title: PAPERCLIP for si-CstF64/64tau, replicate 1

city: Pittsburgh

first: Hun-Way

last: Hwang

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

description:
Index 3: ACTAGCTC
PAPERCLIP protocol
processed data file: CSTF2_2T.distal.prox.edgeR.pA.2sites.FDR.0.05.txt

data_processing:
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014).  In brief, the raw reads were filtered based on quality score.
Filtered reads with the exact sequence were collapsed into one.
The 5′ degenerate linker was removed.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011).  Only reads that are at least 25-nt in length are retained for mapping to reference genome (hg19 or mm10).
Mapping was performed using Novoalign (http://www.novocraft.com) without trimming.  A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single tag as previously described (Moore et al. 2014).  All reads went through the entire process are referred to as “unique reads” and were used for poly(A) site annotation and other downstream analysis.
Poly(A) site usage for each library was determined by the count of reads aligning up to 100-nt upstream of a PAPERCLIP identified poly(A) site.  Genes with poly(A) sites closer than 100-nt apart were not considered in the APA shift analysis.  Also, we restricted the APA shift analysis to genes with two distinct PAPERCLIP defined poly(A) sites.  Additionally, for the HeLa siRNA comparisons, at least one of the poly(A) site was required to be present in the control experiment.  EdgeR package (Robinson et al. 2010) was used to statistically test significant APA shifts between two experimental conditions, while accounting for biological and technical variability between experimental replicates.  Each replicate dataset was first normalized to account for library size and compositional bias using the TMM methodology (Robinson and Oshlack 2010).  Next, we model the poly(A) site PAPERCLIP read count data as a negative binomial distribution and fitted a Generalized Linear Model (GLM) with explanatory variables for batch, experimental condition (e.g. siRNA treatment, mouse developmental stage), poly(A) location (i.e distal or proximal) and an interaction factor for experimental condition × poly(A) location.  For each gene, GLM likelihood ratio test was conducted to test if the interaction coefficient between experimental condition and poly(A) location was non-zero (i.e poly(A) site usage is dependent on experimental condition).  GLM likelihood ratio test derived p-values were adjusted for multiple hypotheses testing using the qvalue package (Storey and Tibshirani 2003).  In addition to FDR < 0.05 cutoff, we require the average normalized read count ratio of poly(A) locations (proximal vs. distal) to be greater than a twofold change between experimental conditions to identify genes with robust APA shifts.
genome build: hg19
processed data files format and content: txt files for edgeR outputs

source_name: HeLa cells

extract_protocol:
Sample preparation, immunoprecipitation, SDS-PAGE and RNA extraction were adapted from standard HITS-CLIP (Moore et al. 2014).  Mouse monoclonal anti-PABP (Sigma, P6246) was used for immunoprecipitation.
The sequencing library was constructed using BrdU-CLIP method (Weyn-Vanhentenryck et al. 2014) with modification to improve sensitivity.  The library contains a 14-nt degenerate linker sequence at the 5′ end (6-nt random barcode followed by 8-nt sample multiplexing index).  The complete protocol is detailed in Supplemental Method.

value: HeLa

value: replicate 1


title: PAPERCLIP for si-CFIm68, replicate 1

status: Public on Feb 19 2016

type: SRA

state: PA

country: USA

description:
Index 2: AACAGTGC
PAPERCLIP protocol
processed data file: CPSF6.distal.prox.edgeR.pA.2sites.FDR.0.05.txt

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: replicate

tag: antibody

value: Mouse monoclonal anti-PABP (Sigma, P6246)


title: PAPERCLIP for si-CFIm68, replicate 2

description:
Index 3: ACTAGCTC
PAPERCLIP protocol
processed data file: CPSF6.distal.prox.edgeR.pA.2sites.FDR.0.05.txt

value: replicate 2


title: 12-day-old wild type rep. 2

city: Blacksburg

first: Delasa

last: Aghamirzaie

state: VA

address: 101L Price Hall, Virginia Tech

department: GBCB

institute: virginia Tech

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to hard-masked Arabidopsis TAIR10 genome using Tophat2
Transcript assembly was done using StringTie
Assembled transcripts from all samples were merged using Cuffmerge to generate a reference transcriptome GTF file
StringTie-B was used to prepare read coverage tables from aligned reads
Raw count abundance values were normalized to the library size and transcript sizes to obtain Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values.
Genome_build: TAIR10
Supplementary_files_format_and_content: Final FPKM values and raw counts are provided as Expression.txt

organism: Arabidopsis thaliana

source_name: developing embryos

growth_protocol: Normal growth in Farfard superfine germinating mix (Sun Gro Horticulture, Vancouver, British Columbia, Canada) in 2-inch pots. Irrigation was done with deionized water every 3 – 4 days until the plants were 3 – 4 weeks old.  After that, the plants received Miracle Gro All-Purpose Plant Food (1 tsp per 2 gallons) with every watering. Controlled environment at ~115 E, 20/18 oC day/night, 65% humidity, and a 16-hour photoperiod

extract_protocol:
RNA was extracted from frozen embryos using phenol/chloroform and LiCl precipitation and purified by using the Qiagen RNeasy Plant Mini kit.  RNA quality and integrity analysis was performed by the Virginia Bioinformatics Institute (Virginia Tech, Blacksburg, VA).
Reverse transcription of mRNA, library preparation, and paired-end RNA-Seq generating 75-bp reads, including removing low quality reads and adapter sequence trimming, was performed by Beckman Coulter Genomics (Danvers, MA) using established protocols.

treatment_protocol: Seeds and embryos from siliques of defined stages were dissected at low temperatures to slow down any metabolic processes. This was achieved by performing these dissections on wet glass-fiber filters placed on Petri dishes completely filled with frozen water and ensuring that temperatures were maintained between -5 and 5 oC by frequent measurements with an infrared thermometer. We found that these temperatures are the lowest that can be used without freezing the seeds, which would cause cell damage that would be problematic for the subsequent embryo washing steps. Depending on the developmental stage of the embryos, embryo dissection from a single silique (40–60 seeds) took between 10 and 25 minutes.  Wild type and val1 mutant embryos were dissected under dissecting microscopes in parallel by two personnel. Embryos were rinsed off from the glass-fiber filter into ice-cold mass spectrometry-grade water, briefly centrifuged at 4 oC prior to an additional wash to remove any remaining endosperm, snap-frozen in liquid nitrogen, and stored at -80 oC until RNA extraction was performed.

tag: developmental stage

tag: genotype

value: wild type


title: JHU_UM_03

city: Baltimore

first: Srikanth

middle: Srinivas

last: Manda

state: Maryland

address: 733 N Broadway

department: School of Medicine

institute: Johns Hopkins University

data_processing:
The RNA libraries were sequenced on Illumina HiSeq 2000 Platform
The qualities of all sequences in fastq format were assessed using FASTQC . The adaptors and low quality bases were trimmed from the sequence using Trimmomatic. Reads with a phred quality (Q > 20) were used for further alignment and assembly.
Quality trimmed raw reads from all 15 samples were aligned to the human reference genome sequence (GRCh38.79 assembly) separately using HISAT (v 0.1.4) with Gencode V22 junctions as a guided reference annotation.
The aligned reads for each sample were assembled into transcripts using Stringtie (v1.3.3). The transcripts abundance was estimated as Fragments Per Kilobases of exon per Million fragments mapped (FPKM)
Separate GTF files for each sample were generated
Genome_build: GRCh38.79
Supplementary_files_format_and_content: GTF files

source_name: Monocyte Cells

extract_protocol:
CD14-Positive monocytes cells were isolated from PBMC by negative selection method using Miltenyi Monocyte Isolation kit II (Miltenyi biotec).
Total RNA was extracted from monocytes cells using the RNesasy mini kit (QIAGEN)
Messenger RNA isolation and sequencing libraries preparation was performed using TruSeq RNA Sample preparation Kit and SuperScript II Reverse Transcriptase.

tag: cell type

value: Primary Monocyte Cells

tag: age

value: Healthy individuals


title: PAPERCLIP for si-CstF64/64tau, replicate 2

description:
Index 6: ACTTGTAC
PAPERCLIP protocol
processed data file: CSTF2_2T.distal.prox.edgeR.pA.2sites.FDR.0.05.txt


title: PAPERCLIP for si-Ctrl, replicate 2

description:
Index 2: AACAGTGC
PAPERCLIP protocol

data_processing:
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014).  In brief, the raw reads were filtered based on quality score.
Filtered reads with the exact sequence were collapsed into one.
The 5′ degenerate linker was removed.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011).  Only reads that are at least 25-nt in length are retained for mapping to reference genome (hg19 or mm10).
Mapping was performed using Novoalign (http://www.novocraft.com) without trimming.  A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single tag as previously described (Moore et al. 2014).  All reads went through the entire process are referred to as “unique reads” and were used for poly(A) site annotation and other downstream analysis.
Poly(A) site usage for each library was determined by the count of reads aligning up to 100-nt upstream of a PAPERCLIP identified poly(A) site.  Genes with poly(A) sites closer than 100-nt apart were not considered in the APA shift analysis.  Also, we restricted the APA shift analysis to genes with two distinct PAPERCLIP defined poly(A) sites.  Additionally, for the HeLa siRNA comparisons, at least one of the poly(A) site was required to be present in the control experiment.  EdgeR package (Robinson et al. 2010) was used to statistically test significant APA shifts between two experimental conditions, while accounting for biological and technical variability between experimental replicates.  Each replicate dataset was first normalized to account for library size and compositional bias using the TMM methodology (Robinson and Oshlack 2010).  Next, we model the poly(A) site PAPERCLIP read count data as a negative binomial distribution and fitted a Generalized Linear Model (GLM) with explanatory variables for batch, experimental condition (e.g. siRNA treatment, mouse developmental stage), poly(A) location (i.e distal or proximal) and an interaction factor for experimental condition × poly(A) location.  For each gene, GLM likelihood ratio test was conducted to test if the interaction coefficient between experimental condition and poly(A) location was non-zero (i.e poly(A) site usage is dependent on experimental condition).  GLM likelihood ratio test derived p-values were adjusted for multiple hypotheses testing using the qvalue package (Storey and Tibshirani 2003).  In addition to FDR < 0.05 cutoff, we require the average normalized read count ratio of poly(A) locations (proximal vs. distal) to be greater than a twofold change between experimental conditions to identify genes with robust APA shifts.
genome build: hg19

