title: Metazome_ML1_sample_0005

source_name: single embryo 5


title: Metazome_ML1_sample_0004

status: Public on Feb 18 2016

type: SRA

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

library_source: transcriptomic

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

molecule: total RNA

organism: Mnemiopsis leidyi

source_name: single embryo 4

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_0008

source_name: single embryo 8


title: Metazome_ML1_sample_0002

source_name: single embryo 2


title: 4 hr TP-0903 Rep 4

city: Salt Lake City

first: Rodney

last: Stewart

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

country: USA

institute: University of Utah

description: 4 hr treatment: 8 somite (13 hpf) - 16 somite (17 hpf)

data_processing:
Reads were aligned to zv9 chromosome sequence + splice junction sequences using Novoalign (v2.08.03), allowing up to 50 alignments for each read. Splice junctions were created by running USeq (v8.8.1) MakeTranscriptome application using Ensembl transcript annotations.
The resulting alignment file was processed with the USeq (v8.8.1) application SamTranscriptomeParser, which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities.  SamTranscriptomeParser also converts splice junction alignment coordinates back to genomic space.
USeq's DefinedRegionDifferentialSeq application was used to determine differentially expressed genes.  The application determines the number of reads aligning to each gene and runs DESeq2 (v1.4.5) on the resulting count table.
Genome_build: zv9
Supplementary_files_format_and_content: tab-delimited file containing Ensembl Ids, log2 fold change, -10 * log10(adjusted p-value), raw counts and FPKMs

organism: Danio rerio

source_name: 35 whole zebrafish embryos

extract_protocol:
RNA was harvested using Qiagen RNeasy kit (Cat # 74104). Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip.
RNA-Seq libraries prepared using illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero (Cat # RS-122-2401).
Sequencing was performed on Illumina HiSeq 2000 and Illumina HiSeq 2500 using 50 cycle single-read sequencing v3 kit (Cat # FC-401-3002).

tag: strain

tag: developmental stage

value: 16 somites (17 hpf)


title: 4 hr DMSO Rep 4


title: 1 hr TP-0903 Rep 2

description: 1 hr treatment: 8 somite (13 hpf) - 10 somite (14 hpf)

value: 10 somites (14 hpf)


title: 4 hr DMSO Rep 2


title: 1 hr DMSO Rep 4


title: 1 hr TP-0903 Rep 3


title: 4 hr DMSO Rep 1


title: 4 hr TP-0903 Rep 1


title: 4 hr DMSO Rep 3


title: 1 hr TP-0903 Rep 1


title: 4 hr TP-0903 Rep 3


title: 1 hr DMSO Rep 1


title: 1 hr DMSO Rep 3


title: 1 hr DMSO Rep 2


title: Metazome_ZF_timecourse_sample_0105

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 Zv9 genome
Read counting with htseq-count version 0.5.4p3. Using on Ensemble Zv9 annotations
Genome_build: Zv9
Supplementary_files_format_and_content: tabular Expression matrix

molecule: polyA RNA

source_name: single embryo

growth_protocol: zebrafish fertilization was performed in the lab of Karina Yaniv (Weizmann Institute, Israel). Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. After females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in (REF). Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro-mouthpipette and the embryo flash frozen in liquid nitrogen.

extract_protocol:
RNA was isolated using TRIzol as previously described (Levin et al., 2012).
The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.

tag: time (min after fertilization)


title: Metazome_ML1_sample_0003

source_name: single embryo 3


title: Metazome_ZF_timecourse_sample_0106


title: Metazome_ZF_timecourse_sample_0103


title: Metazome_ZF_timecourse_sample_0102


title: Metazome_ZF_timecourse_sample_0101


title: Metazome_ZF_timecourse_sample_0100


title: 4 hr TP-0903 Rep 2


title: Metazome_ZF_timecourse_sample_0098


title: Metazome_ZF_timecourse_sample_0099


title: Metazome_ZF_timecourse_sample_0096


title: Metazome_ZF_timecourse_sample_0104


title: Metazome_ZF_timecourse_sample_0095


title: 1 hr TP-0903 Rep 4


title: Metazome_ZF_timecourse_sample_0094


title: Metazome_ZF_timecourse_sample_0093


title: Metazome_ZF_timecourse_sample_0092


title: Metazome_ZF_timecourse_sample_0087


title: Metazome_ZF_timecourse_sample_0091


title: Metazome_ZF_timecourse_sample_0088


title: Metazome_ZF_timecourse_sample_0089


title: Metazome_ZF_timecourse_sample_0086


title: Metazome_ZF_timecourse_sample_0090


title: Metazome_ZF_timecourse_sample_0083


title: Metazome_ZF_timecourse_sample_0085


title: Metazome_ZF_timecourse_sample_0080


title: Metazome_ZF_timecourse_sample_0082


title: Metazome_ZF_timecourse_sample_0084


title: Metazome_ZF_timecourse_sample_0081


title: Metazome_ZF_timecourse_sample_0097


title: Metazome_ZF_timecourse_sample_0079


title: Metazome_ZF_timecourse_sample_0076


title: Metazome_ZF_timecourse_sample_0078


title: Metazome_ZF_timecourse_sample_0072


title: Metazome_ZF_timecourse_sample_0073


title: Metazome_ZF_timecourse_sample_0071


title: Metazome_ZF_timecourse_sample_0077


title: Metazome_ZF_timecourse_sample_0075


title: Metazome_ZF_timecourse_sample_0070


title: Metazome_ZF_timecourse_sample_0069


title: Metazome_Platyhelminthes_timecourse_sample_0132

description: single embryo 132

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 BDGP5
Read counting with htseq-count version 0.5.4p3.
Genome_build: Spol_transcriptome_v1 (NCBI BioProject PRJNA271420)
Supplementary_files_format_and_content: expression matrix

organism: Schmidtea polychroa

source_name: stage 3_single embryo

growth_protocol: Schmidtea polychroa embryos were collected at the lab of Jochen Rink (Max Planck Institute CBG, Dresden, Germany). A population of S.polychroa was maintained in the lab at 20°C as described elsewhere (PMID 18942102). Egg capsules were regularly collected just after deposition and kept in Petri dishes at 20°C. Once at the desired time of development (evenly spread over 15 days of development), capsules were carefully opened using two fine forceps. Embryos were released from capsules and collected individually into eppendorf tubes. After assessment of stage of development (according to system established by Martin-Duran PMID 20100474) excess water was removed and embryos 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. The library was treated with DSN treatment

