title: Adult2

city: Yangling

first: Hui

state: Shaanxi

address: College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China

institute: Northwest A&F University

data_processing:
From the raw FASTQ files, adapter was removed using Trim Galore and filtered data were aligned to the Bos taurus reference genome (bosTau7) from UCSC (http://genome.ucsc.edu/) with TopHat2 (version 2.0.14)
Linear transcripts assembly and abundance estimation were performed using CuffLinks analyzed by LC-Bio (Hangzhou, China). The assembled transcripts were mapped to the reference annotation using a program named Cuffcompare in the Cufflinks site to derive novel genes.
The transcript abundances were normalized as the number of uniquely mapped fragments per kilobase of exon per million fragments mapped (FPKM).
Genome_build: bosTau7
Supplementary_files_format_and_content: Additional file 1: List of differentially expressed gene identified in skeletal muscle.
Supplementary_files_format_and_content: Additional file 2: Heat map of 100 most differentially expressed genes profiling between embryonic stage and adult stage.
Supplementary_files_format_and_content: Additional file 3: 157 terms significantly enriched in molecular function of Gene Ontology enrichment.
Supplementary_files_format_and_content: Additional file 4: 153 terms significantly enriched in cellular component of Gene Ontology enrichment.
Supplementary_files_format_and_content: Additional file 5: 287 terms significantly enriched in biological processes of Gene Ontology enrichment.

source_name: adult longissimus muscle

growth_protocol: Six longissimus muscle samples from Qinchuan cattles of two developmental states (embryonic, 90 d; and adult, 24 M old) were collected from Yiming abattoir, a local slaughterhouse of Xi’An, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer. The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries.
Then the rRNA depleted RNA samples were fragmented and used to synthesize first- and second-strand complementary DNA (cDNA) with random hexamer primers, dNTPs and DNA Polymerase I. The cDNA fragments were cleaned and concentrated using AMPure XP beads, then the ends were repaired and modified with T4 DNA polymerase Klenow DNA polymerase to add A and adapter at the 3’ end of the DNA fragments. The ligated cDNA products were purified with AMPure XP beads and treated with uracil DNA glycosylase to remove the second-strand cDNA.  Purified first-strand cDNA was subjected to PCR amplification, and the libraries were quality controlled with a Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) and sequenced by Illumina HiSeq 2500 (LC Sciences, USA) on a 125 bp paired-end run.

tag: breed

value: Qinchuan

value: skeletal muscle

tag: developmental stage

value: Adult

tag: age

value: 24 M old


title: 490_DMSO_3

status: Public on Jul 11 2017

type: SRA

city: Boston

first: Ramnik

last: Xavier

state: MA

address: 55 Fruit Street

department: Gastroenterology

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
Whole transcriptome: Alignment with Tophat+Bowtie.
Whole transcriptome: Counting of transcripts with htseq-count.
Whole transcriptome: QC with RSeqC.
Whole transcriptome: Differential expression with EdgeR.
3' DGE: Alignment with BWA.
3' DGE: Counting of transcripts with custom python script.
3' DGE: QC with custom python script.
3' DGE: Differential expression with EdgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.namesorted.htseq.txt: Tab-delimited text files include raw counts for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs, DMSO, donor 490

growth_protocol: hPBMCs were isolated and plated and stimulated for a total of 21 hours in human serum at 0.5% in Xvivo15 media.

extract_protocol:
RNA extraction using RNeasy Plus Mini kit from Qiagen using gDNA eliminator columns (no on-column DNase digestion needed).
The smart-seq2 protocol (Picelli et al., 2013) was modified for 20 ng total input RNA.

treatment_protocol: PBMCs were stimulated with 80uM IA or 0.1% DMSO control for 45 min, followed by 1ng/mL LPS stimulation for 20 hours, at which point supernatant was collected and spun down, pellet and adherent cells used for RNA isolation.

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: treatment

value: DMSO, followed by LPS

tag: donor

tag: number of cells

value: 2 million

tag: rna ng/ul

tag: total volume

tag: collection buffer

value: ultrapure water

tag: plate (index)

tag: well

tag: i7 index 1

value: GCTACGCT

tag: s

tag: i5 index 1

value: CTCTCTAT

tag: total rna

value: ATAGAGAG


title: Day 14-Mock 3

city: Galveston

first: Grant

last: Hughes

state: TX

address: 301 University Boulevard

department: Pathology

institute: University of Texas Medical Branch

data_processing:
The quality of raw data from each library was controlled by CLC Genomic Workbench version 7.5.1.  Raw data were stripped of adapters and reads with quality score above 0.05 and less than 2 ambiguous nucleotides were retained. Reads without 3’ adapters and also reads with less than 16 nt were discarded from the libraries. Clean data considered as mappable reads for further analysis.
Tab separated files with the read sequences and their counts were used as input file for novel and homologous miRNA analysis using sRNAtoolbox. All known Ae. aegypti pre-miRNAs reported in miRBase 21 were used as reference for miRNA annotation.
Genome_build: Ae. aegypti genome (AaegL1)
Supplementary_files_format_and_content: text file, miRNA copy number

organism: Aedes aegypti

source_name: Day 14-Mock

extract_protocol:
Total RNA was extracted from infected and non-infected mosquito samples using mirVANA following the manufacturer’s protocol (Life Technologies).
The small RNA libraries were from pools at days 2, 7 and 14 post infection generated from both populations using the  New England Biolabs small RNA library protocol (New England Biolabs) at the UTMB’s Next Generation Sequencing (NGS) Core (Galveston, TX). The purified cDNA libraries were sequenced using the rapid run platform and single end 50 base sequencing by synthesis on an Illumina Hi-Seq 1500 using the TruSeq SBS kit v3.

treatment_protocol: Mosquitoes were provided either a ZIKV infectious blood meal or non-infectious blood meal

tag: strain

value: Galveston

tag: infection

value: Mock

tag: time

value: Day 14

tag: tissue

value: Whole mosquito


title: 1001957_OCT_Contact4

city: Seoul

first: Han Young

last: Chung

address: 1 Gwanak-ro, Gwanak-gu, Seoul 151-742

country: South Korea

institute: Seoul National University

description: Sample 4 (2-2)

data_processing:
The Ribo-Zero rRNA removal kit (Epicentre, USA) was used for ribosomal RNA depletion according to manufacturer instructions.
Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA sample prep kit (Illumina, USA) following the manufacturer’s protocol.
The quality of cDNA libraries was determined by Agilent 2100 Bioanalyzer (Agilent Technologies). Strand-specific paired-ended 100 nucleotide reads from each cDNA library were obtained using HiSeq2500 (Illumina).
For biological replication, two libraries were separately constructed and sequenced from RNAs isolated from two independent filtered culture supernatants of FORC_036.
The reads obtained from RNA-sequencing were mapped to the FORC_036 reference genome using CLC Genomics Workbench ver. 7.5.1 (CLC bio, Aarhus, Denmark). The GenBank (http://www.ncbi.nlm.nih.gov) accession numbers of the reference genome are CP015512 (Chromosome I), CP015513 (Chromosome II), and CP015514 (Plasmid)
Genome_build: ASM211720v1 [CP015512 (Chromosome I), CP015513 (Chromosome II), and CP015514 (Plasmid)]
Supplementary_files_format_and_content: Count calculation by Cuffquant and Cuffdiff

organism: Vibrio vulnificus

source_name: Small Octopus

growth_protocol: FORC_036 was grown to mid-log phase (A600 of 0.8) in VFMG (Vibrio fisheri minimal medium containing glycerol) medium

extract_protocol: Total RNAs were isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer's procedure. The DNA contaminations were removed by TURBO DNase (AMbion, Austin, TX), and then extracted RNAs were cleaned up using RNeasy MinElute Cleanup kit (Qiagen). The extracted RNA was verified by Agilent 2100 Bioanalyzer with Agilent RNA 6000 Nano reagens (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: We artificially contact the FORC_036 strain to small octopus, and contact to small octopus for 1 h, and 4 h. Non-contact strain to crab in VFGM medium also prepared as negative control.

value: Contact

value: 1 h


title: 1001957_OCT_Uncontact4

description: Sample 3 (2-1)

source_name: Vibrio fischeri minimal medium  containing 32.6 mM glycerol (VFMG) media (Non crab)

value: Control (Non-contact)


title: 1001957_OCT_Contact3

description: Sample 2 (1-2)


title: Adult1

last: Li

department: College of Animal Science and Technology

country: China

molecule: polyA RNA

organism: Bos taurus

tag: breed

value: Qinchuan

value: skeletal muscle

tag: developmental stage

tag: age


title: Embryo3

source_name: embryonic longissimus muscle

value: Embryo


title: Day 2-Mock 3

source_name: Day 2-Mock

value: Day 2


title: 1001957_4h_OCT_Uncontact2

description: Sample 7 (4-1)

tag: treatment

value: 4 h


title: Embryo2


title: Day 14-Mock 2


title: 1685_DMSO_2

source_name: PBMCs, DMSO, donor 1685

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

value: DMSO, followed by LPS

tag: donor

tag: number of cells

value: 2 million

tag: rna ng/ul

value: CAGAGAGG

value: TATCCTCT

value: AGAGGATA


title: 1001957_OCT_Uncontact3

description: Sample 1 (1-1)


title: 490_DMSO_1

tag: total volume

tag: collection buffer

value: ultrapure water

tag: plate (index)

tag: well

value: CTCTCTAC

value: CTCTCTAT

value: ATAGAGAG


title: Embryo1


title: Adult3

value: Adult

value: 24 M old


title: 490_IA_2

source_name: PBMCs, IA, donor 490

value: IA, followed by LPS

tag: i7 index 1

value: AAGAGGCA

tag: s

tag: i5 index 1

tag: total rna


title: EpCAM+Tomato+ _1

status: Public on Jul 10 2017

city: Los Angeles

first: Cunyu

last: Wang

state: CA

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using Tophat
Differential expression were calculated using cuffdiff.
Genome_build: mm9

organism: Mus musculus

source_name: Oral cancer

extract_protocol:
Oral cancer samples were minced in cold PBS and digested into single cells using collagenase and dispase. Cells were stained with anti-EpCAM sorted based on EpCAM and Tomato expression. mRNA were isolated using Qiagen RNeasy Micro Kit.
RNA libraries were prepared for sequencing using KAPA kit

tag: strain

tag: sample type

value: Oral cancer


title: EpCAM+Tomato+ _2


title: EpCAM+Tomato- _2


title: 490_IA_1

value: CGAGGCTG


title: Input rep1

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: UBC

library_source: genomic

data_processing:
Fastq files were aligned to saccer3 using BWA
Samtools was used to filter for mapped reads with a mapping quality score of at least 10
Bedtools and AWK were used to convert the BAM files into bed files of mapped DNA fragments
Fragments smaller than 1000bp were selected for using AWK
Read coverage wig files were generated using the java-genomics-toolkit base.align.count function
Genome_build: sacCer3
Supplementary_files_format_and_content: wig files, coverage in 1bp intervals