treatment_protocol: si-Ctrl


title: PAPERCLIP for HEK293 cells, replicate 2

description:
Index 1: ACGATGTC
PAPERCLIP protocol
processed data file: HEK293_BC2_16414_GeneAssigned.bed

data_processing:
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014).  In brief, the raw reads were filtered based on quality score.
Filtered reads with the exact sequence were collapsed into one.
The 5′ degenerate linker was removed.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011).  Only reads that are at least 25-nt in length are retained for mapping to reference genome (hg19 or mm10).
Mapping was performed using Novoalign (http://www.novocraft.com) without trimming.  A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single tag as previously described (Moore et al. 2014).  All reads went through the entire process are referred to as “unique reads” and were used for poly(A) site annotation and other downstream analysis.
Unique reads from both replicates were merged.  CIMS software package was used to cluster overlapping reads and to determine the read counts (PH) for each cluster.  Only clusters that contained more than 2 (for mouse cortex) or 3 (for cultured cells) unique reads were used for downstream analysis.  For each filtered cluster, the most abundant 3′ end from all reads in the cluster was assigned as the poly(A) site.  The 3′ most position was selected if there was a tie in abundance for multiple 3′ ends.  Please refer to the citation for further information.
genome build: hg19
processed data files format and content: bed files for annotated poly(A) sites

source_name: HEK293 cells


title: 10-day-old wild type rep. 3


title: PAPERCLIP for HEK293 cells, replicate 1

description:
Index 6: ACTTGTAC
PAPERCLIP protocol
processed data file: HEK293_BC2_16414_GeneAssigned.bed


title: PAPERCLIP for si-Ctrl, replicate 1

description:
Index 1: ACGATGTC
PAPERCLIP protocol


title: PAPERCLIP for HeLa cells, replicate 1

description:
Index 1: ACGATGTC
PAPERCLIP protocol
processed data file: HeLa_No1No6_BC2_17652_GeneAssigned.bed


title: PAPERCLIP for HeLa cells, replicate 2

description:
Index 6: ACTTGTAC
PAPERCLIP protocol
processed data file: HeLa_No1No6_BC2_17652_GeneAssigned.bed


title: RNA-seq for embryo mouse cortex, replicate 2

data_processing:
RNA-Seq reads were mapped to the mm10 genome assembly using STAR aligner using default parameters and providing splicing junctions from the Ensembl version 80 release.
HTSeq package was used to count the number of overlapping reads per gene definition.
Replicate raw gene read counts were used as input to EdgeR for differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file; cpm for each gene

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Trizol (Invitrogen) and Dynabeads mRNA Purification Kit for mRNA Purification (Invitrogen)
ScriptSeq V2 kit (Epicentre)

tag: tissue

value: whole brain cortex

tag: strain


title: RNA-seq for embryo mouse cortex, replicate 1


title: RNA-seq for adult mouse cortex, replicate 2


title: RNA-seq for adult mouse cortex

description:
No index
processed data file: 00081814.remake.bedgraph.gz

data_processing:
Reads were aligned to the mouse genome (mm10) using bowtie2 (version 2.1.0) and converted the resulting sample to a bam file containing only the properly mapped paired-reads. The bam file was then converted to a paired-end bed file using bed tools (version 2.20.1), which was in turn used to create a bed graph file (tag2profile, CIMS package).
genome build: mm10
processed data files format and content: bedgraph files for coverage


title: Islet cell Sample 619

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (mouse: GRCm38) using CLC bio Genomics Workbench Version 7.0 (CLC Bio) allowing one mismatch.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Pancreatic islets

extract_protocol:
Single islet cells were captured with C1 Integrated Fluidic Circuit. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (Protocol #100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (Protocol #100-7168 E1).

value: Pancreatic islets


title: Islet cell Sample 617


title: Islet cell Sample 615


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title: Islet cell Sample 598


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title: Islet cell Sample 592


title: Islet cell Sample 587


title: Islet cell Sample 611


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title: Islet cell Sample 211


title: Islet cell Sample 208


title: Islet cell Sample 207


title: Islet cell Sample 206


title: Islet cell Sample 205


title: Islet cell Sample 209


title: Islet cell Sample 204


title: Islet cell Sample 203


title: Islet cell Sample 201


title: Islet cell Sample 202


title: Islet cell Sample 199


title: Islet cell Sample 197


title: Islet cell Sample 198


title: Islet cell Sample 196


title: Islet cell Sample 195


title: Islet cell Sample 194


title: Islet cell Sample 191


title: Islet cell Sample 193


title: H3K4me3 D11, H3K27ac D11, and H3K27me3 D11 input

city: San Francisco

last: Cao

state: CA

address: 1650 Owens Street

department: Department of Pharmaceutical Chemistry

institute: gladstone institute of cardiovascular disease

library_source: genomic

data_processing:
base-calling was done using CASAVA 1.8.4.
The alignment was done using bowtie (version 1.1.0) with human genome build hg19, reporting only reads with unique genome alignments. The result was then filtered by removed potential PCR duplications with with samtools (version 0.1.19)
peak calling for H3k4me3 and H3K27Ac was done using Macs (version 1.4), using the corresponding input DNA as control for each samples. Default parameters from Macs were used. Peak calling for H3K27me3 was done using Macs (version 2.0: macs2 callpeak -t $treatment -c $control --broad -g hs -n $name -B --no-model)
Genome_build: hg19
Supplementary_files_format_and_content: MACS peak files

molecule: genomic DNA

source_name: foreskin

growth_protocol: Cells were grown in standard fibroblast culture medium (HFFs), reprogramming medium (D6), and cardiac induction medium (D11) at 37°C.

extract_protocol:
Histones and DNA were cross-linked by 1% formaldehyde and extracted using a Magna ChIP G kit (Millipore). The chromatin was then sonicated to an average DNA fragment length of 200-300 bp.
Illumina sequencing libraries were generated according to the manufacturer’s instructions. Briefly, 5-50 ng of ChIP product was end repaired, a-tailed and ligated to Illumina single end adapters by using an NEB Next kit (New England Biolabs). Adaptor-ligated DNA with a size of 200-300 bp was purified by running a gel and enriched via 19 cycles of PCR amplification with Phusion High-Fidelity DNA Polymerase, followed by sequencing on an Illumina HiSeq 2000 system.

treatment_protocol: Cells were treated with reprogramming small molecules for 6 days (D6), and then treated with cardiac inductive molecules for another 5 days (D11).

value: foreskin fibroblast

tag: treatment

value: reprogramming

tag: time

tag: chip antibody

value: none (input)


title: Islet cell Sample 212


title: Islet cell Sample 192


title: H3K4me3 D6 input


title: Islet cell Sample 190


title: H3K27ac D6 and H3K27me3 D6 input


title: Islet cell Sample 187


title: Islet cell Sample 188


title: Islet cell Sample 189


title: H3K4me3 HFFs and H3K27ac HFFs input

value: control


title: Islet cell Sample 186


title: H3K27ac D11

value: H3K27ac (Millipore, catalog# 17-683, lot# 2510209)


title: Islet cell Sample 185


title: Islet cell Sample 183


title: H3K27ac HFFs


title: H3K27me3 D11

value: H3K27me3 (Millipore, catalog# 17-622, lot# 2135434)


title: Islet cell Sample 179


title: Islet cell Sample 200


title: H3K27ac D6


title: Islet cell Sample 184


title: Islet cell Sample 178


title: Islet cell Sample 180


title: H3K4me3 D6

value: H3K4me3 (Millipore, catalog# 17-614, lot# 2109590)


title: Islet cell Sample 176


title: H3K4me3 D11


title: H3K27me3 HFFs


title: H3K27me3 D6


title: H3K4me3 HFFs


title: Islet cell Sample 182


title: EX172588_V1N

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

description: high RNA integrity group

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Reads were aligned by TopHat 2.0.6 using the hg19 genome build and bowtie1 aligner option. Mean and standard deviation of fragment size were estimated by sampling the first 100,000 read pairs that were uniquely mapped.
Raw count, FPM and FPKM were calcualted using RSeQC (v2.3.6) with parameters "-d '1+-,1-+,2++,2--'
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Processed files are Tab separated plain text files. Each file contains 9 columns: Chromosome, gene start coordinate, gene end coordinate, gene symbol, score size, strand, raw fragment count, FPM (fragment per million) and FPKM.

source_name: Prostate cancer (Bone metastasis)

extract_protocol:
Tissues were snap frozen with liquid nitrogen, and RNA was harvested using Rneasy Plus Mini Ki t(Qiagen). Ribo-zero rRNA remove Kit was used. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used
RNA libraries were prepared according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA).  The liquid handling Eppendorf (Hamburg, GER) EpMotion 5075 robot was employed for TruSeq library construction.  All AMPure bead clean up, mRNA isolation, end repair and A-tailing reactions was completed on the 5075 robot.  Reverse transcription and adaptor ligation steps were performed manually.    Briefly, poly-A mRNA was purified from total RNA using oligo dT magnetic beads. The purified mRNA was fragmented at 95°C for 8 minutes, eluted from the beads and primed for first strand cDNA synthesis. The RNA fragments were then copied into first strand cDNA using SuperScript III reverse transcriptase and random primers (Invitrogen, Carlsbad, CA).  Next, second strand cDNA synthesis was performed using DNA polymerase I and RNase H. The double-stranded cDNA was purified using a single AMPure XP bead (Agencourt, Danvers, MA) clean-up step.   The cDNA ends were repaired and phosphorylated using Klenow, T4 polymerase, and T4 polynucleotide kinase followed by a single AMPure XP bead clean-up.  The blunt-ended cDNAs were modified to include a single 3’ adenylate (A) residue using Klenow exo- (3’ to 5’ exo minus).  Paired-end DNA adaptors (Illumina) with a single “T” base overhang at the 3’ end were immediately ligated to the ‘A tailed’ cDNA population.  Unique indexes, included in the standard TruSeq Kits (12-Set A and 12-Set B) were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells.  The resulting constructs were purified by 2 consecutive AMPure XP bead clean-up steps.   The adapter-modified DNA fragments were enriched by 12 cycles of PCR using primers included in the Illumina Sample Prep Kit. The concentration and size distribution of the libraries were determined on an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA).  A final quantification, using Qubit fluorometry (Invitrogen, Carlsbad, CA), was done to confirm sample concentration. mRNA libraries are loaded 2 per lane onto Illumina TruSeq v3 paired end flow cells at concentrations of 9 pM to generate cluster densities of 600,000-800,000/mm2 following Illumina’s standard protocol using the Illumina cBot and TruSeq Rapid Paired end cluster kit version 3.