tag: time/developmental stage according to pmid 15599763

tag: tissue

value: single embryo


title: Metazome_Platyhelminthes_timecourse_sample_0130

description: single embryo 130


title: Metazome_Platyhelminthes_timecourse_sample_0131

description: single embryo 131


title: Metazome_ZF_timecourse_sample_0068


title: Metazome_Platyhelminthes_timecourse_sample_0129

description: single embryo 129


title: Metazome_ZF_timecourse_sample_0067


title: Metazome_ZF_timecourse_sample_0066


title: Metazome_ZF_timecourse_sample_0064


title: Metazome_Platyhelminthes_timecourse_sample_0126

description: single embryo 126


title: Metazome_ZF_timecourse_sample_0065


title: Metazome_Platyhelminthes_timecourse_sample_0127

description: single embryo 127


title: Metazome_Platyhelminthes_timecourse_sample_0124

description: single embryo 124


title: Metazome_ZF_timecourse_sample_0062


title: Metazome_ZF_timecourse_sample_0063


title: Metazome_ZF_timecourse_sample_0061


title: Metazome_Platyhelminthes_timecourse_sample_0122

description: single embryo 122


title: Metazome_Platyhelminthes_timecourse_sample_0123

description: single embryo 123


title: Metazome_ZF_timecourse_sample_0060


title: Metazome_Platyhelminthes_timecourse_sample_0121

description: single embryo 121


title: Metazome_ZF_timecourse_sample_0074


title: Metazome_ZF_timecourse_sample_0059


title: Metazome_Platyhelminthes_timecourse_sample_0119

description: single embryo 119

source_name: stage 2_single embryo


title: Metazome_ZF_timecourse_sample_0057


title: Metazome_Platyhelminthes_timecourse_sample_0118

description: single embryo 118


title: Metazome_ZF_timecourse_sample_0056


title: Metazome_ZF_timecourse_sample_0055


title: Metazome_Platyhelminthes_timecourse_sample_0128

description: single embryo 128


title: Metazome_ZF_timecourse_sample_0054


title: Metazome_Platyhelminthes_timecourse_sample_0117

description: single embryo 117


title: Metazome_Platyhelminthes_timecourse_sample_0116

description: single embryo 116


title: Metazome_Platyhelminthes_timecourse_sample_0115

description: single embryo 115


title: Metazome_Platyhelminthes_timecourse_sample_0120

description: single embryo 120


title: Metazome_ZF_timecourse_sample_0053


title: Metazome_ZF_timecourse_sample_0052


title: Metazome_Platyhelminthes_timecourse_sample_0114

description: single embryo 114


title: Metazome_Platyhelminthes_timecourse_sample_0125

description: single embryo 125


title: Metazome_Platyhelminthes_timecourse_sample_0113

description: single embryo 113


title: Metazome_Platyhelminthes_timecourse_sample_0112

description: single embryo 112


title: Metazome_ZF_timecourse_sample_0051


title: Metazome_ZF_timecourse_sample_0048


title: Metazome_Platyhelminthes_timecourse_sample_0110

description: single embryo 110


title: Metazome_ZF_timecourse_sample_0049


title: Metazome_Platyhelminthes_timecourse_sample_0108

description: single embryo 108

source_name: stage 1_single embryo


title: Metazome_Platyhelminthes_timecourse_sample_0109

description: single embryo 109


title: Metazome_ZF_timecourse_sample_0046


title: Metazome_ZF_timecourse_sample_0058


title: Metazome_Platyhelminthes_timecourse_sample_0106

description: single embryo 106

source_name: stage yolk_single embryo

value: yolk


title: Metazome_Platyhelminthes_timecourse_sample_0107

description: single embryo 107


title: Metazome_ZF_timecourse_sample_0043


title: Metazome_ZF_timecourse_sample_0044


title: Metazome_ZF_timecourse_sample_0045


title: Metazome_Platyhelminthes_timecourse_sample_0103

description: single embryo 103

source_name: stage 8_single embryo


title: Metazome_ZF_timecourse_sample_0041


title: Metazome_ZF_timecourse_sample_0042


title: Metazome_Platyhelminthes_timecourse_sample_0104

description: single embryo 104


title: Metazome_ZF_timecourse_sample_0038


title: Metazome_Platyhelminthes_timecourse_sample_0100

description: single embryo 100


title: Metazome_Platyhelminthes_timecourse_sample_0101

description: single embryo 101


title: Metazome_ZF_timecourse_sample_0040


title: Metazome_Platyhelminthes_timecourse_sample_0102

description: single embryo 102


title: Metazome_ZF_timecourse_sample_0050


title: Metazome_ZF_timecourse_sample_0037


title: Metazome_Platyhelminthes_timecourse_sample_0099

description: single embryo 99


title: Metazome_Platyhelminthes_timecourse_sample_0111

description: single embryo 111


title: Metazome_Platyhelminthes_timecourse_sample_0098

description: single embryo 98


title: Metazome_ZF_timecourse_sample_0047


title: Metazome_ZF_timecourse_sample_0034


title: Metazome_ZF_timecourse_sample_0035


title: Metazome_Platyhelminthes_timecourse_sample_0097

description: single embryo 97


title: Metazome_Platyhelminthes_timecourse_sample_0094

description: single embryo 94


title: Metazome_ZF_timecourse_sample_0032


title: Metazome_ZF_timecourse_sample_0036


title: Metazome_Platyhelminthes_timecourse_sample_0096

description: single embryo 96


title: Metazome_Platyhelminthes_timecourse_sample_0105

description: single embryo 105


title: Metazome_Platyhelminthes_timecourse_sample_0095

description: single embryo 95


title: Metazome_ZF_timecourse_sample_0030


title: Metazome_Platyhelminthes_timecourse_sample_0091

description: single embryo 91


title: Metazome_ZF_timecourse_sample_0029


title: Metazome_Platyhelminthes_timecourse_sample_0092

description: single embryo 92


title: Metazome_Platyhelminthes_timecourse_sample_0093

description: single embryo 93


title: Metazome_ZF_timecourse_sample_0039


title: Metazome_Platyhelminthes_timecourse_sample_0089

description: single embryo 89

source_name: stage 7_single embryo


title: Metazome_Platyhelminthes_timecourse_sample_0088

description: single embryo 88


title: Metazome_ZF_timecourse_sample_0025


title: Metazome_ZF_timecourse_sample_0027


title: Metazome_Platyhelminthes_timecourse_sample_0090

description: single embryo 90


title: Metazome_Platyhelminthes_timecourse_sample_0087

description: single embryo 87


title: Metazome_Platyhelminthes_timecourse_sample_0086

description: single embryo 86


title: Metazome_ZF_timecourse_sample_0024


title: Metazome_Platyhelminthes_timecourse_sample_0085

description: single embryo 85


title: Metazome_ZF_timecourse_sample_0033


title: Metazome_ZF_timecourse_sample_0021


title: Metazome_Platyhelminthes_timecourse_sample_0084

description: single embryo 84


title: Metazome_Platyhelminthes_timecourse_sample_0083

description: single embryo 83


title: Metazome_ZF_timecourse_sample_0022


title: Metazome_Platyhelminthes_timecourse_sample_0082

description: single embryo 82


title: Metazome_ZF_timecourse_sample_0031


title: Metazome_Platyhelminthes_timecourse_sample_0081

description: single embryo 81


title: Metazome_ZF_timecourse_sample_0019


title: Metazome_Platyhelminthes_timecourse_sample_0080

description: single embryo 80


title: Metazome_ZF_timecourse_sample_0028


title: Metazome_Platyhelminthes_timecourse_sample_0079

description: single embryo 79


title: Metazome_ZF_timecourse_sample_0018


title: Metazome_ZF_timecourse_sample_0026


title: Metazome_ZF_timecourse_sample_0017


title: Metazome_Platyhelminthes_timecourse_sample_0078

description: single embryo 78


title: Metazome_Platyhelminthes_timecourse_sample_0076

description: single embryo 76


title: Metazome_ZF_timecourse_sample_0015


title: Metazome_Platyhelminthes_timecourse_sample_0077

description: single embryo 77


title: Metazome_ZF_timecourse_sample_0013


title: Metazome_ZF_timecourse_sample_0014


title: Metazome_Platyhelminthes_timecourse_sample_0075

description: single embryo 75


title: Metazome_Platyhelminthes_timecourse_sample_0074

description: single embryo 74


title: Metazome_ZF_timecourse_sample_0012


title: Metazome_ZF_timecourse_sample_0011


title: Metazome_ZF_timecourse_sample_0010


title: Metazome_Platyhelminthes_timecourse_sample_0073

description: single embryo 73

source_name: stage 6_single embryo


title: Metazome_ZF_timecourse_sample_0016


title: Metazome_ZF_timecourse_sample_0023


title: Metazome_Platyhelminthes_timecourse_sample_0071

description: single embryo 71


title: Metazome_ZF_timecourse_sample_0020


title: Metazome_Platyhelminthes_timecourse_sample_0070

description: single embryo 70


title: Metazome_ZF_timecourse_sample_0009


title: Metazome_Platyhelminthes_timecourse_sample_0069

description: single embryo 69


title: Metazome_ZF_timecourse_sample_0006


title: Metazome_Platyhelminthes_timecourse_sample_0068

description: single embryo 68


title: Metazome_ZF_timecourse_sample_0007


title: Metazome_Platyhelminthes_timecourse_sample_0072

description: single embryo 72


title: Metazome_ZF_timecourse_sample_0004


title: Metazome_Platyhelminthes_timecourse_sample_0066

description: single embryo 66


title: Metazome_Platyhelminthes_timecourse_sample_0067

description: single embryo 67


title: Metazome_Platyhelminthes_timecourse_sample_0065

description: single embryo 65


title: Metazome_ZF_timecourse_sample_0003


title: Metazome_Platyhelminthes_timecourse_sample_0064

description: single embryo 64


title: Metazome_ZF_timecourse_sample_0005


title: Metazome_ZF_timecourse_sample_0001


title: Metazome_Platyhelminthes_timecourse_sample_0061

description: single embryo 61


title: Metazome_Platyhelminthes_timecourse_sample_0060

description: single embryo 60


title: Metazome_Platyhelminthes_timecourse_sample_0062

description: single embryo 62


title: Metazome_Platyhelminthes_timecourse_sample_0063

description: single embryo 63


title: Metazome_Platyhelminthes_timecourse_sample_0059

description: single embryo 59


title: Metazome_Platyhelminthes_timecourse_sample_0058

description: single embryo 58


title: Metazome_Platyhelminthes_timecourse_sample_0055

description: single embryo 55

source_name: stage 5_single embryo


title: Metazome_Platyhelminthes_timecourse_sample_0056

description: single embryo 56


title: Metazome_Platyhelminthes_timecourse_sample_0057

description: single embryo 57


title: Metazome_Platyhelminthes_timecourse_sample_0054

description: single embryo 54


title: Metazome_Platyhelminthes_timecourse_sample_0053

description: single embryo 53


title: Metazome_Platyhelminthes_timecourse_sample_0050

description: single embryo 50


title: Metazome_Platyhelminthes_timecourse_sample_0052

description: single embryo 52


title: Metazome_Platyhelminthes_timecourse_sample_0049

description: single embryo 49


title: Metazome_Platyhelminthes_timecourse_sample_0048

description: single embryo 48


title: Metazome_Platyhelminthes_timecourse_sample_0051

description: single embryo 51


title: Metazome_Platyhelminthes_timecourse_sample_0047

description: single embryo 47


title: Metazome_Platyhelminthes_timecourse_sample_0046

description: single embryo 46


title: Metazome_Platyhelminthes_timecourse_sample_0045

description: single embryo 45


title: Metazome_Platyhelminthes_timecourse_sample_0044

description: single embryo 44

source_name: stage 4_single embryo


title: Metazome_Platyhelminthes_timecourse_sample_0043

description: single embryo 43


title: Metazome_Platyhelminthes_timecourse_sample_0041

description: single embryo 41


title: Metazome_ZF_timecourse_sample_0002


title: Metazome_Platyhelminthes_timecourse_sample_0042

description: single embryo 42


title: Metazome_Platyhelminthes_timecourse_sample_0040

description: single embryo 40


title: Metazome_Platyhelminthes_timecourse_sample_0039

description: single embryo 39


title: Metazome_Platyhelminthes_timecourse_sample_0037

description: single embryo 37


title: Metazome_Platyhelminthes_timecourse_sample_0036

description: single embryo 36


title: Metazome_Platyhelminthes_timecourse_sample_0035

description: single embryo 35


title: Metazome_Platyhelminthes_timecourse_sample_0034

description: single embryo 34


title: Metazome_Platyhelminthes_timecourse_sample_0031

description: single embryo 31

source_name: stage protist_single embryo

value: protist


title: Metazome_Platyhelminthes_timecourse_sample_0032

description: single embryo 32


title: Metazome_Platyhelminthes_timecourse_sample_0030

description: single embryo 30


title: Metazome_Platyhelminthes_timecourse_sample_0028

description: single embryo 28


title: Metazome_Platyhelminthes_timecourse_sample_0029

description: single embryo 29


title: Metazome_Platyhelminthes_timecourse_sample_0024

description: single embryo 24


title: Metazome_Platyhelminthes_timecourse_sample_0027

description: single embryo 27


title: Metazome_Platyhelminthes_timecourse_sample_0023

description: single embryo 23


title: Metazome_Platyhelminthes_timecourse_sample_0026

description: single embryo 26


title: Metazome_Platyhelminthes_timecourse_sample_0017

description: single embryo 17


title: Metazome_Platyhelminthes_timecourse_sample_0025

description: single embryo 25


title: Metazome_Platyhelminthes_timecourse_sample_0022

description: single embryo 22


title: Metazome_Platyhelminthes_timecourse_sample_0016

description: single embryo 16


title: Metazome_Platyhelminthes_timecourse_sample_0020

description: single embryo 20


title: Metazome_Platyhelminthes_timecourse_sample_0019

description: single embryo 19


title: Metazome_Platyhelminthes_timecourse_sample_0018

description: single embryo 18


title: Metazome_Platyhelminthes_timecourse_sample_0015

description: single embryo 15


title: Metazome_Platyhelminthes_timecourse_sample_0013

description: single embryo 13


title: Metazome_Platyhelminthes_timecourse_sample_0011

description: single embryo 11


title: Metazome_Platyhelminthes_timecourse_sample_0021

description: single embryo 21


title: Metazome_Platyhelminthes_timecourse_sample_0014

description: single embryo 14


title: Metazome_Platyhelminthes_timecourse_sample_0012

description: single embryo 12


title: Metazome_Platyhelminthes_timecourse_sample_0009

description: single embryo 9


title: Metazome_Platyhelminthes_timecourse_sample_0010

description: single embryo 10


title: Metazome_Platyhelminthes_timecourse_sample_0008

description: single embryo 8


title: Metazome_Platyhelminthes_timecourse_sample_0007

description: single embryo 7


title: Metazome_Platyhelminthes_timecourse_sample_0003

description: single embryo 3


title: Metazome_Platyhelminthes_timecourse_sample_0038

description: single embryo 38


title: Metazome_Platyhelminthes_timecourse_sample_0006

description: single embryo 6


title: Metazome_Platyhelminthes_timecourse_sample_0004

description: single embryo 4


title: Metazome_Platyhelminthes_timecourse_sample_0002

description: single embryo 2


title: Metazome_Echinodermata_timecourse_sample_0162

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 using parameters "--mp 3,1 -N 1 -L 15"
Read counting with htseq-count version 0.5.4p3.
Genome_build: WHL22 transcriptome (NCBI BioProject PRJNA81157)

