title: Genomic DNA from human placenta 6008581008 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636038 _ R03C02

status: Public on Jun 01 2016

type: genomic

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

country: USA

institute: Rollins School of Public Health at Emory University

description: normal infant placenta tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylatio450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Term placenta

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from Placental samples using Qiagen DNeasy Kit according to standard instructions

tag: gestational age

tag: job1 nightshift

value: No

tag: prepreg smoke

tag: maternal age yrs

tag: arousal

tag: lethargy

tag: ivf

tag: infant gender

value: Male

tag: subfertility

value: Less than 11th grade

tag: maternalrace

value: White

tag: bmi


title: Genomic DNA from human placenta 5806636041 _ R06C01

description: normal infant placenta tissue

value: Yes

value: High school graduate


title: Genomic DNA from human placenta 6008581005 _ R01C02

description: normal infant placenta tissue

tag: batch

tag: birth weight group

value: LGA

tag: attention

tag: quality of movement


title: Genomic DNA from human placenta 5859594028 _ R06C01

description: normal infant placenta tissue

value: College graduate


title: Genomic DNA from human placenta 6008581014 _ R06C01

description: normal infant placenta tissue

value: SGA


title: Genomic DNA from human placenta 5806417045 _ R03C02

description: normal infant placenta tissue

value: AGA


title: Genomic DNA from human placenta 5806636079 _ R03C02

description: normal infant placenta tissue

value: Female

value: Junior college graduate or equivalent


title: Genomic DNA from human placenta 5806636028 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720029 _ R03C01

description: normal infant placenta tissue

value: Other


title: Genomic DNA from human placenta 5859594028 _ R06C02

description: normal infant placenta tissue

value: Any post graduate schooling


title: Genomic DNA from human placenta 6008581005 _ R06C01

description: normal infant placenta tissue

value: Black


title: Genomic DNA from human placenta 5806417009 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636085 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636051 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636042 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581005 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636061 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594009 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636086 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594006 _ R01C02

description: normal infant placenta tissue

value: Asian


title: Genomic DNA from human placenta 6008581014 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636059 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636029 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636036 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594009 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417077 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636037 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417045 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636041 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636079 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417009 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417076 _ R02C01

description: normal infant placenta tissue

value: More than one


title: UM-P17

status: Public on May 13 2016

type: SRA

city: Ann Abor

first: Maureen

last: Sartor

address: 100 Washtenaw Ave.

institute: University of Michigan

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA-1.8.2
RNA-Seq reads were aligned to hg19 with tophat2 (v2.0.11) and gene read counts were quantified by HTseq (0.6.1p1) with option “-m intersection-strict” using gene annotation of UCSC hg19.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq read counts were quantified by HTSeq

molecule: total RNA

source_name: squamous cell carcinoma

extract_protocol:
Using a sterile scalpel, surface scrapings were taken directly from the frozen tissue blocks from the region of tissue identified as having at least 70% tumor cellularity. Tissue scrapings were processed using the Qiagen AllPrep DNA/RNA/Protein Mini Kit (Valencia, CA, USA) as per manufacturer protocol.
Samples were prepped using the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS-122-2001, RS-122-2002) (Illumina, San Diego, CA). Where 0.1-3ug of total RNA was converted to mRNA using a polyA purification. The mRNA is then fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3 prime ends of the cDNA is then adenylated and adapters are ligated.  One of the adapters that is ligated has a 6 nucleotide barcode that will be unique for each sample which allowed us to sequence more than one sample in each lane of a HiSeq flow cell (Illumina). The products are purified and enriched by PCR to create the final cDNA library.

tag: tumor stage

value: IVa

tag: gender

value: M

tag: hpv-status


title: UM-P15


title: UM-P14


title: UM-P13


title: Genomic DNA from human placenta 5859594009 _ R06C01

description: normal infant placenta tissue

tag: gestational age

value: No

value: Male


title: Genomic DNA from human placenta 5806636085 _ R06C01

description: normal infant placenta tissue

tag: job1 nightshift

tag: prepreg smoke

value: White


title: Genomic DNA from human placenta 5806636039 _ R05C01

description: normal infant placenta tissue

tag: maternal age yrs

tag: arousal

value: Yes


title: Genomic DNA from human placenta 5806636019 _ R06C02

description: normal infant placenta tissue

tag: lethargy

tag: ivf

value: High school graduate


title: UM-P16


title: UM-P10

value: III


title: Genomic DNA from human placenta 3999997076 _ R06C02

description: normal infant placenta tissue

tag: infant gender

tag: subfertility


title: UM-P08

value: IVb


title: Genomic DNA from human placenta 5806636063 _ R04C01

description: normal infant placenta tissue

value: College graduate

tag: maternalrace

tag: bmi


title: Genomic DNA from human placenta 5806636028 _ R05C02

description: normal infant placenta tissue


title: UM-P04


title: UM-P05


title: UM-P02


title: UM-P09


title: UM-P07


title: UM-P01


title: UM-P06


title: UM-N18

value: Neg


title: Genomic DNA from human placenta 6190781088 _ R05C01

description: normal infant placenta tissue

value: Female


title: Genomic DNA from human placenta 5806636086 _ R03C02

description: normal infant placenta tissue


title: UM-N17


title: Genomic DNA from human placenta 5806417081 _ R02C01

description: normal infant placenta tissue

tag: batch

tag: birth weight group

value: AGA


title: UM-P03

value: III or IV


title: Genomic DNA from human placenta 5806636083 _ R05C01

description: normal infant placenta tissue

value: Junior college graduate or equivalent


title: Genomic DNA from human placenta 5806636035 _ R03C02

description: normal infant placenta tissue


title: UM-N11


title: UM-N14

value: II

value: F


title: UM-N13

value: IVa


title: UM-N10


title: Genomic DNA from human placenta 3999997080 _ R04C02

description: normal infant placenta tissue

tag: attention

tag: quality of movement

value: Other


title: UM-N15

tag: tumor stage

tag: gender


title: UM-N06

value: M

tag: hpv-status


title: UM-N09


title: UM-N04


title: Genomic DNA from human placenta 5806636086 _ R01C01

description: normal infant placenta tissue

tag: gestational age

tag: job1 nightshift

value: No


title: UM-N05


title: UM-N07


title: UM-N03


title: UM-N08


title: Genomic DNA from human placenta 3999997072 _ R03C02

description: normal infant placenta tissue

value: White


title: Genomic DNA from human placenta 3999997114 _ R04C02

description: normal infant placenta tissue

value: SGA


title: UM-P18


title: UM-N01


title: UM_N07_Blood

description: BT61: UM_N07_Blood

hyb_protocol: standard Illumina hybridisation protocol

scan_protocol: standard Illumina scanning protocol for BeadChip Arrays

data_processing:
The scanned data files were processed by GenomeStudio (Illumina) Genotyping Analysis Modulue (v1.9.4)
Genotype: AA, AB, BB or NC(no call)

label: biotin(C,G) ; dinitrophenyl (A, T)

source_name: Blood

label_protocol: standard Illumina labelling protocol

extract_protocol: The tumor DNA was prepared using Qiagen AllPrep DNA/RNA/protein Mini Kit prep and the blood DNA was isolated using the Qiagen QIAamp Blood DNA Mini Kit.

