title: 14mpf_19


title: PT081_P1_B12

status: Public on Aug 11 2018

type: SRA

city: Boston

first: Simona

last: Cristea

state: Massachusetts

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

country: USA

institute: Dana-Farber Cancer Institute

library_source: transcriptomic

data_processing:
Fastq files were quantified to transcript per million (TPM) expression values with RSEM with default parameters
Low quality cells were filtered as follows: 4 median absolute deviations (MADs) below the median for any of the three metrics concering: i) library size; ii) number of expressed genes; iii) total amount of mRNA
Unexpressed genes were removed as follows: a gene was considered unexpressed if log2(TPM+1) < 0.1 in at least 95% of cells separately for each patient
Data was normalized following a three-step combination approach: i) Transform the TPM values into relative counts with the Census algorithm (Qiu et al, 2017); ii) Normalize the Census counts with the deconvolution strategy implemented in scran (Lun et al 2016); iii) Remove additional sources of variation with RUVSeq (Risso et al, 2014)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files representing: TPM values (tpm_rsem.txt); counts (counts_rsem.txt); normalized data as described above (norm_data.txt)

molecule: total RNA

organism: Homo sapiens

source_name: breast

extract_protocol:
Fresly collected human tumor samples were mechanically and enzymatically digested using tumor dissociation kit (Miltenyi Biotec). Single cells were sorted by flow cytometry, lysed and snap frozen on dry ice immediately.
RNA libraries were prepared using Smart-seq2 protocol (Picelli et al., 2014)

tag: tissue

value: breast

tag: breast cancer subtype

value: TNBC

tag: patient


title: PT081_P1_C12


title: PT081_P1_B11


title: 14mpf_18

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
Trimming using trim_galore using default parameters
Mapping using HISAT2 with default parameters
Counts per gene generated using htseq-count with default parameters
Genome_build: Zebrafish GRCz10