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol:
Yeast strains were grown to midlog and crosslinked with 1% formaldehyde for 15 minutes
Cells were grown in YPD

extract_protocol:
ChIP-SEQ was done as described with a few alterations (Maltby et al. 2012b; 2012a). Briefly, cells were grown in 1 L of yeast, peptone, dextrose media to mid-log phase and cross-linked with 1% formaldehyde for 15 minutes at 30°C. The cross-linking reaction was stopped with 125 mM liquid glycine and cells were washed twice with cold PBS. Cells were resuspended in lysis buffer [50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate], flash frozen in liquid nitrogen and ground in a coffee grinder with dry ice for 10 x 3 minutes. Samples were thawed, normalized by protein content, and sonicated (Biorupter, Diagenode, high output for 30 x 30 sec on/off) to obtain an average DNA fragment length of 200 to 400 bp. The lysate was cleared at 10,000 rpm for 10 minutes, and the supernatant was retained for the whole cell extract. Magnetic Protein-G Dynabeads were added and incubated with the whole cell extract for one hour, then removed. Antibodies were added (15.0 μL of the α-Hho1 antibody, Abcam, ab71833) and incubated with the whole cell extract overnight. Magnetic Protein-G Dynabeads were added and incubated with the sample for 30 minutes. Crosslinks were reversed overnight at 65C and DNA purified by phenol:chloroform:isoamyl alcohol extraction.
Library construction for the Illumina platform was performed using a custom procedure for paired-end sequencing. Briefly, 2–10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. In between each reaction, the material was purified using phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation. The resulting material was then amplified in the Phusion HF master mix (NEB) using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5′ AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3′, where “NNNNNN” corresponds to unique hexamer barcodes]. PCR amplification was performed as follows: denaturation at 98 °C for 60 s; eight cycles of (98 °C, 30 s; 65 °C, 30 s; 72 °C, 30 s), and a final extension at 72 °C for 5 min. Amplified libraries were purified using 0.8 (vol) Agencourt AMPure XP solid phase reversible immobilization paramagnetic beads and eluted in 10 mM Tris⋅HCl pH 8.5. An aliquot of each library was run on an Agilent High Sensitivity chip to check the size distribution and molarity of the PCR products. Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200–600 bp size range were selected on an 8% (wt/vol) Novex TBE PAGE gel (Invitrogen). An aliquot (1 μL) of the library pool was run on an Agilent Tape Station to confirm proper size selection and measure DNA concentration. The pooled libraries were diluted to 15 nM and their concentration was confirmed using the Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen).

treatment_protocol: 1% formaldehyde crosslinking

tag: genotype

value: his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

tag: chip antibody

tag: growth stage

value: Log growth


title: EpCAM+Tomato- _1


title: H3 IP rep2

value: α-H3 (custom rabbit polyclonal antibody raised against the yeast c-terminus of histone H3)


title: Hho1 IP rep1

value: α-Hho1 (Abcam, catalog# ab71833, lot# 586158)


title: H3 IP rep1


title: 490_DMSO_2

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: treatment

value: DMSO, followed by LPS

value: 2 million

value: CAGAGAGG


title: E13.5_P24 [single cell RNA-seq]

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description:
FACS sorted mouse single mouse sympatho-adrenal anlage at E13.5
E13.5_counts.txt.gz

data_processing:
RNA-seq data was aligned using tophat2, read counts were quantified with HTSeq
Genome_build: mm9
Supplementary_files_format_and_content: HTSeq read counts for each cell were combined and written out into a csv file

source_name: surgically extracted symaptho-adrenal anlage from Wnt1-Cre/R26Tomato embryo at E13.5; after dissociation Tomato+ neural crest-derived cells were fluorescently sorted in single cell mode into 384 well plates for sequencing.

extract_protocol:
Timed-pregnant mice were sacrificed by deep anesthesia followed by cervical dislocation. Dissection of embryos and adrenal anlages was carried out using a stereotactic microscope equipped with a fluorescent light source. Biological materials were transferred into DMEM/F12 medium with 0.05% Trypsin/ 0.02% EDTA (Sigma) and incubated at 37⁰ C for 5 min. Single cells were isolated by gentle trituration using P1000 tips and then added cold 10% FCS to stop the enzymatic reaction. After a double wash procedure using PBS with RNAse inhibitor, cells were filtered through a 40 uM nylon cell strainer and collected into a FACS tube on ice. Samples remained on ice throughout the process and total processing time from adrenal anlages isolation to sorting was limited to 1 hour.
Dissection of Wnt1-Cre/Tomato+ sympatho-adrenal anlages at E12.5 and E13.5 stages was carried out using a stereomicroscope equipped with a fluorescent light source. The dissected fragments were transferred into DMEM/F12 medium with 0.05% Trypsin/ 0.02% EDTA (Sigma) and incubated at 37⁰ C for 5 min. Single cells were released by gentle trituration using P1000 tips, and then ice-cold 10% FCS was added to stop the enzymatic reaction. After a double wash procedure using PBS with RNAse inhibitor, cells were filtered through a 40 uM nylon cell strainer and collected into a FACS tube on ice. After that the samples remained on ice or were kept at +4C throughout the rest of the processing that included single cell FACS sorting of Tomato+ cells into 384-well plates with pre-filled lysis buffer.The sequencing libraries were generated using the published protocol for Smartseq2 sequencing (Picelli et al., Nature Protocols 2014). Resulting libraries were sequenced on the Illumina® HiSeqTM 2000 sequencing platform. The extended analysis is published in Furlan, Dyachuk and Kastriti et al., Science 2016".

value: sympatho-adrenal anlage

tag: age


title: E13.5_P23 [single cell RNA-seq]


title: E13.5_P22 [single cell RNA-seq]


title: E13.5_P21 [single cell RNA-seq]


title: E13.5_P20 [single cell RNA-seq]


title: E13.5_P19 [single cell RNA-seq]


title: E13.5_P18 [single cell RNA-seq]


title: E13.5_P16 [single cell RNA-seq]


title: microRNA-seq from midbrain (ENCLB190ZRE)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR152ETW/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR152ETW
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB190ZRE
size range: <30

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

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

value: midbrain

value: tissue

tag: description

value: Midbrain from 88 embyronic 11.5 day mice

tag: biosample encode accession

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

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

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


title: microRNA-seq from midbrain (ENCLB969LUH)

description:
https://www.encodeproject.org/experiments/ENCSR152ETW/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR152ETW
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB969LUH
size range: <30

value: Midbrain of 109 embyronic 11.5 day mice

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


title: Day 14-Mock 1

value: Galveston

tag: infection

value: Mock

tag: time

value: Day 14

tag: tissue

value: Whole mosquito


title: E13.5_P15 [single cell RNA-seq]


title: E13.5_P13 [single cell RNA-seq]


title: E13.5_P14 [single cell RNA-seq]


title: E13.5_P12 [single cell RNA-seq]


title: Input rep2

value: his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: Log growth


title: E13.5_P11 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: Hho1 IP rep2

value: α-Hho1 (Abcam, catalog# ab71833, lot# 586158)


title: E13.5_P7 [single cell RNA-seq]


title: E13.5_P8 [single cell RNA-seq]


title: E13.5_P6 [single cell RNA-seq]


title: E13.5_P9 [single cell RNA-seq]


title: E13.5_P5 [single cell RNA-seq]


title: E13.5_P4 [single cell RNA-seq]


title: E13.5_P3 [single cell RNA-seq]


title: E13.5_P2 [single cell RNA-seq]


title: E13.5_P1 [single cell RNA-seq]


title: E13.5_O24 [single cell RNA-seq]


title: E13.5_O23 [single cell RNA-seq]


title: E13.5_P17 [single cell RNA-seq]


title: E13.5_O19 [single cell RNA-seq]


title: E13.5_O20 [single cell RNA-seq]


title: E13.5_O21 [single cell RNA-seq]


title: E13.5_O17 [single cell RNA-seq]


title: E13.5_O18 [single cell RNA-seq]


title: E13.5_O16 [single cell RNA-seq]


title: E13.5_O14 [single cell RNA-seq]


title: E13.5_O11 [single cell RNA-seq]


title: E13.5_O13 [single cell RNA-seq]


title: E13.5_O12 [single cell RNA-seq]


title: E13.5_O9 [single cell RNA-seq]


title: E13.5_O6 [single cell RNA-seq]


title: E13.5_O7 [single cell RNA-seq]


title: E13.5_O8 [single cell RNA-seq]


title: E13.5_O10 [single cell RNA-seq]


title: E13.5_O3 [single cell RNA-seq]


title: E13.5_O2 [single cell RNA-seq]


title: E13.5_O5 [single cell RNA-seq]


title: E13.5_O4 [single cell RNA-seq]


title: E13.5_O1 [single cell RNA-seq]


title: E13.5_O22 [single cell RNA-seq]


title: E13.5_N23 [single cell RNA-seq]


title: E13.5_P10 [single cell RNA-seq]


title: E13.5_N20 [single cell RNA-seq]


title: E13.5_N24 [single cell RNA-seq]


title: E13.5_O15 [single cell RNA-seq]


title: E13.5_N18 [single cell RNA-seq]


title: E13.5_N15 [single cell RNA-seq]


title: E13.5_N14 [single cell RNA-seq]


title: E13.5_N17 [single cell RNA-seq]


title: E13.5_N16 [single cell RNA-seq]


title: E13.5_N13 [single cell RNA-seq]


title: E13.5_N11 [single cell RNA-seq]


title: E13.5_N12 [single cell RNA-seq]


title: E13.5_N9 [single cell RNA-seq]


title: E13.5_N8 [single cell RNA-seq]


title: E13.5_N5 [single cell RNA-seq]


title: E13.5_N6 [single cell RNA-seq]


title: E13.5_N10 [single cell RNA-seq]


title: E13.5_N3 [single cell RNA-seq]


title: E13.5_N22 [single cell RNA-seq]


title: E13.5_N2 [single cell RNA-seq]


title: E13.5_N4 [single cell RNA-seq]


title: E13.5_M24 [single cell RNA-seq]


title: E13.5_N1 [single cell RNA-seq]


title: E13.5_N19 [single cell RNA-seq]


title: E13.5_N21 [single cell RNA-seq]


title: E13.5_M23 [single cell RNA-seq]


title: E13.5_M22 [single cell RNA-seq]


title: E13.5_M21 [single cell RNA-seq]


title: E13.5_M20 [single cell RNA-seq]


title: E13.5_M17 [single cell RNA-seq]


title: E13.5_M19 [single cell RNA-seq]


title: E13.5_M18 [single cell RNA-seq]


title: E13.5_M16 [single cell RNA-seq]


title: E13.5_M13 [single cell RNA-seq]


title: E13.5_M12 [single cell RNA-seq]


title: E13.5_M10 [single cell RNA-seq]


title: E13.5_M9 [single cell RNA-seq]


title: E13.5_M15 [single cell RNA-seq]


title: E13.5_N7 [single cell RNA-seq]


title: E13.5_M7 [single cell RNA-seq]


title: E13.5_M11 [single cell RNA-seq]