organism: Strongylocentrotus purpuratus

source_name: single embryo 162

tag: time


title: Metazome_Echinodermata_timecourse_sample_0164

source_name: single embryo 164


title: Metazome_Echinodermata_timecourse_sample_0156

source_name: single embryo 156


title: Metazome_Platyhelminthes_timecourse_sample_0033

description: single embryo 33


title: Metazome_Echinodermata_timecourse_sample_0160

source_name: single embryo 160


title: Metazome_Echinodermata_timecourse_sample_0158

source_name: single embryo 158


title: Metazome_Echinodermata_timecourse_sample_0161

source_name: single embryo 161


title: Metazome_Echinodermata_timecourse_sample_0157

source_name: single embryo 157


title: Metazome_Echinodermata_timecourse_sample_0153

source_name: single embryo 153


title: Metazome_Echinodermata_timecourse_sample_0154

source_name: single embryo 154


title: Metazome_Echinodermata_timecourse_sample_0159

source_name: single embryo 159


title: Metazome_Platyhelminthes_timecourse_sample_0005

description: single embryo 5

source_name: stage 2_single embryo


title: Metazome_Echinodermata_timecourse_sample_0165

source_name: single embryo 165


title: Metazome_Echinodermata_timecourse_sample_0152

source_name: single embryo 152


title: Metazome_Echinodermata_timecourse_sample_0155

source_name: single embryo 155


title: Metazome_Echinodermata_timecourse_sample_0151

source_name: single embryo 151


title: Metazome_Echinodermata_timecourse_sample_0148

source_name: single embryo 148


title: Metazome_Echinodermata_timecourse_sample_0146

source_name: single embryo 146


title: Metazome_Echinodermata_timecourse_sample_0149

source_name: single embryo 149


title: Metazome_Echinodermata_timecourse_sample_0150

source_name: single embryo 150


title: Metazome_Echinodermata_timecourse_sample_0144

source_name: single embryo 144


title: Metazome_Echinodermata_timecourse_sample_0145

source_name: single embryo 145


title: Metazome_Echinodermata_timecourse_sample_0147

source_name: single embryo 147


title: Metazome_Echinodermata_timecourse_sample_0143

source_name: single embryo 143


title: Metazome_Platyhelminthes_timecourse_sample_0001

description: single embryo 1

source_name: stage 1_single embryo


title: Metazome_Echinodermata_timecourse_sample_0142

source_name: single embryo 142


title: Metazome_Echinodermata_timecourse_sample_0163

source_name: single embryo 163


title: Metazome_Echinodermata_timecourse_sample_0141

source_name: single embryo 141


title: Metazome_Echinodermata_timecourse_sample_0140

source_name: single embryo 140


title: Metazome_Echinodermata_timecourse_sample_0138

source_name: single embryo 138


title: Metazome_Echinodermata_timecourse_sample_0136

source_name: single embryo 136


title: Metazome_Echinodermata_timecourse_sample_0133

source_name: single embryo 133


title: Metazome_Echinodermata_timecourse_sample_0131

source_name: single embryo 131


title: Metazome_Echinodermata_timecourse_sample_0135

source_name: single embryo 135


title: Metazome_Echinodermata_timecourse_sample_0134

source_name: single embryo 134


title: Metazome_Echinodermata_timecourse_sample_0132

source_name: single embryo 132


title: Metazome_Echinodermata_timecourse_sample_0130

source_name: single embryo 130


title: Metazome_Echinodermata_timecourse_sample_0129

source_name: single embryo 129


title: Metazome_Echinodermata_timecourse_sample_0128

source_name: single embryo 128


title: Metazome_CE_timecourse_sample_0138

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 C. elegans genome WS230
Read counting with htseq-count version 0.5.4p3. Using on WS230 annotations
Genome_build: WormBase WS230
Supplementary_files_format_and_content: tabular Expression matrix

organism: Caenorhabditis elegans

growth_protocol: Standard C. elegans techniques were followed to grow worms (Stiernagle 2006).

treatment_protocol: For the embryo collection of all species adult hermaphrodites or females were collected and cut to obtain embryos. Embryos were washed with a bleach solution (70% DDW, 20% bleach, 10% 5M KOH) for 30 seconds and subsequently with a 5% BSA solution for 30 seconds. 4-cell embryos were collected,washed 4 times in clear DDW and incubated at 20°C for the appropriate time for each species to reach stages 1-10. After incubation embryos were frozen in liquid nitrogen and kept at -80°C until RNA extraction.

tag: time point (minutes after 4-cell)