organism: Danio rerio

source_name: beta-cells

extract_protocol:
FACS
SMART-Seq v4

tag: age

tag: strain

tag: feeding

value: Normal


title: PT081_P1_B10


title: PT081_P1_B08


title: 14mpf_15


title: 14mpf_27


title: 14mpf_16


title: 14mpf_17


title: PT081_P1_B05


title: 14mpf_12


title: 14mpf_11


title: PT081_P1_B03


title: 14mpf_14


title: 14mpf_10


title: 14mpf_21


title: 14mpf_13


title: PT081_P1_B04


title: PT081_P1_B02


title: PT081_P1_A10


title: 14mpf_7


title: 14mpf_9


title: 14mpf_8


title: PT081_P1_B01


title: 14mpf_6


title: PT081_P1_A08


title: PT081_P1_D01


title: PT081_P1_A12


title: PT081_P1_A07


title: PT081_P1_B07


title: 14mpf_5


title: 14mpf_4


title: PT081_P1_A09


title: PT081_P1_A05


title: 14mpf_3


title: 14mpf_2


title: PT081_P1_G05


title: PT081_P1_A03


title: PT081_P1_A02


title: 6mpf_91


title: 6mpf_92


title: PT081_P1_A01


title: PT058_P1_H12


title: PT058_P1_H11


title: PT081_P1_A06


title: PT058_P1_H08


title: PT058_P1_H05


title: PT058_P1_H04


title: PT058_P1_H06


title: 6mpf_86


title: 14mpf_1


title: 6mpf_88


title: 6mpf_85


title: 6mpf_83


title: 6mpf_81


title: 6mpf_82


title: PT058_P1_H01


title: PT058_P1_H02


title: 6mpf_80


title: PT058_P1_G10


title: 6mpf_90


title: 6mpf_79


title: 6mpf_89


title: PT058_P1_H03


title: 6mpf_78


title: 6mpf_77


title: PT058_P1_G07


title: 6mpf_76


title: PT058_P1_G05


title: PT058_P1_G04


title: 6mpf_87


title: PT058_P1_G03


title: 6mpf_84


title: PT058_P1_G02


title: PT058_P1_G01


title: 6mpf_74


title: 6mpf_73


title: PT058_P1_G11


title: 6mpf_72


title: 6mpf_70


title: PT058_P1_F12


title: PT058_P1_F11


title: PT058_P1_F10


title: 6mpf_69


title: 6mpf_75


title: PT058_P1_F09


title: 6mpf_68


title: PT058_P1_F08


title: PT058_P1_F07


title: 6mpf_66


title: PT058_P1_F04


title: 6mpf_65


title: 6mpf_64


title: PT058_P1_F01


title: PT058_P1_F02


title: 6mpf_71


title: PT058_P1_E12


title: PT058_P1_E11


title: PT058_P1_E10


title: 6mpf_61


title: 6mpf_62


title: 6mpf_60


title: PT058_P1_E09


title: 6mpf_67


title: PT058_P1_E07


title: 6mpf_57


title: PT058_P1_E08


title: 6mpf_58


title: 6mpf_63


title: 6mpf_59


title: PT058_P1_E06


title: 6mpf_56


title: PT058_P1_E05


title: PT058_P1_E04


title: PT081_P1_B06


title: 6mpf_54


title: 6mpf_53


title: 6mpf_52


title: PT058_P1_E02


title: PT058_P1_D12


title: PT058_P1_E01


title: 6mpf_55


title: PT058_P1_D11


title: 6mpf_50


title: 6mpf_49


title: PT058_P1_D09


title: 6mpf_47


title: PT058_P1_D06


title: PT058_P1_H07


title: 6mpf_48


title: PT058_P1_D07


title: 6mpf_46


title: 6mpf_45


title: 6mpf_44


title: PT058_P1_D03


title: 6mpf_43


title: PT058_P1_D02


title: PT058_P1_E03


title: 6mpf_42


title: PT058_P1_C12


title: 6mpf_51


title: 6mpf_41


title: PT058_P1_C11


title: 6mpf_40


title: PT058_P1_G08


title: 6mpf_39


title: PT058_P1_C08


title: PT058_P1_C09


title: 6mpf_37


title: 6mpf_38


title: 6mpf_36


title: PT058_P1_C07


title: PT058_P1_D04


title: PT058_P1_D05


title: 6mpf_33


title: 6mpf_35


title: PT058_P1_C05


title: 6mpf_34


title: PT058_P1_C06


title: PT058_P1_C01


title: PT058_P1_C04


title: 6mpf_31


title: PT058_P1_C02


title: PT058_P1_B10


title: PT058_P1_B11


title: 6mpf_30


title: 6mpf_29


title: PT058_P1_C10


title: PT058_P1_B08


title: 6mpf_28


title: 6mpf_27


title: PT058_P1_B06


title: 6mpf_26


title: PT058_P1_B04


title: 6mpf_25


title: PT058_P1_B03


title: PT058_P1_B02


title: 6mpf_24


title: PT058_P1_A12


title: 6mpf_23


title: 6mpf_22


title: PT058_P1_A11


title: 6mpf_32


title: 6mpf_21


title: PT058_P1_A10


title: 6mpf_20


title: 6mpf_19


title: PT058_P1_A06


title: PT058_P1_B09


title: 6mpf_17


title: PT058_P1_A04


title: PT058_P1_A07


title: 6mpf_16


title: PT058_P1_A02


title: 6mpf_18


title: PT058_P1_A01


title: PT058_P1_A05


title: 6mpf_14


title: PT039_P1_F10


title: 6mpf_15


title: PT039_P1_F09


title: 6mpf_13


title: PT039_P1_F07


title: PT039_P1_F08


title: PT058_P1_A08


title: 6mpf_12


title: PT039_P1_F04


title: PT039_P1_F05


title: PT039_P1_F06


title: 6mpf_11


title: PT039_P1_F02


title: PT039_P1_F03


title: 6mpf_10


title: HRDE-1-coIP small RNA

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
Remove  the 3' linker 5'-CTGTAGGCACCATCAATC-3' and the 5' 4-nt inline barcodes
Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis.
The number of reads that map to each 1 kb window throughout the genome is calculated and then normalized to the total number of reads that map to the genome. If a read maps to multiple positions in the genome (N times), it will be counted as 1/N at each position.
Genome_build: WS190(ce6)
Supplementary_files_format_and_content: File format: MS Excel file. The content includes normalized counts for each 1 kb region (row) in the genome for each library (column) used in this study.

