title: longissimus dorsi muscle

city: Yaan

first: jideng

last: Ma

address: Xinkang road

institute: Sichuan Agricultural University(SICAU),

data_processing:
The small sequencing data of LDM and PMM were obtained from the same pigs in our previous study. The raw reads of all these three tissues (PL, PMM and LDM) were then subjected to a series of additional strict filters (i.e. removed these reads: 3′adapter not found, the length less than 16 bases or more than 29 bases, junk reads). Then the mappable reads were then mapped to the precursor miRNAs of pig and 24 other mammals in miRBase 19.0. The following mapping process included two steps: (1) the pre-miRNAs were mapped to the pig genome (Sscrofa10.2) using NCBI Local BLAST; (2) UNAFold [56] was used to predict the hairpin RNA structures of the mappable sequences that not-mapped to pig genome in step 1 from the adjacent 60 nt sequences in either direction.
The expression of miRNAs in three samples were normalized by total mappable reads, program IDEG6 were employed to detected the differentially expressed miRNAs among three libraries (http://telethon.bio.unipd.it/bioinfo/IDEG6_form/). A unique miRNA is considered to be differentially expressed when it simultaneously obtain P < 0.001 under three statistical tests (Audic-Claverie test, Fisher exact test and Chi-squared 2×2 test with the Bonferroni correction by pairwise comparison).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: xlsx format and content with profile of the known porcine miRNAs (miRBase 19.0) with genome locations

source_name: muscle tissues

growth_protocol: All research involving animals was conducted according to the Regulations for the Administration of Affairs Concerning Experimental Animals (Ministry of Science and Technology, China, revised in June 2004) and approved by the Institutional Animal Care and Use Committee in the College of Animal Science and Technology, Sichuan Agricultural University, Sichuan, China under permit No. DKY-B20110807. Animals were allowed access to food and water ad libitum under normal conditions, and were humanely sacrificed as necessary, to ameliorate suffering.

extract_protocol:
Total RNA was extracted from PL using the mirVana™ miRNA isolation kit (Ambion, Austin, TX, USA) following the manufacturer’s procedure. The quantity and purity of total RNA were monitored by NanoDrop ND-1000 spectrophotometer (Nano Drop, DE, USA) at 260/280 nm (ratio > 2.0). The integrity of total RNA was monitored by the Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 6.0. Equal quantities (5 µg) of small RNA isolated from three female Landrace pigs were pooled.
Briefly, approximately 15 µg of small RNA was used for library construction and sequencing. The small RNA fragments (between 10-40 nt) were isolated by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina, San Diego, CA, USA). The small RNA fractions were then converted to cDNA by RT-PCR and the cDNA was sequenced on the Genome Analyzer GA-II (Illumina) following the recommended manufacturer’s protocol.

treatment_protocol: Muscles were obtained from three female Landrace pigs (210-days-old), and immediately frozen in liquid nitrogen, then stored at -80°C until RNA extraction.

tag: breed

value: Landrace

tag: gender

value: female

tag: age

value: 210 days old

value: longissimus dorsi muscle


title: PY9pat

status: Public on Dec 23 2015

type: SRA

city: Cambridge

first: Gavin

last: Kelsey

address: Babraham Research Campus

country: United Kingdom

institute: The Babraham Institute

library_source: genomic

data_processing:
Allelic methylation levels were extracted from the Bismark BAM files for reads with a linear match to the genome using a custom script (Supplementary material in manuscript), which compared the bases in the reads to the expected SNPs designed into the amplicons.
Genome_build: GRCh37
Supplementary_files_format_and_content: Average DNA methylation for each read, with a minimum of 5 informative CpGs, corresponding to allele 1 or allele 2 of SNPs for each assayed region in each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
submitter states "custom" (no  meaningful entry)
DNeasy Blood and Tissue Kit DNA extraction
Parallel PCR reactions to assay 151 imprinted differentially methylated domains (Supplementary material in manuscript) with a final concentration of 1xHotStar PCR buffer, 0.2mM dNTPs, 1U HotStar taq and 0.4uM each primer pair and 2ng DNA were performed in a 15uL reaction volume in 384-well plates.  The plates were prepared on the Agilent Bravo Workstation.  The cycling conditions included a 15 minute 95°C denaturation, followed by 30 cycles of 95°C for 30 seconds, 50°C for 30 seconds, 72°C for 90 seconds, with a 5 minute final extension at 72°C and were performed on the C1000 Touch Thermal Cycler.  PCR products were pooled for each sample and SPRI-purified using Sera-Mag carboxylate-modified Magnetic SpeedBeads as per manufacturer’s recommendations.  A-overhang addition was done using 1x NEB buffer 2, 0.2mM dATP, 12.5U Klenow fragment (3’->5’ exo-) in a 25uL reaction incubated at 37°C for 30 minutes.  Following SPRI purification, Illumina adapters were ligated using the Quick ligation kit in a 40uL reaction.  Following another SPRI purification, libraries were amplified (11 cycles) and barcoded using the Sanger 8-base index in a 50uL reaction containing: 1x High Fidelity buffer, 1U Phusion High Fidelity taq, 0.2mM dNTPs, 0.1uM each primer .  Final libraries were SPRI purified and concentration and quality were assessed by the 2100 Bioanalyzer system and Kapa library quantification.  The 48 barcoded libraries were pooled and multiplexed.

tag: tissue

value: whole blood

tag: developmental stage

value: adult

tag: genotype

value: Control


title: T01

city: Yangling

first: Yuejin

last: Wang

state: Shaanxi

address: Shaanxi, China

country: China

institute: Northwest A&F University

description: E-L 33 rep1

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to grape reference genome using TopHat2
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using a protocol from Trapnell C et al. Nature Biotechnology 2010
Genome_build: Vitis vinifera
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

molecule: total RNA

organism: Vitis vinifera

source_name: Grape skin

extract_protocol:
Total RNA was extracted using  OMEGA plant RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Cabernet Sauvignon

value: Grape skin


title: PM285

source_name: placental villi

value: placental villi

value: 3rd trimester


title: PM273tro

source_name: trophoblast

value: trophoblast


title: PM273


title: PM266tro


title: PM264tro


title: PM266


title: PM266mat


title: PM259tro


title: PM264mat


title: PM243mat


title: PM243


title: PM259mat


title: PM273mat


title: PM259


title: PX23mat


title: PM234tro


title: psoas major muscle

organism: Sus scrofa

value: psoas major muscle


title: PM220tro


title: PM220mat


title: PM234


title: PM285mat


title: peroneal longu

value: peroneal longu


title: PM210.2


title: PM264


title: Cell74

city: Cincinnati

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

country: USA

institute: Cincinnati Children's Hospital

description: total RNA from single-cells

data_processing:
Illumina Off-Line Basecaller(OLB) v1.9.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, mapped to mm10 whole genome using tophat v2.0.9 –p 4 –G (UCSC gtf)
Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

organism: Mus musculus

source_name: Nephron_progenitors_e14 single cell

extract_protocol:
Single-cell were loaded onto a Fluidigm Single-cell 10uM-17uM chip using the C-1 Autoprep system.   Cells were lysed and cDNAs generated following manufacturer's protocol.
The construction of RNA libraries were generated using Illumina Tagmentation following manufactuer's protocols

treatment_protocol: Nephron progenitors from various embryonic stages were purifed from the kidneys of Cited1-GFP transgenic mice by FACS.

tag: strain

value: Mixed

value: Kidney

value: embryonic day 14


title: PM243tro


title: PM193tro


title: PM234mat


title: PM193mat


title: H3K27me3_Pax6_G1

city: Worcester

first: Troy

middle: W.

last: Whitfield

address: 55 Lake Ave. N.

institute: University of Massachusetts Medical School

data_processing:
ChIP-Seq
Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6, Illumina).
Reads were mapped to the human genome (GRCh37, hg19) using bowtie (version 0.12.8) with up to two mismatches allowed.
For each cellular condition (i.e. defined by cell cycle phase and differentiation state), genome-wide enrichment profiles were generated from pooled ChIP-seq replicates versus input for H3K27me3 and H3K4me3, respectively using SPP. The resulting enrichment profiles are conservative (alpha=0.01) statistical estimates of log2 fold-enrichment  across the genome.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq: BigWig files correspond to enrichment profiles that are conservative (alpha=0.01) statistical estimates of log2 fold-enrichment  across the genome.
RNA-Seq
Base calls and sequence reads were generated by Illumina CASAVA software (CASAVA 1.8 pipeline, Illumina).
Raw sequences from RNA-seq libraries were mapped using TopHat (version 2.0.8b) with the parameters of “--b2-sensitive -r 80 -g 10”.
Mapped reads were analyzed using SeqMonk software (v0.27.0; Babraham Bioinformatics Institute). Expression profiles were calculated using the RNA-seq quantitation pipeline and normalized by adjusting globally count distributions at the 75th percentile. Differential expression was calculated using the intensity difference statistical test included in the software. Differential expression was called on log2 transformed counts by selecting transcripts that changed with a significance of p < 0.05 after Benjamini and Hochberg correction using a null model constructed from the 1% of transcripts showing the closest average level of observation to estimate experimental noise.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: Tab-delimited text files include RPKM values for each sample.

source_name: H9 Human ESCs-derived PAX6 positive cells

growth_protocol: The H9 human ESC line from WiCell Research Institute (Madison, WI) was maintained on hESC-qualified Matrigel (BD Bioscience, Catalog number 354277) in mTeSR-1 medium (Stemcell Technologies, Catalog number 05850) or Essential E8 medium (Life Technologies, Catalog number A1517001), as recommended by the supplier. Cells were expanded every 5–6 days, using non-enzymatic passaging following WiCell standard protocols. To generate PAX6 cells, undifferentiated ESCs were incubated in mTeSR-1 medium supplemented with 10 mM of Retinoic Acid (Sigma-Aldrich, Catalog number R2625-50MG) for 5 days. The treatment started one day after plating the cells, and medium was changed every day. hESC research was approved by the Institutional Embryonic Stem Cell Research Oversight Committee at University of Vermont.

extract_protocol:
Immunoprecipitated DNA or Input DNA for each cell cycle phase, cellular condition (ESC vs PAX6 cells), and biological replicate were end repaired using the End-It DNA End-Repair Kit (Epicenter), extended using a Klenow fragment (3′-5′ exo) (Epicenter), and ligated to sequencing adaptor oligos (Illumina) by following manufacturers´ recommendations. Each library was then subjected to 15 cycles of PCR amplification using PFU Ultra II Hotstart Master Mix (Agilent), and a size selected in range of 300 ± 50 bp. The final libraries were quantified by using both Qubit fluorimeter (Life Technologies) and Bioanalyzer system (Agilent Technologies), and submitted for sequencing.
Before every cell sorting experiment, cells were allowed to establish robust colonies. Normally, they were collected 4-5 days after plating. To improve the yield of sorting, we synchronized hESCs at either G2/M or G1 phase of the cell cycle one day before the collection, by incubation with Nocodazole (Sigma–Aldrich, Catalog number M1404-2MG) (200 ng/ml for 16 hr when cells were grown in mTeSR-1) (Figure 2B). Blocking of hESCs in G2/M phase was reversible, and cells were able to resume the cell cycle and progress into G1 after withdrawing of Nocodazole from the culture medium (Figure 1C). For cells growing in E8 medium, 25 ng/ml of Nocodazole for 16 hr was enough to block most of the cells in G2/M and allowed progression into G1 after withdrawing of Nocodazole from the medium (data not shown). After synchronization, cells were collected as single cells by treatment with Acutase (MP Biomedicals, Catalog number 1000449), and subsequently fixed with 1% formaldehyde for 10 minutes followed by 5 minutes of incubation with 0.125M glycine (Sigma-aldrich, Catalog number G8790-100G). Cells were counted and stored at -80ºC.
Pure populations of cells at G2, mitosis or G1 phase of the cell cycle were isolated by FACS, taking advantage of differences in DNA content that allow us to distinguish cells in G2/M from cells in G1, and the exclusive presence of histone H3 phosphorylated in serine 28 (H3S28p) in mitosis that permits us to discriminate between cells in G2 or M phase. Subsequent to cell synchronization and fixation, cells were permeabilized for 10 minutes using a mild permeabilization/wash buffer containing Saponin (BD Bioscience, Catalog number 51-2091KZ). For ESCs isolation, staining was performed with antibodies against OCT4 (PE-conjugated, BD Bioscience, Material number 561556), H3S28p (Alexa fluor 647-conjugated, BD Bioscience, Material number 558609), for 30 min. For PAX6 cells, staining was performed with antibodies against PAX6, instead of OCT4 (PE-conjugated, BD Bioscience, Material number 561552). After staining, cells were washed with permeabilization/wash buffer, resuspended in 2% fetal bovine serum (FBS) in phosphate buffer saline (PBS) and counterstained with 1 μg/ml DAPI (Life Technologies, Catalog number D1306) for 30 min. FACS was performed on a BD FACSAria II using linear FSC and SSC scaling, followed by height and area-based doublets discrimination. Compensation was calculated using FACS Diva autocompensation algorithms, and supplemented by manual compensation to correct for autofluorescence. Cells with sub-normal DNA content were filtered out during the gating and only samples with a purity of 95% or higher were used in the following experiments.
Cells at specific phases of the cell cycle, obtained from 3-4 different cell-sorting experiments, were pooled and treated as a single sample (or biological replicate). Two biological replicates were analyzed for each cell cycle phase, and for each cellular condition (ESCs and PAX6 cells). Cells were washed twice with PBS and subjected to extraction of nuclei according to (Siegel et al., 2009) with modifications. Isolated nuclei were sonicated using a Misonix S-4000 Ultrasonic Processor (QSonica,) to obtain sheared chromatin ranging from 0.2 to 0.6 kilobases (Figure S1). 4 μg of sheared chromatin were immunoprecipitated with either anti H3K4me3 (Abcam, ab1012) or anti H3K27me3 (Millipore, 07-449). Immunoprecipitated complexes were purified by Protein-G Dynabeads (Invitrogen), eluted, reverse crosslinked, quantified, and subjected to library preparation.