title: E13.5_M6 [single cell RNA-seq]


title: E13.5_M8 [single cell RNA-seq]


title: E13.5_M4 [single cell RNA-seq]


title: E13.5_M5 [single cell RNA-seq]


title: E13.5_L23 [single cell RNA-seq]


title: E13.5_M1 [single cell RNA-seq]


title: E13.5_L24 [single cell RNA-seq]


title: E13.5_M2 [single cell RNA-seq]


title: E13.5_L21 [single cell RNA-seq]


title: E13.5_L20 [single cell RNA-seq]


title: E13.5_L19 [single cell RNA-seq]


title: E13.5_L17 [single cell RNA-seq]


title: E13.5_L15 [single cell RNA-seq]


title: E13.5_L22 [single cell RNA-seq]


title: E13.5_L14 [single cell RNA-seq]


title: E13.5_L13 [single cell RNA-seq]


title: E13.5_L12 [single cell RNA-seq]


title: E13.5_L16 [single cell RNA-seq]


title: E13.5_L11 [single cell RNA-seq]


title: E13.5_L9 [single cell RNA-seq]


title: E13.5_L7 [single cell RNA-seq]


title: E13.5_L6 [single cell RNA-seq]


title: E13.5_L5 [single cell RNA-seq]


title: E13.5_L8 [single cell RNA-seq]


title: E13.5_L10 [single cell RNA-seq]


title: E13.5_L4 [single cell RNA-seq]


title: E13.5_L1 [single cell RNA-seq]


title: E13.5_L2 [single cell RNA-seq]


title: E13.5_M3 [single cell RNA-seq]


title: E13.5_K24 [single cell RNA-seq]


title: E13.5_L18 [single cell RNA-seq]


title: E13.5_K22 [single cell RNA-seq]


title: E13.5_K21 [single cell RNA-seq]


title: E13.5_K20 [single cell RNA-seq]


title: E13.5_K23 [single cell RNA-seq]


title: E13.5_K19 [single cell RNA-seq]


title: E13.5_M14 [single cell RNA-seq]


title: E13.5_K17 [single cell RNA-seq]


title: E13.5_K16 [single cell RNA-seq]


title: E13.5_K18 [single cell RNA-seq]


title: E13.5_K15 [single cell RNA-seq]


title: E13.5_K12 [single cell RNA-seq]


title: E13.5_K11 [single cell RNA-seq]


title: E13.5_K8 [single cell RNA-seq]


title: E13.5_K10 [single cell RNA-seq]


title: E13.5_K9 [single cell RNA-seq]


title: E13.5_L3 [single cell RNA-seq]


title: E13.5_K6 [single cell RNA-seq]


title: E13.5_K5 [single cell RNA-seq]


title: E13.5_K7 [single cell RNA-seq]


title: E13.5_K3 [single cell RNA-seq]


title: E13.5_K4 [single cell RNA-seq]


title: E13.5_K2 [single cell RNA-seq]


title: E13.5_J23 [single cell RNA-seq]


title: E13.5_J24 [single cell RNA-seq]


title: E13.5_K1 [single cell RNA-seq]


title: E13.5_J22 [single cell RNA-seq]


title: E13.5_J21 [single cell RNA-seq]


title: E13.5_J20 [single cell RNA-seq]


title: E13.5_K14 [single cell RNA-seq]


title: E13.5_J17 [single cell RNA-seq]


title: E13.5_J18 [single cell RNA-seq]


title: E13.5_J19 [single cell RNA-seq]


title: E13.5_J13 [single cell RNA-seq]


title: E13.5_J14 [single cell RNA-seq]


title: E13.5_J12 [single cell RNA-seq]


title: E13.5_J15 [single cell RNA-seq]


title: E13.5_J16 [single cell RNA-seq]


title: E13.5_K13 [single cell RNA-seq]


title: E13.5_J11 [single cell RNA-seq]


title: E13.5_J10 [single cell RNA-seq]


title: E13.5_J8 [single cell RNA-seq]


title: E13.5_J6 [single cell RNA-seq]


title: E13.5_J5 [single cell RNA-seq]


title: E13.5_J7 [single cell RNA-seq]


title: E13.5_J4 [single cell RNA-seq]


title: E13.5_J9 [single cell RNA-seq]


title: E13.5_J1 [single cell RNA-seq]


title: E13.5_J2 [single cell RNA-seq]


title: E13.5_I22 [single cell RNA-seq]


title: E13.5_I23 [single cell RNA-seq]


title: E13.5_I24 [single cell RNA-seq]


title: E13.5_I19 [single cell RNA-seq]


title: E13.5_I21 [single cell RNA-seq]


title: E13.5_I18 [single cell RNA-seq]


title: E13.5_I17 [single cell RNA-seq]


title: E13.5_I16 [single cell RNA-seq]


title: E13.5_I15 [single cell RNA-seq]


title: E13.5_I14 [single cell RNA-seq]


title: E13.5_I12 [single cell RNA-seq]


title: E13.5_I6 [single cell RNA-seq]


title: E13.5_I11 [single cell RNA-seq]


title: E13.5_I9 [single cell RNA-seq]


title: E13.5_I8 [single cell RNA-seq]


title: E13.5_I7 [single cell RNA-seq]


title: E13.5_I13 [single cell RNA-seq]


title: E13.5_I5 [single cell RNA-seq]


title: E13.5_I4 [single cell RNA-seq]


title: E13.5_I10 [single cell RNA-seq]


title: E13.5_J3 [single cell RNA-seq]


title: E13.5_I1 [single cell RNA-seq]


title: E13.5_I3 [single cell RNA-seq]


title: E13.5_H24 [single cell RNA-seq]


title: E13.5_H23 [single cell RNA-seq]


title: E13.5_I2 [single cell RNA-seq]


title: E13.5_H20 [single cell RNA-seq]


title: E13.5_H22 [single cell RNA-seq]


title: E13.5_H17 [single cell RNA-seq]


title: E13.5_H19 [single cell RNA-seq]


title: E13.5_H15 [single cell RNA-seq]


title: E13.5_H18 [single cell RNA-seq]


title: E13.5_H14 [single cell RNA-seq]


title: E13.5_H16 [single cell RNA-seq]


title: E13.5_I20 [single cell RNA-seq]


title: E13.5_H13 [single cell RNA-seq]


title: E13.5_H12 [single cell RNA-seq]


title: E13.5_H11 [single cell RNA-seq]


title: E13.5_H8 [single cell RNA-seq]


title: E13.5_H9 [single cell RNA-seq]


title: E13.5_H1 [single cell RNA-seq]


title: E13.5_H2 [single cell RNA-seq]


title: E13.5_G24 [single cell RNA-seq]


title: E13.5_H10 [single cell RNA-seq]


title: E13.5_H7 [single cell RNA-seq]


title: E13.5_H3 [single cell RNA-seq]


title: E13.5_H6 [single cell RNA-seq]


title: E13.5_H4 [single cell RNA-seq]


title: E13.5_H5 [single cell RNA-seq]


title: E13.5_H21 [single cell RNA-seq]


title: E13.5_G23 [single cell RNA-seq]


title: E13.5_G18 [single cell RNA-seq]


title: E13.5_G21 [single cell RNA-seq]


title: E13.5_G17 [single cell RNA-seq]


title: E13.5_G19 [single cell RNA-seq]


title: E13.5_G22 [single cell RNA-seq]


title: E13.5_G20 [single cell RNA-seq]


title: E13.5_G13 [single cell RNA-seq]


title: E13.5_G14 [single cell RNA-seq]


title: E13.5_G12 [single cell RNA-seq]


title: E13.5_G11 [single cell RNA-seq]


title: E13.5_G15 [single cell RNA-seq]


title: E13.5_G10 [single cell RNA-seq]


title: E13.5_G9 [single cell RNA-seq]


title: E13.5_G8 [single cell RNA-seq]


title: E13.5_G7 [single cell RNA-seq]


title: E13.5_G6 [single cell RNA-seq]


title: E13.5_G5 [single cell RNA-seq]


title: E13.5_G2 [single cell RNA-seq]


title: E13.5_G3 [single cell RNA-seq]


title: E13.5_G4 [single cell RNA-seq]


title: E13.5_G1 [single cell RNA-seq]


title: E13.5_G16 [single cell RNA-seq]


title: E13.5_F21 [single cell RNA-seq]


title: E13.5_F23 [single cell RNA-seq]


title: E13.5_F22 [single cell RNA-seq]


title: E13.5_F20 [single cell RNA-seq]


title: E13.5_F17 [single cell RNA-seq]


title: E13.5_F18 [single cell RNA-seq]


title: E13.5_F24 [single cell RNA-seq]


title: E13.5_F14 [single cell RNA-seq]


title: E13.5_F16 [single cell RNA-seq]


title: E13.5_F15 [single cell RNA-seq]


title: E13.5_F12 [single cell RNA-seq]


title: E13.5_F11 [single cell RNA-seq]


title: E13.5_F13 [single cell RNA-seq]


title: E13.5_F10 [single cell RNA-seq]


title: E13.5_F9 [single cell RNA-seq]


title: E13.5_F7 [single cell RNA-seq]


title: E13.5_F6 [single cell RNA-seq]


title: E13.5_F8 [single cell RNA-seq]


title: E13.5_F5 [single cell RNA-seq]


title: E13.5_F4 [single cell RNA-seq]


title: E13.5_F1 [single cell RNA-seq]


title: E13.5_F3 [single cell RNA-seq]


title: E13.5_F2 [single cell RNA-seq]


title: E13.5_F19 [single cell RNA-seq]


title: E13.5_E24 [single cell RNA-seq]


title: E13.5_E21 [single cell RNA-seq]


title: E13.5_E17 [single cell RNA-seq]


title: E13.5_E19 [single cell RNA-seq]


title: E13.5_E20 [single cell RNA-seq]


title: E13.5_E14 [single cell RNA-seq]


title: E13.5_E15 [single cell RNA-seq]


title: E13.5_E18 [single cell RNA-seq]


title: E13.5_E16 [single cell RNA-seq]


title: E13.5_E11 [single cell RNA-seq]


title: E13.5_E13 [single cell RNA-seq]


title: E13.5_E12 [single cell RNA-seq]


title: E13.5_E10 [single cell RNA-seq]


title: E13.5_E9 [single cell RNA-seq]


title: E13.5_E8 [single cell RNA-seq]


title: E13.5_D23 [single cell RNA-seq]


title: E13.5_E6 [single cell RNA-seq]


title: E13.5_D24 [single cell RNA-seq]


title: E13.5_E1 [single cell RNA-seq]


title: E13.5_E3 [single cell RNA-seq]


title: E13.5_E7 [single cell RNA-seq]


title: E13.5_D22 [single cell RNA-seq]


title: E13.5_D21 [single cell RNA-seq]


title: E13.5_D20 [single cell RNA-seq]


title: E13.5_E23 [single cell RNA-seq]


title: E13.5_E22 [single cell RNA-seq]


title: E13.5_D19 [single cell RNA-seq]


title: E13.5_D18 [single cell RNA-seq]