organism: Caenorhabditis elegans

source_name: C. elegans young adults

extract_protocol:
We used FLAG Immunoprecipitation kit (Sigma Catalog# FLAGIPT1) and followed the the manufacture’s protocol to pull-down FLAG-StrepII-HRDE-1 and its bound siRNA.  Briefly, the frozen worm grind (5000-10000 adult animals, previously ground with mortar and pestle in liquid nitrogen) was first resuspended in 1ml of Lysis Buffer, 10ul of 100xHALT protease inhibitor (ThermoFisher), and 10ul of RNaseOUT (ThermoFisher).  The lysis were sonicated three times, 8 minutes each time, at 4°C using a Bioruptor (Diagenode) at high setting and 30 second on/off cycle.  Then the lysis were centrifuged at top speed for 4 minutes at 4°C.  The supernatant was mixed with ANTI-FLAG M2 affinity gel (washed and collected from 40ul resin provided by kit) and was rotated at 4°C overnight.  On the next day, the sample was centrifuged at 8,200xg for 30 seconds at 4°C and the supernatant was removed.  The resin was washed three times with 0.5ml of 1x Wash Buffer at 4°C.  FLAG-StrepII-HRDE-1 was eluted from resin with 15ug of 3xFLAG Peptide in 100ul of 1x Elution Buffer by rotating 30 minutes at 4°C. RNA was extracted from IP using TRIzol reagent.
Small RNA-seq was performed using a 5’-monophosphate-independent small RNA cloning procedure described in Gent, J.I. et al. A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference. Genetics 183, 1297–1314 (2009).

tag: developmental stage

value: young adult

tag: Sex

value: hermaphrodite

tag: inline barcode at the 5' end

value: mixture of 'CTGG','ACTG','GAAG','TGCC'


title: small RNA from N2


title: cytoplasmic enriched RNA-seq, N2, 23C for four generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib42

data_processing:
Remove the 5' 4-nt inline barcodes
Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis.
The number of reads that map to each 1 kb window throughout the genome is calculated and then normalized to the total number of reads that map to the genome. If a read maps to multiple positions in the genome (N times), it will be counted as 1/N at each position.
Genome_build: WS190(ce6)
Supplementary_files_format_and_content: File format: MS Excel file. The content includes normalized counts for each 1 kb region (row) in the genome for each library (column) used in this study.

extract_protocol:
Nuclei and cytoplasm factions were obtained using Nuclei PURE Prep kit (Sigma-Aldrich NUC-201) according to manufacture’s instruction. All procedure was performed at 4°C. Briefly, worm grinds were re-suspended in 10ml Lysis Solution with 1mM DTT and 0.1% Triton X-100. Proper grinding was confirmed by DAPI staining the lysis and microscopic examination.  The lysis was mixed with 18ml 1.8M Sucrose Cushion, loaded on top of 10ml 1.8M Sucrose Cushion Solution, and ultra-centrifuged at 30,000xg for 45 minutes at 4°C in a SW28 rotor. The clear sucrose cushion layer was collected as cytoplasm fraction and used for RNA extraction immediately.  The pellet of purified nuclei was wash with Nuclei PURE Storage Buffer, and was used as nuclear fraction for RNA extraction immediately.  RNA extraction was performed using the TRIzol Reagent. Ribosomal RNA (rRNA) was removed from the total RNA using RNase H and anti-rRNA oligo mixture. 1.25 µg of anti-rRNA oligos were mixed with 0.5 µg total RNA in 1x Hybridization Buffer (100 mM Tris-HCl pH 7.4, 200mM NaCl) in a final volume of 8 µl.  The sample was denatured at 95°C for 2 minutes, and then cooled at −0.1 °C /sec to 45°C.  Equal volumes of Hybridase Thermostable RNase H (5U/µl,Epicentre) and 10x RNaseH Reaction Buffer (500 mM Tris-HCl pH 7.4, 1 M NaCl, 200 mM MgCl2) were mixed and preheated to 45°C before use. 2 µl of the enzyme mix was added to each reaction mix, which was then incubated at 45°C for 1 hr. To remove DNA oligos, 5 µl TURBO DNase buffer, 3 µl TURBO DNase (Invitrogen), and 32 µl diH2O were added to the reaction mix, followed by 37˚C incubation for 30 minutes.  To purify RNA, 300 µl STOP solution (1 M ammonium acetate, 10 mM EDTA) was added to the reaction mix, followed by phenol/chloroform (1:1) extraction and ethanol precipitation.
The resulting RNA (without poly(A) selection) was used to prepare the RNA-seq library using the standard Illumina RNA-seq library construction protocol.