title: Metazome_Echinodermata_timecourse_sample_0126

source_name: single embryo 126


title: Metazome_Echinodermata_timecourse_sample_0124

source_name: single embryo 124


title: Metazome_Echinodermata_timecourse_sample_0123

source_name: single embryo 123


title: Metazome_Echinodermata_timecourse_sample_0120

source_name: single embryo 120


title: Metazome_CE_timecourse_sample_0139

source_name: single embryo 139


title: Metazome_Echinodermata_timecourse_sample_0122

source_name: single embryo 122


title: Metazome_CE_timecourse_sample_0137

source_name: single embryo 137


title: Metazome_Echinodermata_timecourse_sample_0121

source_name: single embryo 121


title: Metazome_Echinodermata_timecourse_sample_0118

source_name: single embryo 118


title: Metazome_Echinodermata_timecourse_sample_0137


title: Metazome_CE_timecourse_sample_0135


title: Metazome_Echinodermata_timecourse_sample_0117

source_name: single embryo 117


title: Metazome_CE_timecourse_sample_0132


title: Metazome_Echinodermata_timecourse_sample_0119

source_name: single embryo 119


title: Metazome_CE_timecourse_sample_0134


title: Metazome_Echinodermata_timecourse_sample_0125

source_name: single embryo 125


title: Metazome_Echinodermata_timecourse_sample_0139


title: Metazome_Echinodermata_timecourse_sample_0116

source_name: single embryo 116


title: Metazome_Echinodermata_timecourse_sample_0114

source_name: single embryo 114


title: Metazome_CE_timecourse_sample_0130

source_name: single embryo 130


title: Metazome_CE_timecourse_sample_0133

source_name: single embryo 133


title: Metazome_CE_timecourse_sample_0131

source_name: single embryo 131


title: Metazome_Echinodermata_timecourse_sample_0111

source_name: single embryo 111


title: Metazome_CE_timecourse_sample_0127

source_name: single embryo 127


title: Metazome_CE_timecourse_sample_0126

source_name: single embryo 126


title: Metazome_Echinodermata_timecourse_sample_0127


title: Metazome_Echinodermata_timecourse_sample_0115

source_name: single embryo 115


title: Metazome_Echinodermata_timecourse_sample_0109

source_name: single embryo 109


title: Metazome_CE_timecourse_sample_0129

source_name: single embryo 129


title: Metazome_CE_timecourse_sample_0136

source_name: single embryo 136


title: Metazome_Echinodermata_timecourse_sample_0113

source_name: single embryo 113


title: Metazome_Echinodermata_timecourse_sample_0107

source_name: single embryo 107


title: Metazome_CE_timecourse_sample_0122

source_name: single embryo 122


title: Metazome_Echinodermata_timecourse_sample_0110

source_name: single embryo 110


title: Metazome_CE_timecourse_sample_0128

source_name: single embryo 128


title: Metazome_CE_timecourse_sample_0120

source_name: single embryo 120


title: Metazome_CE_timecourse_sample_0125

source_name: single embryo 125


title: Metazome_Echinodermata_timecourse_sample_0103

source_name: single embryo 103


title: Metazome_Echinodermata_timecourse_sample_0105

source_name: single embryo 105


title: Metazome_Echinodermata_timecourse_sample_0106

source_name: single embryo 106


title: Metazome_CE_timecourse_sample_0123

source_name: single embryo 123


title: Metazome_CE_timecourse_sample_0114

source_name: single embryo 114


title: Metazome_CE_timecourse_sample_0119

source_name: single embryo 119


title: Metazome_CE_timecourse_sample_0121

source_name: single embryo 121


title: Metazome_CE_timecourse_sample_0118

source_name: single embryo 118


title: Metazome_Echinodermata_timecourse_sample_0098

source_name: single embryo 98


title: Metazome_ZF_timecourse_sample_0008

source_name: single embryo


title: Metazome_Echinodermata_timecourse_sample_0096

source_name: single embryo 96


title: Metazome_Echinodermata_timecourse_sample_0104

source_name: single embryo 104


title: Metazome_CE_timecourse_sample_0115

source_name: single embryo 115


title: Metazome_Echinodermata_timecourse_sample_0102

source_name: single embryo 102


title: Metazome_Echinodermata_timecourse_sample_0094

source_name: single embryo 94


title: Metazome_Echinodermata_timecourse_sample_0095

source_name: single embryo 95


title: Metazome_CE_timecourse_sample_0117

source_name: single embryo 117


title: Metazome_Echinodermata_timecourse_sample_0101

source_name: single embryo 101


title: Metazome_CE_timecourse_sample_0108

source_name: single embryo 108


title: Metazome_CE_timecourse_sample_0110

source_name: single embryo 110


title: Metazome_Echinodermata_timecourse_sample_0093

source_name: single embryo 93


title: Metazome_Echinodermata_timecourse_sample_0092

source_name: single embryo 92


title: Metazome_CE_timecourse_sample_0124

source_name: single embryo 124


title: Metazome_Echinodermata_timecourse_sample_0108


title: Metazome_Echinodermata_timecourse_sample_0099

source_name: single embryo 99


title: Metazome_CE_timecourse_sample_0107

source_name: single embryo 107


title: Metazome_CE_timecourse_sample_0113

source_name: single embryo 113


title: Metazome_Echinodermata_timecourse_sample_0112

source_name: single embryo 112


title: Metazome_CE_timecourse_sample_0112


title: Metazome_CE_timecourse_sample_0111

source_name: single embryo 111


title: Metazome_CE_timecourse_sample_0116

source_name: single embryo 116


title: Metazome_Echinodermata_timecourse_sample_0089

source_name: single embryo 89


title: Metazome_Echinodermata_timecourse_sample_0088

source_name: single embryo 88


title: Metazome_Echinodermata_timecourse_sample_0100

source_name: single embryo 100


title: Metazome_CE_timecourse_sample_0103

source_name: single embryo 103


title: Metazome_CE_timecourse_sample_0109

source_name: single embryo 109


title: Metazome_Echinodermata_timecourse_sample_0091

source_name: single embryo 91


title: Metazome_Echinodermata_timecourse_sample_0090

source_name: single embryo 90


title: Metazome_CE_timecourse_sample_0106

source_name: single embryo 106


title: Metazome_CE_timecourse_sample_0105

source_name: single embryo 105


title: Metazome_CE_timecourse_sample_0104

source_name: single embryo 104


title: Metazome_CE_timecourse_sample_0102

source_name: single embryo 102


title: Metazome_CE_timecourse_sample_0101

source_name: single embryo 101


title: Metazome_Echinodermata_timecourse_sample_0086

source_name: single embryo 86


title: Metazome_Echinodermata_timecourse_sample_0085

source_name: single embryo 85


title: Metazome_CE_timecourse_sample_0100


title: Metazome_Echinodermata_timecourse_sample_0083

source_name: single embryo 83


title: Metazome_Echinodermata_timecourse_sample_0082

source_name: single embryo 82


title: Metazome_Echinodermata_timecourse_sample_0084

source_name: single embryo 84


title: Metazome_CE_timecourse_sample_0096

source_name: single embryo 96


title: Metazome_CE_timecourse_sample_0097

source_name: single embryo 97


title: Metazome_CE_timecourse_sample_0099

source_name: single embryo 99


title: Metazome_CE_timecourse_sample_0095

source_name: single embryo 95


title: Metazome_Echinodermata_timecourse_sample_0087

source_name: single embryo 87


title: Metazome_Echinodermata_timecourse_sample_0080

source_name: single embryo 80


title: Metazome_Echinodermata_timecourse_sample_0077

source_name: single embryo 77


title: Metazome_Echinodermata_timecourse_sample_0076

source_name: single embryo 76


title: Metazome_Echinodermata_timecourse_sample_0079

source_name: single embryo 79


title: Metazome_Echinodermata_timecourse_sample_0075

source_name: single embryo 75


title: Metazome_Echinodermata_timecourse_sample_0081

source_name: single embryo 81


title: Metazome_Echinodermata_timecourse_sample_0078

source_name: single embryo 78


title: Metazome_CE_timecourse_sample_0089

source_name: single embryo 89


title: Metazome_CE_timecourse_sample_0092

source_name: single embryo 92


title: Metazome_CE_timecourse_sample_0088

source_name: single embryo 88


title: Metazome_CE_timecourse_sample_0093

source_name: single embryo 93


title: Metazome_CE_timecourse_sample_0091

source_name: single embryo 91


title: Metazome_CE_timecourse_sample_0090

source_name: single embryo 90


title: Metazome_Echinodermata_timecourse_sample_0073

source_name: single embryo 73


title: Metazome_CE_timecourse_sample_0098

source_name: single embryo 98


title: Metazome_Echinodermata_timecourse_sample_0074

source_name: single embryo 74


title: Metazome_CE_timecourse_sample_0094

source_name: single embryo 94


title: Metazome_Echinodermata_timecourse_sample_0071

source_name: single embryo 71


title: Metazome_CE_timecourse_sample_0086

source_name: single embryo 86


title: Metazome_CE_timecourse_sample_0087

source_name: single embryo 87


title: Metazome_Echinodermata_timecourse_sample_0072

source_name: single embryo 72


title: Metazome_CE_timecourse_sample_0085

source_name: single embryo 85


title: Metazome_Echinodermata_timecourse_sample_0070

source_name: single embryo 70


title: Metazome_Echinodermata_timecourse_sample_0068

source_name: single embryo 68


title: Metazome_CE_timecourse_sample_0084

source_name: single embryo 84


title: Metazome_Echinodermata_timecourse_sample_0067

source_name: single embryo 67


title: Metazome_CE_timecourse_sample_0082

source_name: single embryo 82


title: Metazome_CE_timecourse_sample_0080

source_name: single embryo 80


title: Metazome_Echinodermata_timecourse_sample_0066

source_name: single embryo 66


title: Metazome_Echinodermata_timecourse_sample_0065

source_name: single embryo 65


title: Metazome_Echinodermata_timecourse_sample_0064

source_name: single embryo 64


title: Metazome_CE_timecourse_sample_0081

source_name: single embryo 81


title: Metazome_CE_timecourse_sample_0078

source_name: single embryo 78


title: Metazome_Echinodermata_timecourse_sample_0062

source_name: single embryo 62


title: Metazome_CE_timecourse_sample_0079

source_name: single embryo 79


title: Metazome_Echinodermata_timecourse_sample_0060

source_name: single embryo 60


title: Metazome_Echinodermata_timecourse_sample_0059

source_name: single embryo 59


title: Metazome_CE_timecourse_sample_0074

source_name: single embryo 74


title: Metazome_Echinodermata_timecourse_sample_0058

source_name: single embryo 58


title: Metazome_Echinodermata_timecourse_sample_0069

source_name: single embryo 69


title: Metazome_Echinodermata_timecourse_sample_0057

source_name: single embryo 57


title: Metazome_CE_timecourse_sample_0083

source_name: single embryo 83


title: Metazome_CE_timecourse_sample_0072

source_name: single embryo 72


title: Metazome_CE_timecourse_sample_0071

source_name: single embryo 71


title: Metazome_Echinodermata_timecourse_sample_0056

source_name: single embryo 56


title: Metazome_CE_timecourse_sample_0073

source_name: single embryo 73


title: Metazome_CE_timecourse_sample_0070

source_name: single embryo 70


title: Metazome_CE_timecourse_sample_0069


title: Metazome_Echinodermata_timecourse_sample_0053

source_name: single embryo 53


title: Metazome_Echinodermata_timecourse_sample_0052

source_name: single embryo 52


title: Metazome_CE_timecourse_sample_0067

source_name: single embryo 67


title: Metazome_Echinodermata_timecourse_sample_0063

source_name: single embryo 63


title: Metazome_Echinodermata_timecourse_sample_0051

source_name: single embryo 51


title: Metazome_CE_timecourse_sample_0077

source_name: single embryo 77


title: Metazome_Echinodermata_timecourse_sample_0061

source_name: single embryo 61


title: Metazome_CE_timecourse_sample_0066

source_name: single embryo 66


title: Metazome_Echinodermata_timecourse_sample_0050

source_name: single embryo 50


title: Metazome_CE_timecourse_sample_0075

source_name: single embryo 75


title: Metazome_Echinodermata_timecourse_sample_0049

source_name: single embryo 49


title: Metazome_Echinodermata_timecourse_sample_0048

source_name: single embryo 48


title: Metazome_CE_timecourse_sample_0065

source_name: single embryo 65


title: Metazome_Echinodermata_timecourse_sample_0047

source_name: single embryo 47


title: Metazome_Echinodermata_timecourse_sample_0046

source_name: single embryo 46


title: Metazome_CE_timecourse_sample_0064

source_name: single embryo 64


title: Metazome_Echinodermata_timecourse_sample_0045

source_name: single embryo 45


title: Metazome_Echinodermata_timecourse_sample_0044

source_name: single embryo 44


title: Metazome_Echinodermata_timecourse_sample_0054

source_name: single embryo 54


title: Metazome_Echinodermata_timecourse_sample_0043

source_name: single embryo 43


title: Metazome_CE_timecourse_sample_0063

source_name: single embryo 63


title: Metazome_Echinodermata_timecourse_sample_0055

source_name: single embryo 55


title: Metazome_CE_timecourse_sample_0062

source_name: single embryo 62


title: Metazome_Echinodermata_timecourse_sample_0042

source_name: single embryo 42


title: Metazome_Echinodermata_timecourse_sample_0040

source_name: single embryo 40


title: Metazome_CE_timecourse_sample_0068

source_name: single embryo 68


title: Metazome_CE_timecourse_sample_0061

source_name: single embryo 61


title: Metazome_Echinodermata_timecourse_sample_0039

source_name: single embryo 39


title: Metazome_Echinodermata_timecourse_sample_0038

source_name: single embryo 38


title: Metazome_CE_timecourse_sample_0060

source_name: single embryo 60


title: Metazome_CE_timecourse_sample_0076

source_name: single embryo 76


title: Metazome_Echinodermata_timecourse_sample_0037

source_name: single embryo 37


title: Metazome_Echinodermata_timecourse_sample_0035

source_name: single embryo 35


title: Metazome_CE_timecourse_sample_0059

source_name: single embryo 59


title: Metazome_CE_timecourse_sample_0058

source_name: single embryo 58


title: Metazome_Echinodermata_timecourse_sample_0033

source_name: single embryo 33


title: Metazome_CE_timecourse_sample_0057

source_name: single embryo 57


title: Metazome_Echinodermata_timecourse_sample_0031

source_name: single embryo 31


title: Metazome_CE_timecourse_sample_0056

source_name: single embryo 56


