantification based on GENCODE v24 GTF file.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count and normalized RPKM values in gene count matrix file format for all samples

molecule: polyA RNA

growth_protocol: HepAD38 were cultured in the presence of 2 mM PFA from day 2 to day 6 after tet removal.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq tranded_mRNA Dual_Index library prep kit following manufacturer's protocols.

treatment_protocol: followed with DMSO or B02 (20 uM) treatment for 7 h. Total RNA was extracted by TRIzol.

tag: cell line

tag: cell type

value: Hepatocyte

tag: treatment

tag: time

value: 7 hour


title: HepAD38 mRNA, DMSO, 7h, rep1 [s13]

value: DMSO


title: HepAD38 mRNA, B02 (20 uM), 7h, rep1 [s16]


title: HepAD38 mRNA, DMSO, 7h, rep3 [s15]


title: HepAD38 mRNA, DMSO, 7h, rep2 [s14]


title: M7_2

city: Guiyang

first: Jiao

last: Xu

address: Dongqing South Road, Huaxi District

institute: Guizhou University of traditonal Chinese Medicine

description: biol rep 2

data_processing:
The data quality control was used by FastQC
The data filtered using fastx_toolkit Version 0.0.14（http://hannonlab.cshl.edu/fastx_toolkit/）
Then all clean reads were used for de novo assembly with Trinity, (http://trinityrnaseq.sourceforge.net/).
The TPM was calculated by RSEM（http://deweylab.github.io/RSEM/ software）.

organism: Dipsacus asperoides

source_name: root

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Promega). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The roots of one-leaf stage (L1), two-leaf stage (L2), and plants that had been growing for 7 months (M7)

value: root

value: WT

tag: developmental stage

value: the root of plants that had been growing for 7 months


title: M7_1

description: biol rep 1


title: M7_3

description: biol rep 3


title: Sl ChIP-Seq GLK1 Solyc07g053630 replicate 2

city: Hong Kong

first: Sibo

last: REN

address: Sha tin CUHK

institute: The Chinese University of Hong Kong

library_source: genomic

data_processing:
ChIP-seq reads 100 bp from 3’ end were trimmed with the bowtie2 parameter -3 100.
ChIP-seq reads were aligned to plant reference genomes (Arabidopsis thaliana TAIR10, Nicotiana benthamiana version 2.5.1, Solanum lycopersicum SL4.0, Oryza sativa MSU7.0 and Zea mays RefGen_v4) using Bowtie 2 (version 2.3.2).
The ENCODE2 ChIP-seq pipline with MACS2 (version 2.2.1) and IDR (version 2.0.4.2) were used for peak calling. Peak summit positions were retrieved by using the “--call-summits” function in MACS2. The regions +/- 75bp from the summit position with signal fold-change in NarrowPeak format were then supplied to IDR, and the regions passed the IDR 0.01 and summit signal foldchange cut-off were kept and resized back to 150bp.
BigWig files were generated using the samtools view with binsize 1bp.
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

organism: Solanum lycopersicum

source_name: Leaf

extract_protocol:
The nuclei were then isolated by filtration and centrifugation, and the chromatin was sonicated to sub-kb fragments using Bioruptor.
ChIP-seq libraries were prepared using the HiSeq X Ten.

value: Leaf

tag: replicate

value: replicate 2

tag: chip antibody

value: Rabbit polyclonal anti-GFP, Invitrogen, Cat# A-11122


title: Sl ChIP-Seq GLK1 Solyc07g053630 replicate 1

value: replicate 1

value: Rabbit monoclonal anti-HA (clone C29F4), Cell Signaling Technology, Cat# 3724


title: Sl ChIP-Seq GLK2 Solyc10g008160 replicate 1


title: Sl ChIP-Seq GLK2 Solyc10g008160 replicate 2

value: Rabbit polyclonal anti-GFP, Invitrogen, Cat# A-11122; Rabbit monoclonal anti-HA (clone C29F4), Cell Signaling Technology, Cat# 3735


title: L2_3

description: biol rep 3

value: roots of two-leaf stage


title: L2_2

description: biol rep 2


title: Reindeer_1A__Antler__day_0 62137

value: Antler

value: FALSE


title: HepAD38 mRNA, B02 (20 uM), 7h, rep3 [s18]


title: L1_3

description: biol rep 3

value: roots of one-leaf stage


title: L1_2

description: biol rep 2


title: bulk RNA sequencing of primary tumor

city: Pittsburgh

first: Kai

last: Ding

address: 204 Craft Ave

institute: University of Pittsburgh

description:
Primary_bulk
bulk RNA
BoM_primary_bulkRNA.txt

data_processing:
FastQC for quality, Salmon for reads mapping, log2 trimmed mean counts per million for data normalization.
Assembly: GRCh38
Supplementary files format and content: PDOs_LogCounts.txt: text file of normalized counts, with row as gene column as cell.
Supplementary files format and content: BoM_primary_bulkRNA.txt: text file of normalized counts, with row as gene column as sample.