tag: generations


title: RNA-seq, hrde-1(tm1200) mutant, 23C for four generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib43


title: PT039_P1_F01


title: 6mpf_9


title: nuclear enriched RNA-seq, hrde-1(tm1200) mutant, 23C for four generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib44


title: PT039_P1_E11


title: nuclear enriched RNA-seq, N2, 23C for four generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib41


title: cytoplasmic enriched RNA-seq, hrde-1(tm1200) mutant, 23C for four generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib45


title: PT039_P1_E09


title: RNA-seq, N2, 23C for four generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib40


title: 6mpf_8


title: PT039_P1_E10


title: PT039_P1_E08


title: 6mpf_7


title: PT039_P1_E07


title: PT039_P1_E06


title: 6mpf_6


title: nuclear enriched RNA-seq, hrde-1(tm1200) mutant, 23C for three generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib38


title: PT039_P1_E05


title: PT039_P1_E03


title: RNA-seq, hrde-1(tm1200) mutant, 23C for three generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib37


title: PT039_P1_E02


title: 6mpf_4


title: cytoplasmic enriched RNA-seq, N2, 23C for three generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib36


title: 6mpf_2


title: PT039_P1_E01


title: PT039_P1_D10


title: 6mpf_1


title: PT039_P1_D07


title: nuclear enriched RNA-seq, N2, 23C for three generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib35


title: PT039_P1_D08


title: PT039_P1_D11


title: PT039_P1_D09


title: 3mpf_90


title: PT039_P1_D05


title: cytoplasmic enriched RNA-seq, hrde-1(tm1200) mutant, 23C for three generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib39


title: PT039_P1_E04


title: 6mpf_5


title: PT039_P1_D03


title: HO-20-9R

type: genomic

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: cell culture of strain HO-20-9R

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: JSC25 cells were grown in 7 mL YPD overnight to reach an OD600 of 0.2. Yeast cells (5×107) were collected by centrifugation and arrested in G1 in 1 mL YPD containing 2.5 μg α-factor at 30 degree  After two hours, H2O2 was added into the cell culture. Cell culture was incubated at  30 degree for another hour. Yeast cells were then washed twice to remove α-factor and H2O2 before plating. Yeast  cells were cultured at 30 degree  for 3 days and sectored colonies were selected for chromosome IV SNP-specific microarrays.