title: Metazome_Echinodermata_timecourse_sample_0030

source_name: single embryo 30


title: Metazome_Echinodermata_timecourse_sample_0041

source_name: single embryo 41


title: Metazome_Echinodermata_timecourse_sample_0029

source_name: single embryo 29


title: Metazome_CE_timecourse_sample_0055

source_name: single embryo 55


title: Metazome_CE_timecourse_sample_0053

source_name: single embryo 53


title: Metazome_Echinodermata_timecourse_sample_0025

source_name: single embryo 25


title: Metazome_CE_timecourse_sample_0054

source_name: single embryo 54


title: Metazome_Echinodermata_timecourse_sample_0024

source_name: single embryo 24


title: Metazome_Echinodermata_timecourse_sample_0026

source_name: single embryo 26


title: Metazome_Echinodermata_timecourse_sample_0027

source_name: single embryo 27


title: Metazome_Echinodermata_timecourse_sample_0023

source_name: single embryo 23


title: Metazome_Echinodermata_timecourse_sample_0036

source_name: single embryo 36


title: Metazome_Echinodermata_timecourse_sample_0034

source_name: single embryo 34


title: Metazome_CE_timecourse_sample_0051

source_name: single embryo 51


title: Metazome_Echinodermata_timecourse_sample_0022

source_name: single embryo 22


title: Metazome_CE_timecourse_sample_0050

source_name: single embryo 50


title: Metazome_CE_timecourse_sample_0052

source_name: single embryo 52


title: Metazome_Echinodermata_timecourse_sample_0032

source_name: single embryo 32


title: Metazome_Echinodermata_timecourse_sample_0021

source_name: single embryo 21


title: Metazome_Echinodermata_timecourse_sample_0017

source_name: single embryo 17


title: Metazome_Echinodermata_timecourse_sample_0019

source_name: single embryo 19


title: Metazome_Echinodermata_timecourse_sample_0016

source_name: single embryo 16


title: Metazome_Echinodermata_timecourse_sample_0020

source_name: single embryo 20


title: Metazome_CE_timecourse_sample_0049

source_name: single embryo 49


title: Metazome_Echinodermata_timecourse_sample_0018

source_name: single embryo 18


title: Metazome_Echinodermata_timecourse_sample_0015

source_name: single embryo 15


title: Metazome_Echinodermata_timecourse_sample_0014

source_name: single embryo 14


title: Metazome_Echinodermata_timecourse_sample_0028

source_name: single embryo 28


title: Metazome_Echinodermata_timecourse_sample_0012

source_name: single embryo 12


title: Metazome_CE_timecourse_sample_0048

source_name: single embryo 48


title: Metazome_CE_timecourse_sample_0047

source_name: single embryo 47


title: Metazome_Echinodermata_timecourse_sample_0010

source_name: single embryo 10


title: Metazome_Echinodermata_timecourse_sample_0008

source_name: single embryo 8


title: Metazome_CE_timecourse_sample_0046

source_name: single embryo 46


title: Metazome_Echinodermata_timecourse_sample_0007

source_name: single embryo 7


title: Metazome_Echinodermata_timecourse_sample_0009

source_name: single embryo 9


title: Metazome_Echinodermata_timecourse_sample_0006

source_name: single embryo 6


title: Metazome_CE_timecourse_sample_0044

source_name: single embryo 44


title: Metazome_CE_timecourse_sample_0045

source_name: single embryo 45


title: Metazome_CE_timecourse_sample_0043

source_name: single embryo 43


title: Metazome_Echinodermata_timecourse_sample_0001

source_name: single embryo 1


title: Metazome_Echinodermata_timecourse_sample_0003

source_name: single embryo 3


title: Metazome_Echinodermata_timecourse_sample_0005

source_name: single embryo 5


title: Metazome_CE_timecourse_sample_0041

source_name: single embryo 41


title: Metazome_CE_timecourse_sample_0038

source_name: single embryo 38


title: Metazome_CE_timecourse_sample_0042

source_name: single embryo 42


title: Metazome_Echinodermata_timecourse_sample_0002

source_name: single embryo 2


title: Metazome_CE_timecourse_sample_0037

source_name: single embryo 37


title: Metazome_CE_timecourse_sample_0036

source_name: single embryo 36


title: Metazome_CE_timecourse_sample_0039

source_name: single embryo 39


title: Metazome_CE_timecourse_sample_0035

source_name: single embryo 35


title: Metazome_CE_timecourse_sample_0034

source_name: single embryo 34


title: Metazome_Echinodermata_timecourse_sample_0011

source_name: single embryo 11


title: Metazome_CE_timecourse_sample_0033

source_name: single embryo 33


title: Metazome_CE_timecourse_sample_0032

source_name: single embryo 32


title: Metazome_CE_timecourse_sample_0031

source_name: single embryo 31


title: Metazome_CE_timecourse_sample_0030

source_name: single embryo 30


title: Metazome_CE_timecourse_sample_0029

source_name: single embryo 29


title: Metazome_CE_timecourse_sample_0025

source_name: single embryo 25


title: Metazome_CE_timecourse_sample_0027

source_name: single embryo 27


title: Metazome_CE_timecourse_sample_0026

source_name: single embryo 26


title: Metazome_CE_timecourse_sample_0024

source_name: single embryo 24


title: Metazome_CE_timecourse_sample_0022

source_name: single embryo 22


title: Metazome_CE_timecourse_sample_0040

source_name: single embryo 40


title: Metazome_CE_timecourse_sample_0021

source_name: single embryo 21


title: Metazome_CE_timecourse_sample_0020

source_name: single embryo 20


title: Metazome_CE_timecourse_sample_0023

source_name: single embryo 23


title: Metazome_CE_timecourse_sample_0018

source_name: single embryo 18


title: Metazome_CE_timecourse_sample_0019

source_name: single embryo 19


title: Metazome_CE_timecourse_sample_0016

source_name: single embryo 16


title: Metazome_CE_timecourse_sample_0017

source_name: single embryo 17


title: Metazome_CE_timecourse_sample_0015

source_name: single embryo 15


title: BSG1469_IP_ScpB

city: Martinsried

first: Stephan

last: Gruber

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

description:
ChIP using ScpB antibody
1307_AI_processed.txt

library_source: genomic

data_processing:
Genome mapping with Bowtie in Galaxy
Binning and normalization of total numbers of reads  with SeqMonk software
Relative quantification of input and ChIP with SeqMonk software
Genome_build: NC_000964.3
Supplementary_files_format_and_content: tab-delimited text files including: Start/End basepairs of bins in the genome used for mapping; Corresponding Start/End basepairs of bins in the reference genome; Ratio of reads for IP/Input samples

molecule: genomic DNA

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells

growth_protocol: Cells were grown in minimal medium at 37°C to mid exponential phase. Cells were treated with a formaldehyde-containing fixing solution, washed and lysed in the presence of protease inhibitors.

extract_protocol: Lysed cells were sonicated and cleared lysates were kept as the input samples. The IP samples were incubated with Protein G coupled dynabeads (Invitrogen), coupled to the respective antibodies (Smc, ParB or ScpB). DNA was purified by phenol chloroform extraction and ethanol precipitation.

tag: genotype

tag: chip antibody

value: anti-ScpB


title: Metazome_CE_timecourse_sample_0014

source_name: single embryo 14


title: BSG1470_IP_ScpB

description:
ChIP using ScpB antibody
1307_BJ_processed.txt


title: BSG1470_input_ScpB

description:
Total DNA
1307_BJ_processed.txt

value: input material


title: Metazome_Echinodermata_timecourse_sample_0004

source_name: single embryo 4


title: BSG1052_input_ScpB

description:
Total DNA
698_KL_processed.txt

value: smc ftsY::ermB delta-parB::kanR


title: BSG1469_input_ScpB

description:
Total DNA
1307_AI_processed.txt


title: BSG1052_IP_ScpB

description:
ChIP using ScpB antibody
698_KL_processed.txt


title: 8 hr TP-0903 Rep 3

description: 8 hr treatment: 8 somite (13 hpf) - 21 somite (19.5 hpf)

source_name: 35 whole zebrafish embryos

value: 21 somites (19.5 hpf)


title: BSG1002_input_ScpB

description:
Total DNA
698_EF_processed.txt

value: smc ftsY::ermB


title: Metazome_CE_timecourse_sample_0012

source_name: single embryo 12


title: Metazome_CE_timecourse_sample_0028

source_name: single embryo 28


title: 8 hr TP-0903 Rep 2


title: BSG1002_IP_ScpB

description:
ChIP using ScpB antibody
698_EF_processed.txt


title: 8 hr TP-0903 Rep 1


title: Metazome_CE_timecourse_sample_0011

source_name: single embryo 11


title: BSG1470_input_ParB

description:
Total DNA
1265_HL_processed.txt


title: Metazome_CE_timecourse_sample_0013

source_name: single embryo 13


title: BSG1471_input_Smc

description:
Total DNA
1265_EM_processed.txt

value: smc (E1118Q) ftsY::ermB, delta-amyE::parS359::cat


title: BSG1470_IP_ParB

description:
ChIP using ParB antibody
1265_HL_processed.txt

value: anti-ParB


title: 8 hr DMSO Rep 4


title: Metazome_CE_timecourse_sample_0010

source_name: single embryo 10


title: 8 hr TP-0903 Rep 4


title: BSG1008_IP_Smc

description:
ChIP using Smc antibody
1265_BJ_processed.txt

value: smc(E1118Q) ftsY::ermB

value: anti-Smc


title: BSG1002_input_Smc

description:
Total DNA
1265_AI_processed.txt


title: BSG1008_input_Smc

description:
Total DNA
1265_BJ_processed.txt


title: Metazome_Echinodermata_timecourse_sample_0013


title: Metazome_CE_timecourse_sample_0007

source_name: single embryo 7


title: 8 hr DMSO Rep 3


title: Metazome_Amphimedon_timecourse_sample_0124

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 A. queenslandica genome  Aqu1
Read counting with htseq-count version 0.5.4p3. Using on Ensemble Aqu2.1 annotations
Genome_build: Aqu1
Supplementary_files_format_and_content: AQ_exp.tab is a tabular Expression matrix

organism: Amphimedon queenslandica

source_name: single embryo 124

growth_protocol: Embryos, larvae and post-larvae were collected individually at Heron Island, the Great Barrier Reef, Australia.

treatment_protocol: samples staged by morphology and imaged before being stored in 20 μl RNA later.

value: adult


title: BSG1002_IP_Smc

description:
ChIP using Smc antibody
1265_AI_processed.txt


title: 8 hr DMSO Rep 1


title: 8 hr DMSO Rep 2


title: FigS5_Smc3_WT_PK_WCE

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: Candida glabrata spike-in for calibration only

data_processing:
Library sequencing was carried out on the Ion Torrent Proton
The quality of the raw sequence data was examined using FastQC (Galaxy tool version 1.0.0) and trimming of reads was carried out using “trim sequences” (Galaxy tool version 1.0.0)
Any reads smaller than 50bp were removed using ‘Filter FASTQ’
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, genolevures) using Bowtie2 (Galaxy tool version 0.2) with the default (--sensitive) parameters
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Genome_build: SacCer3
Supplementary_files_format_and_content: bigwig files

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNAse A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270

value: sac cer strain  BR733

value: can gla strain  K23308

tag: antibody

value: none (input)


title: Metazome_CE_timecourse_sample_0002

source_name: single embryo 2


title: Metazome_CE_timecourse_sample_0005

source_name: single embryo 5


title: Metazome_CE_timecourse_sample_0006

source_name: single embryo 6


title: FigS5_Smc3_D1161E_PK_WCE

value: sac cer strain  BR736


title: BSG1471_IP_Smc

description:
ChIP using Smc antibody
1265_EM_processed.txt


title: Metazome_CE_timecourse_sample_0008

source_name: single embryo 8


title: Fig4_Smc3_L1126V_WCE

value: sac cer strain  BR777


title: Metazome_Amphimedon_timecourse_sample_0122

source_name: single embryo 122

value: tent-pole-formation


title: Metazome_Amphimedon_timecourse_sample_0119

source_name: single embryo 119

value: mat-formation


title: Fig4_Smc3_L1126V_IP

value: anti-PK antibody (Bio-Rad)


title: Metazome_Amphimedon_timecourse_sample_0118

source_name: single embryo 118


title: Fig4_Smc1_WT_WCE

value: sac cer strain  BR645


title: Metazome_CE_timecourse_sample_0009

source_name: single embryo 9


title: Metazome_Amphimedon_timecourse_sample_0121

source_name: single embryo 121

value: chamber-formation


title: Fig4_Smc1_WT_IP


title: Metazome_CE_timecourse_sample_0003

source_name: single embryo 3


title: Metazome_Amphimedon_timecourse_sample_0117

source_name: single embryo 117

value: settelment


title: FigS5_Smc3_WT_PK_IP


title: FigS5_Smc3_D1161E_PK_IP


title: Fig4_Smc3_WT_WCE

value: sac cer strain  BR776


title: Metazome_CE_timecourse_sample_0004

source_name: single embryo 4


title: Metazome_Amphimedon_timecourse_sample_0120

source_name: single embryo 120


title: Fig4_Smc3_WT_IP


title: Metazome_CE_timecourse_sample_0001

source_name: single embryo 1


title: Fig4_Smc1_L1129V_WCE

value: sac cer strain  BR625


title: Metazome_Amphimedon_timecourse_sample_0123

source_name: single embryo 123

value: juvenile


title: Fig6_Smc3_E1155Q_IP

value: sac cer strain K17409

value: can gla strain K23308


title: Fig6_Smc3_E1155Q_WCE


title: Fig4_Smc1_L1129V_IP


title: Metazome_Amphimedon_timecourse_sample_0112

source_name: single embryo 112


title: Sample_Set1a_RNAi

city: Shanghai

first: Jiemin

last: Wong

address: 500 Dongchuan Road

country: China

institute: Institute of Biomedical Sciences and School of Life Sciences, East China Normal University

data_processing:
Basecalls performed using CASAVA.
mRNA-Seq data processing: RNA-Seq reads of each sample were firstly mapped to the mm9 genome assembly using TopHat 2.0.12 with default parameters.
Read counts were obtained from TopHat-generated BAM files using SAMtools 0.1.16.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RefSeq id and RPKM values for each Sample

organism: Mus musculus

source_name: CGR8 ESC

growth_protocol: CGR8 cells were cultured feeder-free in GMEM containing 15% FBS, 2mM L-glutamine, 0.1mM β-mercaptoethanol, LIF and penicillin/streptomycin at 37℃, 5% CO2. The culture surface was pre-coated with 0.2% (w/v) gelatin.

extract_protocol:
collecting the cells in Trizol Reagent ( Invitrogen, 15596026)
according to Jinneng Co., Ltd. Protocol.

treatment_protocol: Transfection twice of negative siRNA or Set1a siRNA in CGR8 cells within 72 hours.