title: E13.5_D17 [single cell RNA-seq]


title: E13.5_D13 [single cell RNA-seq]


title: E13.5_D15 [single cell RNA-seq]


title: E13.5_D14 [single cell RNA-seq]


title: E13.5_D16 [single cell RNA-seq]


title: E13.5_D11 [single cell RNA-seq]


title: E13.5_E5 [single cell RNA-seq]


title: E13.5_D10 [single cell RNA-seq]


title: E13.5_E2 [single cell RNA-seq]


title: E13.5_E4 [single cell RNA-seq]


title: E13.5_D8 [single cell RNA-seq]


title: E13.5_D9 [single cell RNA-seq]


title: E13.5_D5 [single cell RNA-seq]


title: E13.5_D4 [single cell RNA-seq]


title: E13.5_D3 [single cell RNA-seq]


title: E13.5_C22 [single cell RNA-seq]


title: E13.5_C24 [single cell RNA-seq]


title: E13.5_D2 [single cell RNA-seq]


title: E13.5_C23 [single cell RNA-seq]


title: E13.5_C18 [single cell RNA-seq]


title: E13.5_C19 [single cell RNA-seq]


title: E13.5_C17 [single cell RNA-seq]


title: E13.5_C21 [single cell RNA-seq]


title: E13.5_C16 [single cell RNA-seq]


title: E13.5_C15 [single cell RNA-seq]


title: E13.5_D12 [single cell RNA-seq]


title: E13.5_C11 [single cell RNA-seq]


title: E13.5_C9 [single cell RNA-seq]


title: E13.5_D7 [single cell RNA-seq]


title: E13.5_C10 [single cell RNA-seq]


title: E13.5_D6 [single cell RNA-seq]


title: E13.5_C8 [single cell RNA-seq]


title: E13.5_C7 [single cell RNA-seq]


title: E13.5_C12 [single cell RNA-seq]


title: E13.5_C4 [single cell RNA-seq]


title: E13.5_C5 [single cell RNA-seq]


title: E13.5_C13 [single cell RNA-seq]


title: E13.5_D1 [single cell RNA-seq]


title: E13.5_C1 [single cell RNA-seq]


title: E13.5_C6 [single cell RNA-seq]


title: E13.5_B24 [single cell RNA-seq]


title: E13.5_C20 [single cell RNA-seq]


title: E13.5_B23 [single cell RNA-seq]


title: E13.5_B21 [single cell RNA-seq]


title: E13.5_B22 [single cell RNA-seq]


title: E13.5_B20 [single cell RNA-seq]


title: E13.5_B19 [single cell RNA-seq]


title: E13.5_B18 [single cell RNA-seq]


title: E13.5_B17 [single cell RNA-seq]


title: E13.5_C14 [single cell RNA-seq]


title: E13.5_B16 [single cell RNA-seq]


title: E13.5_B15 [single cell RNA-seq]


title: E13.5_B14 [single cell RNA-seq]


title: E13.5_B13 [single cell RNA-seq]


title: E13.5_C3 [single cell RNA-seq]


title: E13.5_C2 [single cell RNA-seq]


title: E13.5_B12 [single cell RNA-seq]


title: E13.5_B10 [single cell RNA-seq]


title: E13.5_B3 [single cell RNA-seq]


title: E13.5_B5 [single cell RNA-seq]


title: E13.5_B7 [single cell RNA-seq]


title: E13.5_B2 [single cell RNA-seq]


title: E13.5_B1 [single cell RNA-seq]


title: E13.5_A21 [single cell RNA-seq]


title: E13.5_B11 [single cell RNA-seq]


title: E13.5_A23 [single cell RNA-seq]


title: E13.5_B8 [single cell RNA-seq]


title: E13.5_B9 [single cell RNA-seq]


title: E13.5_B4 [single cell RNA-seq]


title: E13.5_B6 [single cell RNA-seq]


title: E13.5_A19 [single cell RNA-seq]


title: E13.5_A18 [single cell RNA-seq]


title: E13.5_A17 [single cell RNA-seq]


title: E13.5_A22 [single cell RNA-seq]


title: E13.5_A15 [single cell RNA-seq]


title: E13.5_A14 [single cell RNA-seq]


title: E13.5_A16 [single cell RNA-seq]


title: E13.5_A12 [single cell RNA-seq]


title: E13.5_A13 [single cell RNA-seq]


title: E13.5_A11 [single cell RNA-seq]


title: E13.5_A10 [single cell RNA-seq]


title: E13.5_A9 [single cell RNA-seq]


title: E13.5_A6 [single cell RNA-seq]


title: E13.5_A8 [single cell RNA-seq]


title: E12.5_P24 [single cell RNA-seq]

description:
FACS sorted mouse single mouse sympatho-adrenal anlage at E12.5
E12.5_counts.txt.gz

source_name: surgically extracted symaptho-adrenal anlage from Wnt1-Cre/R26Tomato embryo at E12.5; after dissociation Tomato+ neural crest-derived cells were fluorescently sorted in single cell mode into 384 well plates for sequencing.


title: E13.5_A4 [single cell RNA-seq]


title: E13.5_A2 [single cell RNA-seq]


title: E13.5_A7 [single cell RNA-seq]


title: E12.5_P23 [single cell RNA-seq]


title: E12.5_P21 [single cell RNA-seq]


title: E12.5_P14 [single cell RNA-seq]


title: E12.5_P13 [single cell RNA-seq]


title: E12.5_P16 [single cell RNA-seq]


title: E13.5_A5 [single cell RNA-seq]


title: E12.5_P20 [single cell RNA-seq]


title: E13.5_A20 [single cell RNA-seq]


title: E13.5_A24 [single cell RNA-seq]


title: E13.5_A3 [single cell RNA-seq]


title: E12.5_P9 [single cell RNA-seq]


title: E13.5_A1 [single cell RNA-seq]


title: E12.5_P10 [single cell RNA-seq]


title: E12.5_P18 [single cell RNA-seq]


title: E12.5_P12 [single cell RNA-seq]


title: E12.5_P8 [single cell RNA-seq]


title: E12.5_P7 [single cell RNA-seq]


title: E12.5_P6 [single cell RNA-seq]


title: E12.5_P5 [single cell RNA-seq]


title: E12.5_P11 [single cell RNA-seq]


title: E12.5_P19 [single cell RNA-seq]


title: E12.5_P22 [single cell RNA-seq]


title: E12.5_P15 [single cell RNA-seq]


title: E12.5_P17 [single cell RNA-seq]


title: E12.5_P4 [single cell RNA-seq]


title: E12.5_P2 [single cell RNA-seq]


title: E12.5_O22 [single cell RNA-seq]


title: E12.5_P1 [single cell RNA-seq]


title: E12.5_O21 [single cell RNA-seq]


title: E12.5_O18 [single cell RNA-seq]


title: E12.5_O15 [single cell RNA-seq]


title: E12.5_P3 [single cell RNA-seq]


title: E12.5_O24 [single cell RNA-seq]


title: E12.5_O23 [single cell RNA-seq]


title: E12.5_O14 [single cell RNA-seq]


title: E12.5_O13 [single cell RNA-seq]


title: E12.5_O11 [single cell RNA-seq]


title: E12.5_O10 [single cell RNA-seq]


title: E12.5_O9 [single cell RNA-seq]


title: E12.5_O19 [single cell RNA-seq]


title: E12.5_O17 [single cell RNA-seq]


title: E12.5_O16 [single cell RNA-seq]


title: E12.5_O5 [single cell RNA-seq]


title: E12.5_O4 [single cell RNA-seq]


title: E12.5_O7 [single cell RNA-seq]


title: E12.5_O12 [single cell RNA-seq]


title: E12.5_O6 [single cell RNA-seq]


title: E12.5_O3 [single cell RNA-seq]


title: E12.5_O2 [single cell RNA-seq]


title: E12.5_N23 [single cell RNA-seq]


title: E12.5_O1 [single cell RNA-seq]


title: E12.5_N24 [single cell RNA-seq]


title: E12.5_O20 [single cell RNA-seq]


title: E12.5_N18 [single cell RNA-seq]


title: E12.5_O8 [single cell RNA-seq]


title: E12.5_N19 [single cell RNA-seq]


title: E12.5_N20 [single cell RNA-seq]


title: E12.5_N15 [single cell RNA-seq]


title: E12.5_N16 [single cell RNA-seq]


title: E12.5_N21 [single cell RNA-seq]


title: E12.5_N14 [single cell RNA-seq]


title: E12.5_N13 [single cell RNA-seq]


title: E12.5_N11 [single cell RNA-seq]


title: E12.5_N10 [single cell RNA-seq]


title: E12.5_N7 [single cell RNA-seq]


title: E12.5_N6 [single cell RNA-seq]


title: E12.5_N8 [single cell RNA-seq]


title: E12.5_N12 [single cell RNA-seq]


title: E12.5_M24 [single cell RNA-seq]


title: E12.5_N5 [single cell RNA-seq]


title: E12.5_N9 [single cell RNA-seq]


title: E12.5_N3 [single cell RNA-seq]


title: E12.5_M22 [single cell RNA-seq]


title: E12.5_N2 [single cell RNA-seq]


title: E12.5_M20 [single cell RNA-seq]


title: E12.5_M21 [single cell RNA-seq]


title: E12.5_N22 [single cell RNA-seq]


title: E12.5_N17 [single cell RNA-seq]


title: E12.5_M23 [single cell RNA-seq]


title: E12.5_M18 [single cell RNA-seq]


title: E12.5_M19 [single cell RNA-seq]


title: E12.5_M17 [single cell RNA-seq]


title: E12.5_M16 [single cell RNA-seq]


title: E12.5_M14 [single cell RNA-seq]


title: E12.5_N4 [single cell RNA-seq]


title: E12.5_N1 [single cell RNA-seq]


title: E12.5_M13 [single cell RNA-seq]


title: E12.5_M11 [single cell RNA-seq]


title: E12.5_M12 [single cell RNA-seq]


title: E12.5_M8 [single cell RNA-seq]


title: E12.5_M10 [single cell RNA-seq]


title: E12.5_M7 [single cell RNA-seq]


title: E12.5_M6 [single cell RNA-seq]


title: E12.5_M5 [single cell RNA-seq]


title: E12.5_M3 [single cell RNA-seq]


title: E12.5_M2 [single cell RNA-seq]


title: E12.5_M4 [single cell RNA-seq]


title: E12.5_L24 [single cell RNA-seq]


title: E12.5_M1 [single cell RNA-seq]


title: E12.5_L23 [single cell RNA-seq]


title: E12.5_L22 [single cell RNA-seq]


title: E12.5_L21 [single cell RNA-seq]


title: E12.5_L20 [single cell RNA-seq]


title: E12.5_L18 [single cell RNA-seq]


title: E12.5_L17 [single cell RNA-seq]


title: E12.5_L16 [single cell RNA-seq]


title: E12.5_L19 [single cell RNA-seq]


title: E12.5_L15 [single cell RNA-seq]


title: E12.5_L14 [single cell RNA-seq]