tag: cell type

tag: passages

tag: chip antibody


title: Input_Pax6_M_K27_R1

description: Input matched to sample from R1 of M-phase H3K27me3 experiment in Pax6 positive cells.

data_processing:
Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6, Illumina).
Reads were mapped to the human genome (GRCh37, hg19) using bowtie (version 0.12.8) with up to two mismatches allowed.
For each cellular condition (i.e. defined by cell cycle phase and differentiation state), genome-wide enrichment profiles were generated from pooled ChIP-seq replicates versus input for H3K27me3 and H3K4me3, respectively using SPP. The resulting enrichment profiles are conservative (alpha=0.01) statistical estimates of log2 fold-enrichment  across the genome.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files correspond to enrichment profiles that are conservative (alpha=0.01) statistical estimates of log2 fold-enrichment  across the genome.

extract_protocol:
Before every cell sorting experiment, cells were allowed to establish robust colonies. Normally, they were collected 4-5 days after plating. To improve the yield of sorting, we synchronized hESCs at either G2/M or G1 phase of the cell cycle one day before the collection, by incubation with Nocodazole (Sigma–Aldrich, Catalog number M1404-2MG) (200 ng/ml for 16 hr when cells were grown in mTeSR-1) (Figure 2B). Blocking of hESCs in G2/M phase was reversible, and cells were able to resume the cell cycle and progress into G1 after withdrawing of Nocodazole from the culture medium (Figure 1C). For cells growing in E8 medium, 25 ng/ml of Nocodazole for 16 hr was enough to block most of the cells in G2/M and allowed progression into G1 after withdrawing of Nocodazole from the medium (data not shown). After synchronization, cells were collected as single cells by treatment with Acutase (MP Biomedicals, Catalog number 1000449), and subsequently fixed with 1% formaldehyde for 10 minutes followed by 5 minutes of incubation with 0.125M glycine (Sigma-aldrich, Catalog number G8790-100G). Cells were counted and stored at -80ºC.
Pure populations of cells at G2, mitosis or G1 phase of the cell cycle were isolated by FACS, taking advantage of differences in DNA content that allow us to distinguish cells in G2/M from cells in G1, and the exclusive presence of histone H3 phosphorylated in serine 28 (H3S28p) in mitosis that permits us to discriminate between cells in G2 or M phase. Subsequent to cell synchronization and fixation, cells were permeabilized for 10 minutes using a mild permeabilization/wash buffer containing Saponin (BD Bioscience, Catalog number 51-2091KZ). For ESCs isolation, staining was performed with antibodies against OCT4 (PE-conjugated, BD Bioscience, Material number 561556), H3S28p (Alexa fluor 647-conjugated, BD Bioscience, Material number 558609), for 30 min. For PAX6 cells, staining was performed with antibodies against PAX6, instead of OCT4 (PE-conjugated, BD Bioscience, Material number 561552). After staining, cells were washed with permeabilization/wash buffer, resuspended in 2% fetal bovine serum (FBS) in phosphate buffer saline (PBS) and counterstained with 1 μg/ml DAPI (Life Technologies, Catalog number D1306) for 30 min. FACS was performed on a BD FACSAria II using linear FSC and SSC scaling, followed by height and area-based doublets discrimination. Compensation was calculated using FACS Diva autocompensation algorithms, and supplemented by manual compensation to correct for autofluorescence. Cells with sub-normal DNA content were filtered out during the gating and only samples with a purity of 95% or higher were used in the following experiments.
Cells at specific phases of the cell cycle, obtained from 3-4 different cell-sorting experiments, were pooled and treated as a single sample (or biological replicate). Two biological replicates were analyzed for each cell cycle phase, and for each cellular condition (ESCs and PAX6 cells). Cells were washed twice with PBS and subjected to extraction of nuclei according to (Siegel et al., 2009) with modifications. Isolated nuclei were sonicated using a Misonix S-4000 Ultrasonic Processor (QSonica,) to obtain sheared chromatin ranging from 0.2 to 0.6 kilobases (Figure S1). 4 μg of sheared chromatin were immunoprecipitated with either anti H3K4me3 (Abcam, ab1012) or anti H3K27me3 (Millipore, 07-449). Immunoprecipitated complexes were purified by Protein-G Dynabeads (Invitrogen), eluted, reverse crosslinked, quantified, and subjected to library preparation.
Immunoprecipitated DNA or Input DNA for each cell cycle phase, cellular condition (ESC vs PAX6 cells), and biological replicate were end repaired using the End-It DNA End-Repair Kit (Epicenter), extended using a Klenow fragment (3′-5′ exo) (Epicenter), and ligated to sequencing adaptor oligos (Illumina) by following manufacturers´ recommendations. Each library was then subjected to 15 cycles of PCR amplification using PFU Ultra II Hotstart Master Mix (Agilent), and a size selected in range of 300 ± 50 bp. The final libraries were quantified by using both Qubit fluorimeter (Life Technologies) and Bioanalyzer system (Agilent Technologies), and submitted for sequencing.

value: H9 Human ESCs-derived PAX6 positive cells


title: H3K27me3_Pax6_M


title: PM193


title: H3K27me3_Pax6_G2


title: PM155tro


title: PM161


title: H3K4me3_Pax6_G1


title: H3K4me3_Pax6_M


title: H3K4me3_Pax6_G2


title: Input_Pax6_G1


title: PM220


title: Input_Pax6_M


title: PM210.2mat


title: Input_Pax6_G2


title: PM155mat


title: Input_ES_G1

source_name: H9 Human ESCs

value: H9 Human ESCs


title: Input_ES_G2


title: H3K27me3_ES_G1


title: Input_ES_M


title: H3K27me3_ES_M


title: H3K4me3_ES_G1


title: Input_ES_G1_K4_R2

description: Input matched to sample from R2 of G1-phase H3K4me3 experiment in hES cells.


title: H3K27me3_ES_G2


title: RNA-seq Beta8

city: Philadelphia

first: Paul

state: PA

address: 3700 Hamilton Walk

institute: University of Pennsylvania

data_processing:
ATACseq: Illumina adapters were trimmed by Trimmomatic, and the 50 bp reads were trimmed by 10 bp with fastx_trimmer, then all reads were combined for each sample and aligned to hg18 with bowtie2 using default settings. Reads mapped to mitochrondrial DNA and low quality reads (MAPQ<10, duplicates and reads in Encode blacklist regions) were removed. All reads left were offset by +4 bp for + strand and −5 bp for – strand. Peaks were called for each sample using MACS2 with parameters “-q 0.05 --nomodel --shift 37 --extsize 73”.
RNAseq: High quality RNA-seq reads were aligned to the human genome and transcriptome (hg18) using the RNA-seq Unified Mapper (RUM). Aligned reads were filtered for rRNA reads using BLAST alignment against the known rRNA sequences, and all reads aligning to the mitochondrial genome were also discarded. Aligned reads were used to determine unambiguous read counts for each gene in the refGene database using HTSeq, i.e., only reads uniquely assigned to a single gene were counted. All differential expression analysis was performed using the GLM functions in the EdgeR package.
Genome_build: hg18
Supplementary_files_format_and_content: bed files from MACS2 for ATACseq peak summit locations;  tab-delimited text files include read counts for each RNAseq ample

source_name: pancreatic islets

growth_protocol: Islets were cultured either in CMRL1066 with 0.5% human albumin, 2 mM L-glutamine, 1% heparin, and 1% penicillin/streptomycin or in Prodo PIM(S) media supplemented with 5% PIM(ABS) and 1% PIM(G) at 37oC with 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen AllPrep DNA/RNA Mini Kit (Part# 80204).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded Total RNA LT Sample Prep Kit (Part# RS-122-2301).

treatment_protocol: Islets underwent fluorescence-activated cell sorting using cell-surface antibodies (HIC1-2B4, HIC3-2D12, and HIC1-1C10) to separate alpha, beta, and acinar cells.

value: beta

tag: donor


title: PM161mat


title: H3K4me3_ES_M


title: RNA-seq Beta5

extract_protocol:
Total RNA was extracted using the Ambion mirVana miRNA Isolation Kit (Part# AM1560).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded Total RNA LT Sample Prep Kit (Part# RS-122-2301).


title: RNA-seq Beta4


title: 3OL8_CDL_V

city: St Andrews,

first: Darren

middle: James

last: Parker

state: Fife

address: Dyers Brae House

department: Centre for Biological Diversity

institute: University of St. Andrews

data_processing:
Raw sequence reads were trimmed using SOLiD TRIM (with run options: -p 3 -q 22 -y y -e 2 -d 10)
Reads were then error corrected using SOLiD Accuracy Enhancer Tools (SAET)
Remaining low quality bases at the end of the reads were then trimmed using CLC Genomics Workbench 5.0.1 (quality score: 0.02)
Reads for each sample were mapped individually to the reference transcriptome using CLC Bio (default values).
HTSeq was used then to quantify the number of reads mapping uniquely to each of the reference contigs.
Genome_build: The Transcriptome Shotgun Assembly used has been deposited at DDBJ/EMBL/GenBank under the accession GECM00000000. The version described in this paper is the first version, GECM01000000.
Supplementary_files_format_and_content: Data files contain 3 columns: Col1: contigs reads are mapped to, Col2: Top Blast Hit Accession number for each contig, Col3: Uniquely mapping read counts from HTseq

molecule: polyA RNA

organism: Drosophila montana

source_name: pooled flies (10)

extract_protocol:
RNA was extracted from each sample using Tri Reagent (Sigma-Aldrich) followed by RNeasy Mini kit (Qiagen) purification with DNase treatment.
RNA libraries were prepared for sequencing using standard SOLiD protocols

tag: Sex

value: female

value: 21 days post eclosion

tag: diapause state

value: non-diapause

tag: light

value: dark cycle:17.5:5.5


title: RNA-seq Beta6


title: RNA-seq Beta3


title: 3OL8_CDL_D

value: Diapause


title: PM155

value: Control


title: 265OJ8_CDL_V


title: 265OJ8_CDL_D


title: 175OJ8_V_3

value: dark cycle:22:2


title: RNA-seq Beta1


title: RNA-seq Beta2


title: 175OJ8_V_2


title: RNA-seq Alpha6

value: alpha


title: RNA-seq Alpha7


title: 175OJ8_D_3

value: dark cycle:16:8


title: 175OJ8_V_1


title: RNA-seq Alpha5


title: 175OJ8_D_2


title: RNA-seq Alpha4


title: 175OJ8_D_1


title: 175OJ8_CDL_V


title: RNA-seq Beta7


title: RNA-seq Alpha3


title: H3K4me3_ES_G2


title: RNA-seq Alpha2


title: RNA-seq Alpha1


title: HPC CD31+G2V+KITint

status: Public on Dec 22 2015

city: Edinburgh

first: Elaine

last: Dzierzak

address: 47 Little France Crescent

department: MRC Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
Map reads from fastq file to mouse genome mm10 using tophat
perform corrections (fragment-bias and multi-read) using cufflinks
calculate FPKMs using cufflinks
calculate gene counts using HTSeq tool and mouse genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: counts.txt file reports count measurements, genes.fpkm_tracking file reports abundance measurements