tag: cell line

value: CGR8 embryonic stem cells

tag: transfection

value: Set1a siRNA 72 hours


title: Sample_NC

value: negative siRNA 72 hours


title: Metazome_Amphimedon_timecourse_sample_0113

source_name: single embryo 113


title: Fig4_Smc1_D1164E_WCE

source_name: Saccharomyces cerevisiae cells

value: sac cer strain  BR627

value: can gla strain  K23308

value: none (input)


title: Fig4_Smc1_D1164E_IP


title: Metazome_Amphimedon_timecourse_sample_0105

source_name: single embryo 105


title: Fig6_Smc3_QQ_E1155Q_WCE

value: sac cer strain K25260


title: Fig6_Smc3_QQ_E1155Q_IP


title: Metazome_Amphimedon_timecourse_sample_0115

source_name: single embryo 115


title: Metazome_Amphimedon_timecourse_sample_0114

source_name: single embryo 114

value: tent-pole-formation


title: Metazome_Amphimedon_timecourse_sample_0110

source_name: single embryo 110

value: mat-formation


title: Metazome_Amphimedon_timecourse_sample_0104

source_name: single embryo 104


title: Metazome_Amphimedon_timecourse_sample_0102

source_name: single embryo 102


title: Metazome_Amphimedon_timecourse_sample_0109

source_name: single embryo 109


title: Metazome_Amphimedon_timecourse_sample_0108

source_name: single embryo 108

value: adult


title: Metazome_Amphimedon_timecourse_sample_0107

source_name: single embryo 107


title: Metazome_Amphimedon_timecourse_sample_0103

source_name: single embryo 103


title: Metazome_Amphimedon_timecourse_sample_0101

source_name: single embryo 101


title: Metazome_Amphimedon_timecourse_sample_0116

source_name: single embryo 116


title: Metazome_Amphimedon_timecourse_sample_0099

source_name: single embryo 99

value: cleavage


title: Metazome_Amphimedon_timecourse_sample_0100

source_name: single embryo 100


title: Metazome_Amphimedon_timecourse_sample_0095

source_name: single embryo 95

value: late spot


title: Metazome_Amphimedon_timecourse_sample_0111

source_name: single embryo 111


title: Metazome_Amphimedon_timecourse_sample_0096

source_name: single embryo 96

value: free-swimming


title: Metazome_Amphimedon_timecourse_sample_0092

source_name: single embryo 92


title: Metazome_Amphimedon_timecourse_sample_0094

source_name: single embryo 94


title: Metazome_Amphimedon_timecourse_sample_0097

source_name: single embryo 97


title: Metazome_Amphimedon_timecourse_sample_0098

source_name: single embryo 98

value: late ring


title: Metazome_Amphimedon_timecourse_sample_0090

source_name: single embryo 90


title: Metazome_Amphimedon_timecourse_sample_0089

source_name: single embryo 89


title: Metazome_Amphimedon_timecourse_sample_0088

source_name: single embryo 88


title: Metazome_Echinodermata_timecourse_sample_0097


title: Metazome_Amphimedon_timecourse_sample_0084

source_name: single embryo 84


title: Metazome_Amphimedon_timecourse_sample_0082

source_name: single embryo 82


title: Metazome_Amphimedon_timecourse_sample_0083

source_name: single embryo 83

value: juvenile


title: Metazome_Amphimedon_timecourse_sample_0081

source_name: single embryo 81


title: Metazome_Amphimedon_timecourse_sample_0085

source_name: single embryo 85

value: ring


title: Metazome_Amphimedon_timecourse_sample_0087

source_name: single embryo 87

value: spot


title: Metazome_Amphimedon_timecourse_sample_0079

source_name: single embryo 79


title: Metazome_Amphimedon_timecourse_sample_0078

source_name: single embryo 78


title: Metazome_Amphimedon_timecourse_sample_0077

source_name: single embryo 77


title: Metazome_Amphimedon_timecourse_sample_0075

source_name: single embryo 75


title: Metazome_Amphimedon_timecourse_sample_0076

source_name: single embryo 76


title: Metazome_Amphimedon_timecourse_sample_0074

source_name: single embryo 74


title: Metazome_Amphimedon_timecourse_sample_0072

source_name: single embryo 72


title: Metazome_Amphimedon_timecourse_sample_0073

source_name: single embryo 73


title: Metazome_Amphimedon_timecourse_sample_0071

source_name: single embryo 71


title: Metazome_Amphimedon_timecourse_sample_0091

source_name: single embryo 91

value: settelment


title: Metazome_Amphimedon_timecourse_sample_0093

source_name: single embryo 93


title: Metazome_Amphimedon_timecourse_sample_0069

source_name: single embryo 69


title: Metazome_Amphimedon_timecourse_sample_0067

source_name: single embryo 67


title: Metazome_Amphimedon_timecourse_sample_0065

source_name: single embryo 65


title: Metazome_Amphimedon_timecourse_sample_0070

source_name: single embryo 70


title: Metazome_Amphimedon_timecourse_sample_0064

source_name: single embryo 64

value: cloud


title: Metazome_Amphimedon_timecourse_sample_0068

source_name: single embryo 68


title: Metazome_Amphimedon_timecourse_sample_0066

source_name: single embryo 66


title: Metazome_Amphimedon_timecourse_sample_0086

source_name: single embryo 86


title: Metazome_Amphimedon_timecourse_sample_0063

source_name: single embryo 63

value: brown


title: tra, esg>traF female rep3

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina Casava1.8.2  software used for basecalling.
Sequenced reads were mapped to dm3 whole genome using tophat v2.0.11 with parameters -p 8 -r 100.
Gene Based read counts were obtained with HTSeq counts module v0.5.3p9
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

organism: Drosophila melanogaster

growth_protocol: Flies were transferred to fresh vials every 3 days and fly density was kept to a maximum of 15 flies per vial

extract_protocol:
Midguts were dissected (x30 by replicate), and RNA were extracted using Trizol reagent. Illumina Truseq mRNA stranded library prep kit was used with 500ng of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols
Library quality was checked on a Bioanalyser HS DNA chip and concentrations were estimated by Qubit measurement. Libraries were pooled in equimolar quantities and sequenced on a Hiseq2500 using paired end 100bp reads

treatment_protocol: Flies were raised and aged for 3 days at 18C and then shifted at 29C 10 days to induce transgene expresssion

tag: strain background

tag: gender

value: female

tag: age

value: virgin 15 day-old

tag: genotype/variation:

value: dissected midgut (30x)


title: Metazome_Amphimedon_timecourse_sample_0080

source_name: single embryo 80


title: Metazome_Amphimedon_timecourse_sample_0061

source_name: single embryo 61


title: tra, esg>traF female rep2


title: tra, esg>traF female rep1


title: Metazome_Amphimedon_timecourse_sample_0060

source_name: single embryo 60


title: tra female rep3

source_name: tra mutant_female_midgut


title: WT female control rep3


title: tra female rep1


title: WT female control rep2


title: tra female rep2


title: Metazome_Amphimedon_timecourse_sample_0058

source_name: single embryo 58


title: Metazome_Amphimedon_timecourse_sample_0059

source_name: single embryo 59


title: WT female control rep1


title: WT female rep1

growth_protocol: Flies were kept at 29C. Flies were transferred to fresh vials every 3 days and fly density was kept to a maximum of 15 flies per vial

extract_protocol:
Midguts were dissected (x30 by replicate), and RNA was extracted using Trizol reagent. Illumina Truseq mRNA stranded library prep kit was used with 500ng of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols
Library quality was checked on a Bioanalyser HS DNA chip and concentrations were estimated by Qubit measurement. Libraries were pooled in equimolar quantities and sequenced on a Hiseq2500 using paired end 100bp reads


title: Metazome_Amphimedon_timecourse_sample_0057

source_name: single embryo 57


title: WT male rep2

value: male


title: Metazome_Amphimedon_timecourse_sample_0106

source_name: single embryo 106

value: tent-pole-formation


title: Metazome_Amphimedon_timecourse_sample_0055

source_name: single embryo 55

value: mat-formation


title: WT female rep3


title: WT male rep1


title: WT male rep3


title: Metazome_Drosophila_timecourse_sample_0090

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 BDGP5
Read counting with htseq-count version 0.5.4p3. Using on Ensemble BDGP5.76 annotations
Genome_build: BDGP5
Supplementary_files_format_and_content: DM_exp.tab is  a tabular Expression matrix reporting read counts.

source_name: single embryo 90

growth_protocol: Drosophila melanogaster embryos were collected using the protocol published in (PMID:21357063). In short, agar plates with apple juice smeared with freshly prepared yeast were used to make young adult flies lay a lot of eggs. Cages consisting of such plates were set up with at least 20 flies and left for roughly one day for the flies to acclimatize to the cage. In order to make sure to use only newly laid eggs the apple juice plates were replaced with fresh ones twice in one hour interval in the morning to clear the embryos held by the mothers overnight as fresh food stimulates egg laying. The third apple juice plate contained embryos that were further processed for embryo collection. Drosophila embryos are covered with a non-transparent chorion which has to be removed prior to live imaging by dechorionation. Shortly after being laid embryos were washed off from plates into a plastic sieve using tap water and a fine brush to loosen the embryos. In the sieve embryos were submerged into 50% bleach solution for exactly two minutes. Embryos were washed off from bleach on the sieve with cold tap water by spraying with a plastic squirt. Embryos were finally rinses by dipping the plastic sieve three times into white plastic weighing baskets filled with fresh water and then left in the last basket until further handling. Using a needle pick 20 embryos were placed in a row on a strip of agar placed on a glass slide. n-Heptane glue was applied in a thin layer on a big glass cover slip. This cover slip was carefully put upside down on top of the embryos on the agar strip so that embryos adhere to the glue layer. Embryos were covered with PBS and kept in humid chambers in a 25°C incubator. Embryos on the slip were observed under light microscope and for each embryo time of cellularization was noted. Reaching respective time after cellularization embryos were carefully removed from slide using needle pick and flash frozen in an Eppendorf tube 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 cellularization stage)