title: E12.5_L13 [single cell RNA-seq]


title: E12.5_L12 [single cell RNA-seq]


title: E12.5_L11 [single cell RNA-seq]


title: E12.5_L10 [single cell RNA-seq]


title: E12.5_L8 [single cell RNA-seq]


title: E12.5_L9 [single cell RNA-seq]


title: E12.5_M15 [single cell RNA-seq]


title: E12.5_L7 [single cell RNA-seq]


title: E12.5_L6 [single cell RNA-seq]


title: E12.5_L5 [single cell RNA-seq]


title: E12.5_L4 [single cell RNA-seq]


title: E12.5_K23 [single cell RNA-seq]


title: E12.5_K24 [single cell RNA-seq]


title: E12.5_L1 [single cell RNA-seq]


title: E12.5_K21 [single cell RNA-seq]


title: E12.5_K19 [single cell RNA-seq]


title: E12.5_K20 [single cell RNA-seq]


title: E12.5_K22 [single cell RNA-seq]


title: E12.5_K18 [single cell RNA-seq]


title: E12.5_K16 [single cell RNA-seq]


title: E12.5_K17 [single cell RNA-seq]


title: E12.5_K15 [single cell RNA-seq]


title: E12.5_K14 [single cell RNA-seq]


title: E12.5_K13 [single cell RNA-seq]


title: E12.5_K12 [single cell RNA-seq]


title: E12.5_K11 [single cell RNA-seq]


title: E12.5_K10 [single cell RNA-seq]


title: E12.5_M9 [single cell RNA-seq]


title: E12.5_L3 [single cell RNA-seq]


title: E12.5_K9 [single cell RNA-seq]


title: E12.5_K7 [single cell RNA-seq]


title: E12.5_K8 [single cell RNA-seq]


title: E12.5_L2 [single cell RNA-seq]


title: E12.5_K5 [single cell RNA-seq]


title: E12.5_K4 [single cell RNA-seq]


title: E12.5_J24 [single cell RNA-seq]


title: E12.5_K1 [single cell RNA-seq]


title: E12.5_K6 [single cell RNA-seq]


title: E12.5_K3 [single cell RNA-seq]


title: E12.5_K2 [single cell RNA-seq]


title: E12.5_J23 [single cell RNA-seq]


title: E12.5_J21 [single cell RNA-seq]


title: E12.5_J22 [single cell RNA-seq]


title: E12.5_J20 [single cell RNA-seq]


title: E12.5_J17 [single cell RNA-seq]


title: E12.5_J18 [single cell RNA-seq]


title: E12.5_J15 [single cell RNA-seq]


title: E12.5_J14 [single cell RNA-seq]


title: E12.5_J19 [single cell RNA-seq]


title: E12.5_J13 [single cell RNA-seq]


title: E12.5_J12 [single cell RNA-seq]


title: E12.5_J11 [single cell RNA-seq]


title: E12.5_J9 [single cell RNA-seq]


title: E12.5_J8 [single cell RNA-seq]


title: E12.5_J7 [single cell RNA-seq]


title: E12.5_J6 [single cell RNA-seq]


title: E12.5_J10 [single cell RNA-seq]


title: E12.5_J5 [single cell RNA-seq]


title: E12.5_J4 [single cell RNA-seq]


title: E12.5_J2 [single cell RNA-seq]


title: E12.5_J3 [single cell RNA-seq]


title: E12.5_J1 [single cell RNA-seq]


title: E12.5_I23 [single cell RNA-seq]


title: E12.5_I24 [single cell RNA-seq]


title: E12.5_I20 [single cell RNA-seq]


title: E12.5_I17 [single cell RNA-seq]


title: E12.5_I21 [single cell RNA-seq]


title: E12.5_I19 [single cell RNA-seq]


title: E12.5_J16 [single cell RNA-seq]


title: E12.5_I18 [single cell RNA-seq]


title: E12.5_I16 [single cell RNA-seq]


title: E12.5_I14 [single cell RNA-seq]


title: E12.5_I12 [single cell RNA-seq]


title: E12.5_I11 [single cell RNA-seq]


title: E12.5_I9 [single cell RNA-seq]


title: E12.5_I8 [single cell RNA-seq]


title: E12.5_I13 [single cell RNA-seq]


title: E12.5_I6 [single cell RNA-seq]


title: E12.5_I10 [single cell RNA-seq]


title: UAMS1_wildtype_6h

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

description: total RNA, rRNA-depleted

data_processing:
Raw data files (.sff) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The accession number for the Genbank genome file used as references was NC_002952
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium (dextrose depleted) at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

tag: strain

value: wild-type

tag: growth medium

value: TSB (dextrose depleted)

tag: growth conditions


title: GFP_Batch2_Rep2

city: Cambridge

first: Jong Wook

last: Kim

address: 45 Main Street

department: Cancer Program

institute: Broad Institute

data_processing:
bam conversion (picard)
Re-calibrate BAM (prada)
RNAseqMatrics
Cuff-Link
Genome_build: HG19
Supplementary_files_format_and_content: KRAS_RNAseq.rpkm.v2.gct

extract_protocol:
RNA Isolation Kit: RNeasy Mini Kit - QIAGEN
Tru-Seq Standard & Strand- Specific RNA-Seq (high coverage-50M paired reads)

value: Small Airway Epithelial Cells

tag: genotype/variation

value: GFP

tag: agent

value: puromycin


title: UAMS1_nos_6h

description: total RNA, rRNA-depleted

tag: genotype

value: nos mutant


title: GFP_Batch1_Rep2

tag: cell type

value: blasticidin


title: E12.5_I22 [single cell RNA-seq]

tag: age


title: UAMS1_nos_4h

description: total RNA, rRNA-depleted


title: GFP_Batch2_Rep1


title: E12.5_I7 [single cell RNA-seq]


title: GFP_Batch1_Rep1


title: KRAS_Batch3_Rep1

value: KRAS G12V


title: E12.5_I5 [single cell RNA-seq]


title: KRAS_Batch3_Rep2


title: E12.5_I15 [single cell RNA-seq]


title: KRAS_Batch2_Rep2


title: E12.5_I4 [single cell RNA-seq]


title: E12.5_I3 [single cell RNA-seq]


title: KRAS_Batch2_Rep1


title: YAPC_RG1

description: (YAPC-Cas9 cells with Random gRNA1)

data_processing:
bam conversion (picard)
Re-calibrate BAM (prada)
RNAseqMatrics

source_name: YAPC_Cas9 Cell Line

extract_protocol:
RNA Isolation Kit: RNeasy Mini Kit - QIAGEN
Illumina stranded mRNA Library Prep

tag: cell line

value: YAPC

tag: grnas

value: RG


title: E12.5_I1 [single cell RNA-seq]


title: KRAS_Batch1_Rep1


title: YAPC_RG2

description: (YAPC-Cas9 cells with Random gRNA2)


title: KRAS_Batch1_Rep2


title: E12.5_I2 [single cell RNA-seq]


title: YAPC_RFP1

description: (YAPC-Cas9 cells with RFP gRNA1)

value: RFP


title: YAPC_RFP2

description: (YAPC-Cas9 cells with RFP gRNA2)


title: YAPC_JUN_3

description: (YAPC-Cas9 cells with JUN gRNA3)

value: JUN


title: YAPC_JUN_2

description: (YAPC-Cas9 cells with JUN gRNA2)


title: YAPC_FOS_3

description: (YAPC-Cas9 cells with FOS gRNA3)

value: FOS


title: YAPC_JUN_1

description: (YAPC-Cas9 cells with JUN gRNA1)


title: YAPC_FOS_2

description: (YAPC-Cas9 cells with FOS gRNA2)


title: YAPC_FOS_1

description: (YAPC-Cas9 cells with FOS gRNA1)


title: E12.5_H22 [single cell RNA-seq]


title: YAPC_FOSL1_1

description: (YAPC-Cas9 cells with FOSL1 gRNA1)


title: E12.5_H21 [single cell RNA-seq]


title: YAPC_FOSL1_3

description: (YAPC-Cas9 cells with FOSL1 gRNA3)


title: E12.5_H20 [single cell RNA-seq]


title: YAPC_E2F1_2

description: (YAPC-Cas9 cells with E2F1 gRNA2)


title: YAPC_E2F1_1

description: (YAPC-Cas9 cells with E2F1 gRNA1)


title: E12.5_H18 [single cell RNA-seq]


title: HCC44_RG1

description: (HCC44-Cas9 cells with Random gRNA1 gRNA3)

source_name: HCC44_Cas9 Cell Line


title: HCC44_RFP1

description: (HCC44-Cas9 cells with RFP1 gRNA3)


title: E12.5_H19 [single cell RNA-seq]


title: E12.5_H17 [single cell RNA-seq]


title: HCC44_ZEB1_2

description: (HCC44-Cas9 cells with ZEB1 gRNA2)


title: HCC44_ZEB1_1

description: (HCC44-Cas9 cells with ZEB1 gRNA1)


title: E12.5_H24 [single cell RNA-seq]


title: HCC44_ZEB1_3

description: (HCC44-Cas9 cells with ZEB1 gRNA3)


title: E12.5_H23 [single cell RNA-seq]


title: total RNA-seq from erythroblast (ENCLB723EFA)

description:
https://www.encodeproject.org/experiments/ENCSR247IMK/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse ERY 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR247IMK
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB723EFA
size range: 200-764
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J erythroblast primary cell male adult (5-6 weeks)

value: erythroblast

value: primary cell

tag: biosample encode accession

tag: dev stage

value: adult

value: Ross Hardison, PennState

value: 5-6 week

value: unknown

tag: Sex

value: male

value: ENCBS584MBS at ENCODE; https://www.encodeproject.org/ENCBS584MBS/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: E12.5_H14 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: E12.5_H16 [single cell RNA-seq]


title: total RNA-seq from common myeloid progenitor (ENCLB350XMQ)

description:
https://www.encodeproject.org/experiments/ENCSR133SAI/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse CMP 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR133SAI
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB350XMQ
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J common myeloid progenitor primary cell male adult (5-6 weeks)

value: common myeloid progenitor

tag: description

tag: lab

tag: health state

tag: link

value: ENCBS041EEZ at ENCODE; https://www.encodeproject.org/ENCBS041EEZ/


title: total RNA-seq from erythroblast (ENCLB586YJU)

description:
https://www.encodeproject.org/experiments/ENCSR247IMK/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse ERY 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR247IMK
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB586YJU
size range: 138-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: ENCBS102ASI at ENCODE; https://www.encodeproject.org/ENCBS102ASI/


title: YAPC_E2F1_3

description: (YAPC-Cas9 cells with E2F1 gRNA3)

value: YAPC


title: E12.5_H13 [single cell RNA-seq]


title: E12.5_H12 [single cell RNA-seq]


title: HCC44_GFP1

description: (HCC44-Cas9 cells with GFP1 gRNA3)

value: GFP


title: E12.5_H15 [single cell RNA-seq]


title: E12.5_H11 [single cell RNA-seq]


title: total RNA-seq from hematopoietic stem cell (ENCLB720BIA)