source_name: embryonic day 11 aortic hematopoietic progenitor cells

extract_protocol:
RNA was prepared with the mirVana miRNA Kit (Ambion) and SMARTER protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cell sorting based on expression Gata2Venus transgene

tag: genotype/variation

value: Gata2Venus +

value: aorta

value: hematopoietic progenitor cells (HPCs)


title: TMRM High

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: TMRM High

data_processing:
Basecalls performed using CASAVA 1.8 and Raw reads were aligned to the mm9 genome assembly using Bowtie 0.12.9
Aligned reads are converted to BED format using bamtools 1.0.2 and RPKM (Reads Per Kilobase per Million mapped reads) values are calculated using unpublished python scripts
Differential gene expression is analyzed using R package edgeR
Genome_build: mm9
Supplementary_files_format_and_content: BED files are generated using bamtools and unpublished python scripts

source_name: Pre-activated CD8+ T cells

growth_protocol: CD8+ T cells from pmel-1 mice were stimulated in vitro with 1 μM hgp10025–33 peptide and expanded for 4 days in culture medium containing 10 ng•ml–1 IL-2 (Chiron). Membrane potential was assessed using the potentiometric dye tetramethyl rhodamine methyl ester (TMRM; Sigma Aldrich) at a final concentration of 25 nm for 30 min at 37°C. For sorting of cells with different mitochondrial membrane potential, CD8+ gated cells were sorted into two pools corresponding to the cells with the lowest (7-10%) and highest (7-10%) TMRM fluorescence. Cell sorting was performed with a FACS Aria instrument (BD Biosciences).

extract_protocol:
Total RNA was used to synthesize cDNA. 220-400 bp fragments were isolated using 2% E-Gel (Invitrogen), ends were repaired, adaptor was added using T4 DNA ligase (New England Biolabs), and amplified for 17 cycles using PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs).
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform

treatment_protocol: Activated T cells were sorted for low and high TMRM

value: Spleen


title: TMRM Low

description: TMRM Low


title: MC_AGMex_CD31nKITnBREp

data_processing:
Map reads from fastq file to mouse genome mm10 using tophat
perform corrections (fragment-bias and multi-read) using cufflinks
calculate FPKMs using cufflinks
calculate gene counts using HTSeq tool and mouse genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: .txt files report counts

source_name: embryonic day 11 AGM cells

growth_protocol: Either directly after dissection, or after explant culture defined condition with/without cyclopamine treatment.

treatment_protocol: cell sorting based on expression BRE-GFP transgene expression.

value: C57BL6 BRE-GFP reporter strain

tag: region

value: aorta-gonadmesonephros (AGM)

tag: enriched for

value: mesenchymal cells

tag: cell markers

value: CD31 negative, c-Kit negative

tag: bre-gfp status

value: positive

tag: protocol

value: AGM after explant culture


title: MC_AGMcy_CD31nKITnBREp

tag: developmental stage

tag: tissue

value: AGM after explant in presence of cyclopamine


title: MC_AGM11_CD31nKITnBREp

value: fresh AGMs


title: MC_AGMcy_CD31nKITnBREn

value: negative


title: HPSC_AGMex_CD31pKITpBREn

value: hematopoietic progenitor/stem cell

value: CD31 positive, c-Kit positive


title: HPSC_AGMex_CD31pKITpBREp


title: HPSC_AGMcy_CD31pKITpBREp


title: HPSC_AGMcy_CD31pKITpBREn


title: HPSC_AGM11_CD31pKITpBREn


title: HPSC_AGM11_CD31pKITpBREp


title: EC_AGMex_CD31pKITnBREp

value: endothelial cells

value: CD31 positive, c-Kit negative


title: EC_AGMex_CD31pKITnBREn


title: EC_AGMcy_CD31pKITnBREp


title: EC_AGMcy_CD31pKITnBREn


title: EC_AGM11_CD31pKITnBREp


title: EC_AGM11_CD31pKITnBREn


title: OtA8543

city: Farmington

first: Julia

last: Svedova

state: CT

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

data_processing:
base-calling Illumina (Otogenetics)
Advanced RNAseq analysis via DNANexus
mapping against mouse genome mm9 with STAR (2.4.0j)
expression measurement in FPKM (Fragments Per Kilobase per Million mapped) with cufflinks 2.2.1
differential expression (DE) analysis/comparison with cuffdiff 2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: Comparisons between RNAseq FPKM expression reports between either Vehicle Vβ3+ T cells and SEA Vβ3+ T cells or SEA Vβ3+ T cells and SEA Vβ14+ T cells from individual experiments

source_name: sorted T cells

growth_protocol: C57BL/6J mice were kept in the Central Animal Facility at the Uconn Health in accordance with federal guidelines.

extract_protocol:
Lymph nodes were harvested from mice 40 min after SEA or vehicle inhalation and cruched into single cell suspensions. The cells were stained with live/dead stain and anti-Vβ3 and anti-Vβ14 antibodies and sorted by FACS Aria II. Total RNA was obtained from the sorted cell lysates using RNeasy Mini kit (Qiagen) and sent to Otogenetics (Norcross, GA) for analysis. All samples passed the required quality control and underwent ultra low RNA input polyA cDNA preparation.
Low input RNA library were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice received either 1 μg of SEA in 50 μL of BSS or BSS alone (vehicle) intranasally.

tag: age

value: 8-10 weeks

value: V{beta}14+ T cells

tag: agent

value: SEA


title: OtA8542

tag: strain

tag: cell type


title: OtA8540

description:
OtA8537_vs_OtA8540_gene_exp.diff
OtA8540_vs_OtA8543_gene_exp.diff

value: V{beta}3+ T cells


title: OtA8539

description:
OtA8536_vs_OtA8539_gene_exp.diff
OtA8539_vs_OtA8542_gene_exp.diff


title: OtA8538

description:
OtA8535_vs_OtA8538_gene_exp.diff
OtA8538_vs_OtA8541_gene_exp.diff


title: OtA8541


title: 175OJ8_CDL_D

value: female

value: 21 days post eclosion

value: Diapause

value: dark cycle:17.5:5.5


title: MC_AGMex_CD31nKITnBREn

value: C57BL6 BRE-GFP reporter strain

value: aorta

value: aorta-gonadmesonephros (AGM)

value: mesenchymal cells

value: CD31 negative, c-Kit negative


title: HPC CD31+G2V-KITint

value: Gata2Venus -

value: hematopoietic progenitor cells (HPCs)


title: OtA8537

value: Vehicle


title: MC_AGM11_CD31nKITnBREn

value: negative

value: fresh AGMs


title: OtA8535

value: 8-10 weeks


title: OtA8536


title: FA_Day28_rep2

city: Boston

first: Kathryn

last: Pellegrini

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Renal Division, Department of Medicine

institute: Brigham and Women's Hospital, Harvard Medical School

description: Day 28 - sample 2

data_processing:
Basecalls determined with Illumina CASAVA version 1.8 software
Sequence reads trimmed, aligned to mm9 genome build, and annotated against miRBase v19 using miRDeep2 software.
Read counts were normalized against the library size for each sample (including only the mapped, aligned reads)and expressed as counts per million reads (cpm)
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file with read counts for each miRNA normalized as counts per million reads

growth_protocol: All mice were maintained under standard housing conditions in accordance with NIH guidelines for the care and use of laboratory animals.

extract_protocol:
Total RNA was isolated from homogenized kidney tissue from mice using Trizol. The yield, purity, and quality of extracted RNA was assessed using an RNA Pico chip on an Agilent Bioanalyzer.
Libraries were prepared using the Illumina TruSeq Small RNA Sample Preparation Kit and individually barcoded with TruSeq Small RNA Indices.

treatment_protocol: Male BALB/c mice (Charles River Laboratories) were injected with 250mg/kg of folic acid (prepared in 0.3M sodium bicarbonate) and kidney tissues were collected at 0, 1, 2, 3, 7, 14, and 28 days.

value: BALB/c

tag: gender

value: male

tag: time point

value: 28 day after folic acid injection

value: kidney


title: CTD-K7me2 ChIP-seq

city: Berlin

first: Elena

last: Torlai Triglia

state: Deutschland

address: Robert Rössle Str 10

department: BIMSB

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
QSEQ files were converted to FASTQ using qseq2fastq-1.1 and processed with Flexbar 2.5
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie 2.0.5 with default parameters
Data were filtered using a 95% quantile threshold for read duplication
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig program from UCSC

source_name: ES cells

growth_protocol: Mouse ES-OS25 cells were grown on 0.1% gelatin-coated surfaces in GMEM-BHK21 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 1% MEM non-essential amino acids, 1 mM sodium pyruvate (all from Gibco), 50 μM 2-mercaptoethanol, 1000 U/ml of human recombinant leukaemia inhibitory factor (Chemicon) and 0.1 mg/ml Hygromycin (Roche).

extract_protocol:
ChIP for RNAPII modifications was performed using chromatin from ESCs fixed in 1% formaldehyde (Sigma) at 37°C for 10 min, as described (associated paper, Brookes et al., 2012; Stock et al., 2007). 50μg of antibody and 600-700 μg of chromatin were used for immunoprecipitation.
ChIP-seq libraries were prepared from 10 ng of immunoprecipitated genomic DNA (quantified by Picogreen and Qubit) using the Next ChIP-Seq Library Prep Master Mix Set from Illumina (NEB, # E6240) following NEB protocol with some modifications. Samples were PCR amplified prior to size selection on an agarose gel. Libraries were quantified by Qubit (Invitrogen) and qPCR Kapa Library Quantification Universal Kit (KapaBiosytems, # KK4824), and library size was assessed by Bioanalyzer (Agilent).

value: OS25 ES cells

tag: antibody

tag: chromatin

value: Fixed chromatin


title: FA_Day28_rep3

description: Day 28 - sample 3


title: CTD-K7me1 ChIP-seq

value: K7me1 3D3


title: FA_Day14_rep3

description: Day 14 - sample 3

value: 14 day after folic acid injection


title: FA_Day14_rep2

description: Day 14 - sample 2


title: FA_Day14_rep1

description: Day 14 - sample 1


title: FA_Day7_rep2

description: Day 7 - sample 2

value: 7 day after folic acid injection


title: FA_Day7_rep3

description: Day 7 - sample 3


title: FA_Day28_rep1

description: Day 28 - sample 1


title: FA_Day7_rep1

description: Day 7 - sample 1


title: FA_Day3_rep3

description: Day 3 - sample 3

value: 3 day after folic acid injection


title: FA_Day3_rep1

description: Day 3 - sample 1


title: FA_Day2_rep3

description: Day 2 - sample 3

value: 2 day after folic acid injection


title: FA_Day1_rep3

description: Day 1 - sample 3

value: 1 day after folic acid injection


title: FA_Day2_rep1

description: Day 2 - sample 1


title: FA_Day0_rep3

description: Day 0 - sample 3

value: 0 day after folic acid injection


title: FA_Day2_rep2

description: Day 2 - sample 2


title: FA_Day1_rep1

description: Day 1 - sample 1


title: FA_Day1_rep2

description: Day 1 - sample 2


title: FA_Day0_rep2

description: Day 0 - sample 2


title: FA_Day0_rep1

description: Day 0 - sample 1


title: PCF SpliceLeader replicate_1 reanalysis

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

description:
GSM1379714
processed as before; but against new genome build

data_processing:
RNAseq reads were aligned to the Tb927 genome TriTrypDB V5.0 using bowtie2 version 2.2.2 in local alignment mode with the following configurations -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
Read counts for each of these regions of all genes were generated using HTSeq {ref} package. Any read overlapping the CDS or 5’ UTR region either partially or fully was assigned to that region. Both unique and multipmapping reads were considered for further analyses.
Raw read counts are analyzed using statistical package edgeR and DESeq from bioconductor project.
Genome_build: Tb927 genome build  V5.1; TriTrypDB V9.0
Supplementary_files_format_and_content: Tab delimited files with raw read count data corresponding to the CDSregion (+46th base until stop codon).