tag: ploidy

value: diploid strain

source_name: cell culture of JSC24

value: control strain JSC24


title: HO-20-9W

source_name: cell culture of strain HO-20-9W


title: 3mpf_89


title: PT039_P1_D02


title: PT039_P1_D01


title: 3mpf_88


title: PT039_P1_C12


title: PT039_P1_D12


title: 6mpf_3


title: PT039_P1_D06


title: RNA-seq, N2, 23C for three generations

description:
RNAseq_Normalized_cov_1kb.xlsx
SG0117_lib34


title: PT039_P1_C07


title: PT039_P1_C08


title: PT039_P1_C09


title: PT039_P1_C06


title: 3mpf_84


title: 3mpf_85


title: HO-20-7W

source_name: cell culture of strain HO-20-7W


title: PT039_P1_D04


title: HO-20-8W

source_name: cell culture of strain HO-20-8W


title: PT039_P1_C05


title: 3mpf_83


title: PT039_P1_C01


title: PT039_P1_C03


title: 3mpf_87


title: PT039_P1_C02


title: PT039_P1_B12


title: PT039_P1_C10


title: 3mpf_81


title: PT039_P1_C11


title: PT039_P1_B11


title: HO-20-8R

source_name: cell culture of strain HO-20-8R


title: PT039_P1_B10


title: PT039_P1_B09


title: 3mpf_80


title: 3mpf_79


title: PT039_P1_B08


title: PT039_P1_C04


title: PT039_P1_B07


title: PT039_P1_B06


title: 3mpf_78


title: 3mpf_82


title: 3mpf_86


title: HO-20-7R

source_name: cell culture of strain HO-20-7R


title: PT039_P1_B04


title: PT039_P1_B02


title: HO-20-4R

source_name: cell culture of strain HO-20-4R


title: 3mpf_77


title: 3mpf_76


title: PT039_P1_B01


title: PT039_P1_A12


title: HO-20-5W

source_name: cell culture of strain HO-20-5W


title: HO-20-47W

source_name: cell culture of strain HO-20-47W


title: HO-20-47R

source_name: cell culture of strain HO-20-47R


title: PT039_P1_A11


title: HO-20-4W

source_name: cell culture of strain HO-20-4W


title: HO-20-6R

source_name: cell culture of strain HO-20-6R


title: HO-20-5R

source_name: cell culture of strain HO-20-5R


title: HO-20-6W

source_name: cell culture of strain HO-20-6W


title: PT039_P1_A09

source_name: breast


title: PT039_P1_A10


title: 3mpf_74

source_name: beta-cells


title: PT039_P1_B05


title: 3mpf_73


title: 3mpf_75


title: PT039_P1_B03


title: HO-20-46W

source_name: cell culture of strain HO-20-46W


title: HO-20-46R

source_name: cell culture of strain HO-20-46R

source_name: cell culture of JSC24


title: PT039_P1_A06


title: PT039_P1_A07


title: PT039_P1_A04


title: PT039_P1_A08


title: 3mpf_72


title: PT039_P1_A05


title: 3mpf_71


title: PT039_P1_A03


title: HO-20-45R

source_name: cell culture of strain HO-20-45R


title: PT039_P1_A01


title: PT039_P1_A02


title: PT039_P11_H12_S96


title: 3mpf_69


title: HO-20-45W

source_name: cell culture of strain HO-20-45W


title: 3mpf_68


title: PT039_P11_H07_S91


title: PT039_P11_H06_S90


title: PT039_P11_H08_S92


title: 3mpf_67


title: PT039_P11_H04_S88


title: 3mpf_66


title: HO-20-3R

source_name: cell culture of strain HO-20-3R


title: PT039_P11_H03_S87


title: HO-20-40R

source_name: cell culture of strain HO-20-40R


title: HO-20-40W

source_name: cell culture of strain HO-20-40W


title: PT039_P11_H02_S86


title: PT039_P11_H01_S85


title: PT039_P11_G12_S84


title: HO-20-3W

source_name: cell culture of strain HO-20-3W


title: HO-20-44W

source_name: cell culture of strain HO-20-44W


title: PT039_P11_H10_S94


title: 3mpf_65


title: 3mpf_64


title: PT039_P11_G10_S82


title: PT039_P11_G09_S81


title: PT039_P11_G08_S80


title: HO-20-39W

source_name: cell culture of strain HO-20-39W


title: PT039_P11_G07_S79


title: HO-20-44R

source_name: cell culture of strain HO-20-44R