treatment_protocol: These 20 mCRPC patients were recruited as part of Prostate Cancer Medically Optimized Genome-Enhanced Therapy (PROMOTE) study. Tissue biopsies from a metastatic rib lesion were obtained before initiating enzalutamide treatment.

value: Bone

tag: tumor stage

value: metastatic castration resistant

tag: rin score

tag: median tin score


title: EX171721_V1N

description: high RNA integrity group


title: EX169285_V1N

description: high RNA integrity group


title: EX178001_V1N

description: high RNA integrity group


title: Islet cell Sample 177


title: Islet cell Sample 175


title: H3K27me3 HFFs input


title: Islet cell Sample 173


title: Islet cell Sample 181


title: Islet cell Sample 171


title: Islet cell Sample 169


title: EX170045_V1N

description: high RNA integrity group


title: Islet cell Sample 170


title: Islet cell Sample 167


title: Islet cell Sample 166


title: Islet cell Sample 164


title: Islet cell Sample 174


title: Islet cell Sample 163


title: Islet cell Sample 168


title: Islet cell Sample 162


title: EX172638_V1N

description: low RNA integrity group


title: Islet cell Sample 172


title: Islet cell Sample 161


title: EX177059_V1N

description: high RNA integrity group


title: EX177867_V1N

description: high RNA integrity group


title: EX178996_V1N

description: low RNA integrity group


title: EX176795_V1N

description: high RNA integrity group


title: EX161328_V1N

description: high RNA integrity group


title: EX174179_V1N

description: low RNA integrity group


title: EX178643_V1N

description: low RNA integrity group


title: EX177392_V1N

description: high RNA integrity group


title: Islet cell Sample 159


title: EX173983_V1N

description: low RNA integrity group


title: EX148171_V1N

description: low RNA integrity group


title: EX178108_V1N

description: low RNA integrity group


title: Islet cell Sample 160


title: EX176721_V1N

description: low RNA integrity group


title: Islet cell Sample 165


title: Islet cell Sample 158


title: EX172587_V1N

description: low RNA integrity group


title: Islet cell Sample 157


title: Islet cell Sample 155


title: Islet cell Sample 154


title: Islet cell Sample 151


title: Islet cell Sample 153


title: Islet cell Sample 149


title: Islet cell Sample 147


title: Islet cell Sample 150


title: Islet cell Sample 152


title: Islet cell Sample 145


title: Islet cell Sample 144


title: Islet cell Sample 140


title: Islet cell Sample 141


title: Islet cell Sample 143


title: Islet cell Sample 142


title: Islet cell Sample 139


title: Islet cell Sample 137


title: Islet cell Sample 138


title: Islet cell Sample 133


title: Islet cell Sample 134


title: Islet cell Sample 136


title: Islet cell Sample 135


title: Islet cell Sample 132


title: EX177582_V1N

description: low RNA integrity group


title: Islet cell Sample 130


title: Islet cell Sample 131


title: Islet cell Sample 156


title: Islet cell Sample 128


title: Islet cell Sample 129


title: Islet cell Sample 148


title: Islet cell Sample 127


title: Islet cell Sample 126


title: Islet cell Sample 146


title: Islet cell Sample 125


title: Islet cell Sample 124


title: Islet cell Sample 122


title: Islet cell Sample 123


title: Islet cell Sample 120


title: Islet cell Sample 118


title: APP-PS Control rep2

first: Iliya

last: Lefterov

address: 100 technology drive

department: Department of environmental and occupational health

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation .
Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file includes raw read counts for each sample

source_name: Brain

extract_protocol:
Qiagene Rneasy Kit
TruSeq Stranded mRNA LT Sample Prep Kit

value: cortex

tag: agent

value: 0.2 mg/kg glycerol


title: APP-PS Control rep3


title: Islet cell Sample 119


title: APP-PS Control rep4


title: Islet cell Sample 117


title: APP-PS Bex rep4

value: bexarotene


title: APP-PS Bex rep3


title: APP-PS Control rep1


title: APP-PS Bex rep1


title: GMP_4C_Klf4promoter

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

country: France

institute: Ecole Normale Superieure

data_processing:
Library strategy: 4C-seq
The reading primer was removed from the read seqeunce using the python script present in the bioconductor package fourCseq demultiplex.py
reads were mapped using STAR (parameters: -outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.1 -alignIntronMax 1 -alignEndsType EndToEnd).
Mapped reads were pre-process using the fourCseq package, and tracks of signal were made using the R package fourCseq, applying a running mean over 5 framgments.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, track of signal

source_name: GMP

growth_protocol: ESCs (E14TG2) were cultured on gelatinized plates in N2B27 media (50 %DMEM/F12, 50% Neurobasal medium, N2 (500X), B27 (1000X)) supplemented with small-molecule inhibitors PD (1 μM, PD0325901), CHIR (3 μM, CHIR99021) and LIF. CD19+ pre-B cells were obtained from bone marrow with monoclonal antibody to CD19 (BD Pharmingen) using MACS sorting (Miltenyi Biotech). The purity of the sorted cell fractions was confirmed by FACS using an LSR2 machine (BD). After isolation, B cells were grown in RPMI medium supplemented with 10% FBS and 10ng/ml IL-7 (Peprotech). All medium contain 100 X L-glutamine, 100X penicillin/streptomycin, 100X nonessential amino acids, 1000X β-mercaptoethanol. All reagents are from Life Technologies unless otherwise specified. Lin- c-Kit+ Sca-1- CD16+/CD32+ CD34+ GMP cells were isolated by FACS sorting using a BD INFLUX sorting machine and culture in STEMSPAN medium (Stemcell technologies) supplemented with 100ng/ml SCF, 50ng/ml IL3, 50ng/ml Flt3L and 50ng/ml mTPO (all from Peprotech). The antibodies used from GMPs isolation were from BD Biosciences.

extract_protocol:
0.5-1.0 million of crosslinked nuclei were digested with Csp6I followed by ligation under dilute conditions. After decrosslinking and DNA purification, samples were digested overnight with DpnII and once more ligated under dilute conditions.
Column purified DNA was directly used as input for inverse PCR using primers with Illumina adapter sequences as overhangs. Several PCR reactions were pooled, purified and sequenced.

treatment_protocol: For the reprogramming experiments B cells were exposed for 18h to 100nM of -Estradiol (E2) in gelatinized plates seeded with a feeder layer of the MEFs in RPMI medium. After E2 washout, the cultures were switched to serum-free N2B27 medium supplemented with 2μg/ml of doxycycline, IL-4 10ng/ml, IL-7 10ng/ml and IL-15 2ng/ml. B cells were seeded at a density of 500 cells/cm2 in 12 well plates.

tag: target

value: Klf4 promoter

tag: first cutter and restriction site sequence

value: Csp6i (GTAC)

tag: second cutter and restriction site sequence

value: DpnII (GATC)

tag: reading primer sequence

value: GACAGGACAAGCGCGTAC

tag: non-reading primer sequence

value: GAGATACCTTTCACCAGGGAT


title: APP-PS Bex rep2

tag: genotype


title: Islet cell Sample 116

value: Pancreatic islets

value: wild type


title: Islet cell Sample 115


title: Islet cell Sample 114


title: ESC_4C_Klf4enhancer

source_name: ES

value: Klf4 enhancer

value: CGCTTTATGTTCTGCCAGTAC

value: TGTCACAGCCCCAGTAGTG


title: Islet cell Sample 113


title: Bcell+Cebpa18h_4C_Klf4enhancer


title: ESC_4C_Klf4promoter


title: Bcell_4C_Klf4enhancer

source_name: Bcell


title: Islet cell Sample 112


title: GMP_slow_RNAseq_bio1

data_processing:
reads were mapped using STAR5 with the Ensembl gene annotation gtf (GRCm38.78) (parameters: -sjdbOverhang 100 -outFilterType BySJout -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.06 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000)
bigwig tracks were obtained with STAR
For quantitative analysis, reads were counted on genes exon using the Rpackage Rsubread (1.16.1)(parameters: GTF.featureType="exon", GTF.attrType="gene_id", isPairedEnd=T, nthreads=12, strandSpecific=0)
Samples scaling and statistical analysis were performed using the Rpackage DESeq2 (1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, track of read signal

extract_protocol:
RNA isolation was performed with the miRNeasy mini kit (Qiagen) following manufacturers instruction. To remove the feeders, cells were pre-plated for 30 minutes before RNA processing. RNA was eluted from the columns using RNase-free water and quantified by Nanodrop. cDNA was produced with the High Capacity RNA-to-cDNA kit (Applied Biosystem).
Libraries were prepared using the SMARTer Universal Low Input RNA Kit (Clontech Laboratories) according to the manufacturer's protocol.

treatment_protocol: For the reprogramming experiments B cells were exposed for 18h to 100nM of β-Estradiol (E2) in gelatinized plates seeded with a feeder layer of the MEFs in RPMI medium. After E2 washout, the cultures were switched to serum-free N2B27 medium supplemented with 2μg/ml of doxycycline, IL-4 10ng/ml, IL-7 10ng/ml and IL-15 2ng/ml. B cells were seeded at a density of 500 cells/cm2 in 12 well plates.