source_name: primary breast cancer

extract_protocol:
Qiagen RNeasy FFPE kit.
Illumina TruSeq Stranded mRNA (Exome/Access) for FFPE kit.

value: primary breast cancer

value: breast cancer and stromal cells


title: bulk RNA sequencing of BoM2

description:
BoM2_bulk
bulk RNA
BoM_primary_bulkRNA.txt

source_name: breast cancer bone metastases

value: breast cancer bone metastases


title: bulk RNA sequencing of BoM1

description:
BoM1_bulk
bulk RNA
BoM_primary_bulkRNA.txt


title: plasma-derived AS-exosomes Nymber 8

city: Toronto

first: Fataneh

last: Tavasolian

state: Ontario

address: 60 leonard Ave

institute: Krembil Research institute

description:
Total RNA extracted form Plasma derived exosomes
Fataneh19

data_processing:
CLC Genomic Workbench20 (version 5.5.2; CLC bio)
Supplementary files format and content: tab-delimited text files

source_name: Plasma

growth_protocol: Plasma was extracted from venous blood samples collected during clinic hours. Heparinized tubes were centrifuged at 460g (1600rpm) for 10 min before plasma was collected. Plasma aliquots, stored at -80 °C until required, underwent only one freeze-thaw cycle. With the remaining cellular layer from the heparin tubes, peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll–Paque PLUS (GE Healthcare Bioscience, ON, Canada) and were transferred to liquid N2 for storage.

extract_protocol:
RNA extraction from exosomes  The entire method for isolating RNA from exosomes with exoRNeasy Midi Kit (Qiagen) consists of two steps: exosome purification and RNA isolation. Isolating RNA from exosomes consisted of two steps: exosome purification and RNA isolation. For exosome purification, the plasma sample was mixed with buffer XBP (1:1) and centrifuged for 1 min at 500 x g to bind to an exoEasy membrane affinity spin column. The bound exosomes were washed with 3.5 ml buffer XWP after 1 min of centrifugation at 500g, and then lysed by adding 700 l QIAzol after 5 min of centrifugation at 5000g.  In the RNA extraction stage, 90 µl chloroform was added to the QIAzol eluate, which was then shaken for 15 seconds. The aqueous phase was then collected and combined with 2 volumes of 100% ethanol. Total RNA, including miRNA, attached to the spin column after 15 seconds of centrifugation at 8000 x g, was washed three times and eluted in 14 lµ RNase-free water.. All protocols were provided by Qiagen. The enzyme Bacteroides I (New England Biolabs, P0735S) and RNase Inhibitor (Enzymatic, Y9240L) were utilized after RNA extraction following the manufacturer's protocol to eliminate residual heparin potentially transferred from the heparin blood collection tubes. After incubation for 1 hr at 30C and 1 min at 99.9C, the RNA was stored at -80°C and then used as RNA templates to produce a cDNA library for sequencing.
MiRNA libraries were prepared using Qiagen’s QIAseq miRNA Library Kit with 5 μl of total RNA from each sample. This was followed by completing universal cDNA synthesis with UMI assignment, cDNA cleaning, library amplification, and library purification. The resulting libraries were quantified using the Denovix hsDNA assay, and quality was assayed using a hsDNA chip on an Agilent Bioanalyzer.

value: Plasma

value: Female

value: BASDAI 7.2

tag: disease state

value: Ankylosing Spondylitis


title: plasma-derived AS-exosomes Nymber 7

description:
Total RNA extracted form Plasma derived exosomes
Fataneh18

tag: tissue

value: BASDAI 6.8


title: plasma-derived AS-exosomes Nymber 5

description:
Total RNA extracted form Plasma derived exosomes
Fataneh16

value: BASDAI 9


title: plasma-derived AS-exosomes Nymber 16

description:
Total RNA extracted form Plasma derived exosomes
Fataneh27

value: BASDAI 5.7


title: plasma-derived AS-exosomes Nymber 10

description:
Total RNA extracted form Plasma derived exosomes
Fataneh21

value: BASDAI 8.1


title: plasma-derived AS-exosomes Nymber 17

description:
Total RNA extracted form Plasma derived exosomes
Fataneh28

value: Male

value: BASDAI 5.5


title: plasma-derived AS-exosomes Nymber 13

description:
Total RNA extracted form Plasma derived exosomes
Fataneh24


title: plasma-derived AS-exosomes Nymber 9

description:
Total RNA extracted form Plasma derived exosomes
Fataneh20

value: BASDAI 8.4


title: plasma-derived AS-exosomes Nymber 4

description:
Total RNA extracted form Plasma derived exosomes
Fataneh15

value: BASDAI 4.7


title: plasma-derived HC-exosomes Nymber 10

description:
Total RNA extracted form Plasma derived exosomes
Fataneh10A

value: healthy control


title: plasma-derived AS-exosomes Nymber 1

description:
Total RNA extracted form Plasma derived exosomes
Fataneh11

value: BASDAI 7.6


title: plasma-derived AS-exosomes Nymber 2

description:
Total RNA extracted form Plasma derived exosomes
Fataneh13

value: BASDAI 8.7