tag: turmor stage


title: UM_N08_Blood

description: BT62: UM_N08_Blood


title: UM_N18_Blood

description: BT72: UM_N18_Blood


title: UM_N06_Blood

description: BT60: UM_N06_Blood


title: UM-N02


title: UM-N12


title: UM_N15_Blood

description: BT69: UM_N15_Blood


title: Genomic DNA from human placenta 5806417064 _ R06C02

description: normal infant placenta tissue

tag: prepreg smoke

tag: maternal age yrs

tag: arousal


title: UM_N05_Blood

description: BT59: UM_N05_Blood


title: UM_N04_Blood

description: BT58: UM_N04_Blood


title: UM_N03_Blood

description: BT57: UM_N03_Blood


title: UM_N13_Blood

description: BT67: UM_N13_Blood


title: UM_N12_Blood

description: BT66: UM_N12_Blood


title: UM_N17_Blood

description: BT71: UM_N17_Blood


title: UM_N14_Blood

description: BT68: UM_N14_Blood


title: UM_P18_Blood

description: BT54: UM_P18_Blood


title: UM_N10_Blood

description: BT64: UM_N10_Blood


title: UM_N11_Blood

description: BT65: UM_N11_Blood


title: UM_N16_Blood

description: BT70: UM_N16_Blood


title: UM_P17_Blood

description: BT53: UM_P17_Blood


title: UM_P08_Blood

description: BT44: UM_P08_Blood


title: UM_N02_Blood

description: BT56: UM_N02_Blood


title: UM_N01_Blood

description: BT55: UM_N01_Blood


title: UM_N09_Blood

description: BT63: UM_N09_Blood


title: UM_P14_Blood

description: BT50: UM_P14_Blood


title: UM_P10_Blood

description: BT46: UM_P10_Blood


title: UM_P04_Blood

description: BT40: UM_P04_Blood


title: UM_P16_Blood

description: BT52: UM_P16_Blood


title: UM_P07_Blood

description: BT43: UM_P07_Blood


title: UM_P15_Blood

description: BT51: UM_P15_Blood


title: UM_P11_Blood

description: BT47: UM_P11_Blood


title: UM_P13_Blood

description: BT49: UM_P13_Blood


title: UM_P05_Blood

description: BT41: UM_P05_Blood


title: UM_P12_Blood

description: BT48: UM_P12_Blood


title: UM_N18_Tumor

description: BT36: UM_N18_Tumor

source_name: Head and neck squamous cell carcinoma


title: UM_P09_Blood

description: BT45: UM_P09_Blood


title: UM_P02_Blood

description: BT38: UM_P02_Blood


title: UM_P03_Blood

description: BT39: UM_P03_Blood


title: UM_N16_Tumor

description: BT34: UM_N16_Tumor


title: UM_N07_Tumor

description: BT25: UM_N07_Tumor


title: UM_N14_Tumor

description: BT32: UM_N14_Tumor


title: UM_N05_Tumor

description: BT23: UM_N05_Tumor


title: UM_P06_Blood

description: BT42: UM_P06_Blood


title: UM_P01_Blood

description: BT37: UM_P01_Blood


title: UM_N10_Tumor

description: BT28: UM_N10_Tumor


title: UM_N08_Tumor

description: BT26: UM_N08_Tumor


title: UM_N15_Tumor

description: BT33: UM_N15_Tumor


title: UM_N06_Tumor

description: BT24: UM_N06_Tumor


title: UM_N13_Tumor

description: BT31: UM_N13_Tumor


title: UM_N02_Tumor

description: BT20: UM_N02_Tumor


title: UM_N11_Tumor

description: BT29: UM_N11_Tumor


title: UM_N03_Tumor

description: BT21: UM_N03_Tumor


title: UM_N09_Tumor

description: BT27: UM_N09_Tumor


title: UM_P18_Tumor

description: BT18: UM_P18_Tumor


title: UM-N16


title: UM_P17_Tumor

description: BT17: UM_P17_Tumor


title: UM_N17_Tumor

description: BT35: UM_N17_Tumor


title: UM_P08_Tumor

description: BT8: UM_P08_Tumor


title: UM_P10_Tumor

description: BT10: UM_P10_Tumor


title: UM_P16_Tumor

description: BT16: UM_P16_Tumor


title: UM_P15_Tumor

description: BT15: UM_P15_Tumor


title: UM_P05_Tumor

description: BT5: UM_P05_Tumor


title: UM_P06_Tumor

description: BT6: UM_P06_Tumor


title: UM_P11_Tumor

description: BT11: UM_P11_Tumor


title: UM_P12_Tumor

description: BT12: UM_P12_Tumor

value: IVB


title: UM_N12_Tumor

description: BT30: UM_N12_Tumor


title: UM_P03_Tumor

description: BT3: UM_P03_Tumor


title: UM_N04_Tumor

description: BT22: UM_N04_Tumor


title: UM_P04_Tumor

description: BT4: UM_P04_Tumor

value: III


title: UM_P13_Tumor

description: BT13: UM_P13_Tumor


title: UM-P12


title: UM_P09_Tumor

description: BT9: UM_P09_Tumor

value: IVb


title: UM_P01_Tumor

description: BT1: UM_P01_Tumor


title: UM_P02_Tumor

description: BT2: UM_P02_Tumor


title: WT_RF_ZT10_B_RFP

status: Public on Nov 10 2015

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

description: Ribosome-protected mRNA fragments

data_processing:
Library strategy: Ribosome profiling
Footprint sequences were first aligned against rRNA and tRNA sequences (obtained using http://genome.ucsc.edu/, filtered on rRNA and tRNA) using STAR 2.3.0 with options --seedSearchStartLmax 15 --clip3pAdapterSeq TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC --outReadsUnmappedFastx.
Unmapped reads were then aligned with the same options to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions
A custom Perl script was used to quantify reads. For each Ensembl gene, all the exons of the respective annotated protein-coding transcripts were used. Reads up to one mismatch with size between 29 nt and 35 nt were quantified considering read orientation. Uniquely mapping and multi-mapping reads were reported independently
Reads count were normalized by the respective library size and average size of transcripts coding region. Log2 expression levels were calculated
Genome_build: mm10
Supplementary_files_format_and_content: Log2 Normalized read count (RPKM)