organism: Trypanosoma brucei

source_name: Tb927 PCF in SDM79 medium

growth_protocol: In vivo T brucei TREU927 were grown in irradiated Wistar rats infected with 107-108 parasites.  The parasites were harvested on day 3 at a parasitemia of 4´107-1.2´108 cells/ml.  In vitro procyclic TREU927 cell were grown in SDM-79 to a cell density of 5´106-1.2´107 cells/ml.  In vitro bloodform Lister427 was grown in HMI-9 to a density of 8´105 to 1.5´106 cells/ml.

extract_protocol:
For in vivo blood form parasites, the blood from 2-3 infects rats was pooled and centrifuged and the buffy coat extracted and placed into 20 ml HMI-9 without serum pre-warmed to 37°C.  To arrest translation, cycloheximide was added to 100 μg/ml and incubated for 2 minutes at 37°.  To rapidly chill the cells, 300 ml of ice-cold phosphate buffered saline with glucose (PSG) was added and the cells were pelleted at 4°.  Only parasite populations with greater than 99% slender cells were used.  In vitro grown parasites were pelleted at 5000g and resuspended in 50 mls of media lacking serum.  Cycloheximide was added to 100 mg/ml at the cell incubated for 2min at room temperature (procyclic cells) or 37° (bloodform cells). Following cycloheximide treatment the cells were rapidly chilled with PSG and pelleted at 5000g.  Lysates from both type of parasite pellets were then prepared as following. Cell pellets were resuspended in Buffer A (10 mM Tris pH 7.4, 300 mM KCl, 10 mM MgCl2 plus protease inhibitors to approximately 1.3x109/ml.  Approximately one-third of the sample was placed into TRIzol (Life Technologies) for RNA extraction following manufacturer’s suggested protocol.  To the remainder, one-sixth volume of buffer A containing 0.2M sucrose and 1.2% Triton N-101 was added and the samples were dounced (30 strokes in a chilled homogenizer). After transfer to a prechilled microfuge tube, the samples were clarified by centrifugation in a microfuge at 15000 rpm for one minute.  The supernatant was withdrawn, pooled if needed, and then aliquots flash frozen in liquid nitrogen for storage at -70°C.
After thawing on ice, RNase I (Ambion) was added at 30 units/OD260 of lysate.  Samples were then incubated for 1 hour at room temperature.  RNase digestion was stopped by adding 400 units RNasin (Promega).  Samples were them layered over a 1 ml 1M sucrose cushion prepared in buffer A and ribosomes were pelleted by centrifuging for 4 hours at 70,000g in an SW55 rotor.  After removing the supernatant, the ribosomal pellet was resuspended in 500 μl buffer A with the MgCl2 replaced with 10 mM EDTA to dissociate the ribosomes and deplete larger rRNA fragments.  The protected fragments were then separated from contaminating ribosomal RNA by passage through an Amicon Ultra-4 or YM-100 column with 100,000 MW cutoff. After more than 400 μl had flowed through the membrane the RNA in the flow-through was extracted with phenol:CHCl3:iAA and the RNA precipitated.  Poly(A)+ RNA was isolated using Dynabeads mRNA Direct (Life Technologies).  RNA was fragmented as described Ingolia et all 2011.  Ribosomal protected fragments between 28 and 31 nucleotides and fragmented Poly(A)+ RNA between 30 and 70 nucleotides was isolated from 15% accrylimide gels and libraries prepared for sequencing.  For detailed protocol on generating sequencing libraries for both the ribosome protected and fragmented mRNA library see Ingolia et a 2011.  Briefly, following dephosphorylation the adapter Linker-1 (IDT) was ligated to the 3’ end of the fragment and the ligated product gel purified.  The adapter was used for priming reverse.  Following gel purification the cDNA was circularized with Circ Ligase (Epicenter Biotechnologies).  Circles containing ribosomal RNA were subtracted using biotinylated primers .  The final library was generated by PCR..To map the 5’ end of the transcripts, libraries enriched for the 5’ ends of mRNAs were constructed from three biological samples of strain 927 (2 PCF and 1 slBF selected from the biological samples above).  SL libraries were constructed as described Mittra B et al 2013.  In brief, RNA was prepared and cDNA synthesized using primer ending in a random 6 bases.  Second strand synthesis was primed using a primer that matches the T. brucei SL sequence.  The sequencing library was generated by PCR. Duplexed libraries were sequenced using Illumina GA II machines at the High Throughput Genomics Unit at the University of Washington to generate ~36 nt reads.
RNAseq, Ribosome Profiling Seq, Splice Leader RNAseq

treatment_protocol: Cells were treated with 100 µg/ml cycloheximide for 2 min at either room temperature (procylic cells) or 37° (bloodform cells) to arrest elongating ribosomes.

value: Procyclic Form


title: cBF SpliceLeader replicate_1 reanalysis

description:
GSM1379717
processed as before; but against new genome build

source_name: Tb427 grown in vitro in HMI-9 medium

value: cultrured bloodstream Form


title: slBF SpliceLeader replicate_1 reanalysis

description:
GSM1379716
processed as before; but against new genome build

source_name: Tb927 BF grown in irradiated Wistar rat

value: Slender bloodstream Form


title: PCF SpliceLeader replicate_2 reanalysis

description:
GSM1379715
processed as before; but against new genome build


title: cBF mRNA replicate_3 reanalysis

description:
mRNA control for cBF3r
GSM1379713
processed as before; but against new genome build


title: cBF mRNA replicate_1 reanalysis

description:
mRNA control for cBF1r
GSM1379711
processed as before; but against new genome build


title: PCF mRNA replicate_2 reanalysis

description:
mRNA control for PCF2r
GSM1379706
processed as before; but against new genome build


title: slBF mRNA replicate_3 reanalysis

description:
mRNA control for slBF3r
GSM1379710
processed as before; but against new genome build


title: slBF mRNA replicate_1 reanalysis

description:
mRNA control for slBF1r
GSM1379708
processed as before; but against new genome build


title: PCF mRNA replicate_3 reanalysis

description:
mRNA control for PCF3r
GSM1379707
processed as before; but against new genome build


title: cBF RiboProf replicate_3 reanalysis

description:
Pairs with cBF3m
GSM1379704
processed as before; but against new genome build


title: PCF mRNA replicate_1 reanalysis

description:
mRNA control for PCF1r
GSM1379705
processed as before; but against new genome build


title: FA_Day3_rep2

description: Day 3 - sample 2


title: slBF mRNA replicate_2 reanalysis

description:
mRNA control for slBF2r
GSM1379709
processed as before; but against new genome build


title: cBF RiboProf replicate_2 reanalysis

description:
Pairs with cBF2m
GSM1379703
processed as before; but against new genome build


title: slBF RiboProf replicate_1 reanalysis

description:
Pairs with slBF1m
GSM1379699
processed as before; but against new genome build


title: slBF RiboProf replicate_2 reanalysis

description:
Pairs with slBF2m
GSM1379700
processed as before; but against new genome build


title: PCF RiboProf replicate_1 reanalysis

description:
Pairs with PCF1m
GSM1379696
processed as before; but against new genome build


title: PCF RiboProf replicate_3 reanalysis

description:
Pairs with PCF3m
GSM1379698
processed as before; but against new genome build


title: KBM7_100kb2

city: Vienna

first: Aleksandra E

last: Kornienko

address: Lazarettgasse 14, AKH BT 25.3, 3rd floor

country: Austria

institute: CeMM  Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
RNA sequencing data was aligned to the hg19 human genome using STAR (version 2.3) with default settings
FPKM and differential expression was calculated using Cuffdiff software (Cufflinkks package version 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: .diff file contains the output of differential expression analysis performed using Cuffdiff

growth_protocol: KBM7 cell lines were obtained frozen from Horizon Genomics GmbH (http://www.horizon-genomics.com/) and were cultured in filter cap flasks in IMDM (Sigma) medium (with L-Glutamine, supplemented with Penicillin/Streptomycin and 10% Fetal Bovine Serum (PAA Laboratories (GE Healthcare)) at 37oC with 5% CO2. KBM7 are suspension cells. Cell concentration and cell size were measured using Casy cell counter (Schärfe System GmbH).

extract_protocol:
RNA was isolated using TRIreagent (Sigma)
RNA for total RNA-seq was depleted for Ribosomal RNA using the RiboZero rRNA removal kit (Human/Mouse/Rat) (Epicentre) according to manufacturer's protocol. Pretreeated RNA was then subject to library preparation. Strand-specific RNA-seq libraries were prepared employing the TruSeq RNA Sample Prep Kit v2 (Illumina) modified to obtain strand-specificity using dUTP incorporation and UDGase treatment. RNA-seq was performed by the Biomedical Sequencing Facility (BSF) in Vienna using the Illumina HiSeq 2000 platform.

treatment_protocol: Gene trap cassettes were inserted into C1, C2, 3kb1, 3kb2, 100kb1 and 100kb2 cell lines as described in

value: Chronic myelogenous leukemia cell line

tag: cell line

tag: passages


title: KBM7_3kb2


title: KBM7_100kb1


title: KBM7_C2


title: KBM7_3kb1


title: KBM7_C1


title: KBM7_WT3


title: cBF mRNA replicate_2 reanalysis

description:
mRNA control for cBF2r
GSM1379712
processed as before; but against new genome build


title: KBM7_WT2


title: H3.1 rep1

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie 0.12.7 using option of --best -v 2 --strata -m 1
We used homer tool to pool the two replicates and allowed only one tag per base by using an option -tbp 1.
BedGraph files were generated using the command using UCSC files which normalizeds the reads to 10e7.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph

source_name: Hela

growth_protocol: HeLa S3 cells stably expressing either FLAG-tagged H3.1, and H3.3 were grown in suspension in Joklik media containing 10% newborn calf serum (Hyclone), 1% GlutaMAX (Invitrogen), and 1% penicillin-streptomycin, and cells were harvested at log phase.

extract_protocol: Nuclei were isolated, mononucleosomes were subsequently obtained from these cell lines.  Cells were lysed in hypotonic TMSD buffer to isolate nuclei, which were then digested with micrococcal nuclease. The resulting mononucleosomes were immunoprecipitated with anti-FLAG M2-agarose beads (Sigma) and eluted with FLAG peptide (Sigma)

value: HeLa

value: cervical cancer

tag: replicate

value: H3.1 FLAG tagged


title: H3.3 rep1

value: H3.3 FLAG tagged


title: H3.3 rep2


title: H3.1 rep2


title: cBF RiboProf replicate_1 reanalysis

description:
Pairs with cBF1m
GSM1379702
processed as before; but against new genome build


title: slBF RiboProf replicate_3 reanalysis

description:
Pairs with slBF3m
GSM1379701
processed as before; but against new genome build


title: N675

city: Bronx

first: Steven

middle: K

last: Libutti

state: NY

address: 1300 Morris Park Ave

department: Surgery

institute: Albert Einstein College of Medicine

description: HpaII

data_processing:
library strategy: HELP-tagging
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions ELAND - 1.7.0)
Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence)
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser. We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.
For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions
To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample
Genome_build: hg19
Supplementary_files_format_and_content: The angle files were generated using in house pipeline; Scores represent degree of unmethylation. tid: ID for reference, chr: chromosome, pos: position of HpaII site, angle: degree of DNA hypomethylation, conf: degree of confidence, higher values have higher confidency

source_name: Non-tumor control tissue

extract_protocol:
All tissues were collected from individuals operated on the National Cancer iNstitute (NCI) and the Albert Einstein College of Medicine (Einstein). All tissues were snap-frozen, stored at -80°C and carefully evaluated by an experienced pathologist. All patients signed consent for a prospective clinical trial to obtain these tissues, and this study was approved by the IRB at both the NCI and Einstein.
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  Five micrograms of genomic DNA were digested with HpaII and MspI in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA or 1 μg of MspI-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).
HELP-tagging (HELP pipeline is described in Suzuki et al. Genome Biol 2010 (PMID: 20359321).)

