title: Sample infected with Anaplasma phagocytophilum NY18 (ISE6-NY3)

source_name: ISE6 cells, infected with Anaplasma phagocytophilum NY18

value: Anaplasma phagocytophilum human NY18 isolate


title: C57BL/6 mice injected with rIL-31 (20µg/50ul) for 14 days via i.d._2

status: Public on Mar 19 2016

type: SRA

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

country: USA

institute: University of Cincinnati

library_source: transcriptomic

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: raw counts with genes in rows and samples in columns

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

tag: tissue

value: Skin

tag: treatment

value: treated


title: C57BL/6 mice injected with rIL-31 (20µg/50ul) for 14 days via i.d._1


title: EA  rep1

status: Public on Mar 20 2016

city: Nanjing

first: Bing-Mei

last: Zhu

state: Jiangsu

address: 138 Xianlin Avenue

country: China

institute: Nanjing university of Chinese Medicine

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC RN4 whole genome using tophat v2.0.6
Differential gene and transcript expression analysis using a protocol from Cole Trapnell et al., nature protocols, 2012.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Rattus norvegicus

source_name: myocardium

extract_protocol:
Hearts were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Sprague Dawley

value: heart

tag: weight


title: C57BL/6 mice injected with saline (50ul) for 14 days via i.d._1

value: controls


title: C57BL/6 mice injected with rIL-31 (20µg/50ul) for 14 days via i.d._3


title: C57BL/6 mice injected with saline (50ul) for 14 days via i.d._2


title: ETP old sample 1

city: Los Angeles

first: Kenneth

last: Dorshkind

state: California

address: 10833 Le Conte Avenue

department: Pathology and Laboratory Medicine

institute: David Geffen School of Medicine at UCLA

data_processing:
Reads were aligned to the Mus musculus genome (mm10 build) using STAR v2.3.0 (Dobin et al. doi:10.1093/bioinformatics/bts635) in supervised mode using the Ensemble GRCm38.71 gene annotation as template. Relevant alignment parameters are: --outFilterMultimapScoreRange 0.75  --outFilterMultimapNmax 100 --outFilterMismatchNmax 25 --outFilterScoreMinOverLread 0.75 --outFilterMatchNminOverLread 0.75 --outFilterMismatchNoverLmax 0.25 --sjdbOverhang 99
Two different methods were used for differential expression analysis on the UCSC (mm10 build) set of gene models. First, Cufflinks v2.1.1 (Trapnell et al. doi:10.1038/nbt.2450) was used to compute the matrix of expression estimates in units of fpkms, and the Cuffdiff tool to compute differential expression statistics (relevant parameters: --total-hits-norm, -u, -c 10, --library-norm-method geometric, --dispersion-method per-condition).
Alternatively, HTSeq-count v0.5.4p3 (Simon Anders, http://www-huber.embl.de/users/anders/HTSeq/) was used to compute the matrix of raw counts (relevant paramters: --mode=intersection-strict). This matrix was used as input for DESeq v1.12.1 to assess pair-wise differential expression with "per-condition" expression estimates. Finally, moderate fold-changes (mfc) between two experimental conditions were computed from variance stabilized data (as provided by DESeq with "pooled" dispersion estimates). For each method above, genes were tagged as differentially expressed if abs(mfc)>.7 and p-value<0.05.
Genome_build: GRCm38.71/mm10
Supplementary_files_format_and_content: Cuffdiff genes tracking output file: UCSC gene id / condition / replicate / number of mapped fragments / scale factors / fpkm /

source_name: ETP purified from thymus_old

growth_protocol: Total thymocytes were isolated and cells were labelled with appropriate antibodies to resolve ETP. ETP were then purified by fluorescence activated cell sorting

extract_protocol:
Total RNA was isolated using Qiagen miRNAeasy micro kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were lysed directly after sort

tag: Sex

value: female

tag: age

value: 72 weeks

value: thymus

tag: cell type

value: Early T-cell Progenitors (ETP)


title: ETP young sample 2

source_name: ETP purified from thymus_young

value: 4-6 weeks


title: ETP young sample 1

description: KDBBmmETPYo


title: total RNA-seq from lung (ENCLB123VIC)

status: Public on Mar 18 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR992WBR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse lung
experiment encode accession: ENCSR992WBR
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB123VIC
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

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

value: lung

value: tissue

tag: description

value: Lung pooled from embyonic 16.5 day mice

tag: biosample encode accession

tag: dev stage

value: embryonic

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

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

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


title: total RNA-seq from forebrain (ENCLB177SFU)

description:
https://www.encodeproject.org/experiments/ENCSR970EWM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR970EWM
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB177SFU
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

value: forebrain

value: Forebrain from embryonic 13.5 day mice

value: ENCBS273RVL at ENCODE; https://www.encodeproject.org/ENCBS273RVL/


title: total RNA-seq from lung (ENCLB626WMA)

description:
https://www.encodeproject.org/experiments/ENCSR992WBR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse lung
experiment encode accession: ENCSR992WBR
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB626WMA
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: Lung from 41 embyonic 16.5 day mice

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


title: total RNA-seq from lung (ENCLB544VIE)

description:
https://www.encodeproject.org/experiments/ENCSR982MRY/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse lungs
experiment encode accession: ENCSR982MRY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB544VIE
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: 2 lungs from pup3 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