value: bone marrow

tag: cell type

value: GMP


title: Bcell+Cebpa18h_4C_Klf4promoter


title: Bcell_4C_Klf4promoter


title: Islet cell Sample 111


title: Islet cell Sample 121


title: GMP_fast_RNAseq_bio1


title: GMP_RNAseq_bio1


title: ES_RNAseq_bio2

value: ES


title: Islet cell Sample 109


title: ES_RNAseq_bio1


title: Bcell_RNAseq_bio2

value: B cell


title: Islet cell Sample 108


title: Bcell_RNAseq_bio1


title: Islet cell Sample 110


title: Bcell_Cebpa18h_RNAseq_bio2


title: Islet cell Sample 107


title: Bcell_Cebpa18h_RNAseq_bio1


title: Bcell_Cebpa18h_OKSMd2_RNAseq_bio2


title: Bcell_Cebpa18h_OKSMd2_RNAseq_bio1


title: Islet cell Sample 105


title: Bcell_Cebpa18h_OKSMd1_RNAseq_bio1


title: Bcell_Cebpa18h_OSKM1d_ChIPseq_H3K4me3

data_processing:
reads were mapped using STAR (parameters: -outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.1 -alignIntronMax 1 -alignEndsType EndToEnd).
Duplicates reads were removed using picard
For quantitative analysis, reads were counted on genes exon using the Rpackage Rsubread (1.16.1)(parameters: GTF.featureType="exon", GTF.attrType="gene_id", isPairedEnd=T, nthreads=12, strandSpecific=0)
bigwig tracks were made using DeepTools BamCompare to subtract the input from the ChIP (parameters: -scaleFactorsMethod SES -ratio subtract -normalizeUsingRPKM -fragmentLength 200 -binSize 1)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, track of fragment signal (elongated to 200b)

extract_protocol:
ChIP was performed as described in Jakobsen et al, BMC genomics, 16, 46 (2015)
Amplification of 2 ng ChIP DNA was essentially performed as described by the manufacturer (NEB, cat#E6240S), with the use of precast 2% SYBR agarose gels (Invitrogen, cat#G5218-02) and excision of band size 175–400 bp. Key modifications consisted of a 30 minute ligation step, 30 minute gel solubilization at 37°C of excised gel fragments, and a prolonged, double run-through elution step (each three minutes) with preheated (55°C) elution buffer for all column purifications (Qiagen, cats#28104,28704,28004) to ensure robust recovery.

value: ChIP H3K4me3

tag: antibody

value: Diagenode, C15410003


title: Bcell_Cebpa18h_ChIPseq_H3K4me3

tag: tissue


title: Islet cell Sample 106

tag: strain


title: Bcell_ChIPseq_H3K4me3


title: Islet cell Sample 103


title: Islet cell Sample 102


title: Islet cell Sample 101


title: Bcell_Cebpa18h_OSKM2d_ChIPseq_input

value: none (input)


title: Bcell_Cebpa18h_ChIPseq_input


title: GMP_ATAC

description: Transposase accessible chromatin

data_processing:
Library strategy: ATAC-seq
reads were mapped using STAR (parameters: -outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.06 -alignIntronMax 1 -alignEndsType EndToEnd -alignMatesGapMax 2000, which forbids read splitting and results in a mapping similar to a classical genomic mapper, and allow a maximum of 2kb between two reads of a pair).
Duplicates reads were removed using Picard (http://picard.sourceforge.net./) (function MarkDuplicates, parameter REMOVE_DUPLICATES=true).
bigwig tracks were made using DeepTools BamCoverage (1.5.9.1) (parameters: -binSize 1 -normalizeUsingRPKM).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, track of fragments signal

extract_protocol:
ATACseq was performed as in (Buenrostro et al, Nature methods 10, 1213-1218 (2013)) with the following modifications. 100.000 cells were washed once with 100µl PBS and resuspended in 50µl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630). The nuclei suspension was then centrifuged for 10min at 500g at 4C. The 50µl transposition reaction (25µl TD buffer, 2.5µl Tn5 Transposase and 22.5µl Nuclease Free H2O) was added to the isolated nuclei and incubated at 37C for 45min. DNA was isolated using Qiagen MinElute Kit following the manufacturer instructions.
Library amplification was done by two sequential PCR reactions (8 and 5 cycles, respectively). After the first PCR reaction the library was size selected (for fragments below 700bp) with AmpureXP beads followed by a second PCR reaction. Libraries were purified with Qiaquick PCR purification and integrity checked on a Bionalyzer before sequencing.


title: Bcell_ChIPseq_input


title: Bcell_Cebpa18h_OSKM1d_ChIPseq_input


title: Bcell_OKSMd2_ATAC

description: Transposase accessible chromatin


title: Islet cell Sample 100


title: Bcell_OKSMd1_ATAC

description: Transposase accessible chromatin


title: Islet cell Sample 98


title: Islet cell Sample 104


title: Bcell_ATAC

description: Transposase accessible chromatin


title: CAD-FBS2

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

institute: University of Colorado Anschutz Medical Campus

description: CAD cells post differentiation Rep2

data_processing:
Reads were aligned to the mm9 genome using either Tophat version 2.0.12 or STAR 2.0.4d
Expression values were calculated using Cufflinks version 2.1.1
Alternative isoform abundances were calculated using MISO
Genome_build: mm9 supplemented with alternative isoforms identified in Merkin et al (Science) 2012

source_name: CAD cells differentiated

extract_protocol:
Cells were fractionated using porous membranes into soma and neurite fractions.
For all N2A and CAD samples, libraries were prepared using the standard "dUTP" strand-specific method.  For cortical neuron samples, libraries were prepared using the Clontech Low Input Kit.

tag: cell line

value: CAD cells differentiated


title: Bcell_Cebpa18h_ATAC

description: Transposase accessible chromatin


title: ES_ATAC

description: Transposase accessible chromatin


title: CAD-FBS1

description: CAD cells post differentiation Rep1


title: Islet cell Sample 99


title: Bcell_Cebpa18h_OKSMd1_RNAseq_bio2


title: CAD+FBS2

description: CAD cells pre differentiation Rep2

source_name: CAD cells undifferentiated

value: CAD cells undifferentiated


title: CAD+FBS1

description: CAD cells pre differentiation Rep1


title: Bcell_Cebpa18h_OSKM2d_ChIPseq_H3K4me3


title: Islet cell Sample 96


title: MbnlsiRNANeurite3

description: Mbnl siRNA Neurite Rep3

source_name: CAD cells Mbnl1/2 siRNA neurite

value: CAD cells

tag: compartment

value: neurite

tag: knockdown

value: Mbnl siRNA


title: MbnlsiRNANeurite2

description: Mbnl siRNA Neurite Rep2


title: Islet cell Sample 94

value: Pancreatic islets


title: Islet cell Sample 95

value: wild type


title: MbnlsiRNASoma3

description: Mbnl siRNA Soma Rep3

source_name: CAD cells Mbnl1/2 siRNA soma

value: soma


title: MbnlsiRNASoma2

description: Mbnl siRNA Soma Rep2


title: MbnlsiRNASoma1

description: Mbnl siRNA Soma Rep1


title: CtrlsiRNANeurite2

description: Ctrl siRNA Neurite Rep2

source_name: CAD cells Ctrl siRNA neurite

value: control siRNA


title: CtrlsiRNANeurite1

description: Ctrl siRNA Neurite Rep1


title: CtrlsiRNANeurite3

description: Ctrl siRNA Neurite Rep3


title: MbnlsiRNANeurite1

description: Mbnl siRNA Neurite Rep1


title: Islet cell Sample 97


title: Islet cell Sample 92


title: CtrlsiRNASoma3

description: Ctrl siRNA Soma Rep3

source_name: CAD cells Ctrl siRNA soma


title: Islet cell Sample 91


title: CADSoma3

description: CAD cells Soma Rep3

source_name: CAD cells soma


title: CtrlsiRNASoma1

description: Ctrl siRNA Soma Rep1


title: Islet cell Sample 88


title: CADNeurite2

description: CAD cells neurite Rep2

source_name: CAD cells neurite


title: Islet cell Sample 90


title: CADSoma2

description: CAD cells Soma Rep2


title: CADSoma1

description: CAD cells Soma Rep1


title: Islet cell Sample 87


title: N2ANeurite2

description: N2A cells neurite Rep2

source_name: N2A cells neurite

value: N2A cells


title: Islet cell Sample 86


title: Islet cell Sample 89


title: N2ANeurite3

description: N2A cells neurite Rep3


title: N2ANeurite1

description: N2A cells neurite Rep1


title: Islet cell Sample 93


title: N2ASoma3

description: N2A cells Soma Rep3

source_name: N2A cells soma


title: Islet cell Sample 85

source_name: Pancreatic islets


title: Islet cell Sample 83


title: PAPERCLIP for embryonic mouse cortex, replicate 1

description:
Index 2: AACAGTGC
PAPERCLIP protocol
processed data file: B6_EmbryoCortex_BC2_13413_GeneAssigned4.bed

data_processing:
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014).  In brief, the raw reads were filtered based on quality score.
Filtered reads with the exact sequence were collapsed into one.
The 5′ degenerate linker was removed.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011).  Only reads that are at least 25-nt in length are retained for mapping to reference genome (hg19 or mm10).
Mapping was performed using Novoalign (http://www.novocraft.com) without trimming.  A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single tag as previously described (Moore et al. 2014).  All reads went through the entire process are referred to as “unique reads” and were used for poly(A) site annotation and other downstream analysis.
Unique reads from both replicates were merged.  CIMS software package was used to cluster overlapping reads and to determine the read counts (PH) for each cluster.  Only clusters that contained more than 2 (for mouse cortex) or 3 (for cultured cells) unique reads were used for downstream analysis.  For each filtered cluster, the most abundant 3′ end from all reads in the cluster was assigned as the poly(A) site.  The 3′ most position was selected if there was a tie in abundance for multiple 3′ ends.  Please refer to the citation for further information.
genome build: mm10
processed data files format and content: bed files for annotated poly(A) sites

value: whole brain cortex

tag: replicate

value: replicate 1

value: Mouse monoclonal anti-PABP (Sigma, P6246)


title: CADNeurite1

description: CAD cells neurite Rep1


title: N2ASoma1

description: N2A cells Soma Rep1


title: Islet cell Sample 84


title: PAPERCLIP for adult mouse cortex, replicate 1

description:
Index 3: ACTAGCTC
PAPERCLIP protocol
processed data file: B6_AdultCortex_BC2_10117_GeneAssigned4.bed