organism: Mus musculus

source_name: Liver Total RNA

extract_protocol:
Ribosome unprotected-mRNAs were digested with RNAse I (350 U/mg of protein, Invitrogen) and resulting footprints were isolated and extracted with classical methods using guanidium  thiocyanate lysis buffer.
Eluted RNA (50 – 250 ng) was heat denatured 3 min at 65°C. The 3’-terminal cyclophosphate resulting from the RNAse I digestion was removed in a 50 L reaction with 10 U of T4 PNK (New England Biolabs) in the absence of ATP. After 60 min incubation at 37°C, ATP is supplemented to a final concentration of 1 mM together with an addition of 10 U T4 PNK and reaction is further incubated 60 min at 37°C. Libraries were generated using Truseq Small RNA kit  (Illumina) or NEXTflex™ Small RNA Sequencing Kit v2. For both methods, manufacturer's recommendations were stricly followed.

treatment_protocol: Immediately after the organ collection, livers were homogenized in lysis buffer containing 20 mM HEPES (pH 7.6), 250 mM NaCl, 10 mM MgCl2, 10 mM DTT, 20 µg/ml cycloheximide, 10 U/µl RNase inhibitor (New England Biolabs), and a protease inhibitor cocktail containing 0.5 mM PMSF, 10 µg/ml Aprotinin, 0.7 µg/ml Pepstatin A, and 0.7 µg/ml Leupeptin.

tag: strain

tag: tissue

value: Liver

tag: age

value: 10-14 weeks

tag: feeding

value: Night restricted

tag: genotype

value: Wild type


title: UM_N01_Tumor

description: BT19: UM_N01_Tumor

value: Neg


title: WT_RF_ZT06_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT14_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT02_B_RFP

description: Ribosome-protected mRNA fragments


title: UM_P14_Tumor

description: BT14: UM_P14_Tumor


title: WT_RF_ZT14_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT06_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT22_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT18_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT10_A_RFP

description: Ribosome-protected mRNA fragments


title: UM_P07_Tumor

description: BT7: UM_P07_Tumor


title: UM-P11


title: WT_RF_ZT02_A_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT22_D_RFP

description: Ribosome-protected mRNA fragments

value: Bmal -/-


title: WT_RF_ZT18_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT22_B_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT10_D_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT14_D_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT06_D_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT18_C_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT02_D_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT10_C_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT22_C_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT14_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT22_D_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT02_C_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT06_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT14_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT10_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT06_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT18_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT02_D_RFP

description: Ribosome-protected mRNA fragments


title: KO_RF_ZT18_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT22_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT14_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT18_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT06_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT22_D_RFP

description: Ribosome-protected mRNA fragments

value: Ad Libitum


title: WT_AL_ZT20_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT14_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT10_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT12_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT08_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT06_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT18_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT04_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT22_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT00_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT20_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT02_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT18_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT14_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT10_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT02_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT10_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT12_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT08_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT16_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT16_D_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT02_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT04_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT20_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT22_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT18_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT00_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT16_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT14_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT12_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT10_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT08_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT00_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT22_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT06_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT02_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT16_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT20_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT04_B_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT18_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT10_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT06_C_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT14_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT08_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT02_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT12_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT06_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_AL_ZT04_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT22_B_RNA

data_processing:
Paired end reads were aligned to the  genome index build with Ensembl annotation index using STAR with option --alignIntronMax 1000000
Using Ensembl annotations, we defined a gene body by merging all the respective transcripts using Bedtools(70). A region is defined as exonic if it occurs in a least one of the transcripts while an intronic region has to be shared between all the transcripts. Using a custom Perl script, we assigned uniquely mapping paired-reads to exonic region (exon/exon and complete exon reads) or intronic region (intron-exon and complete intron reads) considering reads orientation
Reads count were normalized by the total library size and size of the sum of the respective intronic or exonic region. Log2 expression levels were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Log2 Normalized read count (RPKM)

extract_protocol:
Liver RNAs were extracted as previously described (Gachon et al, 2006) with classical methods using guanidium  thiocyanate lysis buffer.
Libraries were prepared using the TruSeq Stranded Total RNA Sample Prep Kit with the Ribo-Zero Gold depletion set (Illumina) following the manufacturer’s protocol. We used 250 ng total RNA as starting material and performed 11 PCR cycles from library amplification (optimal cycle determined with the same method as the small RNA, see above). Samples were pooled by 24, denatured, spiked with 3% PhiX and loaded onto a paired-end read flow cell v3 at a final concentration of 11 pM for a paired-end 100 cycles run, strictly following Illumina’s recommendations. Sequencing depth was equivalent to 3 samples per lane.