value: unknown

tag: clinical information

value: Normal parathyroid tissue

tag: location

tag: tissue type

value: Normal Parathyroid


title: N623

description: HpaII


title: Nor

description: HpaII


title: N14

description: HpaII


title: N320

description: HpaII


title: N48

description: HpaII


title: N350

description: HpaII


title: N402

description: HpaII

value: F

value: Normal right lower parathyroid


title: PCF RiboProf replicate_2 reanalysis

description:
Pairs with PCF2m
GSM1379697
processed as before; but against new genome build


title: MF4

description: HpaII

source_name: Hyperplasia

value: familial MEN1 hyperplasia

value: Human MEN1-parathyroid tumor


title: MG7

description: HpaII


title: MJ

description: HpaII


title: ME7

description: HpaII


title: MD5

description: HpaII


title: ME1

description: HpaII


title: MD8

description: HpaII


title: M87

description: HpaII


title: M213

description: HpaII

value: Right lower parathyroid


title: M112

description: HpaII


title: Ca204

description: HpaII

source_name: Primary malignant Tumor

value: Carcinoma (malignant)

value: Human Parathyroid Carcinoma


title: Ca353

description: HpaII


title: Ad12

description: HpaII

source_name: Adenoma (Primary benign tumor)

value: M

value: Adenoma (benign)

value: Left parathyroid

value: Human Parathyroid Adenoma


title: Ca155

description: HpaII


title: M107

description: HpaII


title: Ad10

description: HpaII


title: Ca354

description: HpaII


title: N215

description: HpaII


title: Ad8

description: HpaII

value: thymic parathyroid


title: Ad7

description: HpaII


title: Ad4

description: HpaII

value: Left lower parathyroid


title: Ad

description: HpaII

value: Right upper parathyroid


title: Ad2

description: HpaII


title: Ad3

description: HpaII


title: M126

description: HpaII

value: unknown


title: A21

description: HpaII


title: A17

description: HpaII


title: A20

description: HpaII

value: Right parathyroid


title: MM1.RL_Dex1uM_2h_Input

city: Chicago

first: Nancy

last: Krett

state: IL

address: 840 South Wood Street, 740 CSB

department: Medicine

institute: University of Illinois Chicago

data_processing:
Trim all reads to the first basepair with a quality score less than 20
Remove all reads with fewer than 25 basepairs
Map all reads to human genome  using BWA
Call peaks using MACS2
Genome_build: UCSC hg19/NCBI 37
Supplementary_files_format_and_content: Peak files in BED format

extract_protocol:
Trizol
ChIP-Seq

tag: treatment

value: Dex 1uM

tag: chip antibody

value: Input


title: MM1.S Dex1uM_2h_Input


title: MM1.S_Ctrl_GR

value: Ctrl

value: GR


title: MM1.RL_Dex1uM_2h_GR


title: MM1.RL_Dex1uM_2h_IgG

value: IgG


title: MM1.S Dex1uM_2h_GR


title: MM1.RL_Ctrl_Input


title: MM1.RL_Ctrl_GR


title: MM1.S_Ctrl_Input


title: MM1.S_Ctrl_IgG


title: MM1.S Dex1uM_2h_IgG


title: KLHL9.1-

city: New York

first: James

middle: C

last: Chen

state: NEW YORK

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

data_processing:
Mapping Reads to ref genome hg19 (UCSC): TopHat
Mapping Reads to known genes (Entrez IDs): Genomic Features, R
Expression normalization: DeSeq, R Bioconductor
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited, normalized fkpm

growth_protocol: Adherent cells, standard DMEM10%FBS, 5%CO2

extract_protocol:
RNA was extracted using Qiagen RNA isolation kits using manufacuter protocols
barcodes: 1:ATCACG, 2:CGATGT, 3:TTAGGC, 4:TGACCA, 5:ACAGTG, 6:GCCAAT, 7:CAGATC, 8:ACTTGA, 9:GATCAG (samples already de-convolved)

treatment_protocol: Doxycycline induction, standard protocols

tag: induction

value: no doxycycline

tag: vector


title: KLHL9.3-


title: GFP.3+

value: doxycycline

value: GFP


title: GFP.1+


title: GFP.2+


title: KLHL9.2-


title: KLHL9.3+


title: KLHL9.2+


title: A19

description: HpaII

value: F


title: A18

description: HpaII

value: Adenoma (benign)


title: KLHL9.1+


title: Shh_rep1

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat-2.0.13 with default parameters.
Raw reads number of genes was calculated by HTSeq. cufflinks v2.2.1 was run for relative quantitation of genes expression and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: embryonic back skin

growth_protocol: All mice were maintained in an SPF facility. Isolation of Shh+ and Nfatc1+ cells for RNA-seq was performed using Shh- and Nfatc1-CreER::Rosa-stop-tdTomato::K14-H2BGFP mice.

extract_protocol:
For purification of Nfatc1 expressing cells in hair pegs, embryonic back skin was removed and the whole skin was cut into 6-9 small pieces and placed, dermis side down, in a 0.25% trypsin solution (Gibco) at 37°C for 16 min. Single-cell suspensions were obtained by triturating the skin gently. Cells were then filtered with strainers (70um followed by 40um). For purification of Shh-expressing hair peg cells at E17.5, embryonic back skin was cut into 9 pieces and placed, dermis side down, in dispase (Life Technologies, 0.4mg/ml) dissolved in PBS for 1hr at 37°C. Epidermis containing placodes and hair germs were removed. Dermis samples containing only hair pegs were placed in a 0.25% trypsin solution at 37°C for 10 min. Single-cell suspensions were obtained by triturating the skin gently. Cells were then filtered with strainers (70µm followed by 40µm).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For purification of Nfatc1 expressing cells in hair pegs, pregnant mice were administered a single dose of Tamoxifen at E15.5.

tag: tissue

value: embryo

tag: developmental stage

value: skin


title: Shh_rep2


title: Nfatc1_rep2


title: Nfatc1_rep1


title: CD8_105 scRNA-seq

city: Cambridge

first: Robert

last: Kimmerling

department: Biological Engineering

institute: MIT

description: CD8 scRNA-seq

data_processing:
Illumina bcl2fastq2.15.0.4 was used to generat .fastq files from .bcl files.
tophat2 was used to align the scRNA-seq data
rsem-1.2.3 generated an expression matrix in transcripts per million.
mm10 ucsc genomestudio
Genome_build: mm10
Supplementary_files_format_and_content: RSEM transcripts per million matrix with genes as rows and samples as columns.

source_name: Single CD8+ cells grown for multiple generations on-chip after 30h activation in vitro with anti-CD3/28

growth_protocol: L1210 cells were cultured in the device in RPMI 1640 (Gibco) with 10% FBS and 1% penicillin-streptomycin solution (Gibco). CD8+ T cells were cultured in the device in RPMI 1640 (Gibco) with 10% FBS, 55μM 2-mercaptoethanol (Gibco), 1% penicillin-streptomycin solution (Gibco) and 100 U/mL IL2 (PeproTech) after 30h activation in vitro (see below).

extract_protocol:
Single cells were flushed from the device with 5 ul of PBS directly in to 5 ul of 2X TCL lysis buffer (Qiagen) resulting in a total volume of 10 ul of single-cell lysate. These samples were immediately frozen on dry ice and subsequently stored at -80°C prior to library preperation and sequencing.
Libraries were constructed using the Smart-Seq2 protocol for single cells.

treatment_protocol: The CD8+ T cells were activated with 5 μg/mL plate-bound anti-mouse CD3 (clone: 145-2C11, BioLegend catalog number 100314) and 2 μg/mL of anti-mouse CD28 (clone: 37.51, BioLegend catalog number 102112) in solution for 30h prior to loading in to the device.

tag: cell type

value: Activated CD8+ T cells

tag: strain

tag: hours since division

tag: sister

tag: cousin 1

tag: cousin 2

tag: doublet?