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


title: single cell RNA-seq from liver (ENCLB791CRT)

description:
https://www.encodeproject.org/experiments/ENCSR950BNG/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse liver (13pgs)
experiment encode accession: ENCSR950BNG
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB791CRT
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

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

extract_protocol:
extraction method: Ambion mirVana
extraction protocol: https://www.encodeproject.org/documents/428a184d-7fa1-4599-9d8d-749c2eba7edd/@@download/attachment/cms_055740.pdf, extraction protocol: https://www.encodeproject.org/documents/f0cc5a7f-96a5-4970-9f46-317cc8e2d6a4/@@download/attachment/cms_055423.pdf, general protocol: https://www.encodeproject.org/documents/5f5193b0-0c61-40c6-a286-b1f6d6f0c0da/@@download/attachment/SmartSeqProtocol.pdf

tag: antibody

value: Control

value: liver

value: tissue

value: single liver from pup 3

value: ENCBS301RUA at ENCODE; https://www.encodeproject.org/ENCBS301RUA/


title: single cell RNA-seq from pyramidal neuron (ENCLB996ZCL)

description:
https://www.encodeproject.org/experiments/ENCSR953TKB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC775)
experiment encode accession: ENCSR953TKB
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB996ZCL
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl pyramidal neuron primary cell adult (8 months)

value: pyramidal neuron

value: primary cell

value: 8 month

value: adult

value: ENCBS338YVH at ENCODE; https://www.encodeproject.org/ENCBS338YVH/

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


title: total RNA-seq from lung (ENCLB810TRL)

description:
https://www.encodeproject.org/experiments/ENCSR982MRY/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse lungs
experiment encode accession: ENCSR982MRY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB810TRL
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: lung

value: 2 lungs from pup1 pregnant 1

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


title: single cell RNA-seq from Purkinje cell (ENCLB183ZSO)

description:
https://www.encodeproject.org/experiments/ENCSR948NDP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR948NDP
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB183ZSO
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl Purkinje primary cell male adult (8 months)

value: Purkinje cell

value: male

value: ENCBS670JKK at ENCODE; https://www.encodeproject.org/ENCBS670JKK/


title: total RNA-seq from forebrain (ENCLB807ODU)

description:
https://www.encodeproject.org/experiments/ENCSR970EWM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR970EWM
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB807ODU
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: forebrain

value: Forebrain from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS793ZRY at ENCODE; https://www.encodeproject.org/ENCBS793ZRY/


title: single cell RNA-seq from liver (ENCLB356IIP)

description:
https://www.encodeproject.org/experiments/ENCSR950BNG/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse liver (13pgs)
experiment encode accession: ENCSR950BNG
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB356IIP
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: liver

value: tissue

value: single liver from pup 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS094UZQ at ENCODE; https://www.encodeproject.org/ENCBS094UZQ/


title: total RNA-seq from skeletal muscle tissue (ENCLB704CYQ)

description:
https://www.encodeproject.org/experiments/ENCSR946HWC/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse skeletal muscle
experiment encode accession: ENCSR946HWC
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB704CYQ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: skeletal muscle tissue

value: 1 skeletal muscle from pup2 pregnant 1

value: ENCBS098FMC at ENCODE; https://www.encodeproject.org/ENCBS098FMC/

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


title: single cell RNA-seq from Purkinje cell (ENCLB562LNT)

description:
https://www.encodeproject.org/experiments/ENCSR940DVT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR940DVT
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB562LNT
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: ENCBS465NJY at ENCODE; https://www.encodeproject.org/ENCBS465NJY/


title: total RNA-seq from intestine (ENCLB030NEC)

description:
https://www.encodeproject.org/experiments/ENCSR932TRU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR932TRU
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB030NEC
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: intestine

value: tissue

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

value: embryonic

value: pooled male and female

value: ENCBS475HQA at ENCODE; https://www.encodeproject.org/ENCBS475HQA/


title: total RNA-seq from intestine (ENCLB156EMG)

description:
https://www.encodeproject.org/experiments/ENCSR932TRU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR932TRU
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB156EMG
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: Barbara Wold, Caltech

value: ENCBS110AZU at ENCODE; https://www.encodeproject.org/ENCBS110AZU/


title: C57BL/6 mice injected with saline (50ul) for 14 days via i.d._3

value: Skin

value: controls


title: single cell RNA-seq from pyramidal neuron (ENCLB658PNH)

description:
https://www.encodeproject.org/experiments/ENCSR927IOO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC763)
experiment encode accession: ENCSR927IOO
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB658PNH
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: not collected

value: ENCBS453UTH at ENCODE; https://www.encodeproject.org/ENCBS453UTH/

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


title: total RNA-seq from neural tube (ENCLB214UZM)

description:
https://www.encodeproject.org/experiments/ENCSR928OXI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse neural tube
experiment encode accession: ENCSR928OXI
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB214UZM
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: neural tube

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

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


title: total RNA-seq from neural tube (ENCLB377PCX)

description:
https://www.encodeproject.org/experiments/ENCSR928OXI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse neural tube
experiment encode accession: ENCSR928OXI
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB377PCX
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: tissue