title: WT_RF_ZT18_B_RNA


title: WT_RF_ZT14_B_RNA


title: WT_RF_ZT10_B_RNA


title: WT_RF_ZT02_B_RNA


title: WT_RF_ZT22_A_RNA


title: WT_RF_ZT10_A_RNA


title: WT_RF_ZT18_A_RNA


title: WT_RF_ZT14_A_RNA


title: WT_RF_ZT06_B_RNA


title: WT_AL_ZT00_A_RFP

description: Ribosome-protected mRNA fragments


title: WT_RF_ZT06_A_RNA


title: WT_RF_ZT02_A_RNA


title: KO_RF_ZT14_D_RNA


title: KO_RF_ZT10_D_RNA


title: KO_RF_ZT22_C_RNA


title: KO_RF_ZT06_D_RNA


title: KO_RF_ZT06_C_RNA


title: KO_RF_ZT18_C_RNA


title: KO_RF_ZT02_D_RNA


title: KO_RF_ZT10_C_RNA


title: KO_RF_ZT14_C_RNA


title: KO_RF_ZT22_D_RNA


title: WT_RF_ZT10_D_RNA


title: WT_RF_ZT22_D_RNA


title: KO_RF_ZT02_C_RNA


title: WT_RF_ZT14_D_RNA


title: WT_RF_ZT18_D_RNA


title: WT_RF_ZT06_D_RNA


title: WT_RF_ZT02_D_RNA


title: WT_RF_ZT22_C_RNA


title: WT_RF_ZT14_C_RNA


title: WT_RF_ZT06_C_RNA


title: WT_AL_ZT16_D_RNA


title: WT_AL_ZT18_D_RNA


title: KO_RF_ZT18_D_RNA


title: WT_AL_ZT14_D_RNA


title: WT_AL_ZT22_D_RNA


title: WT_RF_ZT10_C_RNA


title: WT_RF_ZT02_C_RNA


title: WT_AL_ZT10_D_RNA


title: WT_AL_ZT08_D_RNA


title: WT_AL_ZT12_D_RNA


title: WT_AL_ZT04_D_RNA


title: WT_AL_ZT06_D_RNA


title: WT_AL_ZT00_D_RNA


title: WT_AL_ZT02_D_RNA


title: WT_RF_ZT18_C_RNA


title: WT_AL_ZT22_C_RNA


title: WT_AL_ZT20_C_RNA


title: WT_AL_ZT16_C_RNA


title: WT_AL_ZT14_C_RNA


title: WT_AL_ZT04_C_RNA


title: WT_AL_ZT10_C_RNA


title: WT_AL_ZT12_C_RNA


title: WT_AL_ZT22_B_RNA


title: WT_AL_ZT20_D_RNA


title: WT_AL_ZT02_C_RNA


title: WT_AL_ZT18_C_RNA


title: WT_AL_ZT06_C_RNA


title: WT_AL_ZT00_C_RNA


title: WT_AL_ZT18_B_RNA


title: WT_AL_ZT16_B_RNA


title: WT_AL_ZT20_B_RNA


title: WT_AL_ZT12_B_RNA


title: WT_AL_ZT14_B_RNA


title: WT_AL_ZT10_B_RNA


title: WT_AL_ZT04_B_RNA


title: WT_AL_ZT02_B_RNA


title: WT_AL_ZT08_C_RNA


title: WT_AL_ZT00_B_RNA


title: WT_AL_ZT10_A_RNA


title: WT_AL_ZT22_A_RNA


title: WT_AL_ZT16_A_RNA


title: WT_AL_ZT18_A_RNA


title: WT_AL_ZT12_A_RNA


title: WT_AL_ZT14_A_RNA


title: WT_AL_ZT20_A_RNA


title: WT_AL_ZT08_A_RNA


title: Piwi-associated smRNA from EGFP artificial piRNA expressed OSCs

status: Public on Jun 05 2015

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

description: OSC cell line is described in Saito et al., Nature 2009 [PMID 19812547]

data_processing:
For Piwi-bound small RNA-seq, reads were processed as described previously (Nishida et al., 2015).
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: CLIP-seq: Unique CLIP tag sequences with length in the range of 30-50nt.
Supplementary_files_format_and_content: Piwi-associated small RNA-seq (RIP-seq): Small RNA sequences and their read counts for small RNAs with length in the range of 20-30nt and have read count over 100.

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells (OSC), EGFP artificial piRNA expressed, Piwi IP

extract_protocol:
For smRNA library, anti-Piwi antibody (Saito et al., 2006) was used to immunopurify Piwi from OSCs, and libraries were constructed as previously described (Hirano et al., 2014).
For Piwi-associated small RNA-seq (RIP-seq), library was constructed as previously described (Hirano et al., 2014).

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell line

tag: variation

value: EGFP artificial piRNA expressed

tag: ip antibody

value: Piwi antibody (Saito et al., 2006)


title: YbCLIP in non-deleted OSCs

description:
Control for YbCLIP in tj cis-element deleted OSCs (Sample 4).
OSC cell line is described in Saito et al., Nature 2009 [PMID 19812547]

data_processing:
Library strategy: CLIP-Seq
For YbCLIP tags, reads were processed as described previously (Murota et al., 2014).
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: CLIP-seq: Unique CLIP tag sequences with length in the range of 30-50nt.
Supplementary_files_format_and_content: Piwi-associated small RNA-seq (RIP-seq): Small RNA sequences and their read counts for small RNAs with length in the range of 20-30nt and have read count over 100.

molecule: other

source_name: Ovarian Somatic Cells (OSC), no tj cis-element deletion, Yb IP

extract_protocol:
For CLIP, anti-Yb antibody (Murota et al., 2014 [PMID 24953657]) was used to immunopurify Yb from OSC after irradiation by UV (254 nm) for crosslinking. RNAs within the immunoprecipitates were extracted for library construction as described previously (Murota et al., 2014).
For CLIP-seq, library was constructed as described previously (Murota et al., 2014).

value: no tj cis-element deletion

value: Yb antibody (Murota et al., 2014)


title: YbCLIP in OSCs - rep2

source_name: Ovarian Somatic Cells (OSC), Yb CLIP

value: untreated


title: WT_AL_ZT04_A_RNA


title: WT_AL_ZT00_A_RNA


title: WT_AL_ZT08_B_RNA


title: WT_AL_ZT06_A_RNA


title: Piwi-associated smRNA from tj cis-element deleted OSCs 1

source_name: Ovarian Somatic Cells (OSC), tj cis-element deletion, Piwi IP

value: tj cis-element deletion1


title: YbCLIP in OSCs - rep1


title: WT_AL_ZT02_A_RNA


title: Piwi-associated smRNA from tj cis-element deleted OSCs 2

value: tj cis-element deletion2


title: WT_AL_ZT06_B_RNA


title: Piwi-associated smRNA from non-deleted OSCs

source_name: Ovarian Somatic Cells (OSC), no tj cis-element deletion, Piwi IP


title: ectopically expressed myc-AGO3 associated small RNA from krimp knockdown OSC

status: Public on May 28 2015

description: small RNA

data_processing:
Analysis of small RNA libraries were performed as previously described (Saito et al., 2009; Malone et al., 2009) with modifications. Detailed desscription should be published (Sato et al., 2015).
For Hiseq reads (krimp heterozygous and mutant analysis), reads were obtained as single fastq file, and devided into seven fastq files for each sample according to their barcode sequence. Tag sequences were removed at the same time to generate fastq file for each sample.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include small RNA sequences and their read counts for small RNAs with length in the range of 20-30nt and have read count over 100.