description:
https://www.encodeproject.org/experiments/ENCSR085AJX/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse HSC 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR085AJX
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB720BIA
size range: 232-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J hematopoietic stem cell male adult (5-6 weeks)

value: hematopoietic stem cell

value: stem cell

value: Hematopoietic stem cell (HSC)

value: ENCBS188YYN at ENCODE; https://www.encodeproject.org/ENCBS188YYN/


title: total RNA-seq from megakaryocyte-erythroid progenitor cell (ENCLB132RHQ)

description:
https://www.encodeproject.org/experiments/ENCSR121HYR/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse MEP 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR121HYR
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB132RHQ
size range: 215-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J megakaryocyte-erythroid progenitor primary cell male adult (5-6 weeks)

value: megakaryocyte-erythroid progenitor cell

value: primary cell

value: adult

value: ENCBS874FSX at ENCODE; https://www.encodeproject.org/ENCBS874FSX/


title: total RNA-seq from megakaryocyte (ENCLB649PUC)

description:
https://www.encodeproject.org/experiments/ENCSR025JRA/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse MEG 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR025JRA
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB649PUC
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J megakaryocyte primary cell male adult (5-6 weeks)

value: megakaryocyte

value: Ross Hardison, PennState

value: 5-6 week

value: unknown

value: male

value: ENCBS293VNL at ENCODE; https://www.encodeproject.org/ENCBS293VNL/


title: total RNA-seq from megakaryocyte progenitor cell (ENCLB112LYU)

description:
https://www.encodeproject.org/experiments/ENCSR027FCH/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse CFU-Mk 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR027FCH
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB112LYU
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J megakaryocyte progenitor primary cell male adult (5-6 weeks)

value: megakaryocyte progenitor cell

value: ENCBS674IDL at ENCODE; https://www.encodeproject.org/ENCBS674IDL/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from megakaryocyte progenitor cell (ENCLB181ERT)

description:
https://www.encodeproject.org/experiments/ENCSR027FCH/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse CFU-Mk 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR027FCH
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB181ERT
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: ENCBS722RKS at ENCODE; https://www.encodeproject.org/ENCBS722RKS/


title: WGBS from limb (ENCLB123XPU)

description:
https://www.encodeproject.org/experiments/ENCSR377CZO/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR377CZO
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB123XPU
size range: 180-500

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

value: limb

value: tissue

value: Limb from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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

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


title: E12.5_H9 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: total RNA-seq from megakaryocyte (ENCLB991WJK)

description:
https://www.encodeproject.org/experiments/ENCSR025JRA/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse MEG 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR025JRA
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB991WJK
size range: 221-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: megakaryocyte

value: primary cell

value: adult

value: Ross Hardison, PennState

value: 5-6 week

value: unknown

value: ENCBS359KER at ENCODE; https://www.encodeproject.org/ENCBS359KER/


title: total RNA-seq from hematopoietic stem cell (ENCLB161EXX)

description:
https://www.encodeproject.org/experiments/ENCSR085AJX/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse HSC 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR085AJX
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB161EXX
size range: 172-1452
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: hematopoietic stem cell

value: stem cell

value: Hematopoietic stem cell (HSC)

value: male

value: ENCBS383DPY at ENCODE; https://www.encodeproject.org/ENCBS383DPY/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: WGBS from limb (ENCLB819KXZ)

description:
https://www.encodeproject.org/experiments/ENCSR377CZO/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR377CZO
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB819KXZ
size range: 180-500

value: limb

value: tissue

value: Limb from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL


title: Original_Prox1_2

city: New York

first: Kelley

last: Yan

state: NY

department: Medicine

institute: Columbia University

description: GemCode

data_processing:
The Cell Ranger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). For the old Prox1+ samples, UMI=5 was used for the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bam: bam files of individual samples; mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample
Supplementary_files_format_and_content: File description and contents are described at http://software.10xgenomics.com/single-cell/overview/welcome

source_name: small intestine

growth_protocol: primary cell isolates from reporter mice

extract_protocol:
epithelial cell preparation from proximal jejunum of mice
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single-cell GEMs for the "Original Prox1_1" and "Orginal_Prox1_2" samples, which are two technical replicates. Single-cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al. 2017.  The remainder of the libraries were made using the Chromium Single Cell Instrument to generate single-cell GEMs using the Chromium Single Cell 3' Gel Bead and Library Kit from 10x Genomics (#120235, 120234, 120236, 120262).
For the "Original_Prox1_1" and "Original_Prox1_2" samples, the sequencing libraries were loaded at 2.1 pM on an Illumina NextSeq500 with 2 × 75 paired-end kits using the following read length: 98 bp Read1, 14 bp I7 Index, 8 bp I5 Index and 5 bp Read2. Note that these libraries were generated before the official launch of GemCode Single Cell 3’ Gel Bead and Library Kit. Thus 5bp UMI was used (the official GemCode Single Cell 3’ Gel Bead contains 10 bp UMI).  For the remainder of the samples, the sequencing libraries were loaded at 2.1 pM on an Illumina Hiseq4000 with 2 × 75 paired-end kits using the following read length: 26 bp Read1, 8 bp I7 Index and 98 bp Read2.

value: Prox1-GFP(+) cells

tag: treatment

tag: condition

value: sorted Prox1+ cells from Prox1-GFP reporter mouse


title: Original_Prox1_1

description: GemCode


title: total RNA-seq from common myeloid progenitor (ENCLB667VAC)

description:
https://www.encodeproject.org/experiments/ENCSR133SAI/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse CMP 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR133SAI
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB667VAC
size range: 187-1606
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: common myeloid progenitor

value: primary cell

value: adult

value: Ross Hardison, PennState

value: 5-6 week

value: unknown

value: ENCBS680UYK at ENCODE; https://www.encodeproject.org/ENCBS680UYK/


title: WGBS from limb (ENCLB518NLS)

description:
https://www.encodeproject.org/experiments/ENCSR377CZO/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR377CZO
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB518NLS
size range: 180-500

value: Limb from 69 embryonic 10.5 day mice

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

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


title: WGBS from hindbrain (ENCLB047KOB)

description:
https://www.encodeproject.org/experiments/ENCSR324XQF/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR324XQF
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB047KOB
size range: 180-500

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

value: hindbrain

value: tissue

value: Hindbrain from 69 embryonic 10.5 day mice

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


title: E12.5_H7 [single cell RNA-seq]

description:
FACS sorted mouse single mouse sympatho-adrenal anlage at E12.5
E12.5_counts.txt.gz

value: sympatho-adrenal anlage


title: E12.5_H5 [single cell RNA-seq]


title: E12.5_H6 [single cell RNA-seq]


title: WGBS from hindbrain (ENCLB288VOW)

description:
https://www.encodeproject.org/experiments/ENCSR324XQF/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR324XQF
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB288VOW
size range: 180-500

value: Hindbrain from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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


title: E12.5_H10 [single cell RNA-seq]


title: total RNA-seq from megakaryocyte-erythroid progenitor cell (ENCLB030AKH)

description:
https://www.encodeproject.org/experiments/ENCSR121HYR/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse MEP 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR121HYR
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB030AKH
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: megakaryocyte-erythroid progenitor cell

value: primary cell

value: adult

value: Ross Hardison, PennState

value: 5-6 week

value: male

value: ENCBS460OMF at ENCODE; https://www.encodeproject.org/ENCBS460OMF/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: E12.5_H8 [single cell RNA-seq]


title: E12.5_H3 [single cell RNA-seq]


title: E12.5_H4 [single cell RNA-seq]


title: WGBS from limb (ENCLB832CDT)

description:
https://www.encodeproject.org/experiments/ENCSR377CZO/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR377CZO
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB832CDT
size range: 180-500

value: limb

value: tissue

value: Limb from 69 embryonic 10.5 day mice

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

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


title: HOPX_Negative_S176

city: Duarte

first: John

middle: S.

last: Kaddis

address: 1500 East Duarte Road

department: Diabetes and Cancer Discovery Science

institute: City of Hope

data_processing:
This was performed via sequential application of TopHat, CuffLinks –g vs. –G and CuffDiff 2.0+ algorithms to generate FPKM calls.  Hierarchical clustering of all populations and external datasets (Lrig1, LRC) (Buczacki et al., 2013) was performed and dendrogram and p-values for interrelationships generated.  p-values underwent Benjamini-Hochberg correction for multiple testing to control the FDR. The most differentially expressed genes (FDR<0.05) were used for heatmaps. Gene Ontology (GO) pathway analysis of populations was performed with Bioconductor/GOSeq to remove RNA-seq gene length biases.  Gene set enrichment analysis (GSEA) was performed against the Molecular Signatures Database (MSigDB) and ISC marker-positive gene lists.
Genome_build: mm9
Supplementary_files_format_and_content: txt files and fpkm data

source_name: intestinal stem cells

extract_protocol:
A 1.8X volume of AMPure beads (Beckman Coulter, Brea, CA) was added to the thawed cell lysates (~10,000 cells sorted into 500ul Lysis Buffer RLT (Qiagen, Valencia, CA)). After a 30 minute incubation at room temperature, the samples were washed 2X with 70% ethanol and eluted in 22 µl water.  The samples were then digested with 0.6 mAU Proteinase K (Qiagen, Valencia, CA) in the presence of 1X NEB Buffer 1 (New England Biolabs, Ipswitch, MA) at 50C for 20 minutes, followed by a heat inactivation step at 65C for 10 minutes. A DNase digestion was performed using the RNase-Free DNase Set (Qiagen, Valencia, CA) at 37C for 30 minutes. The samples were cleaned with a 1.8X volume of AMPure XP beads (Beckman Coulter, Brea, CA). 1 ng of purified total RNA, as determined by Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA), was processed with the mRNA direct micro kit (Life Technologies, Foster City, CA) to select for poly A RNA.
Each entire sample was input into the Ambion WT Expression Kit (Life Technologies, Foster City, CA) to perform double stranded cDNA synthesis followed by in vitro transcription to generate amplified cRNA. The cRNA was purified following the manufacturer’s instructions and the concentration was determined by a NanoDrop instrument (Thermo Fisher Scientific, Waltham, MA).  1 µg of cRNA was fragmented in 1X Fragmentation Buffer (mRNA-seq Sample Prep Kit, Illumina, Hayward, CA) at 94C for 5 minutes, then placed on ice and the reaction was stopped by the addition of 20 mM EDTA. The fragments were precipitated with 70mM Sodium actetate (Life Technologies, Foster City, CA), 40 µg glycogen (Life Technologies, Foster City, CA) and 70% ethanol at -80C for 1 hour followed by centrifugation and washing with 70% ethanol.  3 µg of random hexamer (Life Technologies, Foster City, CA) was added to the fragmented, purified cRNA and incubated at 70C for 10 minutes to anneal the primer. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8U SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25C for 10 minutes, then 42C for 50 minutes, then 75C for 15 minutes and cooled to 4C. In second strand synthesis, 1X second strand buffer (Illumina, Hayward, CA) and 0.3mM dNTP’s  (Illumina, Hayward, CA) were added and the samples were incubated at 4C for 5 minutes before adding 50 units of DNA Polymerase (NEB, Ipswitch, MA) and 5 units of Rnase H (NEB, Ipswitch, MA). The samples were mixed well and incubated at 16C for 2.5h, followed by purification with the MinElute Kit (Qiagen, Valencia, CA).
To perform library prep, the samples were end repaired using a Quick Blunting Kit (NEB, Ipswitch, MA) and incubated at 20C for 1 hour, then 75C for 30 minutes to inactivate the enzyme. A’ bases were added to the 3’ ends of each fragment with 2 mM dATP and 5 units of Klenow fragment 3’-5’ exo- DNA Polymerase (NEB, Ipswitch, MA) at 37C for 45 minutes, followed by 75C for 30 minutes to inactivate the enzyme. Using a quick ligase kit (NEB, Ipswitch, MA), 0.5uM of adaptors were ligated to the cDNA fragments at 12C for 75 minutes, then 80C for 20 minutes and cooled to 4C. These adaptors contain barcodes to facilitate sample multiplexing during sequencing. The adaptor sequence is preceded by four random nucleotides to add diversity to the pooled library. The samples were pooled by combining 5 µl of each library. After AMPure XP cleanup, one half of the pooled library was run on the Pippin Size Selection Instrument (Sage Sciences, Beverly, MA) to select for 200bp fragments. Library amplification was performed on one half of the Pippin eluate in 1X Phusion GC buffer with 0.2mM dNTP’s, 0.1uM forward primer (IDT, Coralville, IA), 0.1 µM reverse primer, 1 unit of Phusion Hot Start II Polymerase (Thermo Fisher Scientific, Waltham, MA). The reaction was run with the following program: 98C for 30s, then 15 cycles of 98C for 10s, 65C for 30s, 72 for 30s, then 72C for 4 minutes and cooled to 4C. The amplified library was cleaned using a 1X volume of AMPure XP beads and QC was run with the Agilent Bioanalyzer DNA 1000 kit, followed by concentration determination by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA). In order to qualify for sequencing, the library must have a minimum concentration of 4nM and have no trace of low MW (<150bp) primer/dimer product.