title: HO-20-39R

source_name: cell culture of strain HO-20-39R


title: 3mpf_70


title: 3mpf_63


title: HO-20-37W

source_name: cell culture of strain HO-20-37W


title: HO-20-38R

source_name: cell culture of strain HO-20-38R


title: 3mpf_62


title: HO-20-38W

source_name: cell culture of strain HO-20-38W


title: PT039_P11_G05_S77

source_name: breast


title: PT039_P11_G03_S75


title: PT039_P11_G04_S76


title: 3mpf_61

source_name: beta-cells


title: 3mpf_59


title: PT039_P11_F12_S72


title: PT039_P11_F11_S71


title: PT039_P11_G02_S74


title: 3mpf_60


title: PT039_P11_F07_S67


title: PT039_P11_G01_S73


title: HO-20-37R

source_name: cell culture of strain HO-20-37R


title: PT039_P11_F10_S70


title: PT039_P11_F06_S66


title: PT039_P11_F05_S65


title: 3mpf_57


title: PT039_P11_F03_S63


title: HO-20-36W

source_name: cell culture of strain HO-20-36W

source_name: cell culture of JSC24


title: HO-20-36R

source_name: cell culture of strain HO-20-36R


title: 3mpf_56


title: PT039_P11_F02_S62


title: HO-20-35W

source_name: cell culture of strain HO-20-35W


title: PT039_P11_F01_S61


title: HO-20-35R

source_name: cell culture of strain HO-20-35R


title: HO-20-34W

source_name: cell culture of strain HO-20-34W


title: 3mpf_55


title: 3mpf_54


title: PT039_P11_E09_S57


title: 3mpf_58


title: HO-20-34R

source_name: cell culture of strain HO-20-34R


title: PT039_P11_E11_S59


title: 3mpf_53


title: PT039_P11_E05_S53


title: PT039_P11_E03_S51


title: 3mpf_52


title: HO-20-33W

source_name: cell culture of strain HO-20-33W


title: PT039_P11_E01_S49


title: PT039_P11_E04_S52


title: PT039_P11_E02_S50


title: 3mpf_51


title: PT039_P11_D12_S48


title: PT039_P11_D10_S46


title: 3mpf_50


title: HO-20-33R

source_name: cell culture of strain HO-20-33R


title: PT039_P11_D09_S45


title: HO-20-32W

source_name: cell culture of strain HO-20-32W


title: 3mpf_49


title: HO-20-32R

source_name: cell culture of strain HO-20-32R


title: PT039_P11_D08_S44


title: PT039_P11_E12_S60


title: PT039_P11_D07_S43


title: PT039_P11_D05_S41


title: 3mpf_48


title: HO-20-31W

source_name: cell culture of strain HO-20-31W


title: PT039_P11_D04_S40


title: HO-20-2W

source_name: cell culture of strain HO-20-2W


title: PT039_P11_E06_S54


title: 3mpf_47


title: PT039_P11_D03_S39


title: PT039_P11_D02_S38


title: HO-20-31R

source_name: cell culture of strain HO-20-31R


title: PT039_P11_C12_S36

source_name: breast


title: PT039_P11_C11_S35


title: 3mpf_45

source_name: beta-cells


title: PT039_P11_C09_S33


title: HO-20-2R

source_name: cell culture of strain HO-20-2R


title: 3mpf_44


title: HO-20-29W

source_name: cell culture of strain HO-20-29W


title: HO-20-29R

source_name: cell culture of strain HO-20-29R

source_name: cell culture of JSC24


title: PT039_P11_C03_S27


title: PT039_P11_B11_S23


title: 3mpf_43


title: PT039_P11_C05_S29


title: PT039_P11_C06_S30


title: HO-20-28W

source_name: cell culture of strain HO-20-28W


title: PT039_P11_B10_S22


title: 3mpf_41


title: PT039_P11_B09_S21


title: HO-20-28R

source_name: cell culture of strain HO-20-28R


title: 3mpf_46


title: PT039_P11_B08_S20


title: PT039_P11_B07_S19


title: PT039_P11_D01_S37


title: 3mpf_40


title: PT039_P11_B06_S18


title: HO-20-27W

source_name: cell culture of strain HO-20-27W


title: PT039_P11_B05_S17


title: 3mpf_39


title: HO-20-27R

source_name: cell culture of strain HO-20-27R


title: PT039_P11_B02_S14


title: 3mpf_38