title: N2ASoma2

description: N2A cells Soma Rep2


title: CADNeurite3

description: CAD cells neurite Rep3


title: CtrlsiRNASoma2

description: Ctrl siRNA Soma Rep2


title: Tcf7l2_cKO

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads were mapped using TopHat with default settings (http://tophat.cbcb.umd.edu).
TopHat output data were then analyzed by Cufflinks to (1) calculate FPKM values for known transcripts in mouse genome reference mm9; (2) test the changes of gene expression between Tcf7l2 cKO and control.
Genome_build: All sequencing data were mapped to mm9
Supplementary_files_format_and_content: txt files of gene expression FPKM values

source_name: cKO optic nerve

extract_protocol:
RNAs were isolated from the optic nerves of control and Tcf7l2 cKO mice with trizol as recommended by the manufacturer.
RNA-seq libraries were prepared using Illumina RNA-seq preparation Kit (Illumina)

treatment_protocol: No additional treatment

value: Optic nerve

tag: Stage

value: Tcf7l2 c/c; OLig1-cre


title: PAPERCLIP for adult mouse cortex, replicate 2

value: replicate 2


title: PAPERCLIP for embryonic mouse cortex, replicate 2


title: Islet cell Sample 81


title: Islet cell Sample 79


title: Tcf7l2_Ctrl

source_name: control optic nerve

value: Tcf7l2 c/+; OLig1-cre


title: Islet cell Sample 80


title: Islet cell Sample 78


title: Islet cell Sample 75


title: Islet cell Sample 76


title: Islet cell Sample 72


title: Islet cell Sample 74


title: Islet cell Sample 73


title: Islet cell Sample 77


title: Islet cell Sample 69


title: Islet cell Sample 71


title: Islet cell Sample 70


title: Islet cell Sample 68


title: Islet cell Sample 66


title: Islet cell Sample 67


title: Islet cell Sample 64


title: Islet cell Sample 62


title: Islet cell Sample 82


title: PAPERCLIP for pEN2-AR mutant, replicate 2

description: Index 4: TAGC

data_processing:
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014).  In brief, the raw reads were filtered based on quality score.
Filtered reads with the exact sequence were collapsed into one.
The 5′ degenerate linker was removed.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011).  Only reads that are at least 25-nt in length are retained for mapping to reference genome (hg19 or mm10).
Mapping was performed using Novoalign (http://www.novocraft.com) without trimming.  A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Reads mapping to the same genomic positions without distinct barcodes were further collapsed into a single tag as previously described (Moore et al. 2014).  All reads went through the entire process are referred to as “unique reads” and were used for poly(A) site annotation and other downstream analysis.
Unique reads from both replicates were merged.  CIMS software package was used to cluster overlapping reads and to determine the read counts (PH) for each cluster.  Only clusters that contained more than 2 (for mouse cortex) or 3 (for cultured cells) unique reads were used for downstream analysis.  For each filtered cluster, the most abundant 3′ end from all reads in the cluster was assigned as the poly(A) site.  The 3′ most position was selected if there was a tie in abundance for multiple 3′ ends.  Please refer to the citation for further information.
Genome_build: hg19
Supplementary_files_format_and_content: bed files for uniquely mapped reads

source_name: HeLa cells

treatment_protocol: pEN2-AR transfection

value: HeLa cells

tag: type


title: PAPERCLIP for pEN2-GU mutant, replicate 2

description: Index 5: AGTC

treatment_protocol: pEN2-GU transfection


title: Islet cell Sample 63


title: Islet cell Sample 61


title: Islet cell Sample 60


title: PAPERCLIP for si-CstF64/64tau in LN229, replicate 1

description: Index 5: AGTC

source_name: LN229 cells

value: LN229 cells


title: PAPERCLIP for pEN2, replicate 2

description: Index 6: GACT

treatment_protocol: pEN2 transfection


title: PAPERCLIP for pEN2, replicate 1

description: Index 3: CGAT


title: PAPERCLIP for si-CFIm68 in LN229, replicate 1

description: Index 4: TAGC


title: PAPERCLIP for pEN2-AR mutant, replicate 1

description: Index 5: AGTC


title: PAPERCLIP for pEN2-GU mutant, replicate 1

description: Index 4: TAGC


title: PAPERCLIP for si-CstF64/64tau in LN229, replicate 2

description: Index 4: TAGC


title: PAPERCLIP for si-Ctrl in LN229, replicate 1

description: Index 3: CGAT


title: Islet cell Sample 59


title: RNA-seq for HeLa cells

description:
No index
processed data file: 00091013.uniq.bedgraph.gz

data_processing:
Reads were mapped to the annotated human transcriptome (GRCh37) using tophat2 (version 2.0.11). Duplicated reads were then removed using Picardtools (1.107) and the resulting bam file was converted to a bed file. The bed file in turn was used to create the bedgraph.
genome build: hg19
processed data files format and content: bedgraph files for coverage

value: HeLa


title: 3' end sequencing for HeLa cells

description:
No index
3' end sequencing
processed data file: B3p121_3Seq_81117_hg19_EndAssigned_Filtered.bed

data_processing:
The processing of raw reads was performed using the CIMS software package previously described (Moore et al. 2014).  In brief, the raw reads were filtered based on quality score.
Filtered reads with the exact sequence were collapsed into one.
Poly(A) sequence at the 3′ end was then trimmed using CutAdapt (Martin 2011).  Only reads that are at least 25-nt in length are retained for mapping to reference genome (hg19 or mm10).
Mapping was performed using Novoalign (http://www.novocraft.com) without trimming.  A minimum of 25-nt match to the genome sequence was required and only those reads mapped unambiguously to the genome (single hits) were kept for downstream analysis.
Unique reads from both replicates were merged.  CIMS software package was used to cluster overlapping reads and to determine the read counts (PH) for each cluster.  Only clusters that contained more than 2 (for mouse cortex) or 3 (for cultured cells) unique reads were used for downstream analysis.  For each filtered cluster, the most abundant 3′ end from all reads in the cluster was assigned as the poly(A) site.  The 3′ most position was selected if there was a tie in abundance for multiple 3′ ends.  Please refer to the citation for further information.
genome build: hg19
processed data files format and content: bed file for annotated poly(A) site

extract_protocol:
Trizol (Invitrogen) and Dynabeads mRNA Purification Kit for mRNA Purification (Invitrogen)
The sequencing library was constructed from 400ng poly(A) RNA using NEBNext mRNA Library Prep Reagent Set for Illumina (New England Biolabs) following manufacturer's instructions with a custom primer for reverse transcription and custom adaptors for ligation (both are adapted from (Jenal et al. 2012)).


title: Islet cell Sample 58


title: Islet cell Sample 56


title: Islet cell Sample 57


title: Islet cell Sample 53


title: Islet cell Sample 54


title: Islet cell Sample 65


title: Islet cell Sample 52


title: PAPERCLIP for si-CFIm68 in LN229, replicate 2

description: Index 5: AGTC


title: Islet cell Sample 51


title: PAPERCLIP for si-Ctrl in LN229, replicate 2

description: Index 6: GACT


title: Islet cell Sample 50


title: Islet cell Sample 44


title: Islet cell Sample 48


title: Islet cell Sample 47


title: Islet cell Sample 42


title: Islet cell Sample 46


title: Islet cell Sample 39


title: Islet cell Sample 38


title: Islet cell Sample 35


title: Islet cell Sample 34


title: Islet cell Sample 45


title: Islet cell Sample 37


title: Islet cell Sample 41


title: Islet cell Sample 40


title: Islet cell Sample 55


title: Islet cell Sample 32


title: Islet cell Sample 36


title: Islet cell Sample 30


title: Islet cell Sample 31


title: Islet cell Sample 28


title: Islet cell Sample 29


title: Islet cell Sample 26


title: Islet cell Sample 27


title: Islet cell Sample 25


title: Islet cell Sample 49


title: Islet cell Sample 24


title: Islet cell Sample 43


title: Islet cell Sample 23


title: Islet cell Sample 22


title: Islet cell Sample 21


title: Islet cell Sample 20


title: Islet cell Sample 17


title: Islet cell Sample 19


title: Islet cell Sample 18


title: Islet cell Sample 16


title: Islet cell Sample 12


title: Islet cell Sample 33


title: Islet cell Sample 15


title: Islet cell Sample 11


title: Islet cell Sample 14


title: Islet cell Sample 13


title: whole plant_Drought_Black Hills (Sample 195)

city: SPEARFISH

first: Gunbharpur

middle: Singh

last: Gill

state: SOUTH DAKOTA

address: 1200 UNIVERSITY STREET

department: SCHOOL OF NATURAL SCIENCES

institute: BLACK HILLS STATE UNIVERSITY

description:
150813HiSeq_Run_Sample_195_BHSU_Siemens_ATTCCT_L004_R1_001_fastqc
genes.sorted_by_expression.sig-3_1.txt
genes.sorted_by_expression.sig-4_3.txt
genes.sorted_by_expression.sig-4_3_NH.txt

data_processing:
FastQC_0.10.1 was used to check the quality
Tophat2 tool were used to map the reads with the reference
Cufflinks2 and Cuffmerge2 were used to build and merge the transcripts
Cuffdiff2 were used to examine the differential expression of genes due to comparison of treatment with control
Genome_build: Bstricta_278_v1.2.transcript.fa (linked as supplementary file on Series record)
Supplementary_files_format_and_content: .txt files report FPKMS and fold_change

organism: Boechera stricta

source_name: whole plant, Drought, Black Hills

growth_protocol: There were 256 plants total in the experiment distributed among eight flats, each containing 32 pots. We used two uniparental lines per population, and we randomized eight replicates of each line within each flat (2 pops/flat x 2 lines/pop x 8 plants/line = 32 plants/flat).  Seeds were planted in 0.2L pots filled with a soil mix of 2/3 Premier ProMix BX and 1/3 sand.  Pots also contained 45.78 mg of 7:40:6 NPK MagAmp time release fertilizer.  Plants were grown in a BioChambers growth room with a 16/8 hr D/N photoperiod and 23/21 oC D/N temperatures. Light intensity was 360µmoles/m²/s from a combination of 1220mm T5HO fluorescent and halogen lamps.