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

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


title: total RNA-seq from hindbrain (ENCLB312IAF)

description:
https://www.encodeproject.org/experiments/ENCSR921PRX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse hindbrain
experiment encode accession: ENCSR921PRX
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB312IAF
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

value: hindbrain

value: Hindbrain from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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


title: Sample infected with Anaplasma phagocytophilum NY18 (ISE6-NY5)

city: Ciudad Real

first: Jose

last: De La Fuente

state: Ciudad Real

address: Ronda de Toledo s/n

country: Spain

institute: SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM

data_processing:
Reads were mapped using Tophat 2.1.0
Small RNA library preparation but strand specific data for Ixodes scapularis unavailable, so the reads were mapped to the reference genome as if they were from a normal RNAseq experiment. Thus we obtained reads mapping to coding sequences (protein coding and miRNA coding as well) and also to non coding regions.
Transcripts assembly and abundance estimation performed using Cufflinks 2.2.1
Analysis of differentially expressed genes was performed using Cufflinks 2.2.1
Genome_build: JCVI_ISG_i3_1.0 (NZ_ABJB000000000)
Supplementary_files_format_and_content: GTF2 files generated with Cufflinks.  Columns: <seqname> <source> <feature> <start> <end> <score> <strand> <frame> <FPKM values are included in the last column of the file>

organism: Ixodes scapularis

growth_protocol: The I. scapularis embryo-derived tick cell line ISE6 was cultured in L-15B300 medium as described previously (Blouin et al. (2003) Vet. Parasitol 111, 247-260), except that the osmotic pressure was lowered by the addition of one-fourth sterile water by volume. Tick cells were inoculated with A. phagocytophilum (human NY18 isolate) cells as described previously (Munderloh et al. (1999) J. Clin. Microbiol 37, 2518-2524; de la Fuente et al. (2005) Cell. Microbiol 7, 549–559). Uninfected and infected cultures with approximately 107 cells each were sampled at 12 days post-infection (dpi) (percent infected cells 68-73% (Ave±SD, 70±3). The percentage of cells infected with A. phagocytophilum was calculated by examining at least 200 cells using a 100x oil immersion objective.

extract_protocol:
miRNA was extracted using a Purelink miRNA isolation kit (Invitrogen) following manufacturers recommendations. Quality check of all samples was carried out using the Agilent 2100 Bioanalyzer with the Small RNA kit (Agilent) to determine sample quality and concentration of miRNA in each sample. The four samples passed internal QC with good bioanalyzer profiles and enough miRNA in each sample to proceed with library construction.
The libraries were prepared using the TruSeq Small RNA Sample Prep Kit (Illumina), where the miRNA samples were subjected to ligation of the 3’ and 5’ adapters, and reverse transcription. Unique barcodes were incorporated during the PCR enrichment step to ensure sufficient amount of library is generated. Adapter dimers were removed and the small RNA libraries were purified by PAGE. Resulting libraries were run on the Agilent Bioanalyzer with the DNA High Sensitivity Chip to determine library concentration and size distribution profile. Real-time quantification (KAPA qPCR quantification for Illumina systems) was performed to quantify the libraries prior to sequencing on the the most advanced Illumina platform the NextSeq 500, which uses two channel chemistry to reduce the sequencing time while maintaining unparallel accuracies of the data. Samples with different barcodes are pooled together prior to sequencing but were be separated post sequencing through demutiplexing. Resulting miRNA-seq single end reads and Bcl files were converted to Fastq data immediately after the run and used to generate Cufflinks output

treatment_protocol: The cells were centrifuged at 10,000 g for 3 min, and cell pellets were frozen at -80C until used for miRNA extraction

tag: cell line

tag: infection

value: Anaplasma phagocytophilum human NY18 isolate


title: Control immediately after exercise [CON_20_immediate]

status: Public on Mar 21 2016

city: Eugene

first: John

last: Halliwill

state: OR

address: 1370 Franklin Blvd

institute: University of Oregon

data_processing:
.fastq.gz files: Raw, demultiplexed sequence files produced by Illumina HiSeq Control Software 2.2.58 and CASAVA 1.8.2
Sequencing and basecalling by Illumina HiSeq Control Software 2.2.58
BCL conversion and demultiplexing by Illumina CASAVA 1.8.2
FASTQ files aligned to Homo_sapiens.GRCh38.dna.toplevel.fa genome assembly obtained from ENSEMBL.  The Homo_sapiens.GRCh38.78.gtf file from ENSEMBL was used for annotation.  Alignments were performed with STAR 2.4.0i.
Gene count tables were generated from STAR-produced SAM files using HTSeq-count 0.6.1
Genome_build: Homo_sapiens.GRCh38.dna.toplevel.fa
Supplementary_files_format_and_content: .counts.txt files: Gene count tables generated by HTSeq-count from each .sam file for each sample

organism: Homo sapiens

source_name: Control subject biopsy immediately after exercise

extract_protocol:
Trizol RNA extraction protocol (Thermo Fisher)
Kapa Biosystems Stranded mRNA Seq kit

tag: subject id

value: subject 20

tag: subject group

value: control

tag: time point

value: immediately after exercise

value: vastus lateralis muscle


title: total RNA-seq from hindbrain (ENCLB517UIN)

description:
https://www.encodeproject.org/experiments/ENCSR921PRX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse hindbrain
experiment encode accession: ENCSR921PRX
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB517UIN
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