value: No


title: CD8_104 scRNA-seq

description: CD8 scRNA-seq


title: MM1.RL_Ctrl_IgG

tag: cell line


title: CD8_100 scRNA-seq

description: CD8 scRNA-seq


title: CD8_102 scRNA-seq

description: CD8 scRNA-seq


title: CD8_98 scRNA-seq

description: CD8 scRNA-seq


title: CD8_99 scRNA-seq

description: CD8 scRNA-seq


title: CD8_101 scRNA-seq

description: CD8 scRNA-seq


title: CD8_97 scRNA-seq

description: CD8 scRNA-seq


title: CD8_96 scRNA-seq

description: CD8 scRNA-seq


title: CD8_94 scRNA-seq

description: CD8 scRNA-seq


title: CD8_103 scRNA-seq

description: CD8 scRNA-seq


title: CD8_93 scRNA-seq

description: CD8 scRNA-seq


title: CD8_92 scRNA-seq

description: CD8 scRNA-seq


title: CD8_91 scRNA-seq

description: CD8 scRNA-seq


title: CD8_89 scRNA-seq

description: CD8 scRNA-seq


title: CD8_84 scRNA-seq

description: CD8 scRNA-seq


title: CD8_85 scRNA-seq

description: CD8 scRNA-seq


title: CD8_90 scRNA-seq

description: CD8 scRNA-seq


title: CD8_87 scRNA-seq

description: CD8 scRNA-seq


title: CD8_83 scRNA-seq

description: CD8 scRNA-seq


title: CD8_88 scRNA-seq

description: CD8 scRNA-seq


title: CD8_86 scRNA-seq

description: CD8 scRNA-seq


title: CD8_106 scRNA-seq

description: CD8 scRNA-seq


title: CD8_82 scRNA-seq

description: CD8 scRNA-seq


title: CD8_78 scRNA-seq

description: CD8 scRNA-seq


title: CD8_81 scRNA-seq

description: CD8 scRNA-seq


title: CD8_79 scRNA-seq

description: CD8 scRNA-seq


title: CD8_75 scRNA-seq

description: CD8 scRNA-seq


title: CD8_77 scRNA-seq

description: CD8 scRNA-seq


title: CD8_76 scRNA-seq

description: CD8 scRNA-seq


title: CD8_95 scRNA-seq

description: CD8 scRNA-seq


title: CD8_73 scRNA-seq

description: CD8 scRNA-seq


title: CD8_74 scRNA-seq

description: CD8 scRNA-seq


title: CD8_72 scRNA-seq

description: CD8 scRNA-seq


title: CD8_69 scRNA-seq

description: CD8 scRNA-seq


title: CD8_68 scRNA-seq

description: CD8 scRNA-seq


title: CD8_71 scRNA-seq

description: CD8 scRNA-seq


title: CD8_70 scRNA-seq

description: CD8 scRNA-seq


title: CD8_66 scRNA-seq

description: CD8 scRNA-seq


title: CD8_67 scRNA-seq

description: CD8 scRNA-seq


title: CD8_65 scRNA-seq

description: CD8 scRNA-seq


title: CD8_64 scRNA-seq

description: CD8 scRNA-seq

value: Yes


title: CD8_63 scRNA-seq

description: CD8 scRNA-seq


title: CD8_80 scRNA-seq

description: CD8 scRNA-seq


title: CD8_61 scRNA-seq

description: CD8 scRNA-seq


title: CD8_60 scRNA-seq

description: CD8 scRNA-seq


title: CD8_56 scRNA-seq

description: CD8 scRNA-seq


title: CD8_58 scRNA-seq

description: CD8 scRNA-seq


title: CD8_59 scRNA-seq

description: CD8 scRNA-seq


title: CD8_57 scRNA-seq

description: CD8 scRNA-seq


title: CD8_54 scRNA-seq

description: CD8 scRNA-seq


title: CD8_53 scRNA-seq

description: CD8 scRNA-seq


title: CD8_62 scRNA-seq

description: CD8 scRNA-seq


title: CD8_52 scRNA-seq

description: CD8 scRNA-seq


title: CD8_55 scRNA-seq

description: CD8 scRNA-seq


title: CD8_51 scRNA-seq

description: CD8 scRNA-seq


title: CD8_50 scRNA-seq

description: CD8 scRNA-seq


title: CD8_49 scRNA-seq

description: CD8 scRNA-seq


title: CD8_48 scRNA-seq

description: CD8 scRNA-seq


title: CD8_42 scRNA-seq

description: CD8 scRNA-seq


title: CD8_45 scRNA-seq

description: CD8 scRNA-seq


title: CD8_44 scRNA-seq

description: CD8 scRNA-seq


title: CD8_46 scRNA-seq

description: CD8 scRNA-seq


title: CD8_47 scRNA-seq

description: CD8 scRNA-seq


title: CD8_43 scRNA-seq

description: CD8 scRNA-seq


title: CD8_40 scRNA-seq

description: CD8 scRNA-seq


title: CD8_38 scRNA-seq

description: CD8 scRNA-seq


title: CD8_37 scRNA-seq

description: CD8 scRNA-seq


title: CD8_36 scRNA-seq

description: CD8 scRNA-seq


title: CD8_33 scRNA-seq

description: CD8 scRNA-seq


title: CD8_34 scRNA-seq

description: CD8 scRNA-seq


title: CD8_31 scRNA-seq

description: CD8 scRNA-seq


title: CD8_35 scRNA-seq

description: CD8 scRNA-seq


title: CD8_29 scRNA-seq

description: CD8 scRNA-seq


title: CD8_28 scRNA-seq

description: CD8 scRNA-seq


title: CD8_32 scRNA-seq

description: CD8 scRNA-seq


title: CD8_26 scRNA-seq

description: CD8 scRNA-seq


title: CD8_22 scRNA-seq

description: CD8 scRNA-seq


title: CD8_24 scRNA-seq

description: CD8 scRNA-seq


title: CD8_30 scRNA-seq

description: CD8 scRNA-seq


title: CD8_20 scRNA-seq

description: CD8 scRNA-seq


title: CD8_23 scRNA-seq

description: CD8 scRNA-seq


title: CD8_19 scRNA-seq

description: CD8 scRNA-seq


title: CD8_27 scRNA-seq

description: CD8 scRNA-seq


title: CD8_17 scRNA-seq

description: CD8 scRNA-seq


title: CD8_18 scRNA-seq

description: CD8 scRNA-seq


title: CD8_16 scRNA-seq

description: CD8 scRNA-seq


title: CD8_13 scRNA-seq

description: CD8 scRNA-seq


title: CD8_41 scRNA-seq

description: CD8 scRNA-seq


title: CD8_11 scRNA-seq

description: CD8 scRNA-seq


title: CD8_9 scRNA-seq

description: CD8 scRNA-seq


title: CD8_8 scRNA-seq

description: CD8 scRNA-seq


title: CD8_7 scRNA-seq

description: CD8 scRNA-seq


title: CD8_6 scRNA-seq

description: CD8 scRNA-seq


title: CD8_25 scRNA-seq

description: CD8 scRNA-seq


title: CD8_5 scRNA-seq

description: CD8 scRNA-seq


title: CD8_21 scRNA-seq

description: CD8 scRNA-seq


title: CD8_39 scRNA-seq

description: CD8 scRNA-seq


title: CD8_3 scRNA-seq

description: CD8 scRNA-seq


title: CD8_1 scRNA-seq

description: CD8 scRNA-seq


title: CD8_4 scRNA-seq

description: CD8 scRNA-seq


title: CD8_2 scRNA-seq

description: CD8 scRNA-seq


title: L1210_87 scRNA-seq

description: L1210 scRNA-seq

source_name: Single L1210 cells grown for multiple generations on-chip

value: L1210 lymphocytic leukemia (ATCC CCL-219)

value: DBA subline 212


title: L1210_88 scRNA-seq

description: L1210 scRNA-seq


title: L1210_83 scRNA-seq

description: L1210 scRNA-seq


title: L1210_82 scRNA-seq

description: L1210 scRNA-seq


title: L1210_81 scRNA-seq

description: L1210 scRNA-seq


title: L1210_86 scRNA-seq

description: L1210 scRNA-seq


title: CD8_14 scRNA-seq

description: CD8 scRNA-seq


title: L1210_85 scRNA-seq

description: L1210 scRNA-seq


title: L1210_79 scRNA-seq

description: L1210 scRNA-seq


title: L1210_84 scRNA-seq

description: L1210 scRNA-seq


title: CD8_15 scRNA-seq

description: CD8 scRNA-seq


title: L1210_77 scRNA-seq

description: L1210 scRNA-seq


title: CD8_10 scRNA-seq

description: CD8 scRNA-seq


title: CD8_12 scRNA-seq

description: CD8 scRNA-seq


title: L1210_76 scRNA-seq

description: L1210 scRNA-seq


title: L1210_75 scRNA-seq

description: L1210 scRNA-seq


title: L1210_73 scRNA-seq

description: L1210 scRNA-seq


title: L1210_72 scRNA-seq

description: L1210 scRNA-seq


title: L1210_71 scRNA-seq

description: L1210 scRNA-seq


title: L1210_69 scRNA-seq

description: L1210 scRNA-seq


title: L1210_70 scRNA-seq

description: L1210 scRNA-seq


title: L1210_68 scRNA-seq

description: L1210 scRNA-seq


title: L1210_67 scRNA-seq

description: L1210 scRNA-seq


title: L1210_65 scRNA-seq

description: L1210 scRNA-seq


title: L1210_66 scRNA-seq

description: L1210 scRNA-seq


title: L1210_61 scRNA-seq

description: L1210 scRNA-seq


title: L1210_78 scRNA-seq

description: L1210 scRNA-seq


title: L1210_80 scRNA-seq

description: L1210 scRNA-seq


title: L1210_60 scRNA-seq

description: L1210 scRNA-seq


title: L1210_64 scRNA-seq

description: L1210 scRNA-seq


title: L1210_63 scRNA-seq

description: L1210 scRNA-seq


title: L1210_56 scRNA-seq

description: L1210 scRNA-seq


title: L1210_62 scRNA-seq

description: L1210 scRNA-seq


title: L1210_59 scRNA-seq

description: L1210 scRNA-seq


title: L1210_55 scRNA-seq

description: L1210 scRNA-seq


title: L1210_52 scRNA-seq

description: L1210 scRNA-seq


title: L1210_51 scRNA-seq

description: L1210 scRNA-seq


title: L1210_49 scRNA-seq

description: L1210 scRNA-seq


title: L1210_50 scRNA-seq

description: L1210 scRNA-seq


title: L1210_54 scRNA-seq

description: L1210 scRNA-seq


title: L1210_58 scRNA-seq

description: L1210 scRNA-seq


title: L1210_74 scRNA-seq

description: L1210 scRNA-seq


title: L1210_48 scRNA-seq

description: L1210 scRNA-seq


title: L1210_46 scRNA-seq

description: L1210 scRNA-seq


title: L1210_44 scRNA-seq

description: L1210 scRNA-seq


title: L1210_45 scRNA-seq

description: L1210 scRNA-seq


title: L1210_41 scRNA-seq

description: L1210 scRNA-seq


title: L1210_43 scRNA-seq

description: L1210 scRNA-seq


title: L1210_42 scRNA-seq

description: L1210 scRNA-seq


title: L1210_57 scRNA-seq

description: L1210 scRNA-seq


title: L1210_53 scRNA-seq

description: L1210 scRNA-seq


title: L1210_37 scRNA-seq

description: L1210 scRNA-seq


title: L1210_35 scRNA-seq

description: L1210 scRNA-seq


title: L1210_32 scRNA-seq

description: L1210 scRNA-seq


title: L1210_40 scRNA-seq

description: L1210 scRNA-seq


title: L1210_38 scRNA-seq

description: L1210 scRNA-seq


title: L1210_39 scRNA-seq

description: L1210 scRNA-seq


title: L1210_36 scRNA-seq

description: L1210 scRNA-seq


title: L1210_29 scRNA-seq

description: L1210 scRNA-seq


title: L1210_34 scRNA-seq

description: L1210 scRNA-seq


title: L1210_27 scRNA-seq

description: L1210 scRNA-seq


title: L1210_25 scRNA-seq

description: L1210 scRNA-seq


title: L1210_23 scRNA-seq

description: L1210 scRNA-seq


title: L1210_33 scRNA-seq

description: L1210 scRNA-seq


title: L1210_24 scRNA-seq

description: L1210 scRNA-seq


title: L1210_47 scRNA-seq

description: L1210 scRNA-seq


title: L1210_26 scRNA-seq

description: L1210 scRNA-seq


title: L1210_31 scRNA-seq

description: L1210 scRNA-seq


title: L1210_28 scRNA-seq

description: L1210 scRNA-seq


title: L1210_30 scRNA-seq

description: L1210 scRNA-seq


title: L1210_21 scRNA-seq

description: L1210 scRNA-seq


title: L1210_20 scRNA-seq

description: L1210 scRNA-seq


title: L1210_22 scRNA-seq

description: L1210 scRNA-seq


title: L1210_17 scRNA-seq

description: L1210 scRNA-seq


title: S

city: Nanjing

first: Feifei

last: Luo

state: Jiangsu Province

address: #1 Weigang

department: College of Animal Science & Technology

institute: Nanjing Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, low-quality sequences, reads with many N, and reads <25nt were filtered out using SeqPrep and ConDeTri_v2.0.pl software. Clean reads were mapped to the sheep genome using Tophat software, allowing up to two base mismatches.
RNA-seq analysis was calculated and normalized to FPKM using Cuffdiff software.FDR (false discovery rate) < 0.05 was used as the threshold to judge the significance of difference. Filtered DEGs were visualized with Cummerbund software.
Next, hierarchical clustering analysis was performed on the significant DEGs. Cluster distance was calculated using the complete linkage algorithm. The distance of samples and genes was evaluated via Spearman’s rank method and Pearson correlation analysis, respectively.
Genome_build: Ovis aries (assembly Oar_v3.1)
Supplementary_files_format_and_content: xls file includes FPKM values for each gene, and the fold change of each gene between two groups.

organism: Ovis aries

source_name: Granulosa cell

growth_protocol: The experiment was conducted at the Shen Ning Sheep & Goat Farm (Xuzhou , Jiangsu, China). Sixteen multiparous Hu sheep (3-4 years; 42.2 ± 1.2 kg) were randomly assigned to two groups: the short-term nutrient-supplemented group (S; n=8), and the dietary restricted group (R; n=8). All ewes were fed in individual pens (1.27 m×2.55 m) and received two equivalent meals at 9:00 and 17:00 every day. Water was available to the sheep ad libitum.

extract_protocol:
All visible follicles (>2.5mm in diameter) from the ovaries were dissected free from the ovarian stroma into 1 ml D-PBS. The granulosa cell layer was then gently scraped into D-PBS. RNA was extracted from granulosa cells using the RNeasy Micro Kit (Qiagen, Germany) according to the manufacturer's protocol.
RNA-seq transcriptome libraries were prepared following the TruSeq RNA sample preparation Kit (Illumina, San Diego, CA). 5 microgram of RNA from each group was used to synthesize the cDNA.The cDNA was then eluted with EB buffer for end repair and poly (A) addition. Finally, sequencing adapters were ligated to the fragments, followed by PCR amplification (15 cycles) using Veriti 96 Well Fast Thermal Cycler (Applied Biosystems) to create cDNA libraries.

treatment_protocol: During the Luteal Phase, Sheep in the group S were fed 1.5×Maintenance Diet (1560 g/ewe per day) while those in the group R received 0.5×Maintenance Diet (520 g/ewe per day).

value: Hu Sheep

value: follicle

tag: age

value: 3-4 years

tag: treatment stage

value: luteal phase

tag: diet group

value: nutrient-supplemented


title: R

value: dietary restricted


title: L1210_16 scRNA-seq

description: L1210 scRNA-seq


title: L1210_15 scRNA-seq

description: L1210 scRNA-seq


title: L1210_14 scRNA-seq

description: L1210 scRNA-seq


title: Control 4

city: HAIFA

first: Tamar

last: Lotan

address: 199 Abba Khoushy Ave.   Mount Carmel

country: Israel

institute: University of Haifa

data_processing:
Mapping of 50-bp single-end reads (fastq files) to the N.vectensis genome from the Joint Genome Institute (JGI) was performed using the STAR aligner
Expression levels in raw counts and in reads per kilobase transcript per million (RPKM) were calculated using Partek Genomic Suite
Raw read counts per transcript were submitted to DESeq R package for normalization and differential expression analysis
Genome_build: Nematostella vectensis 1.0
Supplementary_files_format_and_content: normalized counts and statistics

organism: Nematostella vectensis

source_name: Nematostella vectensis_control

growth_protocol: Sea anemones were raised at 18°C in 12.5 ppt artificial seawater (Red Sea, Israel) in the dark.

extract_protocol:
Total RNA was extracted with  Tri-reagent kit (Sigma) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols with TruSeq mRNA kit

treatment_protocol: Experiments were carried out in triplicate groups, each containing five sea anemones aged 2−4 months. For the transcriptome experiments groups were exposed for 24 h to mercury (HgCl2), cadmium (CdCl2), zinc (ZnCl2) and copper (CuCl2), each at a concentration of 100 µg/L, and compared to four untreated groups of sea anemones that served as controls.