extract_protocol:
Total RNAs from ovaries were isolated using ISOGEN according to the manufacturer’s instructions. Piwi proteins were immunopurified from ovaries using specific antibodies, and associated RNAs were extracted using phenol chloroform extraction. Total RNAs and immunopurified RNAs were separated on denaturing polyacrylamide gels. For total RNAs, radioactively labeled 19mer and 28mer RNA oligos were used as size makers to extract 18-29 nt small RNAs.
Small RNA libraries (18-29 nt) were prepared using a TruSeq Small RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

value: OSC (Ovarian Somatic Cell)

tag: Sex

value: female

value: ovary

tag: ip-antibody

value: AGO3-antibody (a kind gift from Dahua Chen, Chinese Academy of Sciences, China)


title: ectopically expressed myc-Aub associated small RNA from krimp knockdown OSC

description: small RNA

value: Aub-antibody (Nishida et al., 2007)


title: AGO3 associated small RNA from aub mutant ovaries

description: small RNA

value: aub mutant

value: AGO3-antibody (Gunawardane et al., 2007)


title: ectopically expressed myc-Piwi associated small RNA from krimp knockdown OSC

description: small RNA

value: myc-antibody (Sigma, C3956)


title: AGO3 associated small RNA from OR (control) ovaries

description: small RNA

value: OregonR wildtype


title: Aub associated small RNA from krimp mutant ovaries

description: small RNA

data_processing:
Analysis of small RNA libraries were performed as previously described (Saito et al., 2009; Malone et al., 2009) with modifications. Detailed desscription should be published (Sato et al., 2015).
For Hiseq reads (krimp heterozygous and mutant analysis), reads were obtained as single fastq file, and devided into seven fastq files for each sample according to their barcode sequence.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include small RNA sequences and their read counts for small RNAs with length in the range of 20-30nt and have read count over 100.

source_name: Aub associated small RNA from krimp mutant (control) ovaries

value: krimp mutant


title: Piwi associated small RNA from krimp mutant ovaries

description: small RNA

value: Piwi-antibody (Saito et al., 2006)


title: total small RNA from krimp mutant ovaries

description: small RNA


title: YbCLIP in tj cis-element deleted OSCs

description:
Sample 4
OSC cell line is described in Saito et al., Nature 2009 [PMID 19812547] and FlyBase (http://flybase.org/reports/FBtc0010001.html).

source_name: Ovarian Somatic Cells (OSC), tj cis-element deletion, Yb IP

value: OSC

value: ovarian somatic cell line


title: Piwi associated small RNA from krimp heterozygous (control) ovaries

description: small RNA

value: krimp heterozygous


title: total small RNA from krimp heterozygous (control) ovaries

description: small RNA


title: AGO3 associated small RNA from krimp heterozygous (control) ovaries

description: small RNA


title: Aub associated small RNA from krimp heterozygous (control) ovaries

description: small RNA


title: BmAGO3 bound piRNAs from BmN4

status: Public on Dec 31 2014

data_processing:
Sequencing of the libraries generated from Siwi, BmAgo3, and Flag-Siwi IP products were performed using MiSeq (illumina). Adapter sequences were removed from obtained reads, and mapped to the B. mori genomic sequence (Mita et al., 2004) using Bowtie2 (Langmead et al., 2012), allowing zero mismatches. The genome-mapped reads were aligned to B. mori transposable element consensus sequences (kind gift from Dr. Kawaoka) using Bowtie2 for further analysis.
Genome_build: genomic sequence from kaikobase (http://sgp.dna.affrc.go.jp/), integretedseq.txt.gz
Supplementary_files_format_and_content: tab-delimited text files include genome-mapped small RNA sequences and their read counts for those with 10 or more read counts

organism: Bombyx mori

source_name: BmN4 cells

growth_protocol: BmN4 cells were grown at 27 degrees on Ex-Cell medium

extract_protocol:
Siwi, BmAgo3, and Flag-Siwi complexes were immunopurified from BmN4 cells (untreated or treated with indicated siRNAs) using anti-Siwi, anti-BmAgo3, and anti-Flag antibody bound to Dynabeads protein G (Invitrogen). The beads were washed three times with binding buffer [30 mM HEPES (pH 7.4), 150 mM potassium acetate, 5 mM magnesium acetate, 5 mM DTT, 0.1 % NP-40, 2 mg/mL pepstatin, 2 mg/mL leupeptin and 0.5% aprotinin] containing 500mM sodium chloride and twice with binding buffer. Total RNAs were eluted from the beads using phenol?chloroform and precipitated using ethanol.
small RNA-seq libraries were prepared using NEBNext Small RNA Library Sample Prep Set (New England BioLabs (NEB), E7330).

treatment_protocol: BmN4 cells were collected and Immno-precipitation was performed using Siwi or BmAGO3 antibody (generated in this study)

tag: antibody

value: anti-BmAGO3 (generated in this study)


title: Yb-CLIP from OSC

status: Public on Jun 24 2014

data_processing:
Illumina Casava1.8.1 software used for basecalling.  The average base-wise quality was checked, and those that passed quality control were subjected to the following analysis.
Raw Yb-CLIP tags were processed using the NCBI BLAST program to detect fragments of adaptor sequences, and the detected sequences were removed.
Reads were then mapped to the Release 5 assembly of the Drosophila melanogaster genome (excluding chuUextra) and to GenBank entry L03284 (the only GenBank entry that recovers hits not present in Release 5), using Burrows-Wheeler Aligner (BWA) software (Li and Durbin, 2009). Up to two mismatches were allowed.
Read realignment was performed using The Genome Analysis Toolkit (McKenna A et al., 2010). To remove potential duplicates resulting from PCR amplification, we collapsed identical reads and mappable reads with the same starting genomic positions.
Genome_build: dm3
Supplementary_files_format_and_content: Yb-CLIP tags which map uniquely to the drosophila genome and their location

source_name: Ovarian Somatic Cells (OSC)

growth_protocol: Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium)

extract_protocol: CLIP was performed basically as described previously (Wang, Z. et al., 2009). Briefly, cells were UV cross-linked by irradiating uncovered with 200 mJ/cm2 of 254 nm UV, followed by RNaseT1 (Roche) treatment. Immunoprecipitation was performed using Protein G magnetic beads (Invitrogen) and 20ug of the Yb-antibody, generated in this study. Dephosphorylation of RNA segments crosslinked to immunoprecipitated proteins was performed by calf intestinal alkaline phosphase (CIP form NEB), and the samples were 5’ end labeled, followed by SDS-page and transfer to the membrane. Protein-bound RNA signal was cut out from the membrane, and RNA was isolated by phenol/chloroform extraction. For library construction, 3’ adapter was ligated to the RNA samples, followed by 5’ adapter ligation. Adapter-ligated RNA samples were reversed transcribed using SuperScript III (Invitrogen), and PCR amplified using Pusion HF PCR master mix (NEB). See the text of the paper for detail.