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


title: single cell RNA-seq from pyramidal neuron (ENCLB517WGI)

description:
https://www.encodeproject.org/experiments/ENCSR909YEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC779)
experiment encode accession: ENCSR909YEQ
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB517WGI
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: primary cell

value: 8 month

value: adult

value: not collected

value: Barbara Wold, Caltech

value: ENCBS197VJV at ENCODE; https://www.encodeproject.org/ENCBS197VJV/


title: total RNA-seq from stomach (ENCLB753FMG)

description:
https://www.encodeproject.org/experiments/ENCSR906YQZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR906YQZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB753FMG
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

value: stomach

value: tissue

value: Stomach from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

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


title: single cell RNA-seq from thymus (ENCLB005HHX)

description:
https://www.encodeproject.org/experiments/ENCSR907JUN/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse thymus (13pgs)
experiment encode accession: ENCSR907JUN
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB005HHX
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

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

value: Control

value: thymus

value: Pup 6 from Charles River C57/Bl6 female 6 mos 10 days old

value: 0 day

value: postnatal

value: ENCBS977KDI at ENCODE; https://www.encodeproject.org/ENCBS977KDI/


title: total RNA-seq from skeletal muscle tissue (ENCLB847UDV)

description:
https://www.encodeproject.org/experiments/ENCSR946HWC/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse skeletal muscle
experiment encode accession: ENCSR946HWC
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB847UDV
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: skeletal muscle tissue

value: 1 skeletal muscle from pup1 pregnant 1

value: ENCBS186LJI at ENCODE; https://www.encodeproject.org/ENCBS186LJI/

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


title: total RNA-seq from stomach (ENCLB110FBI)

description:
https://www.encodeproject.org/experiments/ENCSR906YQZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR906YQZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB110FBI
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: stomach

value: Stomach from 62 embryonic 15.5 day mice

value: Len Pennacchio, LBNL

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


title: total RNA-seq from liver (ENCLB200EFP)

description:
https://www.encodeproject.org/experiments/ENCSR867YNV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR867YNV
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB200EFP
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: liver

value: tissue

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

value: embryonic

value: pooled male and female

value: Barbara Wold, Caltech

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


title: single cell RNA-seq from hindbrain (ENCLB765HDK)

description:
https://www.encodeproject.org/experiments/ENCSR861FGB/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse hindbrain (13pgs)
experiment encode accession: ENCSR861FGB
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB765HDK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

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

value: Control

value: hindbrain

value: single hindbrain from pup 3

value: 0 day

value: postnatal

value: not collected

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


title: total RNA-seq from liver (ENCLB278MMD)

description:
https://www.encodeproject.org/experiments/ENCSR867YNV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR867YNV
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB278MMD
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

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

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


title: single cell RNA-seq from hindbrain (ENCLB238LIR)

description:
https://www.encodeproject.org/experiments/ENCSR861FGB/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse hindbrain (13pgs)
experiment encode accession: ENCSR861FGB
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB238LIR
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: single hindbrain from pup 1

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


title: total RNA-seq from intestine (ENCLB287BOO)

description:
https://www.encodeproject.org/experiments/ENCSR848GST/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse intestine
experiment encode accession: ENCSR848GST
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB287BOO
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

value: intestine

value: tissue

value: Intestine pooled from embyonic 16.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS856EWN at ENCODE; https://www.encodeproject.org/ENCBS856EWN/


title: total RNA-seq from embryonic facial prominence (ENCLB761PCA)

description:
https://www.encodeproject.org/experiments/ENCSR848HOX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR848HOX
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB761PCA
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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: embryonic

value: pooled male and female

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


title: total RNA-seq from intestine (ENCLB008KBU)

description:
https://www.encodeproject.org/experiments/ENCSR848GST/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse intestine
experiment encode accession: ENCSR848GST
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB008KBU
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: Intestine from 41 embyonic 16.5 day mice

value: ENCBS072GMU at ENCODE; https://www.encodeproject.org/ENCBS072GMU/


title: total RNA-seq from embryonic facial prominence (ENCLB331VAA)

description:
https://www.encodeproject.org/experiments/ENCSR848HOX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR848HOX
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB331VAA
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: Craniofacial prominence from 109 embyronic 11.5 day mice

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


title: single cell RNA-seq from pyramidal neuron (ENCLB170GEK)

description:
https://www.encodeproject.org/experiments/ENCSR846FYI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC767)
experiment encode accession: ENCSR846FYI
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB170GEK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: primary cell

value: 8 month

value: adult

value: not collected

value: Barbara Wold, Caltech

value: ENCBS611KWG at ENCODE; https://www.encodeproject.org/ENCBS611KWG/

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


title: total RNA-seq from limb (ENCLB105VLP)

description:
https://www.encodeproject.org/experiments/ENCSR830IVQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse limb
experiment encode accession: ENCSR830IVQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB105VLP
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

value: limb

value: tissue

value: Limb from 62 embryonic 15.5 day mice

value: healthy

value: Len Pennacchio, LBNL

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


title: single cell RNA-seq from Purkinje cell (ENCLB841OTT)

description:
https://www.encodeproject.org/experiments/ENCSR833SOQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR833SOQ
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB841OTT
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: male