extract_protocol:
QIAGEN RNeasy Mini Kit was used for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: Drought

tag: population

value: Black Hills

value: whole plant


title: whole plant_Control_Black Hills (Sample 170)

description:
150813HiSeq_Run_Sample_170_BHSU_Siemens_CGTACG_L004_R1_001_fastqc
genes.sorted_by_expression.sig-4_1.txt
genes.sorted_by_expression.sig-4_3.txt
genes.sorted_by_expression.sig-4_3_NH.txt
genes.sorted_by_expression.sig_4_2.txt
genes.sorted_by_expression.sig4_2NH.txt

source_name: whole plant, Control, Black Hills

value: Control


title: whole plant_Drought_Black Hills (Sample 131)

description:
150813HiSeq_Run_Sample_131_BHSU_Siemens_GTTTCG_L004_R1_001_fastqc
genes.sorted_by_expression.sig-3_1.txt
genes.sorted_by_expression.sig-4_3.txt
genes.sorted_by_expression.sig-4_3_NH.txt


title: whole plant_Drought_Big Horns (Sample 139)

description:
150813HiSeq_Run_Sample_139_BHSU_Siemens_CCGTCC_L003_R1_001_fastqc
genes.sorted_by_expression.sig-3_1.txt
genes.sorted_by_expression.sig-4_3.txt
genes.sorted_by_expression.sig-4_3_BH.txt

source_name: whole plant, Drought, Big Horns

value: Big Horns


title: whole plant_Herbivory_Black Hills (Sample 106)

description:
150813HiSeq_Run_Sample_106_BHSU_Siemens_GTGGCC_L004_R1_001_fastqc
genes.sorted_by_expression.sig-2_1.txt
genes.sorted_by_expression.sig_4_2.txt
genes.sorted_by_expression.sig4_2NH.txt

source_name: whole plant, Herbivory, Black Hills

value: Herbivory


title: Islet cell Sample 9

value: Pancreatic islets

value: wild type


title: whole plant_Drought_Big Horns (Sample 200)

description:
150813HiSeq_Run_Sample_200_BHSU_Siemens_GTCCGC_L003_R1_001_fastqc
genes.sorted_by_expression.sig-3_1.txt
genes.sorted_by_expression.sig-4_3.txt
genes.sorted_by_expression.sig-4_3_BH.txt


title: Islet cell Sample 7


title: whole plant_Herbivory_Big Horns (Sample 110)

description:
150813HiSeq_Run_Sample_110_BHSU_Siemens_ATGTCA_L003_R1_001_fastqc
genes.sorted_by_expression.sig-2_1.txt
genes.sorted_by_expression.sig_4_2.txt
genes.sorted_by_expression.sig4_2BH.txt

source_name: whole plant, Herbivory, Big Horns


title: Islet cell Sample 8


title: whole plant_Both Drought and Herbivory_Big Horns (Sample 84)

description:
150813HiSeq_Run_Sample_84_BHSU_Siemens_AGTTCC_L003_R1_001_fastqc
genes.sorted_by_expression.sig-2_1.txt
genes.sorted_by_expression.sig-3_1.txt
genes.sorted_by_expression.sig-4_1.txt

source_name: whole plant, Both Drought and Herbivory, Big Horns

value: Both Drought and Herbivory


title: whole plant_Both Drought and Herbivory_Big Horns (Sample 79)

description:
150813HiSeq_Run_Sample_79_BHSU_Siemens_AGTCAA_L003_R1_001_fastqc
genes.sorted_by_expression.sig-2_1.txt
genes.sorted_by_expression.sig-3_1.txt
genes.sorted_by_expression.sig-4_1.txt


title: Islet cell Sample 6


title: whole plant_Both Drought and Herbivory_Black Hills (Sample 72)

description:
150813HiSeq_Run_Sample_72_BHSU_Siemens_GTGAAA_L004_R1_001_fastqc
genes.sorted_by_expression.sig-2_1.txt
genes.sorted_by_expression.sig-3_1.txt
genes.sorted_by_expression.sig-4_1.txt

source_name: whole plant, Both Drought and Herbivory, Black Hills


title: Islet cell Sample 5


title: Islet cell Sample 4


title: whole plant_Control_Big Horns (Sample 45)

description:
150813HiSeq_Run_Sample_45_BHSU_Siemens_CTTGTA_L003_R1_001_fastqc
genes.sorted_by_expression.sig-4_1.txt
genes.sorted_by_expression.sig-4_3.txt
genes.sorted_by_expression.sig-4_3_BH.txt
genes.sorted_by_expression.sig_4_2.txt
genes.sorted_by_expression.sig4_2BH.txt

source_name: whole plant, Control, Big Horns


title: Islet cell Sample 3


title: whole plant_Both Drought and Herbivory_Big Horns (Sample 20)

description:
150813HiSeq_Run_Sample_20_BHSU_Siemens_CAGATC_L003_R1_001_fastqc
genes.sorted_by_expression.sig-2_1.txt
genes.sorted_by_expression.sig-3_1.txt
genes.sorted_by_expression.sig-4_1.txt


title: Islet cell Sample 1


title: whole plant_Both Drought and Herbivory_Black Hills (Sample 18)

description:
150813HiSeq_Run_Sample_18_BHSU_Siemens_GTCCGC_L004_R1_001_fastqc
genes.sorted_by_expression.sig-2_1.txt
genes.sorted_by_expression.sig-3_1.txt
genes.sorted_by_expression.sig-4_1.txt


title: Islet cell Sample 10


title: Baudin 48 h

status: Public on Feb 18 2016

city: South Perth

first: Qisen

last: Zhang

state: WA

address: 3 naron Hay Court

country: Australia

institute: Australian Export Grain Innovation Center

description: Baudin 48h

data_processing:
Raw sequencing reads were filtered to clean dirty reads and aligned to reference sequences (Mayer et al., 2012) by using SOAPaligner/SOAP2 (Li et al., 2009)
The transcript levels were expressed by reads per kilo base transcriptome per million mapped reads (RPKM)
SOAPsplice software was used for alternative splicing analysis (read 1 mate-pairs only).
Reference genome used: ASM32608v1
Supplementary_files_format_and_content: Barley_Embryo_RNA_seq_Processed.xlsx includes transcript levels (RPKM) values for each Sample
Supplementary_files_format_and_content: BarleySeqMergedForAS.fa: Used for mapping alternative splicing sites on the sequences

organism: Hordeum vulgare subsp. vulgare

source_name: Germinating seeds

growth_protocol: Seed germinating at 21 oC in dark

extract_protocol:
Total RNA was extracted and mRNA was isolated by oligodT column as described by manufactory
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: varieties

value: Baudin


title: Stirling 48 h

description: Stirling 48h

value: Stirling


title: Islet cell Sample 2


title: Baudin 24 h

description: Baudin 24h


title: Stirling 24 h

description: Stirling 24h


title: Harrington 24 h

description: Harrington 24h

value: Harrington


title: Bass 48 h

description: Bass 48h

value: Bass


title: Harrington 48 h

description: Harrington 48h


title: Metazome_Annelida_timecourse_sample_0091

city: Haifa

first: Itai

last: Yanai

address: Technion City

country: Israel

institute: Technion - Israel Institute of Technology

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against Pdum_transcriptome_v1
Read counting with htseq-count version 0.5.4p3.
Genome_build: Pdum_transcriptome_v1 (NCBI BioProject PRJNA271451)
Supplementary_files_format_and_content: tabular expression matrix

organism: Platynereis dumerilii

source_name: single embryo 91

growth_protocol: Platynereis dumerilii embryos were collected by ML and NM at the lab of Detlev Arendt (EMBL Heidelberg, Germany). In each of several containers, a gravid male and a female were mixed in a small container containing North Sea water. The classical breeding dance was observed after several minutes and the females and males released oocytes and sperm. Fertilized eggs were incubated at 18°C and embryos were collected every hour after fertilization for a period of 5 days. Individual embryos were collected on the cap of a 1.5 ml Eppendorf tube using a micro-mouth pipette. Excessive water was removed and the sample was flash-frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps.
The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used.

tag: time (minutes after fertilization)