tag: marker

value: HopX

tag: sample type

value: Negative


title: HOPX_Positive_S175

value: Positive


title: HOPX_Total_S177

value: Total


title: E12.5_H2 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: HOPX_Total_S174


title: E12.5_H1 [single cell RNA-seq]


title: HOPX_Positive_S172


title: E12.5_G24 [single cell RNA-seq]


title: Bmi1-GFP_Total_S168


title: HOPX_Total_S171


title: Bmi1-GFP_Negative_S167


title: HOPX_Negative_S170


title: E12.5_G23 [single cell RNA-seq]


title: WGBS from hindbrain (ENCLB953HKZ)

description:
https://www.encodeproject.org/experiments/ENCSR324XQF/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR324XQF
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB953HKZ
size range: 180-500

value: hindbrain

value: Hindbrain from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

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


title: Bmi1-GFP_Positive_S166


title: E12.5_G22 [single cell RNA-seq]


title: WGBS from hindbrain (ENCLB911LUF)

description:
https://www.encodeproject.org/experiments/ENCSR324XQF/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR324XQF
assay title: WGBS
assembly: mm10
encode release date: 2016-10-28
lab: Joe Ecker, Salk
library encode accession: ENCLB911LUF
size range: 180-500

value: Hindbrain from 69 embryonic 10.5 day mice

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


title: Bmi1-GFP_Total_S165


title: E12.5_G21 [single cell RNA-seq]


title: Bmi1-GFP_Negative_S164


title: Bmi1-GFP_Positive_S163


title: Bmi1-GFP_Total_S162


title: Bmi1-GFP_Negative_S161


title: HOPX_Negative_S173


title: E12.5_G20 [single cell RNA-seq]


title: HOPX_Positive_S169


title: Dclk1_Negative_S186


title: Bmi1-GFP_Positive_S160


title: E12.5_G19 [single cell RNA-seq]


title: E12.5_G18 [single cell RNA-seq]


title: E12.5_G17 [single cell RNA-seq]


title: Dclk1_Control_S184

value: Control


title: Dclk1_Positive_S185


title: Dclk1_Negative_S183


title: E12.5_G16 [single cell RNA-seq]


title: Dclk1_Control_S181


title: Dclk1_Positive_S182


title: E12.5_G15 [single cell RNA-seq]


title: Dclk1_Positive_S179


title: CD24lo_Interest_S21

value: Interest


title: Dclk1_Negative_S180


title: CD24lo_Negative_S22


title: Dclk1_Control_S178


title: CD24lo_Parent_S20

value: Parent


title: E12.5_G14 [single cell RNA-seq]


title: E12.5_G13 [single cell RNA-seq]


title: CD24lo_Interest_S18


title: CD24lo_Parent_S17


title: E12.5_G11 [single cell RNA-seq]


title: CD24lo_Interest_S15


title: CD24lo_Parent_S14


title: E12.5_G10 [single cell RNA-seq]


title: UpperLowerNonSP_NonSP_S149

value: UpperLowerNonSP

value: NonSP


title: UpperLowerNonSP_Upper_S147

value: Upper


title: UpperLowerNonSP_NonSP_S146


title: CD24lo_Negative_S19

value: Negative


title: E12.5_G8 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: UpperLowerNonSP_Upper_S143


title: E12.5_G6 [single cell RNA-seq]


title: UpperLowerNonSP_Lower_S141

value: Lower


title: E12.5_G5 [single cell RNA-seq]


title: E12.5_G12 [single cell RNA-seq]


title: CD24lo_Negative_S16


title: UpperLowerNonSP_Upper_S140


title: E12.5_G4 [single cell RNA-seq]


title: CD166posCD24neg_High_S55

value: High


title: E12.5_G7 [single cell RNA-seq]


title: CD166posCD24neg_Mid_S50

value: Mid


title: CD166posCD24neg_Negative_S100


title: CD166posCD24neg_Control_S99


title: CD166posCD24neg_Mid_S101


title: CD166posCD24neg_Negative_S49


title: UpperLowerNonSP_Lower_S148


title: E12.5_G3 [single cell RNA-seq]


title: CD166posCD24neg_High_S51


title: CD166posCD24neg_Control_S48


title: E12.5_G2 [single cell RNA-seq]


title: E12.5_G9 [single cell RNA-seq]


title: CD166posCD24neg_Mid_S46


title: CD166posCD24neg_High_S47


title: E12.5_G1 [single cell RNA-seq]


title: UpperLowerNonSP_Lower_S145


title: UpperLowerNonSP_NonSP_S142


title: CD166posCD24neg_Negative_S45


title: E12.5_F24 [single cell RNA-seq]


title: CD166posCD24neg_Control_S44


title: Lgr5_Control_S93


title: Lgr5_Negative_S92


title: E12.5_F23 [single cell RNA-seq]


title: Lgr5_Positive_S91

value: Positive


title: E12.5_F21 [single cell RNA-seq]


title: E12.5_F22 [single cell RNA-seq]


title: Lgr5_Negative_S89


title: Lgr5_Positive_S88


title: Lgr5_Control_S87


title: mTert_Control_S130

value: mTert


title: Lgr5_Negative_S86


title: Lgr5_Positive_S85


title: E12.5_F20 [single cell RNA-seq]


title: E12.5_F18 [single cell RNA-seq]


title: E12.5_F17 [single cell RNA-seq]


title: E12.5_F16 [single cell RNA-seq]


title: mTert_Positive_S128


title: mTert_Control_S127


title: mTert_Negative_S126


title: mTert_Control_S124


title: E12.5_F15 [single cell RNA-seq]


title: mTert_Negative_S123


title: mTert_Positive_S125


title: Lgr5_Control_S90


title: mTert_Positive_S122


title: Lgr5Unfrac_Control_S111


title: E12.5_F14 [single cell RNA-seq]


title: E12.5_F19 [single cell RNA-seq]


title: E12.5_F13 [single cell RNA-seq]


title: mTert_Negative_S129


title: Lgr5Unfrac_Negative_S110


title: Lgr5Unfrac_Positive_S109


title: E12.5_F12 [single cell RNA-seq]


title: Lgr5Unfrac_Control_S108


title: Grp78Neg_Positive_S34


title: Grp78Neg_Negative_S33


title: Lgr5Unfrac_Negative_S103


title: E12.5_F11 [single cell RNA-seq]


title: Lgr5Unfrac_Positive_S105


title: Lgr5Unfrac_Positive_S102


title: Grp78Neg_Negative_S27


title: Grp78Neg_Control_S32


title: Grp78Neg_Positive_S28


title: E12.5_F9 [single cell RNA-seq]


title: Lgr5Unfrac_Control_S104


title: E12.5_F8 [single cell RNA-seq]


title: E12.5_F6 [single cell RNA-seq]


title: E12.5_F7 [single cell RNA-seq]


title: Grp78Neg_Control_S13


title: Grp78Neg_Positive_S24


title: Lgr5Unfrac_Negative_S107


title: Grp78Neg_Control_S26


title: E12.5_F10 [single cell RNA-seq]


title: E12.5_F4 [single cell RNA-seq]


title: Caloric_Restriction_Old_Mouse_20_Methylation

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Library protocol: DREAM
Illumina HiSeq 2500 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to mm10 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_mm9 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

source_name: Mouse whole blood

extract_protocol:
Puregene-Gentra DNA extraction
Two micrograms of genomic DNA spiked with 20 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

tag: tissue

value: whole blood

tag: strain

tag: gender

value: Male

value: 38 months old

tag: caloric status

value: Caloric Restriction


title: Caloric_Restriction_Old_Mouse_19_Methylation

tag: age

value: 34 months old


title: Caloric_Restriction_Old_Mouse_22_Methylation


title: E12.5_F5 [single cell RNA-seq]

tag: genotype

tag: cell type


title: E12.5_F3 [single cell RNA-seq]


title: Caloric_Restriction_Old_Mouse_02_Methylation

value: Female

value: 32 months old


title: Caloric_Restriction_Old_Mouse_06_Methylation


title: Grp78Neg_Negative_S23


title: Old_Mouse_27_Methylation

value: 33 months old

value: Food Ad Libitum


title: Old_Mouse_25_Methylation


title: Old_Mouse_14_Methylation

value: 30 months old


title: E12.5_F2 [single cell RNA-seq]


title: Old_Mouse_09_Methylation

value: 29 months old


title: Old_Mouse_10_Methylation


title: E12.5_E24 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: Young_Mouse_29_Methylation

value: 4 months old


title: Young_Mouse_30_Methylation


title: Old_Mouse_13_Methylation


title: E12.5_E23 [single cell RNA-seq]


title: Old_Mouse_08_Methylation


title: E12.5_E22 [single cell RNA-seq]


title: E12.5_F1 [single cell RNA-seq]


title: Young_Mouse_28_Methylation


title: E12.5_E21 [single cell RNA-seq]


title: Young_Mouse_16_Methylation


title: Young_Mouse_15_Methylation


title: ChIP-seq from PC-9 (ENCLB902ZJQ)