value: ENCBS465VQO at ENCODE; https://www.encodeproject.org/ENCBS465VQO/


title: ETP old sample 2

source_name: ETP purified from thymus_old

tag: strain

value: female

value: 72 weeks

tag: tissue

value: thymus

value: Early T-cell Progenitors (ETP)


title: single cell RNA-seq from thymus (ENCLB185MNU)

description:
https://www.encodeproject.org/experiments/ENCSR907JUN/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse thymus (13pgs)
experiment encode accession: ENCSR907JUN
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB185MNU
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: Pup 7 from Charles River C57/Bl6 female 6 mos 10 days old

value: 0 day

value: postnatal

tag: Sex

value: not collected

value: ENCBS881SPO at ENCODE; https://www.encodeproject.org/ENCBS881SPO/


title: total RNA-seq from embryonic facial prominence (ENCLB015WCJ)

description:
https://www.encodeproject.org/experiments/ENCSR823VEE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR823VEE
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB015WCJ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

tag: age

value: embryonic

value: pooled male and female

value: Barbara Wold, Caltech

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

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


title: total RNA-seq from bladder (ENCLB817LXB)

description:
https://www.encodeproject.org/experiments/ENCSR772FQU/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse bladder
experiment encode accession: ENCSR772FQU
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB817LXB
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: bladder

value: 1 bladder from pup2 pregnant 1

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


title: total RNA-seq from bladder (ENCLB260QNG)

description:
https://www.encodeproject.org/experiments/ENCSR772FQU/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse bladder
experiment encode accession: ENCSR772FQU
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB260QNG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: 1 bladder from pup1 pregnant 1

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


title: single cell RNA-seq from cerebellar granule layer (ENCLB521CXU)

description:
https://www.encodeproject.org/experiments/ENCSR814JMM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on a dissected area of granule cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR814JMM
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB521CXU
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 50.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl cerebellar granule layer tissue male adult (8 months)

value: Control

value: cerebellar granule layer

value: Mm_C57Bl6_8mo_M_WT_granule_areas 18000 square microns

value: 8 month

value: adult

value: male

value: ENCBS483PMB at ENCODE; https://www.encodeproject.org/ENCBS483PMB/


title: single cell RNA-seq from pyramidal neuron (ENCLB813BFK)

description:
https://www.encodeproject.org/experiments/ENCSR782WIL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC771)
experiment encode accession: ENCSR782WIL
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB813BFK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl pyramidal neuron primary cell adult (8 months)

value: pyramidal neuron

value: primary cell

value: not collected

value: ENCBS895RSM at ENCODE; https://www.encodeproject.org/ENCBS895RSM/


title: total RNA-seq from limb (ENCLB646LEJ)

description:
https://www.encodeproject.org/experiments/ENCSR830IVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse limb
experiment encode accession: ENCSR830IVQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB646LEJ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: limb

value: tissue

value: Limb from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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

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


title: total RNA-seq from liver (ENCLB489BJY)

description:
https://www.encodeproject.org/experiments/ENCSR826HIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse liver
experiment encode accession: ENCSR826HIQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB489BJY
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

value: liver

value: Liver pooled from embyonic 16.5 day mice

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


title: total RNA-seq from midbrain (ENCLB051RZO)

description:
https://www.encodeproject.org/experiments/ENCSR792RJV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse midbrain
experiment encode accession: ENCSR792RJV
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB051RZO
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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


title: total RNA-seq from midbrain (ENCLB426MFX)

description:
https://www.encodeproject.org/experiments/ENCSR792RJV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse midbrain
experiment encode accession: ENCSR792RJV
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB426MFX
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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


title: total RNA-seq from hindbrain (ENCLB061TDP)

description:
https://www.encodeproject.org/experiments/ENCSR760TOE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse hindbrain
experiment encode accession: ENCSR760TOE
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB061TDP
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

value: hindbrain

value: Hindbrain from 88 embyronic 11.5 day mice

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


title: total RNA-seq from hindbrain (ENCLB454ZUS)

description:
https://www.encodeproject.org/experiments/ENCSR760TOE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse hindbrain
experiment encode accession: ENCSR760TOE
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB454ZUS
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: tissue

value: Hindbrain from 109 embyronic 11.5 day mice

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


title: single cell RNA-seq from Purkinje cell (ENCLB604HVJ)

description:
https://www.encodeproject.org/experiments/ENCSR758TAD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on a 50 cell pool of Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR758TAD
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB604HVJ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 50.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl Purkinje primary cell male adult (8 months)

extract_protocol: not provided

value: Control

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: Barbara Wold, Caltech

value: ENCBS786AMU at ENCODE; https://www.encodeproject.org/ENCBS786AMU/


title: single cell RNA-seq from Purkinje cell (ENCLB357UPR)

description:
https://www.encodeproject.org/experiments/ENCSR758TAD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on a 50 cell pool of Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR758TAD
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB357UPR
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 50.0
nucleic acid starting quantity units: cells

value: ENCBS362MIS at ENCODE; https://www.encodeproject.org/ENCBS362MIS/

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


title: total RNA-seq from forebrain (ENCLB373ANW)

description:
https://www.encodeproject.org/experiments/ENCSR752RGN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR752RGN
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB373ANW
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

value: forebrain

value: Forebrain from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS811RMD at ENCODE; https://www.encodeproject.org/ENCBS811RMD/


title: total RNA-seq from liver (ENCLB424YVG)

description:
https://www.encodeproject.org/experiments/ENCSR826HIQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse liver
experiment encode accession: ENCSR826HIQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB424YVG
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: liver

value: tissue

value: Liver from 41 embyonic 16.5 day mice

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


title: total RNA-seq from embryonic facial prominence (ENCLB254AMJ)

description:
https://www.encodeproject.org/experiments/ENCSR823VEE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR823VEE
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB254AMJ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: embryonic facial prominence