title: Metazome_Drosophila_timecourse_sample_0091

source_name: single embryo 91


title: Metazome_Amphimedon_timecourse_sample_0054

source_name: single embryo 54


title: Metazome_Amphimedon_timecourse_sample_0062

source_name: single embryo 62


title: Metazome_Amphimedon_timecourse_sample_0056

source_name: single embryo 56


title: Metazome_Drosophila_timecourse_sample_0089

source_name: single embryo 89


title: Metazome_Drosophila_timecourse_sample_0088

source_name: single embryo 88


title: Metazome_Drosophila_timecourse_sample_0086

source_name: single embryo 86


title: Metazome_Amphimedon_timecourse_sample_0053

source_name: single embryo 53


title: Metazome_Amphimedon_timecourse_sample_0052

source_name: single embryo 52


title: Metazome_Drosophila_timecourse_sample_0085

source_name: single embryo 85


title: Metazome_Drosophila_timecourse_sample_0084

source_name: single embryo 84


title: Metazome_Drosophila_timecourse_sample_0082

source_name: single embryo 82


title: Metazome_Drosophila_timecourse_sample_0083

source_name: single embryo 83


title: Metazome_Drosophila_timecourse_sample_0087

source_name: single embryo 87


title: Metazome_Amphimedon_timecourse_sample_0051

source_name: single embryo 51


title: WT female rep2


title: Metazome_Drosophila_timecourse_sample_0081

source_name: single embryo 81


title: Metazome_Drosophila_timecourse_sample_0080

source_name: single embryo 80


title: Metazome_Amphimedon_timecourse_sample_0050

source_name: single embryo 50


title: Metazome_Drosophila_timecourse_sample_0079

source_name: single embryo 79


title: Metazome_Amphimedon_timecourse_sample_0048

source_name: single embryo 48


title: Metazome_Drosophila_timecourse_sample_0078

source_name: single embryo 78


title: Metazome_Drosophila_timecourse_sample_0077

source_name: single embryo 77


title: Metazome_Drosophila_timecourse_sample_0075

source_name: single embryo 75


title: Metazome_Drosophila_timecourse_sample_0074

source_name: single embryo 74


title: Metazome_Amphimedon_timecourse_sample_0046

source_name: single embryo 46


title: Metazome_Drosophila_timecourse_sample_0073

source_name: single embryo 73


title: Metazome_Amphimedon_timecourse_sample_0045

source_name: single embryo 45


title: Metazome_Amphimedon_timecourse_sample_0047

source_name: single embryo 47


title: Metazome_Drosophila_timecourse_sample_0070

source_name: single embryo 70


title: Metazome_Drosophila_timecourse_sample_0071

source_name: single embryo 71


title: Metazome_Drosophila_timecourse_sample_0069

source_name: single embryo 69


title: Metazome_Drosophila_timecourse_sample_0068

source_name: single embryo 68


title: Metazome_Amphimedon_timecourse_sample_0044

source_name: single embryo 44


title: Metazome_Amphimedon_timecourse_sample_0043

source_name: single embryo 43


title: Metazome_Drosophila_timecourse_sample_0067

source_name: single embryo 67


title: Metazome_Drosophila_timecourse_sample_0066

source_name: single embryo 66


title: Metazome_Amphimedon_timecourse_sample_0042

source_name: single embryo 42


title: Metazome_Drosophila_timecourse_sample_0065

source_name: single embryo 65


title: Metazome_Amphimedon_timecourse_sample_0041

source_name: single embryo 41


title: Metazome_Amphimedon_timecourse_sample_0049

source_name: single embryo 49


title: Metazome_Drosophila_timecourse_sample_0076

source_name: single embryo 76


title: Metazome_Drosophila_timecourse_sample_0063

source_name: single embryo 63


title: Metazome_Drosophila_timecourse_sample_0061

source_name: single embryo 61


title: Metazome_Drosophila_timecourse_sample_0060

source_name: single embryo 60


title: Metazome_Drosophila_timecourse_sample_0064

source_name: single embryo 64


title: Metazome_Drosophila_timecourse_sample_0059

source_name: single embryo 59


title: Metazome_Drosophila_timecourse_sample_0058

source_name: single embryo 58


title: Metazome_Amphimedon_timecourse_sample_0039

source_name: single embryo 39


title: Metazome_Drosophila_timecourse_sample_0072

source_name: single embryo 72


title: Metazome_Drosophila_timecourse_sample_0057

source_name: single embryo 57


title: Metazome_Amphimedon_timecourse_sample_0040

source_name: single embryo 40


title: Metazome_Drosophila_timecourse_sample_0056

source_name: single embryo 56


title: Metazome_Amphimedon_timecourse_sample_0037

source_name: single embryo 37


title: Metazome_Drosophila_timecourse_sample_0055

source_name: single embryo 55


title: Metazome_Drosophila_timecourse_sample_0054

source_name: single embryo 54


title: Metazome_Amphimedon_timecourse_sample_0038

source_name: single embryo 38


title: Metazome_Drosophila_timecourse_sample_0062

source_name: single embryo 62


title: Metazome_Drosophila_timecourse_sample_0053

source_name: single embryo 53


title: Metazome_Drosophila_timecourse_sample_0052

source_name: single embryo 52


title: Metazome_Drosophila_timecourse_sample_0048

source_name: single embryo 48


title: Metazome_Drosophila_timecourse_sample_0051

source_name: single embryo 51


title: Metazome_Drosophila_timecourse_sample_0049

source_name: single embryo 49


title: Metazome_Drosophila_timecourse_sample_0050

source_name: single embryo 50


title: Metazome_Amphimedon_timecourse_sample_0036

source_name: single embryo 36

value: unknown


title: Metazome_Drosophila_timecourse_sample_0044

source_name: single embryo 44


title: Metazome_Drosophila_timecourse_sample_0046

source_name: single embryo 46


title: Metazome_Drosophila_timecourse_sample_0045

source_name: single embryo 45


title: Metazome_Amphimedon_timecourse_sample_0033

source_name: single embryo 33


title: Metazome_Amphimedon_timecourse_sample_0035

source_name: single embryo 35

value: cleavage


title: Metazome_Drosophila_timecourse_sample_0043

source_name: single embryo 43


title: Metazome_Amphimedon_timecourse_sample_0030

source_name: single embryo 30


title: Metazome_Drosophila_timecourse_sample_0041

source_name: single embryo 41


title: Metazome_Amphimedon_timecourse_sample_0029

source_name: single embryo 29


title: Metazome_Drosophila_timecourse_sample_0039

source_name: single embryo 39


title: Metazome_Drosophila_timecourse_sample_0040

source_name: single embryo 40


title: Metazome_Drosophila_timecourse_sample_0038

source_name: single embryo 38


title: Metazome_Drosophila_timecourse_sample_0036


title: Metazome_Amphimedon_timecourse_sample_0034

source_name: single embryo 34


title: Metazome_Amphimedon_timecourse_sample_0028

source_name: single embryo 28


title: Metazome_Drosophila_timecourse_sample_0035


title: Metazome_Drosophila_timecourse_sample_0034


title: Metazome_Drosophila_timecourse_sample_0047

source_name: single embryo 47


title: Metazome_Drosophila_timecourse_sample_0033


title: Metazome_Amphimedon_timecourse_sample_0027

source_name: single embryo 27


title: Metazome_Drosophila_timecourse_sample_0032

source_name: single embryo 32


title: Metazome_Drosophila_timecourse_sample_0030


title: Metazome_Drosophila_timecourse_sample_0031

source_name: single embryo 31


title: Metazome_Amphimedon_timecourse_sample_0026

source_name: single embryo 26


title: Metazome_Amphimedon_timecourse_sample_0032


title: Metazome_Amphimedon_timecourse_sample_0025

source_name: single embryo 25


title: Metazome_Drosophila_timecourse_sample_0029


title: Metazome_Drosophila_timecourse_sample_0028


title: Metazome_Amphimedon_timecourse_sample_0031


title: Metazome_Drosophila_timecourse_sample_0027


title: Metazome_Drosophila_timecourse_sample_0042

source_name: single embryo 42


title: Metazome_Drosophila_timecourse_sample_0026


title: Metazome_Amphimedon_timecourse_sample_0024

source_name: single embryo 24


title: Metazome_Drosophila_timecourse_sample_0037

source_name: single embryo 37


title: Metazome_Amphimedon_timecourse_sample_0023

source_name: single embryo 23


title: Metazome_Drosophila_timecourse_sample_0025


title: Metazome_Drosophila_timecourse_sample_0023


title: Metazome_Drosophila_timecourse_sample_0020

source_name: single embryo 20


title: Metazome_Amphimedon_timecourse_sample_0020


title: Metazome_Drosophila_timecourse_sample_0019

source_name: single embryo 19


title: Metazome_Drosophila_timecourse_sample_0022

source_name: single embryo 22


title: Metazome_Drosophila_timecourse_sample_0018

source_name: single embryo 18


title: Metazome_Amphimedon_timecourse_sample_0019


title: Metazome_Drosophila_timecourse_sample_0021

source_name: single embryo 21


title: Metazome_Amphimedon_timecourse_sample_0018


title: Metazome_Drosophila_timecourse_sample_0016

source_name: single embryo 16


title: Metazome_Amphimedon_timecourse_sample_0017

source_name: single embryo 17


title: Metazome_Drosophila_timecourse_sample_0015

source_name: single embryo 15


title: Metazome_Amphimedon_timecourse_sample_0016


title: Metazome_Drosophila_timecourse_sample_0014

source_name: single embryo 14


title: Metazome_Amphimedon_timecourse_sample_0022


title: Metazome_Drosophila_timecourse_sample_0017


title: Metazome_Amphimedon_timecourse_sample_0015


title: Metazome_Drosophila_timecourse_sample_0024


title: Metazome_Drosophila_timecourse_sample_0012

source_name: single embryo 12


title: Metazome_Drosophila_timecourse_sample_0013

source_name: single embryo 13


title: Metazome_Amphimedon_timecourse_sample_0021

value: late spot


title: Metazome_Amphimedon_timecourse_sample_0014


title: Metazome_Drosophila_timecourse_sample_0006

source_name: single embryo 6


title: Metazome_Amphimedon_timecourse_sample_0013


title: Metazome_Drosophila_timecourse_sample_0008

source_name: single embryo 8


title: Metazome_Drosophila_timecourse_sample_0009

source_name: single embryo 9


title: Metazome_Drosophila_timecourse_sample_0007

source_name: single embryo 7


title: Metazome_Drosophila_timecourse_sample_0010

source_name: single embryo 10


title: Metazome_Drosophila_timecourse_sample_0004

source_name: single embryo 4


title: Metazome_Drosophila_timecourse_sample_0005

source_name: single embryo 5


title: Metazome_Drosophila_timecourse_sample_0003

source_name: single embryo 3


title: Metazome_Amphimedon_timecourse_sample_0011

source_name: single embryo 11


title: Metazome_Drosophila_timecourse_sample_0001

source_name: single embryo 1


title: Metazome_Amphimedon_timecourse_sample_0010


title: Metazome_Drosophila_timecourse_sample_0002

source_name: single embryo 2


title: Sample6_Rep3_Nanog+E-cadherin-

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Department of Regenerative Biology

institute: University of Wisconsin

data_processing:
Low quality reads were removed ( <30) and High quality reads were trimmed and adapters clipped using FASTX-Toolkit
Processed reads were aligned to the mm9 genome using bowtie
Expression level was determined by RSEM 1.2.4 with forward probability of 0.5
Genome_build: mm9
Supplementary_files_format_and_content: txt file containing gene expression values in FPKM, TPM, and expected counts

growth_protocol: Neural Stem Cells were isolated from postnatal day4 mice and expanded in NSC media until confluent, then frozen. Mice were homozygous for a dox-inducible Oct4-Sox2-c-Myc, Klf4 (Stemcca )allele in the ColA1 locus and heterozygous for the reverse tetracycline transcriptional activator (rtta) in the Rosa26 locus.

extract_protocol:
NSC reprogramming culture from day7 was trypsinised, passed thru a 70uM filer, fixed in perm/fix buffer (BD bioscience) then stained with an Alexa fluor conjugated E-cadherin antibody. After washing cells were permeabilized with perm/wash buffer and stained for Alexa-647 conjugated Nanog in the presence of Rnase inhibitors. After washing populations were sorted based on Nanog/E-cadherin expression. Sorted cells were decrosslinked using the PKD buffer from the FFPE kit (Qiagen) and RNA was isolated using RNAeasy kit (Qiagen).
Library was constructed by Illumina TruSeq RNA Sample Preparation Kit following Illumina's protocol

treatment_protocol: NSCs were plated on gelatin coated plates and reprogramming was induced by the addition of doxycycline until day 7.