description:
https://www.encodeproject.org/experiments/ENCSR243INX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR243INX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-01-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB902ZJQ
size range: 200-600

source_name: Homo sapiens PC-9 immortalized cell line

tag: antibody

value: CTCF

tag: line

value: immortalized cell line

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

tag: biosample encode accession

tag: dev stage

value: unknown

value: not collected

value: Bradley Bernstein, Broad

value: ENCBS177ANS at ENCODE; https://www.encodeproject.org/ENCBS177ANS/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/

value: ENCODE dbxrefs Cellosaurus CVCL_B260; http://web.expasy.org/cellosaurus/CVCL_B260


title: E12.5_E20 [single cell RNA-seq]


title: E12.5_E19 [single cell RNA-seq]


title: ChIP-seq from B cell (ENCLB091KVS)

description:
https://www.encodeproject.org/experiments/ENCSR051VDI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR051VDI
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR000AUW
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB091KVS
size range: 200-600

source_name: Homo sapiens B primary cell female adult (27 years)

extract_protocol: not provided

value: B cell

value: primary cell

value: adult

tag: Sex

value: female

value: 27 year

tag: health state

value: normal

tag: lab

value: ENCBS400ARI at ENCODE; https://www.encodeproject.org/ENCBS400ARI/

value: Derived from ENCODE donor ENCDO115AAA; https://www.encodeproject.org/ENCDO115AAA/


title: ChIP-seq from OCI-LY1 (ENCLB048BKX)

description:
https://www.encodeproject.org/experiments/ENCSR155XXB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR155XXB
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR569IIN
encode release date: 2016-10-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB048BKX
size range: 200-600

source_name: Homo sapiens OCI-LY1 immortalized cell line

tag: description

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: male

value: B cell lymphoma

tag: link

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: E12.5_E18 [single cell RNA-seq]

source_name: surgically extracted symaptho-adrenal anlage from Wnt1-Cre/R26Tomato embryo at E12.5; after dissociation Tomato+ neural crest-derived cells were fluorescently sorted in single cell mode into 384 well plates for sequencing.

value: sympatho-adrenal anlage


title: ChIP-seq from DOHH2 (ENCLB387MYL)

description:
https://www.encodeproject.org/experiments/ENCSR084RDK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR084RDK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB387MYL
size range: 200-600

source_name: Homo sapiens DOHH2 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ab9a4628-0877-468f-bdfe-78aada2fdb96/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v8.2_exp.pdf

value: CTCF

value: immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: Bradley Bernstein, Broad

value: ENCBS100ZVH at ENCODE; https://www.encodeproject.org/ENCBS100ZVH/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: E12.5_E16 [single cell RNA-seq]


title: E12.5_E15 [single cell RNA-seq]


title: ChIP-seq from DOHH2 (ENCLB575SFP)

description:
https://www.encodeproject.org/experiments/ENCSR084RDK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR084RDK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB575SFP
size range: 200-600

value: adult

value: refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma

value: ENCBS662OGM at ENCODE; https://www.encodeproject.org/ENCBS662OGM/


title: ChIP-seq from B cell (ENCLB035MZA)

description:
https://www.encodeproject.org/experiments/ENCSR005WWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR005WWZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR805DRF
encode release date: 2017-01-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB035MZA
size range: 200-600

source_name: Homo sapiens B primary cell female adult (43 years)

value: B cell

value: primary cell

value: female

value: 43 year

value: normal

value: ENCBS098ETX at ENCODE; https://www.encodeproject.org/ENCBS098ETX/

value: Derived from ENCODE donor ENCDO114AAA; https://www.encodeproject.org/ENCDO114AAA/


title: E12.5_E14 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: E12.5_E13 [single cell RNA-seq]


title: E12.5_E17 [single cell RNA-seq]


title: E12.5_E10 [single cell RNA-seq]


title: E12.5_E11 [single cell RNA-seq]


title: E12.5_E9 [single cell RNA-seq]


title: E12.5_E8 [single cell RNA-seq]


title: E12.5_E7 [single cell RNA-seq]


title: E12.5_E6 [single cell RNA-seq]


title: E12.5_E2 [single cell RNA-seq]


title: E12.5_E1 [single cell RNA-seq]


title: E12.5_D24 [single cell RNA-seq]


title: E12.5_E3 [single cell RNA-seq]


title: E12.5_D23 [single cell RNA-seq]


title: E12.5_D22 [single cell RNA-seq]


title: E12.5_E4 [single cell RNA-seq]


title: E12.5_D21 [single cell RNA-seq]


title: E12.5_D18 [single cell RNA-seq]


title: E12.5_D19 [single cell RNA-seq]


title: E12.5_D17 [single cell RNA-seq]


title: E12.5_D20 [single cell RNA-seq]


title: 10M H

city: Barcelona

first: Elena

last: Hidalgo

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Universitat Pompeu Fabra

description:
Barcode: ATTCCT
f30310MH

data_processing:
original reads have been inspected by FastQC for their quality
reads have been then aligned to reference genome by using tophat (v2.1.1) and using the annotation as a guide. Annotation was retrieved by iGenomes website,
Annotation was retrieved by iGenomes website,
tophat was run by limiting the size of introns to minimum 20 and maximum 1000 bases.
Htseq-count was used for counting the number of mapped tags
Genome_build: EF2
Supplementary_files_format_and_content: Read count matrix for each gene

organism: Schizosaccharomyces pombe

source_name: exponential cultures, minimal media

growth_protocol: Cells were grown in MM to an OD600=0.5)

extract_protocol:
RNA was obtained through phenol/chloroform extraction.
RNA was enriched for presence of polyA

treatment_protocol: Cells were treated or not with 1 mM of hydrogen peroxide for 15 min.

value: [delta]sty1 HA-Atf1.10M

tag: atf1 phosphorylation status

value: unphosphorylatable Atf1

tag: treatment

value: H2O2 treated (1 mM, 15 min)


title: 10M

description:
Barcode: GAGTGG
f30310M

value: untreated


title: E12.5_D15 [single cell RNA-seq]


title: E12.5_E5 [single cell RNA-seq]


title: E12.5_D16 [single cell RNA-seq]


title: HA H

description:
Barcode: TAGCTT
303H

value: [delta]sty1 HA-Atf1

value: wild-type Atf1


title: E12.5_E12 [single cell RNA-seq]


title: E12.5_D14 [single cell RNA-seq]


title: STY

description:
Barcode: GCCAAT
STY


title: E12.5_D13 [single cell RNA-seq]


title: 10D H

description:
Barcode: CCGTCC
f30310DH

value: [delta]sty1 HA-Atf1.10D

value: phosphomimicking Atf1


title: HA

description:
Barcode: GATCAG
303


title: E12.5_D12 [single cell RNA-seq]


title: WT H

description:
Barcode: TTAGGC
WTH

value: wt


title: STY H

description:
Barcode: ACTTGA
STYH


title: WT

description:
Barcode: ATCACG
WT


title: E12.5_D9 [single cell RNA-seq]


title: E12.5_D8 [single cell RNA-seq]


title: E12.5_D7 [single cell RNA-seq]


title: E12.5_D10 [single cell RNA-seq]


title: Bs.NCIB3610.rhomutant.2

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

data_processing:
The raw data quality was controlled using FastQC (v0.11.3) and  low quality ends were removed using Prinseq (0.20.1; options "-trim_ns_left 0 -trim_ns_right 0 -trim_qual_right 20").
Remnant sequencing adaptors identified with FastQC were removed using Cutadapt (1.8.3; option "-b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG").
Reads were trimmed based on sequencing quality using Sickle (1.200; options "-n -x -q 30 -l 30").
Reads were mapped on AL009126.3 reference genome using Bowtie2 (2.0.6; options "-N 1 -L 16 -R 4").
Stranded and reverse stranded read count aggregation was performed using Htseq-count (0.6.0; standard options).
Genome_build: Genbank AL009126.3
Supplementary_files_format_and_content: CSV with tab-separated columns which contains read-counts aggregated on the sense and antisense strand of transcribed segments (annotated genes and S-segments of Nicolas et al., 2012). Each locus is uniquely identified by its coordinates on AL009126.3 (columns "Start.AL009126.3","End.AL009126.3 ","Strand.AL009126.3") and the read count data for reads with forward (sense) and reverse (antisense) directions are reported in two separate rows distinguished by the value in column "Direction.Of.Reads". Columns "Gene.Name" and "Locus.Tag" contains either the information found AL009126.3 (for annotated genes) or the information from Nicolas et al. (2012) for S-segments.

organism: Bacillus subtilis

growth_protocol: Bacteria were grown in LB medium at 37°C under vigorous agitation up to an OD600nm of ~0.5.

extract_protocol:
RNA preparation and DNase treatment were done as described (Nicolas et al., 2012). Quality and quantity of RNA samples was verified on a Bioanalyzer (Agilent, CA).
Library preparation and sequencing was performed by Plate-forme Transcriptome et Epigénome at Pasteur Institut (Paris, France). Ribosomal RNA were depleted using RIBOZero rRNA removal kit Bacteria (Illumina, San Diego, California). The libraries were then prepared with the Truseq Stranded mRNA sample preparation kit (Illumina) according to manufacturer’s instructions. Strand-specific reads with a 6 nt index used for multiplexing and an orientation reverse to the transcripts (first strand cDNA) were obtained on an Illumina Hiseq2500 platform.

tag: strain

tag: genotype/variation

value: rho-deletion mutant

tag: growth stage

value: Cells grown in LB; early exponential phase

tag: replicate

value: replicate 2


title: Bs.NCIB3610.rhomutant.1

value: replicate 1


title: Bs.NCIB3610.parental.2

value: parental


title: E12.5_D5 [single cell RNA-seq]

tag: genotype

tag: age


title: E12.5_D4 [single cell RNA-seq]

tag: cell type


title: Bs.NCIB3610.parental.1


title: E12.5_D6 [single cell RNA-seq]


title: E12.5_D1 [single cell RNA-seq]


title: E12.5_D2 [single cell RNA-seq]


title: E12.5_D11 [single cell RNA-seq]


title: Young_Monkey_54_Methylation

data_processing:
Library protocol: DREAM
Illumina HiSeq 2500 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to mm10 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: rheMac2
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_rheMac2 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

organism: Macaca mulatta

source_name: Rhesus monkey whole blood

extract_protocol:
PAXgene DNA extraction protocol
Five micrograms of genomic DNA spiked with 20 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

tag: tissue

value: whole blood

tag: gender

value: Male

value: 0.9 years old

tag: caloric status

value: Ad Libitum


title: Young_Monkey_57_Methylation


title: Young_Monkey_52_Methylation

value: Female

value: 0.8 years old


title: Young_Monkey_49_Methylation


title: E12.5_C23 [single cell RNA-seq]

value: sympatho-adrenal anlage


title: E12.5_C22 [single cell RNA-seq]


title: Old_Monkey_33_Methylation

value: 29.3 years old


title: Old_Monkey_24_Methylation

value: 21.9 years old