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

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


title: total RNA-seq from adrenal gland (ENCLB556YSG)

description:
https://www.encodeproject.org/experiments/ENCSR739PEB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on postnatal 0 day mouse adrenal glands
experiment encode accession: ENCSR739PEB
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB556YSG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: adrenal gland

value: 2 adrenals from pup1 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS547NQN at ENCODE; https://www.encodeproject.org/ENCBS547NQN/


title: single cell RNA-seq from pyramidal neuron (ENCLB507SLS)

description:
https://www.encodeproject.org/experiments/ENCSR739YUO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC762)
experiment encode accession: ENCSR739YUO
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB507SLS
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: primary cell

value: 8 month

value: adult

value: ENCBS158HDI at ENCODE; https://www.encodeproject.org/ENCBS158HDI/

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


title: single cell RNA-seq from pyramidal neuron (ENCLB228LHA)

description:
https://www.encodeproject.org/experiments/ENCSR746LUP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC758)
experiment encode accession: ENCSR746LUP
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB228LHA
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: ENCBS062LCW at ENCODE; https://www.encodeproject.org/ENCBS062LCW/


title: single cell RNA-seq from pyramidal neuron (ENCLB579FVG)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 2
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB579FVG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Control

value: ENCBS456CCE at ENCODE; https://www.encodeproject.org/ENCBS456CCE/


title: single cell RNA-seq from pyramidal neuron (ENCLB376XWO)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 7
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB376XWO
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS604AJJ at ENCODE; https://www.encodeproject.org/ENCBS604AJJ/


title: single cell RNA-seq from pyramidal neuron (ENCLB977FBH)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 5
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB977FBH
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS499NNJ at ENCODE; https://www.encodeproject.org/ENCBS499NNJ/


title: single cell RNA-seq from pyramidal neuron (ENCLB679XGZ)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 9
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB679XGZ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS562VHG at ENCODE; https://www.encodeproject.org/ENCBS562VHG/


title: single cell RNA-seq from pyramidal neuron (ENCLB282TJI)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 10
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB282TJI
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS553FFB at ENCODE; https://www.encodeproject.org/ENCBS553FFB/


title: single cell RNA-seq from pyramidal neuron (ENCLB292TWB)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 13
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB292TWB
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS226LFK at ENCODE; https://www.encodeproject.org/ENCBS226LFK/


title: single cell RNA-seq from pyramidal neuron (ENCLB231DLC)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 4
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB231DLC
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: not collected

value: ENCBS910XAG at ENCODE; https://www.encodeproject.org/ENCBS910XAG/


title: single cell RNA-seq from pyramidal neuron (ENCLB264HUG)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 14
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB264HUG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Barbara Wold, Caltech

value: ENCBS794PQQ at ENCODE; https://www.encodeproject.org/ENCBS794PQQ/


title: single cell RNA-seq from pyramidal neuron (ENCLB945FTP)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 6
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB945FTP
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: pyramidal neuron

value: primary cell

value: ENCBS488VUW at ENCODE; https://www.encodeproject.org/ENCBS488VUW/


title: single cell RNA-seq from pyramidal neuron (ENCLB670TAW)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 11
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB670TAW
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: 8 month

value: adult

value: ENCBS393OMB at ENCODE; https://www.encodeproject.org/ENCBS393OMB/


title: single cell RNA-seq from pyramidal neuron (ENCLB301VGJ)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 15
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB301VGJ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Control

value: ENCBS531TQU at ENCODE; https://www.encodeproject.org/ENCBS531TQU/

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


title: single cell RNA-seq from pyramidal neuron (ENCLB861EZL)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 12
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB861EZL
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS157VHS at ENCODE; https://www.encodeproject.org/ENCBS157VHS/


title: single cell RNA-seq from pyramidal neuron (ENCLB774TWW)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 1
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB774TWW
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS622XGI at ENCODE; https://www.encodeproject.org/ENCBS622XGI/


title: total RNA-seq from heart (ENCLB931ORG)

description:
https://www.encodeproject.org/experiments/ENCSR727FHP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse heart
experiment encode accession: ENCSR727FHP
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB931ORG
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: heart

value: tissue

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

value: embryonic

value: pooled male and female

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


title: single cell RNA-seq from pyramidal neuron (ENCLB151YVV)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 8
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB151YVV
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: pyramidal neuron

value: not collected

value: Barbara Wold, Caltech

value: ENCBS222YVM at ENCODE; https://www.encodeproject.org/ENCBS222YVM/


title: total RNA-seq from heart (ENCLB584VFZ)

description:
https://www.encodeproject.org/experiments/ENCSR727FHP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse heart
experiment encode accession: ENCSR727FHP
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB584VFZ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