tag: metal

value: none (control)

value: 2-4 months


title: Control 3


title: Control 1


title: Zn2

source_name: Nematostella vectensis_Zn

value: Zn


title: Zn3


title: L1210_13 scRNA-seq

description: L1210 scRNA-seq


title: L1210_10 scRNA-seq

description: L1210 scRNA-seq


title: L1210_19 scRNA-seq

description: L1210 scRNA-seq


title: L1210_9 scRNA-seq

description: L1210 scRNA-seq


title: wc_RNA-seq

first: Julie

last: Secombe

state: United states

address: 1300 Morris park ave. Ullmann 809

institute: Albert einstein college of medicne

data_processing:
After the sequencing platform generated the sequencing images, the pixel-level raw data collection, image analysis, and base calling were performed by Illumina's Real Time Analysis (RTA) software on a Dell PC attached to the HiSeq2000 sequencer
The base call files (*.BCL) were converted to qseq files by the Illumina's BCL Converter, and the qseq files were subsequently converted to FASTQ files for downstream analysis
The RNA-Seq reads from the FASTQ files were mapped to the Drosophila reference genome (dm3) using SOAP (Short Oligonucleotide Analysis Package
The output files in BAM (binary alignment/map) format were analyzed by Cufflinks to estimate the transcript abundance and the presence of putative novel mRNA isoforms.
The transcript assembly of transcript structure predictions of Cufflinks is compared with reference annotation, Ensembl GTF version 65 by Cuffcompare
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Drosophila melanogaster

source_name: whole animal_wildtype_control

growth_protocol: Flies were reared and maintained at 25°C, 50% relative humidity and a 12-hour light/dark cycle

extract_protocol:
RNA was extracted from groups of five adult flies (1-3 days old) using TRIZOL (Invitrogen) and cleaned up using DNA-free (Ambion)
cDNA libraries were prepared using an Illumina TruSeq RNA sample prep kit using three micrograms of total RNA. Briefly, poly-A containing mRNAs were using poly-T primers, RNA fragmented, first and second strand cDNA syntheses, end repair, adaptor ligation, and PCR amplification performed. The average size of the libraries cDNAs was 150 bp (excluding the adapters). Prior to sequencing the integrity and quality of cDNA libraries were assessed using an Agilent 2100 Bioanalyzer and an ABI StepOnePlus real-time PCR system

treatment_protocol: Control genotype flies were w1118 and kdm5 mutant flies were w1118; kdm5K6801/10424. Flies were subjected to contol conditions (5% sucrose for 6 hours) or conditions of oxidative stress (paraquat; six hours of 20mM paraquat in 5% sucose)

tag: genotype

value: whole animal

tag: gender

value: female

value: adult

value: 1-3 days


title: kc_RNA-seq

source_name: whole animal_kdm5mutant_control


title: wt_H3K4me3_ChIPSeq

data_processing:
Basecalls performed using CASAVA version 1.4
To map KDM5 and H3K4me3 binding sites, we pooled the raw reads (about 20 million reads per sample) from into one data file and aligned it to Drosophila reference genome using SOAP for KDM5 and Bowtie short read aligner  for H3K4me3
Peak-calling  of KDM5 and H3K4me3  were determined using macs2.0
Genome_build: dm3
Supplementary_files_format_and_content: bed files were generated using macs2.0

source_name: Female whole animal_wildtype

extract_protocol:
To identify KDM5 binding sites, ChIP-seq was carried out using HA-tagged KDM5 genomic rescue transgene flies with anti-HA (with or without paraquat treatment for 6 hours). Wildtype w1118 adults were used for  KDM5 and anti-H3K4me3 ChIP-seq.
Libraries were prepared using Tru-Seq adaptors and then size-selected (150 bp-350 bp) and purified by agarose gel

treatment_protocol: Flies were subjected to contol conditions(C1_HA and C2_HA) (5% sucrose for 6 hours) or conditions of oxidative stress (P1_HA and P2_HA; paraquat; six hours of 20mM paraquat in 5% sucose)

tag: chip antibody


title: L1210_12 scRNA-seq

description: L1210 scRNA-seq

value: No


title: L1210_11 scRNA-seq

description: L1210 scRNA-seq


title: wp_RNA-seq

source_name: whole animal_wildtype_paraquat

tag: tissue


title: wt_KDM5_ChIPSeq


title: Zn1


title: Cd2

source_name: Nematostella vectensis_Cd

value: Cd


title: wt_input


title: L1210_8 scRNA-seq

description: L1210 scRNA-seq

value: L1210 lymphocytic leukemia (ATCC CCL-219)


title: L1210_18 scRNA-seq

description: L1210 scRNA-seq

value: DBA subline 212


title: L1210_7 scRNA-seq

description: L1210 scRNA-seq


title: Cd1


title: P_input

source_name: Female whole animal_paraquat


title: Control 2


title: L1210_6 scRNA-seq

description: L1210 scRNA-seq


title: kp_RNA-seq

source_name: whole animal_kdm5mutant_paraquat

tag: developmental stage


title: Cu3

source_name: Nematostella vectensis_Cu

value: Cu


title: Cd3


title: P2_HA_ChIPSeq

value: HA


title: Cu2


title: Cu1


title: L1210_4 scRNA-seq

description: L1210 scRNA-seq

tag: cell type


title: P1_HA_ChIPSeq


title: Hg3

source_name: Nematostella vectensis_Hg

value: Hg


title: C-input

source_name: Female whole animal_control_no_paraquat


title: C2_HA_ChIPSeq


title: L1210_5 scRNA-seq

description: L1210 scRNA-seq

tag: strain


title: Hg2


title: L1210_3 scRNA-seq

description: L1210 scRNA-seq

tag: hours since division


title: Hg1


title: Neurospora_wildtype_rep1

status: Public on Dec 21 2015

city: Athens

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

institute: University of Georgia

data_processing:
Data were mapped to the Neurospora crassa (version 12) reference genome
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: GCF_000182925.2
Supplementary_files_format_and_content: tab delimited text file
Column1: chromosome
Column2: cytosine position
Column3: strand
Column4: CNN (N = A, T, C, G)
Column5: methylated cytosines in this site
Column6: totally detected cytosines in this site
Column7: binomial test, 1 means pass, 0 means fail

organism: Neurospora crassa

source_name: Wild type rep1

growth_protocol: Grown in liquid VMM for 48 hours at 32 degrees C.

extract_protocol: Genomic DNA (gDNA) was isolated using standard methods for Neurospora (Pomraning et al. 2009; Methods). MethylC-seq libraries were constructed according to Urich et al. MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols (2015).

tag: genotype/variation

value: wild type


title: L1210_1 scRNA-seq

description: L1210 scRNA-seq

tag: sister

tag: cousin 1


title: Neurospora_crf5_F2_rep2

source_name: Δcrf5-1 F2 rep2

value: {delta}crf5-1 F2


title: Neurospora_dim2


title: Neurospora_crf5_F1_rep2

source_name: Δcrf5-1 F1 rep2

value: {delta}crf5-1 F1


title: Neurospora_crf5_F1_rep1

source_name: Δcrf5-1 F1 rep1


title: Neurospora_wildtype_rep2

source_name: Wild type rep2


title: DGRP229 M_E3_5_L2

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
EP7A032
Drosophila Genetic Reference Panel 229, Male, Environment 3, Fly 5, Library 2

data_processing:
We performed single-end 76 bp sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego, CA) according to the manufacturer.  De-multiplexed reads (Chastity > 0.6) FASTQ output was from Illumina CASAVA v.1.8.2. Reads were mapped to FlyBase release 5 version 57 (FlyBase file: dmel-all-chromosome-r5.57.fasta) and release 6 version 01 (FlyBase file: dmel-all-chromosome-r6.01.fasta) of the Drosophila melanogaster genome and appended sequence corrected ERCC sequences (ERCC_reference.fa, See Jiang et al., Genome Research, 2011, PMID 21816910) and annotations using TopHat2 (v2.0.10) with parameters  "-g 1 --library-type fr-firststrand" (Kim et al., Genome Biol, 2013, PMID 23618408).  We aligned to Drosophila melanogaster chromosome scaffolds only (release 5 chrU and chrUextra were excluded).  We used a Perl script to convert the dmel-all-r5.57.gff to a GTF file (dme5_57_ERCC.gtf) compatible with TopHat2 and HTSeq (v0.5.4p1) (Anders et al., Bioinformatics, 2015, PMID 25260700).  We extracted features, including pre-miRNAs, pseudogenes, mRNAs, ncRNAs, rRNAs, snoRNAs, snRNAs, tRNAs, genes, CDSs and exons, and changed the 304 features for “miRNA” to “exon”.   We changed the following features: 9 mRNA transcripts without strand assignment were assigned to the parent gene strand; 11 Exons and 9 CDSs without strand assignment were assigned to the parent transcript strand; and 10 CDSs, with ends longer than the parent, were truncated to fit the parent ends.  TopHat2 called Bowtie 2 (v2.1.0) to make indexes. We used SAMtools (v0.1.19) (Li et al., Bioinformatics, 2009, PMID 19505943) to index chromosomes, to sort and merge alignments, and for read statistics.  Mapped reads at the gene-level were counted by HTSeq with parameter "--stranded=reverse -i gene_id -t exon".
Supplementary_files_format_and_content: There are five supplemental files.  The tab-delimited 5_57_HTSeq_raw_read_counts.txt and 6_01_HTSeq_raw_read_counts.txt files contain the gene-level output, for each library, for genome releases 5.57 and 6.01 respectively. Column 1 and 2 are FlyBase FBgn#s and gene symbols, or ERCC  identifiers as applicable.  The remaining columns are library names (as GEO GSM#s).  The GEO_run_summary.xls file contains detailed information on each sequencing run and a readme sheet with field definitions.  The dme5_57_ERCC.gtf file contains the annotation for the alignment to release 5.57 plus the ERCC spike-ins.  ERCC_reference.fa is a FASTA file of the sequence corrected ERCCs.

source_name: Whole body

growth_protocol: We grew and aged Drosophila Genetic Reference Panel (DGRP) inbred lines derived from the Raleigh, NC, USA wild population (Mackay et al., Nature, 2012, PMID 22318601; Huang et al., Genome Res, 2014, PMID 24714809).  We randomly chose the following 16 DGRP lines after excluding 5 lines from the population that were slow-growing: DGRP-93, DGRP-229, DGRP-320, DGRP-352, DGRP-370, DGRP-563, DGRP-630, DGRP-703, DGRP-761, DGRP-787, DGRP-790, DGRP-804, DGRP-812, DGRP-822, DGRP-850, and DGRP-900. We collected 8 virgin male and 8 virgin female flies from the 16 DGRP genotypes in three replicated environments to produce RNA sequence profiles.  We controlled the environmental conditions in the following ways. We seeded the fly cultures with 5 male and 5 female parents.  We reared the progeny in a single incubator on standard Drosophila food (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/bloomfood.htm) at 25°C, 60% humidity, and a 12:12-hour light:dark  cycle.  We collected and maintained male and female virgins at 20 flies to a same-sex vial for four days prior to RNA extraction to control for social exposure.