value: whole embryo


title: Metazome_Annelida_timecourse_sample_0095

source_name: single embryo 95


title: Metazome_Annelida_timecourse_sample_0097

source_name: single embryo 97


title: Metazome_Annelida_timecourse_sample_0093

source_name: single embryo 93


title: Bass 24 h

description: Bass 24h


title: Metazome_Annelida_timecourse_sample_0094

source_name: single embryo 94


title: Metazome_Annelida_timecourse_sample_0087

source_name: single embryo 87


title: Metazome_Annelida_timecourse_sample_0088

source_name: single embryo 88


title: Metazome_Annelida_timecourse_sample_0089

source_name: single embryo 89


title: Metazome_Annelida_timecourse_sample_0096

source_name: single embryo 96


title: Metazome_Annelida_timecourse_sample_0086

source_name: single embryo 86


title: Metazome_Annelida_timecourse_sample_0084

source_name: single embryo 84


title: Metazome_Annelida_timecourse_sample_0083

source_name: single embryo 83


title: Metazome_Annelida_timecourse_sample_0085

source_name: single embryo 85


title: Metazome_Annelida_timecourse_sample_0082

source_name: single embryo 82


title: Metazome_Annelida_timecourse_sample_0079

source_name: single embryo 79


title: Metazome_Annelida_timecourse_sample_0081

source_name: single embryo 81


title: Metazome_Annelida_timecourse_sample_0078

source_name: single embryo 78


title: Metazome_Annelida_timecourse_sample_0092

source_name: single embryo 92


title: Metazome_Annelida_timecourse_sample_0076

source_name: single embryo 76


title: Metazome_Annelida_timecourse_sample_0090

source_name: single embryo 90


title: Metazome_Annelida_timecourse_sample_0077

source_name: single embryo 77


title: Metazome_Annelida_timecourse_sample_0073

source_name: single embryo 73


title: Metazome_Annelida_timecourse_sample_0075

source_name: single embryo 75


title: Metazome_Annelida_timecourse_sample_0071

source_name: single embryo 71


title: Metazome_Annelida_timecourse_sample_0065

source_name: single embryo 65


title: Metazome_Annelida_timecourse_sample_0067

source_name: single embryo 67


title: Metazome_Annelida_timecourse_sample_0066

source_name: single embryo 66


title: Metazome_Annelida_timecourse_sample_0068

source_name: single embryo 68


title: Metazome_Annelida_timecourse_sample_0069

source_name: single embryo 69


title: Metazome_Annelida_timecourse_sample_0070

source_name: single embryo 70


title: Metazome_Annelida_timecourse_sample_0064

source_name: single embryo 64


title: Metazome_Annelida_timecourse_sample_0061

source_name: single embryo 61


title: Metazome_Annelida_timecourse_sample_0080

source_name: single embryo 80


title: Metazome_Annelida_timecourse_sample_0062

source_name: single embryo 62


title: Metazome_Annelida_timecourse_sample_0057

source_name: single embryo 57


title: Metazome_Annelida_timecourse_sample_0056

source_name: single embryo 56


title: Metazome_Annelida_timecourse_sample_0055

source_name: single embryo 55


title: Metazome_Annelida_timecourse_sample_0054

source_name: single embryo 54


title: Metazome_Annelida_timecourse_sample_0060

source_name: single embryo 60


title: Metazome_Annelida_timecourse_sample_0053

source_name: single embryo 53


title: Metazome_Annelida_timecourse_sample_0050

source_name: single embryo 50


title: Metazome_Annelida_timecourse_sample_0072

source_name: single embryo 72


title: Metazome_Annelida_timecourse_sample_0052

source_name: single embryo 52


title: Metazome_Annelida_timecourse_sample_0049

source_name: single embryo 49


title: Metazome_Annelida_timecourse_sample_0048

source_name: single embryo 48


title: Metazome_Annelida_timecourse_sample_0074

source_name: single embryo 74


title: Metazome_Annelida_timecourse_sample_0051

source_name: single embryo 51


title: Metazome_Annelida_timecourse_sample_0047

source_name: single embryo 47


title: Metazome_Annelida_timecourse_sample_0063

source_name: single embryo 63


title: Metazome_Annelida_timecourse_sample_0045

source_name: single embryo 45


title: Metazome_Annelida_timecourse_sample_0044

source_name: single embryo 44


title: Metazome_Annelida_timecourse_sample_0046

source_name: single embryo 46


title: Metazome_Annelida_timecourse_sample_0041

source_name: single embryo 41


title: Metazome_Annelida_timecourse_sample_0042

source_name: single embryo 42


title: Metazome_Annelida_timecourse_sample_0040

source_name: single embryo 40


title: Metazome_Annelida_timecourse_sample_0039

source_name: single embryo 39


title: Metazome_Annelida_timecourse_sample_0058

source_name: single embryo 58


title: Metazome_Annelida_timecourse_sample_0059

source_name: single embryo 59


title: Metazome_Annelida_timecourse_sample_0036

source_name: single embryo 36


title: Metazome_Annelida_timecourse_sample_0035

source_name: single embryo 35


title: Metazome_Annelida_timecourse_sample_0033

source_name: single embryo 33


title: Metazome_Annelida_timecourse_sample_0038

source_name: single embryo 38


title: Metazome_Annelida_timecourse_sample_0034

source_name: single embryo 34


title: Metazome_Annelida_timecourse_sample_0031

source_name: single embryo 31


title: Metazome_Annelida_timecourse_sample_0030

source_name: single embryo 30


title: Metazome_Annelida_timecourse_sample_0027

source_name: single embryo 27


title: Metazome_Annelida_timecourse_sample_0024

source_name: single embryo 24


title: Metazome_Annelida_timecourse_sample_0029

source_name: single embryo 29


title: Metazome_Annelida_timecourse_sample_0043

source_name: single embryo 43


title: Metazome_Annelida_timecourse_sample_0021

source_name: single embryo 21


title: Metazome_Annelida_timecourse_sample_0023

source_name: single embryo 23


title: Metazome_Annelida_timecourse_sample_0019

source_name: single embryo 19


title: Metazome_Annelida_timecourse_sample_0022

source_name: single embryo 22


title: Metazome_Annelida_timecourse_sample_0026

source_name: single embryo 26


title: Metazome_Annelida_timecourse_sample_0013

source_name: single embryo 13


title: Metazome_Annelida_timecourse_sample_0016

source_name: single embryo 16


title: Metazome_Annelida_timecourse_sample_0014

source_name: single embryo 14


title: Metazome_Annelida_timecourse_sample_0018

source_name: single embryo 18


title: Metazome_Annelida_timecourse_sample_0011

source_name: single embryo 11


title: Metazome_Annelida_timecourse_sample_0037

source_name: single embryo 37


title: Metazome_Annelida_timecourse_sample_0012

source_name: single embryo 12


title: Metazome_Annelida_timecourse_sample_0017

source_name: single embryo 17


title: Metazome_Annelida_timecourse_sample_0020

source_name: single embryo 20


title: Metazome_Annelida_timecourse_sample_0009

source_name: single embryo 9


title: Metazome_Annelida_timecourse_sample_0032

source_name: single embryo 32


title: Metazome_Annelida_timecourse_sample_0010

source_name: single embryo 10


title: Metazome_Annelida_timecourse_sample_0015

source_name: single embryo 15


title: Metazome_Annelida_timecourse_sample_0008

source_name: single embryo 8


title: Metazome_Annelida_timecourse_sample_0007

source_name: single embryo 7


title: Metazome_Annelida_timecourse_sample_0005

source_name: single embryo 5


title: Metazome_Annelida_timecourse_sample_0028

source_name: single embryo 28


title: Metazome_Annelida_timecourse_sample_0004

source_name: single embryo 4


title: Metazome_Annelida_timecourse_sample_0006

source_name: single embryo 6


title: Metazome_Annelida_timecourse_sample_0003

source_name: single embryo 3


title: Metazome_Annelida_timecourse_sample_0025

source_name: single embryo 25


title: Metazome_Annelida_timecourse_sample_0002

source_name: single embryo 2


title: Metazome_NV_timecourse_sample_0121

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0
Read counting with htseq-count version 0.5.4p3.
Genome_build: Nematostella Reference transcriptome Nv.T1 from http://cnidarians.bu.edu/stellabase/assembly/NvT1.fasta
Supplementary_files_format_and_content: Read counting

organism: Nematostella vectensis

source_name: single embryo 121

growth_protocol: Eggs and sperms were mixed and egg jelly was dissolved as previously described43 using 4% cysteine (pH 7.4–7.6) to make single embryos accessible for collection. The embryos were washed of cysteine six times using 30% of sea water. Fertilized embryos were observed under light microscope and embryos reaching 4-cell stage were deposited in a 10ul drop of 30% salt water on the cap of a 1.5ml Eppendorf tube. Tubes were closed and incubated for respective periods at 20°C. At collection timings embryos were inspected for viability and excessive water was removed using a micro-mouthpipette. The embryo was then flash-frozen in liquid nitrogen. Stages ranged from 4-cell stage and every 20 minutes for up to 48 hours when embryos reached the late planula stage.

extract_protocol:
Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps.
The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. The library was treated with DSN treatment