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


title: single cell RNA-seq from pyramidal neuron (ENCLB637WDO)

description:
https://www.encodeproject.org/experiments/ENCSR734SOQ/
***************
biological replicate number: 1
technical replicate number: 3
description: LC_805-819_C57Bl6_layer_V_pyramidal_neuron_pool-split
experiment encode accession: ENCSR734SOQ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB637WDO
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Control

value: primary cell

value: 8 month

value: adult

value: ENCBS091SVT at ENCODE; https://www.encodeproject.org/ENCBS091SVT/


title: single cell RNA-seq from Purkinje cell (ENCLB035MJZ)

description:
https://www.encodeproject.org/experiments/ENCSR708EHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR708EHJ
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB035MJZ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: male

value: ENCBS387ADD at ENCODE; https://www.encodeproject.org/ENCBS387ADD/

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


title: total RNA-seq from heart (ENCLB601XLL)

description:
https://www.encodeproject.org/experiments/ENCSR691OPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse heart
experiment encode accession: ENCSR691OPQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB601XLL
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

value: heart

value: tissue

value: Heart from 109 embyronic 11.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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


title: total RNA-seq from midbrain (ENCLB080NNG)

description:
https://www.encodeproject.org/experiments/ENCSR719NAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR719NAJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB080NNG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
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: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

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


title: single cell RNA-seq from Purkinje cell (ENCLB891HIS)

description:
https://www.encodeproject.org/experiments/ENCSR691PPV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR691PPV
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB891HIS
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: ENCBS365NUH at ENCODE; https://www.encodeproject.org/ENCBS365NUH/


title: single cell RNA-seq from Purkinje cell (ENCLB809SWT)

description:
https://www.encodeproject.org/experiments/ENCSR710QXP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR710QXP
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB809SWT
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: ENCBS785DRB at ENCODE; https://www.encodeproject.org/ENCBS785DRB/

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


title: single cell RNA-seq from cerebellar granule layer (ENCLB969JPS)

description:
https://www.encodeproject.org/experiments/ENCSR814JMM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on a dissected area of granule cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR814JMM
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB969JPS
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 50.0
nucleic acid starting quantity units: cells

value: Control

value: cerebellar granule layer

value: tissue

value: Mm_C57Bl6_8mo_M_WT_granule_areas 18000 square microns

value: ENCBS569SMF at ENCODE; https://www.encodeproject.org/ENCBS569SMF/


title: total RNA-seq from midbrain (ENCLB180OTB)

description:
https://www.encodeproject.org/experiments/ENCSR719NAJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR719NAJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB180OTB
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: midbrain

value: single midbrain from pup 3

value: 0 day

value: postnatal

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


title: total RNA-seq from forebrain (ENCLB567JQE)

description:
https://www.encodeproject.org/experiments/ENCSR752RGN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR752RGN
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB567JQE
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: forebrain

value: Forebrain from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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


title: total RNA-seq from adrenal gland (ENCLB803HJK)

description:
https://www.encodeproject.org/experiments/ENCSR739PEB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on postnatal 0 day mouse adrenal glands
experiment encode accession: ENCSR739PEB
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB803HJK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: adrenal gland

value: 2 adrenals from pup2 pregnant 1

value: not collected

value: Barbara Wold, Caltech

value: ENCBS386FVC at ENCODE; https://www.encodeproject.org/ENCBS386FVC/

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


title: total RNA-seq from heart (ENCLB347FRI)

description:
https://www.encodeproject.org/experiments/ENCSR691OPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse heart
experiment encode accession: ENCSR691OPQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB347FRI
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: heart

value: tissue

value: Heart from embryonic 11.5 day mice

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


title: total RNA-seq from neural tube (ENCLB790ZKD)

description:
https://www.encodeproject.org/experiments/ENCSR667TOX/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse neural tube
experiment encode accession: ENCSR667TOX
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB790ZKD
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: neural tube

value: single neural tube from pup 1 pregnant 1

value: 0 day

value: postnatal

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


title: single cell RNA-seq from Purkinje cell (ENCLB284YTS)

description:
https://www.encodeproject.org/experiments/ENCSR662UPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR662UPQ
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB284YTS
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: ENCBS931RDM at ENCODE; https://www.encodeproject.org/ENCBS931RDM/


title: single cell RNA-seq from pyramidal neuron (ENCLB449JEZ)

description:
https://www.encodeproject.org/experiments/ENCSR650MMK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC780)
experiment encode accession: ENCSR650MMK
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB449JEZ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: not collected

value: Barbara Wold, Caltech

value: ENCBS185CJV at ENCODE; https://www.encodeproject.org/ENCBS185CJV/


title: single cell RNA-seq from Purkinje cell (ENCLB384GBY)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 10
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB384GBY
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Control

value: ENCBS746KRI at ENCODE; https://www.encodeproject.org/ENCBS746KRI/

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


title: single cell RNA-seq from Purkinje cell (ENCLB219UWV)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 7
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB219UWV
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS659MMZ at ENCODE; https://www.encodeproject.org/ENCBS659MMZ/


title: total RNA-seq from neural tube (ENCLB319NLX)

description:
https://www.encodeproject.org/experiments/ENCSR667TOX/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse neural tube
experiment encode accession: ENCSR667TOX
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB319NLX
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: neural tube