value: Ovarian Somatic Cells (OSC)

tag: clip-antibody

value: Yb-antibody (generated in this study)


title: Flag-Siwi bound piRNAs from Vasa siRNA treated BmN4

description: RNA (immunoprecipitated)

data_processing:
Sequencing of the libraries generated from Siwi, BmAgo3, and Flag-Siwi IP products were performed using MiSeq (illumina). Adapter sequences were removed from obtained reads, and mapped to the B. mori genomic sequence (Mita et al., 2004) using Bowtie2 (Langmead et al., 2012), allowing zero mismatches. The genome-mapped reads were aligned to B. mori transposable element consensus sequences (kind gift from Dr. Kawaoka) using Bowtie2 for further analysis.
Genome_build: genomic sequence from kaikobase (http://sgp.dna.affrc.go.jp/), integretedseq.txt.gz
Supplementary_files_format_and_content: tab-delimited text files include genome-mapped small RNA sequences and their read counts for small RNAs with 10 or more read counts

extract_protocol:
Siwi, BmAgo3, and Flag-Siwi complexes were immunopurified from BmN4 cells (untreated or treated with indicated siRNAs) using anti-Siwi, anti-BmAgo3, and anti-Flag antibody bound to Dynabeads protein G (Invitrogen). The beads were washed three times with binding buffer [30 mM HEPES (pH 7.4), 150 mM potassium acetate, 5 mM magnesium acetate, 5 mM DTT, 0.1 % NP-40, 2 mg/mL pepstatin, 2 mg/mL leupeptin and 0.5% aprotinin] containing 500mM sodium chloride and twice with binding buffer. Total RNAs were eluted from the beads using phenol–chloroform and precipitated using ethanol.
small RNA-seq libraries were prepared using NEBNext Small RNA Library Sample Prep Set (New England BioLabs (NEB), E7330).

treatment_protocol: BmN4 cells were collected and Immuno-precipitation was performed using Flag (for Flag-Siwi expressed in RNAi samples) antibody.

tag: treatment

value: Vasa siRNA

value: anti-Flag M2 (Sigma)


title: Flag-Siwi bound piRNAs from BmAGO3 siRNA treated BmN4

description: RNA (immunoprecipitated)

value: BmAGO3 siRNA


title: Flag-Siwi bound piRNAs from Luc siRNA treated BmN4

description: RNA (immunoprecipitated)

value: Luc siRNA


title: Total smRNA-seq

status: Public on Jun 01 2014

data_processing:
small RNA-seq and MARWI-IP-seq: Adapter sequences were removed from obtained reads, and mapped to the marmoset reference genome (calJac3, WUSTL 3.2) using Bowtie (Langmead et al., 2009) allowing zero mismatches. Annotation of the reads was determined according to UCSC genome browser (Meyer et al., 2013) and Ensembl databases (Flicek et al., 2013).
RNA-seq: Adapter sequences were removed, and the reads were mapped to the marmoset reference genome (calJac3, WUSTL 3.2) using Bowtie (Langmead et al., 2009) with default parameters. Expression of each transcript was determined using TopHat (Trapnell et al., 2009) and Cufflinks (Trapnell et al., 2010), except for Argonaute proteins as these sequences were unavailable within the Ensembl data (C_jacchus3.2.1) (Flicek et al., 2013). We determined the expression of marmoset Argonaute/Piwi mRNAs by calculating the number of reads that uniquely map to the transcript sequence of each Argonaute/Piwi mRNA. These mapped reads were normalized by the length of each transcript and the total number of genome mapped reads to calculate Reads pre Kilobase per Million mapped reads (RPKM).
Genome_build: WUGSC 3.2/calJac3
Supplementary_files_format_and_content: tab-delimited text files include sequences and their read counts for genome-mapped small RNA-seq sample (smRNA-seq_smRNAreads.txt); tab-delimited text files include read counts for genome-mapped MARWI-IP small RNA-seq samples (MARWI-IP_seq_smRNAreads.txt); tab-delimited text files include RPKM values for RNA-seq samples (RNAseq_RPKM.txt).

organism: Callithrix jacchus

source_name: Testis

extract_protocol:
Testis was dissected and frozen. For MARWI-IP samples, immunoprecepitation of MARWI was performed using testis lysates followed by RNA isolation using miRNeasy kit (Qiagen, 217004). For small RNA-seq samples, RNA was harvested from the testes using miRNeasy kit (Qiagen, 217004), and the size fractionation was obtained by gel-purification from total RNA, using the Small RNA Gel Extraction kit (TaKaRa, RR065). RNA-seq samples were prepared by total RNA isolation using miRNeasy kit (Qiagen, 217004).
small RNA-seq libraries were prepared using NEBNext Small RNA Library Sample Prep Set (New England BioLabs (NEB), E7330), and RNA-seq libraries were prepared with the directional mRNA-seq library prep protocol using the TruSeq Small RNA Sample Prep Kit (Illumina, RS-200-0012).

value: Testis

value: 41 month

value: Wild Type


title: MARWI-IP-seq

description: 2 replicates

value: 41 month, 51 month


title: 16-cell_replicate3

status: Public on Feb 09 2014

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

description: pools of 10 embryos

data_processing:
CASAVA 1.6 software was used for basecalling.
Adaptor sequences and the first 5 bases were removed. Additionally, reads were trimmed from the 3'- and 5'-end with a quality cutoff of 20. Reads below a length of 30 were discarded.
Filtered reads were mapped with Tophat2 (v.2.0.3) to the bovine UMD3.1 reference genome with default parameters.
The number of reads falling into exons of genes were counted using HTSeq-count. Read counts were normalized by library size and by a variance stabilizing transformation with DESeq and differential abundances were calculated with an adj. p-value < 0.05.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: tab-delimited text file include normalized values for each gene and sample.