tag: time point


title: Metazome_NV_timecourse_sample_0123

source_name: single embryo 123


title: Metazome_NV_timecourse_sample_0120

source_name: single embryo 120


title: Metazome_NV_timecourse_sample_0118

source_name: single embryo 118


title: Metazome_NV_timecourse_sample_0119

source_name: single embryo 119


title: Metazome_NV_timecourse_sample_0117

source_name: single embryo 117


title: Metazome_NV_timecourse_sample_0122

source_name: single embryo 122


title: Metazome_NV_timecourse_sample_0113

source_name: single embryo 113


title: Metazome_NV_timecourse_sample_0114

source_name: single embryo 114


title: Metazome_NV_timecourse_sample_0116

source_name: single embryo 116


title: Metazome_NV_timecourse_sample_0112

source_name: single embryo 112


title: Metazome_NV_timecourse_sample_0115

source_name: single embryo 115


title: Metazome_NV_timecourse_sample_0109

source_name: single embryo 109


title: Metazome_NV_timecourse_sample_0107

source_name: single embryo 107


title: Metazome_NV_timecourse_sample_0108

source_name: single embryo 108


title: Metazome_NV_timecourse_sample_0111

source_name: single embryo 111


title: Metazome_NV_timecourse_sample_0105

source_name: single embryo 105


title: Metazome_NV_timecourse_sample_0110

source_name: single embryo 110


title: Metazome_NV_timecourse_sample_0104

source_name: single embryo 104


title: Metazome_NV_timecourse_sample_0102

source_name: single embryo 102


title: Metazome_NV_timecourse_sample_0103

source_name: single embryo 103


title: Metazome_NV_timecourse_sample_0100

source_name: single embryo 100


title: Metazome_NV_timecourse_sample_0099

source_name: single embryo 99


title: Metazome_NV_timecourse_sample_0097

source_name: single embryo 97


title: Metazome_NV_timecourse_sample_0098

source_name: single embryo 98


title: Metazome_Annelida_timecourse_sample_0001

source_name: single embryo 1


title: Metazome_NV_timecourse_sample_0106

source_name: single embryo 106


title: Metazome_NV_timecourse_sample_0101

source_name: single embryo 101


title: Metazome_NV_timecourse_sample_0095

source_name: single embryo 95


title: Metazome_NV_timecourse_sample_0096

source_name: single embryo 96


title: Metazome_NV_timecourse_sample_0092

source_name: single embryo 92


title: Metazome_NV_timecourse_sample_0094

source_name: single embryo 94


title: Metazome_NV_timecourse_sample_0091

source_name: single embryo 91


title: Metazome_NV_timecourse_sample_0089

source_name: single embryo 89


title: Metazome_NV_timecourse_sample_0090

source_name: single embryo 90


title: Metazome_NV_timecourse_sample_0087

source_name: single embryo 87


title: Metazome_NV_timecourse_sample_0085

source_name: single embryo 85


title: Metazome_NV_timecourse_sample_0086

source_name: single embryo 86


title: Metazome_NV_timecourse_sample_0082

source_name: single embryo 82


title: Metazome_NV_timecourse_sample_0083

source_name: single embryo 83


title: Metazome_NV_timecourse_sample_0093

source_name: single embryo 93


title: Metazome_NV_timecourse_sample_0080

source_name: single embryo 80


title: Metazome_NV_timecourse_sample_0077

source_name: single embryo 77


title: Metazome_NV_timecourse_sample_0075

source_name: single embryo 75


title: Metazome_NV_timecourse_sample_0078

source_name: single embryo 78


title: Metazome_NV_timecourse_sample_0073

source_name: single embryo 73


title: Metazome_NV_timecourse_sample_0088

source_name: single embryo 88


title: Metazome_NV_timecourse_sample_0079

source_name: single embryo 79


title: Metazome_NV_timecourse_sample_0069

source_name: single embryo 69


title: Metazome_NV_timecourse_sample_0068

source_name: single embryo 68


title: Metazome_NV_timecourse_sample_0084

source_name: single embryo 84


title: Metazome_NV_timecourse_sample_0074

source_name: single embryo 74


title: Metazome_NV_timecourse_sample_0076

source_name: single embryo 76


title: Metazome_NV_timecourse_sample_0072

source_name: single embryo 72


title: Metazome_NV_timecourse_sample_0067

source_name: single embryo 67


title: Metazome_NV_timecourse_sample_0071

source_name: single embryo 71


title: Metazome_NV_timecourse_sample_0064

source_name: single embryo 64


title: Metazome_NV_timecourse_sample_0066

source_name: single embryo 66


title: Metazome_NV_timecourse_sample_0060

source_name: single embryo 60


title: Metazome_NV_timecourse_sample_0065

source_name: single embryo 65


title: Metazome_NV_timecourse_sample_0081

source_name: single embryo 81


title: Metazome_NV_timecourse_sample_0061

source_name: single embryo 61


title: Metazome_NV_timecourse_sample_0062

source_name: single embryo 62


title: Metazome_NV_timecourse_sample_0058

source_name: single embryo 58


title: Metazome_NV_timecourse_sample_0059

source_name: single embryo 59


title: Metazome_NV_timecourse_sample_0063

source_name: single embryo 63


title: Metazome_NV_timecourse_sample_0057

source_name: single embryo 57


title: Metazome_NV_timecourse_sample_0052

source_name: single embryo 52


title: Metazome_NV_timecourse_sample_0056

source_name: single embryo 56


title: Metazome_NV_timecourse_sample_0054

source_name: single embryo 54


title: Metazome_NV_timecourse_sample_0053

source_name: single embryo 53


title: Metazome_NV_timecourse_sample_0050

source_name: single embryo 50


title: Metazome_NV_timecourse_sample_0051

source_name: single embryo 51


title: Metazome_NV_timecourse_sample_0047

source_name: single embryo 47


title: Metazome_NV_timecourse_sample_0048

source_name: single embryo 48


title: Metazome_NV_timecourse_sample_0070

source_name: single embryo 70


title: Metazome_NV_timecourse_sample_0049

source_name: single embryo 49


title: Metazome_NV_timecourse_sample_0046

source_name: single embryo 46


title: Metazome_NV_timecourse_sample_0045

source_name: single embryo 45


title: Metazome_NV_timecourse_sample_0043

source_name: single embryo 43


title: Metazome_NV_timecourse_sample_0044

source_name: single embryo 44


title: Metazome_NV_timecourse_sample_0042

source_name: single embryo 42


title: Metazome_NV_timecourse_sample_0039

source_name: single embryo 39


title: Metazome_NV_timecourse_sample_0040

source_name: single embryo 40


title: Metazome_NV_timecourse_sample_0038

source_name: single embryo 38


title: Metazome_NV_timecourse_sample_0041

source_name: single embryo 41


title: Metazome_NV_timecourse_sample_0037

source_name: single embryo 37


title: Metazome_NV_timecourse_sample_0036

source_name: single embryo 36


title: Metazome_NV_timecourse_sample_0035

source_name: single embryo 35


title: Metazome_NV_timecourse_sample_0055

source_name: single embryo 55


title: Metazome_NV_timecourse_sample_0032

source_name: single embryo 32


title: Metazome_NV_timecourse_sample_0034

source_name: single embryo 34


title: Metazome_NV_timecourse_sample_0033

source_name: single embryo 33


title: Metazome_NV_timecourse_sample_0031

source_name: single embryo 31


title: Metazome_NV_timecourse_sample_0024

source_name: single embryo 24


title: Metazome_NV_timecourse_sample_0028

source_name: single embryo 28


title: Metazome_NV_timecourse_sample_0029

source_name: single embryo 29


title: Metazome_NV_timecourse_sample_0030

source_name: single embryo 30


title: Metazome_NV_timecourse_sample_0022

source_name: single embryo 22


title: Metazome_NV_timecourse_sample_0020

source_name: single embryo 20


title: Metazome_NV_timecourse_sample_0019

source_name: single embryo 19


title: Metazome_NV_timecourse_sample_0021

source_name: single embryo 21


title: Metazome_NV_timecourse_sample_0018

source_name: single embryo 18


title: Metazome_NV_timecourse_sample_0023

source_name: single embryo 23


title: Metazome_NV_timecourse_sample_0017

source_name: single embryo 17


title: Metazome_NV_timecourse_sample_0016

source_name: single embryo 16


title: Metazome_NV_timecourse_sample_0015

source_name: single embryo 15


title: Metazome_NV_timecourse_sample_0014

source_name: single embryo 14


title: Metazome_NV_timecourse_sample_0012

source_name: single embryo 12


title: Metazome_NV_timecourse_sample_0011

source_name: single embryo 11


title: Metazome_NV_timecourse_sample_0010

source_name: single embryo 10


title: Metazome_NV_timecourse_sample_0008

source_name: single embryo 8


title: Metazome_NV_timecourse_sample_0009

source_name: single embryo 9


title: Metazome_NV_timecourse_sample_0005

source_name: single embryo 5


title: Metazome_NV_timecourse_sample_0007

source_name: single embryo 7


title: Metazome_NV_timecourse_sample_0006

source_name: single embryo 6


title: Metazome_NV_timecourse_sample_0003

source_name: single embryo 3


title: Metazome_NV_timecourse_sample_0004

source_name: single embryo 4


title: Metazome_NV_timecourse_sample_0026

source_name: single embryo 26


title: Metazome_NV_timecourse_sample_0025

source_name: single embryo 25


title: Metazome_NV_timecourse_sample_0027

source_name: single embryo 27


title: Metazome_NV_timecourse_sample_0002

source_name: single embryo 2


title: Metazome_NV_timecourse_sample_0013

source_name: single embryo 13


title: Metazome_ML1_sample_0031

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against MlScaffold09
Read counting with htseq-count version 0.5.4p3. on annotations evm2.2
Genome_build: MlScaffold09 [http://research.nhgri.nih.gov/mnemiopsis/download/download.cgi?dl=genome; http://research.nhgri.nih.gov/mnemiopsis/download/proteome/ML2.2.gff3.gz (http://www.sciencemag.org/content/342/6164/1242592.full.pdf?keytype=ref&siteid=sci&ijkey=yaMBwY%2FafqQpk)]
Supplementary_files_format_and_content: ML_exp.tab is a tabular Expression matrix

organism: Mnemiopsis leidyi

source_name: single embryo 31

extract_protocol:
Total RNA was extracted from single embryos using trizol as described in (Levin et al. Developmental cell 2012) including minor adjustments. After the addition of trizol to the embryos the mixture was frozen in liquid nitrogen, thawed at 37 degrees and vortexed for 30 seconds. This procedure was repeated five times. Only then chloroform was added and the sample further processed. Dried total RNA pellet was dissolved in RNAse free water before introduction into subsequent amplification and sequencing library preparation steps.
The CEL-Seq protocol (Hashimshony, et al. Cell reports 2012) was used to amplify and sequence RNA from whole embryos. CEL-seq multiplexing barocdes were used. A slightly different set of barcodes was used that includes Unique Molecular Identifier.

tag: developmental time (hours)


title: Metazome_ML1_sample_0032

source_name: single embryo 32


title: Metazome_ML1_sample_0040

source_name: single embryo 40


title: Metazome_ML1_sample_0034

source_name: single embryo 34


title: Metazome_ML1_sample_0030

source_name: single embryo 30


title: Metazome_ML1_sample_0035

source_name: single embryo 35


title: Metazome_ML1_sample_0037

source_name: single embryo 37


title: Metazome_ML1_sample_0033

source_name: single embryo 33


title: Metazome_ML1_sample_0039

source_name: single embryo 39


title: Metazome_ML1_sample_0029

source_name: single embryo 29


title: Metazome_ML1_sample_0028

source_name: single embryo 28


title: Metazome_ML1_sample_0027


title: Metazome_ML1_sample_0024

source_name: single embryo 24


title: Metazome_ML1_sample_0025


title: Metazome_NV_timecourse_sample_0001

source_name: single embryo 1


title: Metazome_ML1_sample_0018

source_name: single embryo 18


title: Metazome_ML1_sample_0038

source_name: single embryo 38


title: Metazome_ML1_sample_0015

source_name: single embryo 15


title: Metazome_ML1_sample_0023

source_name: single embryo 23


title: Metazome_ML1_sample_0022

source_name: single embryo 22


title: Metazome_ML1_sample_0017

source_name: single embryo 17


title: Metazome_ML1_sample_0021

source_name: single embryo 21


title: Metazome_ML1_sample_0020

source_name: single embryo 20


title: Metazome_ML1_sample_0019

source_name: single embryo 19


title: Metazome_ML1_sample_0014

source_name: single embryo 14


title: Metazome_ML1_sample_0013

source_name: single embryo 13


title: Metazome_ML1_sample_0036

source_name: single embryo 36


title: Metazome_ML1_sample_0016

source_name: single embryo 16


title: Metazome_ML1_sample_0012

source_name: single embryo 12


title: Metazome_ML1_sample_0026

source_name: single embryo 26


title: Metazome_ML1_sample_0010

source_name: single embryo 10


title: Metazome_ML1_sample_0011

source_name: single embryo 11


title: Metazome_ML1_sample_0009

source_name: single embryo 9


title: Metazome_ML1_sample_0001

source_name: single embryo 1


title: Metazome_ML1_sample_0006

source_name: single embryo 6


title: Metazome_ML1_sample_0007

source_name: single embryo 7