value: tissue

value: single neural tube from pup 2 pregnant 1

value: 0 day

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


title: single cell RNA-seq from Purkinje cell (ENCLB030QYZ)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 11
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB030QYZ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Purkinje cell

value: primary cell

value: 8 month

value: ENCBS323MIZ at ENCODE; https://www.encodeproject.org/ENCBS323MIZ/


title: single cell RNA-seq from Purkinje cell (ENCLB577KCS)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 5
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB577KCS
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: adult

value: male

value: ENCBS721LLV at ENCODE; https://www.encodeproject.org/ENCBS721LLV/


title: single cell RNA-seq from Purkinje cell (ENCLB253LOZ)

description:
https://www.encodeproject.org/experiments/ENCSR659SFM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR659SFM
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB253LOZ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Barbara Wold, Caltech

value: ENCBS869ZUE at ENCODE; https://www.encodeproject.org/ENCBS869ZUE/


title: single cell RNA-seq from Purkinje cell (ENCLB462UWC)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 15
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB462UWC
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Control

value: ENCBS610UUG at ENCODE; https://www.encodeproject.org/ENCBS610UUG/


title: single cell RNA-seq from Purkinje cell (ENCLB196QXY)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 8
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB196QXY
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS088CZP at ENCODE; https://www.encodeproject.org/ENCBS088CZP/

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


title: single cell RNA-seq from Purkinje cell (ENCLB033OYZ)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 4
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB033OYZ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS074RTA at ENCODE; https://www.encodeproject.org/ENCBS074RTA/


title: single cell RNA-seq from Purkinje cell (ENCLB863GTU)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 3
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB863GTU
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS881LWZ at ENCODE; https://www.encodeproject.org/ENCBS881LWZ/


title: single cell RNA-seq from Purkinje cell (ENCLB807MQE)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 14
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB807MQE
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS451ZMX at ENCODE; https://www.encodeproject.org/ENCBS451ZMX/


title: single cell RNA-seq from Purkinje cell (ENCLB337IRK)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB337IRK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS107VUQ at ENCODE; https://www.encodeproject.org/ENCBS107VUQ/


title: single cell RNA-seq from Purkinje cell (ENCLB359XUW)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 13
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB359XUW
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Purkinje cell

value: ENCBS825HER at ENCODE; https://www.encodeproject.org/ENCBS825HER/


title: single cell RNA-seq from Purkinje cell (ENCLB950QWJ)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 6
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB950QWJ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: primary cell

value: 8 month

value: ENCBS620SZZ at ENCODE; https://www.encodeproject.org/ENCBS620SZZ/


title: single cell RNA-seq from Purkinje cell (ENCLB435TVJ)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB435TVJ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: adult

value: male

value: ENCBS459UCD at ENCODE; https://www.encodeproject.org/ENCBS459UCD/


title: single cell RNA-seq from Purkinje cell (ENCLB296VEF)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 16
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB296VEF
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Barbara Wold, Caltech

value: ENCBS716XAT at ENCODE; https://www.encodeproject.org/ENCBS716XAT/


title: single cell RNA-seq from Purkinje cell (ENCLB721WMG)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 12
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB721WMG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: Control

value: ENCBS456JNY at ENCODE; https://www.encodeproject.org/ENCBS456JNY/


title: single cell RNA-seq from Purkinje cell (ENCLB430RUN)

description:
https://www.encodeproject.org/experiments/ENCSR637NLF/
***************
biological replicate number: 1
technical replicate number: 9
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR637NLF
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB430RUN
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cell-equivalent

value: ENCBS281KUY at ENCODE; https://www.encodeproject.org/ENCBS281KUY/

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


title: total RNA-seq from embryonic facial prominence (ENCLB256STD)

description:
https://www.encodeproject.org/experiments/ENCSR636CWO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse cranio-facial prominence
experiment encode accession: ENCSR636CWO
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB256STD
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (15.5 days)

value: embryonic facial prominence

value: tissue

value: Embryonic facial prominence from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS900XQR at ENCODE; https://www.encodeproject.org/ENCBS900XQR/


title: total RNA-seq from embryonic facial prominence (ENCLB150ZJS)

description:
https://www.encodeproject.org/experiments/ENCSR636CWO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse cranio-facial prominence
experiment encode accession: ENCSR636CWO
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB150ZJS
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: Embryonic facial prominence from 78 embryonic 15.5 day mice

value: ENCBS543BPM at ENCODE; https://www.encodeproject.org/ENCBS543BPM/


title: total RNA-seq from liver (ENCLB599UVX)

description:
https://www.encodeproject.org/experiments/ENCSR611PTP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse liver
experiment encode accession: ENCSR611PTP
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB599UVX
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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


title: total RNA-seq from spleen (ENCLB590UZK)

description:
https://www.encodeproject.org/experiments/ENCSR579FCW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on postnatal 0 day mouse spleen
experiment encode accession: ENCSR579FCW
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB590UZK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: spleen

value: 1 spleen from pup1 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

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


title: total RNA-seq from spleen (ENCLB318WHF)

description:
https://www.encodeproject.org/experiments/ENCSR579FCW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on postnatal 0 day mouse spleen
experiment encode accession: ENCSR579FCW
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB318WHF
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: tissue

value: 1 spleen from pup2 pregnant 1

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

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