organism: Bos taurus

source_name: embryos

growth_protocol: IVP of bovine embryos was done as described previously . Briefly, cumulus-oocyte complexes (COCs) were aspirated from German Simmental ovaries obtained in a local abattoir and washed twice in preincubated (39°C, 5% CO2 in air) Tissue Culture Medium 199 (TCM 199; Invitrogen) supplemented with l-glutamine (100 mg/L), NaHCO3 (3 g/L), Hepes (1400 mg/L), sodium pyruvate (250 mg/L), l-lactic-Ca-salt (600 mg/L), gentamicin (55 mg/L), and 10% (v/v) estrous cow serum (ECS). For in vitro maturation (IVM) COCs were washed in TCM 199 supplemented with 0.01 U/ml of bovine FSH and bovine LH (both Sioux Biochem), transferred to four-well plates (Nunc), and matured in 400 μl of this medium for 20–24 h at 39°C in an atmosphere of 5% CO2 in humidified air. For in vitro fertilization (IVF) the matured COCs were transferred to 400 μl of Tyrode albumin lactate pyruvate (TALP) medium containing 2.2 mg/ml of sodium pyruvate, 10 μg/ml of heparin sodium salt, and 6 mg/ml of BSA, after three washes in the same medium. Then, the COCs and spermatozoa (artificial insemination straws from a commercially available Zebu bull, subjected to a 90 min swim-up after thawing) were co-incubated for 18 h at 39°C in an atmosphere of 5% CO2 in humidified air. Presumptive zygotes were mechanically denuded by vortexing and gentle pipetting; washed three times in synthetic oviduct fluid (SOF) culture medium enriched with 5% ECS, 20 μl/ml of 100× basal medium (Invitrogen), and 10 μl/ml of 100× minimum essential medium (Invitrogen). Batches of app. 20 embryos were transferred to 400-μl droplets of medium covered with mineral oil and cultured until reaching the respective stages. The culture atmosphere was 5% CO2, 5% O2, and 90% N2 at 39°C and maximum humidity. Pools of ten embryos were picked after visual inspection and snap frozen in liquid nitrogen after washing in PBS. Stages collected for sequencing were: denuded oocytes before and after maturation and embryos at the 4-cell, 8-cell, 16-cell, and blastocyst stages.

extract_protocol:
Frozen pools of ten oocytes or embryos were thawed and lysed in 10 µl of Lysis Buffer (Prelude kit from NuGEN, San Carlos USA). cDNA was generated and amplified with the ovation RNAseq v2 kit (NuGEN, San Carlos, USA).
In brief 1 µl of the lysate was used for mixed random-/polyA-primed first-strand cDNA synthesis. After second strand synthesis the double-stranded cDNA was amplified by single primer isothermal amplification and the amplified cDNA was bead-purified (AmpureXP, Beckman-Coulter, Brea, USA) and fragmented by sonication (Bioruptor, Diagenode, Liege Belgium; 25 cycles 30 sec on/30 sec off). 500 ng of fragmented cDNA were used for preparation of Illumina-compatible sequencing libraries using the NuGEN Rapid library kit according to the manufacturer’s protocol. Adapter ligation was done with sample-specific barcodes. The resulting library was amplified (KAPA hifi polymerase, 8 cycles, 95°C 80 sec, 55°C 30 sec, 72°C 60 sec) and quantified on a Bioanalyzer 2100 (Agilent, Santa Clara, USA). Barcoded libraries were pooled at 10 nM concentration for multiplexed sequencing. Three replicates of each stage were sequenced on an Illumina GAIIx to a mean coverage of 20 Mio reads each. Sequencing runs were done in single-read mode with an 80 base read-length.

tag: Stage

tag: breed

value: German Simmental x Brahman


title: 16-cell_replicate2

description: pools of 10 embryos


title: 16-cell_replicate1

description: pools of 10 embryos


title: PolII ChIP-seq from Mael-KD

status: Public on Aug 01 2013

description: Sample 9

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt software, then mapped to dm3 whole genome and repbase transposable elements using bowtie2 v2.0.0 with default parameters
For calculation of Reads Per Million mapped reads (RPM) of transposable elements, dm3 genome and repbase transposable element mapping result was processed using in-house perl script. In short, number of reads falling in the transposable elements were counted and normalized by the count of genome mapped reads.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include tag density for each transposable element (normalized by Reads Per Million mapped reads (RPM))

source_name: Mael-KD_PolII ChIP-seq

extract_protocol:
Crosslinking chomatin was sheared to 200bp using a Covaris S2 ultrasonicators, immunoprecipitated using anti-Pol II antibody 8WG16 (Santa Cruz). After reversing the cross-linking, samples were treated with RNase A and then DNA was recovered.
The deep sequencing libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (NEB)

treatment_protocol: OSC were transfected once with siRNAs and analyzed after 2 days

tag: transfected with

value: siRNA against Mael

tag: chip antibody

value: anti-Pol II antibody 8WG16

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: RNA-seq from CG3893-KD

description: Sample 5

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt software, discarded reads shorter than 20bp, then mapped to dm3 whole genome and repbase transposable elements using bowtie2 v2.0.0 with default parameters
For calculation of Reads Per Kilobase per Million mapped reads (RPKM) of transposable elements, dm3 genome and repbase transposable element mapping result was processed using in-house perl script. In short, number of reads falling in the transposable elements were counted and normalized by the count of genome mapped reads and the length of each transposable element.
Reads Per Kilobase of exon model per Million mapped reads (RPKM) for transcripts was calculated using TopHat v2.0.7/Cufflinks v.2.0.2 with parameters -G (genes.gtf from Illumina iGenomes) --microexon_search
Genome_build: dm3 (Release 5; GCA_000001215.2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each transcript (*transcript.txt) and transposable elements (*TE.txt)

source_name: RNAi knockdown of CG3893

extract_protocol:
Total RNAs were isolated with the ISOGEN reagent (NipponGene). Poly(A)-RNAs were obtained using Oligo-dT beads.
The deep sequencing libraries were prepared according to TruSeq RNA Sample Prep Kit (Illumina).

value: siRNA against CG3893


title: PolII ChIP-seq from Piwi-KD

description: Sample 8

source_name: Piwi-KD_PolII ChIP-seq

value: siRNA against Piwi


title: PolII ChIP-seq from Control-KD

description: Sample 7

source_name: EGFP-KD_PolII ChIP-seq

value: siRNA against EGFP


title: RNA-seq from HP1a-KD

description: Sample 6

source_name: RNAi knockdown of HP1a

value: Ovarian Somatic Cells (OSC)

value: siRNA against HP1a


title: PolII ChIP-seq from CG3893-KD

description: Sample 10

source_name: CG3893-KD_PolII ChIP-seq


title: RNA-seq from Piwi-KD

description: Sample 2

source_name: RNAi knockdown of Piwi


title: RNA-seq from Mael-KD

description: Sample 4

source_name: RNAi knockdown of Mael


title: RNA-seq from Armi-KD

description: Sample 3

source_name: RNAi knockdown of Armi

value: siRNA against Armi


title: RNA-seq from Control-KD

description: Sample 1

source_name: RNAi knockdown of EGFP

value: siRNA against EGFP (cotnrol)


title: RNA-seq

description: 2 replicates

tag: tissue

tag: age

tag: genotype


title: Siwi bound piRNAs from BmN4

value: anti-Siwi (generated in this study)


title: preT.ETP.Th#8

status: Public on Dec 28 2011

type: RNA

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: preT.ETP.Th#8, Early T Lineage Progenitor