title: 3mpf_42


title: PT039_P11_B03_S15


title: 3mpf_37


title: PT039_P11_A11_S11


title: PT039_P11_A07_S7


title: PT039_P11_A12_S12


title: HO-20-26R

source_name: cell culture of strain HO-20-26R


title: HO-20-26W

source_name: cell culture of strain HO-20-26W


title: 3mpf_36


title: PT039_P11_A09_S9


title: HO-20-25W

source_name: cell culture of strain HO-20-25W


title: PT039_P11_A06_S6


title: 3mpf_35


title: 3mpf_34


title: PT039_P11_A03_S3


title: PT039_P11_A04_S4


title: PT039_P11_A01_S1


title: HO-20-20R

source_name: cell culture of strain HO-20-20R


title: HO-20-25R

source_name: cell culture of strain HO-20-25R


title: HO-20-20W

source_name: cell culture of strain HO-20-20W


title: PT039_P11_B04_S16


title: PT089_P9_H12_S192


title: HO-20-1R

source_name: cell culture of strain HO-20-1R


title: 3mpf_33


title: HO-20-1W

source_name: cell culture of strain HO-20-1W


title: PT089_P9_H10_S190

source_name: breast


title: PT089_P9_H11_S191


title: PT089_P9_H09_S189


title: HO-20-15W

source_name: cell culture of strain HO-20-15W


title: 3mpf_32

source_name: beta-cells


title: PT089_P9_H06_S186


title: PT089_P9_H07_S187


title: PT089_P9_H08_S188


title: 3mpf_30


title: 3mpf_31


title: HO-20-15R

source_name: cell culture of strain HO-20-15R


title: PT039_P11_A02_S2


title: PT089_P9_H01_S181


title: 3mpf_29


title: PT089_P9_H03_S183


title: PT089_P9_H05_S185


title: 3mpf_28


title: PT089_P9_H04_S184


title: PT089_P9_H02_S182


title: 3mpf_27


title: PT089_P9_G12_S180


title: PT089_P9_G11_S179


title: 3mpf_26


title: 3mpf_25


title: PT089_P9_G10_S178


title: HO-20-14W

source_name: cell culture of strain HO-20-14W

source_name: cell culture of JSC24


title: PT089_P9_G08_S176


title: PT089_P9_G09_S177


title: HO-20-13W

source_name: cell culture of strain HO-20-13W


title: HO-20-12W

source_name: cell culture of strain HO-20-12W


title: HO-20-13R

source_name: cell culture of strain HO-20-13R


title: PT089_P9_G07_S175


title: HO-20-12R

source_name: cell culture of strain HO-20-12R


title: 3mpf_24


title: HO-20-14R

source_name: cell culture of strain HO-20-14R


title: 3mpf_23


title: PT089_P9_G05_S173


title: PT089_P9_G04_S172


title: 3mpf_22


title: PT089_P9_G02_S170


title: HO-20-11R

source_name: cell culture of strain HO-20-11R


title: PT089_P9_G01_S169


title: HO-20-10W

source_name: cell culture of strain HO-20-10W


title: PT089_P9_F09_S165


title: PT089_P9_F07_S163


title: PT089_P9_F08_S164


title: PT089_P9_G06_S174


title: HO-20-10R

source_name: cell culture of strain HO-20-10R


title: 3mpf_19


title: PT089_P9_F05_S161


title: HO-20-11W

source_name: cell culture of strain HO-20-11W


title: PT089_P9_F03_S159


title: 3mpf_18


title: PT089_P9_F06_S162


title: PT089_P9_G03_S171


title: PT089_P9_F04_S160


title: 3mpf_21


title: PT089_P9_F01_S157


title: HO-0.5-8R

source_name: cell culture of strain HO-0.5-8R


title: HO-0.5-9R

source_name: cell culture of strain HO-0.5-9R


title: PT089_P9_F02_S158

source_name: breast


title: PT089_P9_E12_S156


title: PT089_P9_E11_S155


title: HO-0.5-9W

source_name: cell culture of strain HO-0.5-9W


title: 3mpf_20

source_name: beta-cells


title: PT089_P9_F11_S167


title: 3mpf_15


title: HO-0.5-7W

source_name: cell culture of strain HO-0.5-7W


title: PT089_P9_E09_S153


title: HO-0.5-7R

source_name: cell culture of strain HO-0.5-7R


title: PT089_P9_E08_S152


title: 3mpf_13


title: 3mpf_14


title: PT089_P9_E05_S149


title: 3mpf_16


title: PT089_P9_E07_S151