tag: strain

value: mixed 129/Black 6

tag: source cell type

value: Neural Stem Cells (NSCs)

tag: sorted population

value: Nanog Positive and E-cadherin Negative population after 7 days of Oct4, Sox2, c-Myc and Klf4 induction


title: Metazome_Drosophila_timecourse_sample_0011


title: Metazome_Amphimedon_timecourse_sample_0009

tag: developmental stage


title: Sample5_Rep3_Nanog+E-cadherin+

value: Nanog Positive and E-cadherin Positive population after 7 days of Oct4, Sox2, c-Myc and Klf4 induction


title: Metazome_Amphimedon_timecourse_sample_0007


title: Sample3_Rep2_Nanog+E-cadherin+


title: Metazome_Amphimedon_timecourse_sample_0008


title: Sample2_Rep1_Nanog+E-cadherin-


title: Metazome_Amphimedon_timecourse_sample_0006


title: Sample1_Rep1_Nanog+E-cadherin+


title: Metazome_Amphimedon_timecourse_sample_0005


title: Sample4_Rep2_Nanog+E-cadherin-


title: Metazome_Amphimedon_timecourse_sample_0002

value: ring


title: Metazome_Amphimedon_timecourse_sample_0004


title: Metazome_Amphimedon_timecourse_sample_0001

value: late ring


title: Metazome_Amphimedon_timecourse_sample_0012


title: Metazome_Amphimedon_timecourse_sample_0003


title: Input_DNA_rep1

city: Berlin

first: Marina

last: Kolesnichenko

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Center

data_processing:
Base-calling with Illumina Casava pipeline
Alignment with bowtie retaining only uniquely mapping reads
Technical replicates were merged after alignment and  likely PCR artifacts were removed using samtools
To obtain comparable total read counts we downsampled the merged bam files to a total read count of 10Mio reads
Peak calling on each biological replicate was performed with macs. Then biological replicates were used to estimate the irreproducible discovery rate (IDR). After IDR analysis reads from biological replicates were merged and jointly analysed with MACS. Final peak calls were defined as regions with IDR < 0.05 and MACS FDR < 0.05.
Overlaps between peaks of different libraries were investigated as follows. First we defined the union of all regions bound in any of the experiments and then determined overlaps with peak calls from each of the individual libraries. Peaks were annotated to the closest gene and the closest TSS within a window of 1Mb according to the annotation of Ensembl version 54.
Genome_build: hg18
Supplementary_files_format_and_content: Tab separated text containing the coordinates of the peak regions. In addition for each NFKB subunit there are the following columns: indicator variable for a peak call, IDR, Macs FDR, fold enrichment over input, read pileup and peak summit.

organism: Homo sapiens

source_name: Hodgkin Lymphoma Cell Line

growth_protocol: 90% RPMI + 10% heat inactivated FBS

extract_protocol:
Cells were fixed with 1% Formaldehyde, lysed with 50 mM Tris-HCl, pH 8, 5mM EDTA, 1% SDS, sonicated with the Bioruptor (12 cycles), Setting M, 30 sec sonication/30 sec break per cycle. Immunoprecipitation and DNA-purification was performed according to the Upstate protocol.
Libraries were prepared using Illumina's ChIP-Seq Sample Prep Kit (#IP-102-1001) according to the instructions of the manufacturer. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, size selection of the library was performed by excision of the region from 175 to 225 bp. DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Each library was validated using an Agilent 2100 bioanalyzer and sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: dsmz no

value: ACC 530


title: Input_DNA_rep3


title: p52_ChIPSeq_rep1

value: NFkB p52 Millipore #05-361, mouse mk Ab


title: Input_DNA_rep2


title: Input_DNA_rep4


title: p52_ChIPSeq_rep2

value: NFkB p52 Millipore #06-413, rabbit pkAb


title: p50_ChIPSeq_rep1

value: NFkB p50 (C-19) #sc-1190, goat pkAb


title: RelA_ChIPSeq_rep1

value: NFkB p65 (C-20) #sc-372, rabbit pkAb


title: p50_ChIPSeq_rep2


title: Input_DNA_rep5


title: Input_DNA_rep6


title: RelB_ChIPSeq_rep2

value: RelB (C-19) #sc-226, rabbit pkAb


title: RelB_ChIPSeq_rep1


title: WT3_LPS_D2

status: Public on Feb 17 2016

city: New York

first: Jane

last: Skok

state: NY

address: 550 First Ave, Smillow 307

institute: NYU

data_processing:
Library strategy: 4C-Seq
Reads were mapped with Bowtie2 not allowing for mismatches
Self ligated and undigested fragments were removed after mapping
Genome_build: mm10
Supplementary_files_format_and_content: TXT; chr, start, end , count per fragment

source_name: Splenic B cells

growth_protocol: Mature splenic CD43 negative cells were activated for 2 days with LPS

extract_protocol:
4C template was prepared by digestion with DpnII and subsequent ligation and then a second digest with Csp6I and another ligation.
Adaptors were introduced in the gene-specific inverse PCR step
Single end 50 cycles

treatment_protocol: Cells were fixed in 2% formaldehyde

tag: genotype/variation

value: Wild-type

tag: day

tag: Stage

value: Activated

tag: cell type

value: Splenic B cells


title: WT2_LPS_D2


title: WT1_LPS_D2


title: MED1KO3_LPS_D2

value: Med1 Mutant


title: HITS-CLIP_Ctrl_2

city: Zurich

first: Claudia

last: Scheckel

address: Schmelzbergstrasse 12

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital Zurich

description: control subject

data_processing:
library strategy: HITS-CLIP
filtering (min:0-4:20,mean:5-29:20)
collapsing of exact sequences
stripping of degenerate linker (5nt; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambigous mapping)
collapsing of PCR duplicates
Genome_build: hg18
Supplementary_files_format_and_content: bed file containing genomic coordinates of unique unambigously mapped reads

growth_protocol: Frozen brain tissue from control and advanced AD subjects was obtained from the Mount Sinai Brain Bank.

extract_protocol: Brain tissue was UV irradiated and subjected to nELAVL HITS-CLIP (detailed description in accompanying paper)

tag: disease status

value: control

tag: tissue

value: brain

tag: tissue subtype

value: dorsolateral prefrontal cortex


title: HITS-CLIP_Ctrl_3

description: control subject


title: MED1KO1_LPS_D2


title: HITS-CLIP_AD_3

description: advanced Alzheimer's Disease subject

source_name: advanced Alzheimer's Disease_brain

value: advanced Alzheimer's Disease


title: HITS-CLIP_AD_1

description: advanced Alzheimer's Disease subject


title: MED1KO2_LPS_D2


title: HITS-CLIP_Ctrl_1

description: control subject


title: ZH3_B

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

data_processing:
Raw reads: adapters and low quality ends trimmed
Alignment to the reference  (STAR)
Transcript counts calculated (Genomic Ranges) and differential expression analysis performed (edgeR)
Alternative exone usage computed (DExSeq)
Discordant alleles called (GATK RNA best practices) and annotated (snpEff)
Discordant alleles  divided into putative polymorphisms and RNA editing sites
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Files with the results of the  two groups comparisons at the gene (obtained with edgeR); they also contain the full matrix of normalized transcripts counts for each sample. They are all tab separated files
Supplementary_files_format_and_content: Files with the results of the  two groups comparison at the exon (with DExSeq) level  They are all tab separated files
Supplementary_files_format_and_content: Files  with the results of the locus-level, RNA editing level from two groups comparisons. They are all tab separated files

source_name: Hippocampus

extract_protocol:
Mice under deep anaesthesia were transcardially perfused with ice-cold PBS heparin treated with diethylpyrocarbonate. Hippocampi were immediately dissected with the help of an adult mouse brain slicer matrix (Zivic Instruments), snap frozen and kept -80°C until homogenization. Total RNA was isolated using the RNeasy Plus universal mini kit (Qiagen), snap frozen, and kept at -80°C until further analysis.
Illumina TruSeq RNA standard

tag: genotype

value: Prnp-/- (coisogenic)

value: 3 months

value: male

value: hippocampus


title: ZH3_D

tag: gender


title: RelA_ChIPSeq_rep2

tag: cell line

value: ACC 530

tag: chip antibody


title: ZH3_C

tag: age


title: ZH3_A

tag: strain


title: ZH1_C

value: Prnp-/- (congenic)


title: ZH1_B


title: B6_D

value: PrnpWT/WT


title: HITS-CLIP_AD_2

description: advanced Alzheimer's Disease subject


title: ZH1_D


title: STR-resubmission rep2

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

institute: University of Bern

description: RB

data_processing:
Illumina reads were trimmed for adapters with flexbar v.2.4 (Dodt et al. 2012)
Reads were aligned against the 18b genome sequence (CP007299.1) with Bowtie2 using default parameters.
Counting over features was done with featureCounts from the Subread package v1.4.6 (Liao, Smyth, and Shi 2013).
DESeq2 (Love, Huber, and Anders 2014) was used to infer differentially expressed genes.
Genome_build: CP007299.1

organism: Mycobacterium tuberculosis

source_name: cell culture

growth_protocol: Mycobacterium tuberculosis 18b was grown at 37°C with shaking in 7H9 broth (Difco) supplemented with 10% albumin-dextrose-catalase (ADC) enrichment, 0.2% glycerol, 0.05% Tween 80, 50 μg/ml STR or on solid Middlebrook 7H10 medium (Difco) supplemented with 0.5% glycerol, 10% oleic acid-albumin-dextrose-catalase (OADC), 50 μg/ml STR.

extract_protocol:
Forty milliliters of replicating (i.e. with STR) or STR-starved M. tuberculosis 18b cultures were pelleted and cells were flash frozen in liquid nitrogen and stored at -80°C until use. Bacteria were re-suspended in 1 ml Trizol (Invitrogen) and added to a 2-ml screw-cap tube containing 0.5 ml zirconia beads (BioSpec Products). Cells were disrupted by bead-beating twice for 1 minute with a 2-minute interval on ice. The cell suspension was then transferred to a new tube, where chloroform-isoamylalcohol (24:1) extraction was performed. RNA was precipitated by adding 1/10 volume of sodium acetate (2 M, pH 5.2) and 0.7 volume of isopropanol, washed with 70% ethanol, air-dried and resuspended in DEPC-treated water. DNase treatment was carried out twice using RQ1 RNase-free DNase (Promega), following the manufacturer’s recommendations, and the reactions were subsequently cleaned up by phenol-chloroform extraction and ethanol precipitation. RNA was stored at -80°C in DEPC-treated water. Amount and purity of RNA were determined spectrophotometrically and by Qubit analysis (Life Technologies), integrity of RNA was assessed on 1% agarose gel and by Fragment Analyzer (Advanced Analytical).
100 ng of total RNA were used for library preparation according to the instructions provided in the TruSeq Stranded mRNA LT kit (Illumina). An aliquot of the library was analyzed on Qubit (Life Technologies) and Agilent Fragment Analyzer (Advanced Analytical) prior to sequencing on Illumina HiSeq 2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3.

treatment_protocol: Non-replicating, STR-starved 18b (SS18b) was generated as follows: 18b was grown to mid-logarithmic phase in STR-containing medium and washed three times in phosphate-buffered saline containing 0.05% Tween 80 (PBST). The final bacterial pellets were resuspended in medium without STR and maintained at an optical density at 600 nm (OD600) between 0.2 and 0.5 for 2 weeks (with the addition of fresh medium if necessary), by which time they had stopped replicating.

tag: condition

value: derived from the resubmission of streptomycin after four weeks of depletion.


title: ZH1_A


title: B6_A


title: STR-depletion_4weeks rep2

value: derived after 4 weeks of streptomycin depletion.


title: STR-resubmission rep1

description: RA


title: B6_B


title: STR-depletion_4weeks rep1