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: thymus

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: Filter/syringe plunger teasing, ACK lysis  Lin+ magnetic depletion (Dynobeads), 2 rounds of sorting, 2d sort directly into trizol

value: 6 weeks

tag: exclusion markers

value: CD19 CD138 B220 IgL-kappa IgL-lamda)

tag: genetic background

tag: phenotype markers

value: Lin-/lo CD25- CD44+ cKit+

tag: separation method

value: dissection/trimming

value: male


title: preT.ETP.Th#7

description: preT.ETP.Th#7, Early T Lineage Progenitor

tag: Sex


title: T.DN4.Th#5

status: Public on Sep 07 2011

description: T.DN4.Th#5, DN4 thymocytes

value: Lin= CD4, CD8a, TCRb, TCRgd, CD11b, CD11c, NK1.1, Gr1, CD19, Ter119

value: Lin-/lo CD25- CD44- CD28+


title: T.DN4.Th#6

description: T.DN4.Th#6, DN4 thymocytes


title: T.DN4.Th#4

description: T.DN4.Th#4, DN4 thymocytes


title: preT.DN3A.Th#3

description: preT.DN3A.Th#3, DN3a thymocytes

value: Lin-/lo CD25hi CD44- CD28-


title: preT.DN3A.Th#2

description: preT.DN3A.Th#2, DN3a thymocytes


title: preT.DN3B.Th#3

description: preT.DN3B.Th#3, DN3b thymocytes

value: Lin-/lo CD25hi CD44- CD28+


title: preT.DN2.Th#5

description: preT.DN2.Th#5, DN2 thymocytes

value: Lin-/lo CD25hi CD44+ cKit+


title: Tgd.Th#3

status: Public on Dec 02 2009

description: Tgd.Th#3, Thymic TCRgamma-delta, all DN

extract_protocol: Glass Tissue Grinder  CD4 & CD8 Dynal Magnetic Bead Depletion  Flow Sorting

value: TCRd+ CD3e+


title: preT.DN3B.Th#1

description: preT.DN3B.Th#1, DN3b thymocytes


title: T.8SP24-.Th#3

status: Public on May 02 2009

description: T.8SP24-.Th#3, CD8 Single-Positive, Mature

extract_protocol: Glass slide teasing  Flow sorting


title: NKT.44+NK1.1+.Th#1

status: Public on Apr 29 2010

description: NKT.44+NK1.1+.Th#1, Developing thymic iNKT cells, stage 3

extract_protocol: homogenize, stain  MACS, doube sort FACS Aria

value: Ter119 CD19 CD11c CD11b Ly6/Gr-1 CD8a PI CD8a

value: aGC CD1d tet CD3e CD44 NK1.1


title: NKT.44+NK1.1+.Th#4

description: NKT.44+NK1.1+.Th#4, Developing iNKT cells from thymus, stage 3

extract_protocol: homogenize, stain  MACS, double sort (Aria)


title: preT.ETP.Th#6

description: preT.ETP.Th#6, Early T Lineage Progenitor

value: Lin= CD4 CD8a TCRb TCRgd CD11b CD11c NK1.1 Gr1 Ter119 CD19


title: NKT.44+NK1.1+.Th#2

description: NKT.44+NK1.1+.Th#2, Developing thymic iNKT cells, stage 3


title: preT.DN3B.Th#2

description: preT.DN3B.Th#2, DN3b thymocytes


title: T.ISP.Th#3

description: T.ISP.Th#3, Immature Single-Positive


title: Tgd.Th#2

description: Tgd.Th#2, Thymic TCRgamma-delta, all DN


title: T.ISP.Th#2

description: T.ISP.Th#2, Immature Single-Positive


title: Tgd.Th#1

description: Tgd.Th#1, Thymic TCRgamma-delta, all DN


title: preT.DN2.Th#6

description: preT.DN2.Th#6, DN2 thymocytes


title: preT.DN3A.Th#1

description: preT.DN3A.Th#1, DN3a thymocytes


title: T.ISP.Th#1

description: T.ISP.Th#1, Immature Single-Positive


title: T.8SP24-.Th#1

description: T.8SP24-.Th#1, CD8 Single-Positive, Mature


title: T.DP.Th#2

description: T.DP.Th#2, Double-Positive, All


title: T.8SP24-.Th#2

description: T.8SP24-.Th#2, CD8 Single-Positive, Mature


title: T.DP.Th#1

description: T.DP.Th#1, Double-Positive, All


title: T.DP.Th#3

description: T.DP.Th#3, Double-Positive, All


title: preT.DN2.Th#4

description: preT.DN2.Th#4, DN2 thymocytes


title: ADM day 2 to 4 miRNA

status: Public on Jul 02 2010

city: Tsu

first: Naohito

last: Aoki

address: 1577 Kurimamachiya-cho

department: Graduate School of Bioresources

institute: Mie University

description: miRNA profiles of ADMs secreted by 3T3-L1 adipocytes (Day 2-4)

hyb_protocol: Hybridization was done by using miRNA labeling Reagent & Hybridization Kit (5190-0408, Agilent).

scan_protocol: Scanned on an Agilent Microarray scanner.  Images were quantified using Agilent Feature Extraction Software (version 9.5.3).

data_processing: Agilent GeneSpingGX Software was used for data processing.

source_name: ADM, Day2-4, 3T3-L1 adipocyte

label_protocol: 100 ng of total RNA was first dephosphorylated by using  calf intestine alkaline phosphatase (TaKaRa) and labeled by using miRNA labeling Reagent & Hybridization Kit (5190-0408, Agilent).

extract_protocol: Total RNAs were extracted using Trizol reagenet (invitrogen) following manufacturer's instructions

treatment_protocol: 3T3-L1 cells were cultured in DMEM (high glucose) containing 10% FCS and  induced into adipocytes with insulin (10µg/ml), dexamethasone (0.25µM) and 3-isobutyl-1-methylxanthine (0.5mM).  The 48h-conditioned medium of Day2-4 and Day8-10 3T3-L1 adipocytes was harvested and the ADMs were prepared by ultracentrifugation followed by RNA preparation.

tag: cell line

tag: sample type

value: microvesicles


title: ADM day 8 to 10 miRNA

description: miRNA profiles of ADMs secreted by 3T3-L1 adipocytes (Day 8-10)

source_name: ADM, Day8-10, 3T3-L1 adipocyte