extract_protocol:
Single flies frozen on dry ice were placed into each well of Axygen 96 Deep Well Plates (Corning, Corning, NY) pre-loaded with 200µL of 1 mm glass beads (Biospec Products, Bartlesville, OK).  Fly placement in the wells of each plate was randomized within a replicated environment. We isolated total RNA using the RNeasy 96 Plate Kit according to the manufacturer using either vacuum or centrifugation technology (Qiagen, Valencia, CA), with the following modifications. We added 200µl RLT buffer to each well, sealed the plates with Axygen Sealing Mats (Corning, Corning, NY), and homogenized flies at room temperature for 30sec using a fixed-speed Mini Bead Beater (Biospec Products, Bartlesville, OK).  We added 200µl of 70% ethanol to the crude homogenate, mixed by pipetting several times, and transferred the supernatant to RNeasy plates.  We measured total RNA yield using the Quant-iTTM RiboGreen(R) RNA Assay Kit (Invitrogen, Carlsbad, CA) in black FLUORTRAC 600 384-well PS plates (Greiner Bio-One, Inc., Longwood, FL) using a Gemini EM Fluorescence Microplate Reader (Molecular Devices, Sunnyvale, CA).  We used Dynabeads Oligo (dT) 25 (Life Technologies, Carlsbad, CA) to purify polyA RNA according to manufacturer instructions, except that we used 50-200ng of total RNA depending on yield, adjusted the volume to 50µl with distilled H2O, added 10µl of the washed Dynabeads in a 50µl binding buffer slurry, heated the samples at 65°C for 5min, and immediately chilled the samples on ice.  To prepare RNA-Seq stranded libraries we modified an existing protocol (Wang et al., PLoS One, 2011, PMID 22039485).  All steps were done in 96-well plate format. We incubated all reactions in a Tetrad PTC-225 Thermal Cycler (MJ Research, Waltham, MA). To clean up enzymatic reactions and size select at any of several steps below, we used 0.1% w/v carboxyl-modified Sera-Mag Magnetic Speed-beads (MagNA beads, Thermo Fisher Scientific, Waltham, MA) in XP buffer [20% PEG 8000, 2.5 M NaCl, (Sigma Aldrich, St. Louis, MO)] following the protocol in (Rohland et al., Genome Res, 2012, PMID 22267522), except that we incubated samples with beads for 10 min and used 80% ethanol for washing.  The volume of MagNA beads in XP buffer and corresponding concentration of PEG in the solution was 1.6× XP buffer for no size-selection (except where noted) and 1× XP buffer for selecting fragments > 200bp. Unless noted, we left the beads in the sample after each step.  We used 96-well PCR plates (USA Scientific, Ocala, Fl) paired with Alpaqua 96R Ring Magnet Plates (Alpaqua, Beverly, MA) for magnetic bead separation. We measured RNA quantity with Quant-iTTM RiboGreen(R) and DNA with Quant-iTTM PicoGreen(R) (Invitrogen, Carlsbad, CA) in 384-well plates, PS, FLUOROTRAC 600, black (Greiner Bio-One Inc, Longwood, Fl) using a Gemini EM Fluorescence Microplate Reader (Molecular Devices, Sunnyvale, CA) according to manufacturer instructions.  We used Agilent Bioanalyzer RNA chips and High Sensitivity DNA chips on the 2100 Bioanalyzer system (Agilent, Santa Clara, CA) according to manufacturer instructions and visually inspected electrophoregrams for RNA degradation, library size (DNA), and adapter dimer contamination (DNA).
We fragmented polyA RNA bound to Dynabeads at 94°C for 8min in 16µl of 1.25× first strand MMuLV RT buffer (New England Biolabs, Beverly, MA), with 100ng random primers (Invitrogen, Carlsbad, CA), and 10pg ERCC spike-in controls (Jiang et al., Genome Res, 2011, PMID 21816910) from pools 78A and 78B (Zook et al., PLoS ONE, 2012, PMID 22859977) obtained from Marc Salit (National Institute of Standards and Technology, Gaithersburg MD).  We chilled the samples immediately on ice for 2min and eluted from the beads.  We transferred 15µl of the eluate to a fresh 96-well PCR plate. We added 5µl of the first strand synthesis mixture [0.3mM dNTPs, 5mM DTT, and 10U M-MuLV RT (New England Biolabs, Beverly, MA), and 0.5U SuperRase-In (Life Technologies, Carlsbad, CA)] to the fragmented RNA in the fragmentation buffer and performed a reverse transcription reaction. We bound RNA/cDNA hybrid with 32µl MagNA bead XP buffer slurry, washed, and eluted samples in 16µl of distilled H2O.  We then performed a second strand synthesis with dUTP by adding 5µl of 1× NEB buffer2 (New England Biolabs, Beverly, MA), with 1mM each of dATP, dCTP, dGTP and 2mM dUTP (Thermo Fisher Scientific, Waltham, MA), 10U DNA PolI, 2.5U RNAseH, and 2.5mM DTT (New England Biolabs, Beverly, MA) and incubated at 16°C for 5 hours.  We rebound, washed, and eluted as above. We repaired ends by adding 4µl of NEBNext End Repair Module (New England Biolabs, Beverly, MA) to the eluate following manufacturer instructions.  We then rebound samples to MagNA beads, washed, and eluted as above. Next we performed dA-tailing by adding 4µl of 1× Blue Buffer, with 1U Klenow 3’-5’ exo- (Enzymatics, Beverly, MA) and 1mM dATP, to the eluate and incubated at 37°C for 30min.  We then rebound samples to MagNA beads and washed as above, eluted with 21µl distilled H2O, and transferred 10µl of cDNA to each of two fresh plates. One plate was used in the following steps and one plate was frozen as a back-up.  We ligated RNA Adapter Indexes (Illumina, San Diego, CA) to dsDNA by adding 1µl of an adapter to each 10µl sample and 13µl of 1× Rapid Ligation Buffer with 30U T4 DNA Ligase (Enzymatics, Beverly, MA), and incubated at 25°C for 10min. We stopped reactions with a final concentration of 0.01M EDTA. We added 25µl of MagNA beads in XP buffer (final PEG = 13.6%), bound cDNA to the beads, washed and eluted in 30µl of distilled H2O as above.  We size-selected libraries by adding 1× XP buffer (30µl), washed, eluted samples with 24µl distilled H2O, and transferred 23µl of cDNA to a fresh plate. 11.5µl of the eluate was transferred to another plate and used in the next step; the remaining samples were frozen as a back-up.  We mixed dsDNA product with 2.5U (0.5µl) of Uracil DNA Glycosylase (New England Biolabs, Beverly, MA) and 3µl of PCR Primer Cocktail (Illumina, San Diego, CA) and incubated at 37°C for 30min to digest the second strand DNA.  We added 15µl 2× KAPA HiFi HotStart ReadyMix (Kapa Biosystems, Woburn, MA) directly to the UDG digested DNA mixture and performed a PCR amplification with the following programmed cycle: 95°C for 2min, followed by 12 cycles of 98°C for 20sec, 65°C for 30sec, and 72°C for 30sec; then 72°C for 5min. We purified the product by adding 30µl MagNA beads in 1× XP buffer, eluted in 30µl distilled H2O and transferred 29µl of cDNA library to a fresh plate as described above. To assay plate-level failure, we took 11 samples from each 96-well plate and examined electropherograms for a strong signal in the 300-350 bp library target size and weak signal in the 100-150bp range (primer dimer products).  Each 96-well plate was composed of 4 sets of samples with 24 unique indexes. We pooled equal amounts (5-15 ng) of each library into pools for multiplex sequencing.  All multiplexed libraries were again quantified and checked for quality as above.  Excess library pools were frozen for re-sequencing if required.

value: Adult

tag: Sex

value: Male

value: Whole body


title: DGRP320 M_E3_5_L2

description:
EP7D032
Drosophila Genetic Reference Panel 320, Male, Environment 3, Fly 5, Library 2


title: DGRP850 M_E3_1_L2

description:
EP8F122
Drosophila Genetic Reference Panel 850, Male, Environment 3, Fly 1, Library 2


title: L1210_2 scRNA-seq

description: L1210 scRNA-seq

source_name: Single L1210 cells grown for multiple generations on-chip

tag: cousin 2

tag: doublet?


title: DGRP761 F_E3_3_L1

description:
EP6H121
Drosophila Genetic Reference Panel 761, Female, Environment 3, Fly 3, Library 1

value: Female


title: Neurospora_crf5_F2_rep1

source_name: Δcrf5-1 F2 rep1


title: DGRP563 F_E3_2_L2

description:
EP6H062
Drosophila Genetic Reference Panel 563, Female, Environment 3, Fly 2, Library 2


title: C1_HA_ChIPSeq

value: whole animal

value: female

tag: age


title: DGRP563 M_E3_2_L2

description:
EP7C122
Drosophila Genetic Reference Panel 563, Male, Environment 3, Fly 2, Library 2


title: DGRP229 F_E3_2_L1

description:
EP6H111
Drosophila Genetic Reference Panel 229, Female, Environment 3, Fly 2, Library 1


title: DGRP812 M_E3_3_L1

description:
EP6H081
Drosophila Genetic Reference Panel 812, Male, Environment 3, Fly 3, Library 1


title: DGRP93 F_E3_5_L1

description:
EP6H101
Drosophila Genetic Reference Panel 93, Female, Environment 3, Fly 5, Library 1


title: DGRP563 F_E3_2_L1

description:
EP6H061
Drosophila Genetic Reference Panel 563, Female, Environment 3, Fly 2, Library 1


title: DGRP787 F_E3_6_L1

description:
EP6G111
Drosophila Genetic Reference Panel 787, Female, Environment 3, Fly 6, Library 1


title: DGRP370 F_E3_5_L1

description:
EP6H041
Drosophila Genetic Reference Panel 370, Female, Environment 3, Fly 5, Library 1


title: DGRP761 M_E3_8_L2

description:
EP6H032
Drosophila Genetic Reference Panel 761, Male, Environment 3, Fly 8, Library 2


title: DGRP370 M_E3_2_L2

description:
EP6H012
Drosophila Genetic Reference Panel 370, Male, Environment 3, Fly 2, Library 2


title: DGRP790 M_E3_3_L2

description:
EP6G072
Drosophila Genetic Reference Panel 790, Male, Environment 3, Fly 3, Library 2


title: DGRP804 F_E3_8_L1

description:
EP6G101
Drosophila Genetic Reference Panel 804, Female, Environment 3, Fly 8, Library 1


title: DGRP630 M_E3_6_L2

description:
EP6G082
Drosophila Genetic Reference Panel 630, Male, Environment 3, Fly 6, Library 2


title: DGRP804 F_E3_3_L1

description:
EP6G121
Drosophila Genetic Reference Panel 804, Female, Environment 3, Fly 3, Library 1


title: DGRP93 F_E3_2_L1

description:
EP6G041
Drosophila Genetic Reference Panel 93, Female, Environment 3, Fly 2, Library 1


title: DGRP370 M_E3_6_L2

description:
EP6G052
Drosophila Genetic Reference Panel 370, Male, Environment 3, Fly 6, Library 2


title: DGRP850 M_E3_7_L2

description:
EP6G012
Drosophila Genetic Reference Panel 850, Male, Environment 3, Fly 7, Library 2


title: DGRP790 M_E3_2_L2

description:
EP6G062
Drosophila Genetic Reference Panel 790, Male, Environment 3, Fly 2, Library 2


title: DGRP804 F_E3_7_L2

description:
EP8D122
Drosophila Genetic Reference Panel 804, Female, Environment 3, Fly 7, Library 2


title: DGRP370 F_E3_7_L1

description:
EP6G021
Drosophila Genetic Reference Panel 370, Female, Environment 3, Fly 7, Library 1


title: DGRP822 M_E3_3_L2

description:
EP6H052
Drosophila Genetic Reference Panel 822, Male, Environment 3, Fly 3, Library 2


title: DGRP352 M_E3_4_L2

description:
EP6F112
Drosophila Genetic Reference Panel 352, Male, Environment 3, Fly 4, Library 2


title: DGRP630 M_E3_1_L2

description:
EP6H022
Drosophila Genetic Reference Panel 630, Male, Environment 3, Fly 1, Library 2


title: DGRP703 F_E3_1_L1

description:
EP6F101
Drosophila Genetic Reference Panel 703, Female, Environment 3, Fly 1, Library 1


title: DGRP703 M_E3_1_L2

description:
EP6F082
Drosophila Genetic Reference Panel 703, Male, Environment 3, Fly 1, Library 2


title: DGRP787 M_E3_4_L2

description:
EP6F072
Drosophila Genetic Reference Panel 787, Male, Environment 3, Fly 4, Library 2


title: DGRP563 F_E3_7_L1

description:
EP6F061
Drosophila Genetic Reference Panel 563, Female, Environment 3, Fly 7, Library 1


title: DGRP900 F_E3_3_L1

description:
EP6F051
Drosophila Genetic Reference Panel 900, Female, Environment 3, Fly 3, Library 1


title: DGRP229 F_E3_5_L1

description:
EP6F011
Drosophila Genetic Reference Panel 229, Female, Environment 3, Fly 5, Library 1


title: DGRP804 M_E3_7_L2

description:
EP6F042
Drosophila Genetic Reference Panel 804, Male, Environment 3, Fly 7, Library 2


title: DGRP630 F_E3_5_L1

description:
EP6E121
Drosophila Genetic Reference Panel 630, Female, Environment 3, Fly 5, Library 1