title: PT089_P9_E06_S150


title: HO-0.5-6W

source_name: cell culture of strain HO-0.5-6W

source_name: cell culture of JSC24


title: PT089_P9_E03_S147


title: 3mpf_17


title: HO-0.5-6R

source_name: cell culture of strain HO-0.5-6R


title: 3mpf_12


title: 3mpf_11


title: HO-0.5-5W

source_name: cell culture of strain HO-0.5-5W


title: PT089_P9_D12_S144


title: PT089_P9_E10_S154


title: PT089_P9_E02_S146


title: 3mpf_10


title: PT089_P9_D11_S143


title: HO-0.5-5R

source_name: cell culture of strain HO-0.5-5R


title: PT089_P9_D09_S141


title: 3mpf_8


title: PT089_P9_E04_S148


title: HO-0.5-4W

source_name: cell culture of strain HO-0.5-4W


title: HO-0.5-4R

source_name: cell culture of strain HO-0.5-4R


title: PT089_P9_D08_S140


title: PT039_P11_C07_S31


title: PT089_P9_E01_S145


title: 3mpf_7


title: PT089_P9_D06_S138


title: HO-0.5-3W

source_name: cell culture of strain HO-0.5-3W


title: HO-0.5-3R

source_name: cell culture of strain HO-0.5-3R


title: 3mpf_6


title: PT089_P9_D02_S134


title: 3mpf_5


title: PT089_P9_D05_S137


title: 3mpf_9


title: PT089_P9_D03_S135


title: PT089_P9_D04_S136


title: PT089_P9_D10_S142


title: PT089_P9_D01_S133


title: 3mpf_4


title: PT089_P9_C11_S131


title: 3mpf_3


title: PT089_P9_C10_S130


title: PT089_P9_C09_S129


title: 3mpf_2


title: PT089_P9_D07_S139


title: PT089_P9_C08_S128


title: HO-0.5-28W

source_name: cell culture of strain HO-0.5-28W


title: 3mpf_1


title: PT089_P9_C07_S127


title: HO-0.5-27W

source_name: cell culture of strain HO-0.5-27W


title: HO-0.5-28R

source_name: cell culture of strain HO-0.5-28R


title: PT089_P9_C05_S125

source_name: breast


title: HO-0.5-2W

source_name: cell culture of strain HO-0.5-2W


title: 1mpf_90

source_name: beta-cells


title: HO-0.5-2R

source_name: cell culture of strain HO-0.5-2R


title: PT089_P9_C12_S132


title: 1mpf_89


title: PT089_P9_C02_S122


title: PT089_P9_C03_S123


title: PT089_P9_C01_S121


title: HO-0.5-27R

source_name: cell culture of strain HO-0.5-27R


title: HO-0.5-26W

source_name: cell culture of strain HO-0.5-26W


title: HO-0.5-26R

source_name: cell culture of strain HO-0.5-26R

source_name: cell culture of JSC24


title: PT089_P9_B12_S120


title: 1mpf_88


title: PT089_P9_B11_S119


title: HO-0.5-25W

source_name: cell culture of strain HO-0.5-25W


title: PT089_P9_B10_S118


title: PT089_P9_C06_S126


title: 1mpf_87


title: 1mpf_86


title: 1mpf_85


title: PT089_P9_B06_S114


title: HO-0.5-25R

source_name: cell culture of strain HO-0.5-25R


title: PT089_P9_B09_S117


title: PT089_P9_B07_S115


title: PT089_P9_B08_S116


title: 1mpf_84


title: HO-0.5-24W

source_name: cell culture of strain HO-0.5-24W


title: PT089_P9_B05_S113


title: PT089_P9_C04_S124


title: PT089_P9_B04_S112


title: HO-0.5-24R

source_name: cell culture of strain HO-0.5-24R


title: PT089_P9_B03_S111


title: PT089_P9_B02_S110


title: PT089_P9_B01_S109


title: HO-0.5-23W

source_name: cell culture of strain HO-0.5-23W


title: HO-0.5-23R

source_name: cell culture of strain HO-0.5-23R


title: 1mpf_82


title: PT089_P9_A12_S108


title: PT089_P9_A11_S107


title: HO-0.5-22W

source_name: cell culture of strain HO-0.5-22W


title: 1mpf_81


title: PT089_P9_A10_S106


title: PT089_P9_A09_S105


title: 1mpf_80


title: PT089_P9_A08_S104


title: HO-0.5-22R

source_name: cell culture of strain HO-0.5-22R


title: PT089_P9_A06_S102


title: PT089_P9_A07_S103


title: 1mpf_79


title: PT089_P9_A05_S101


title: 1mpf_83


title: PT089_P9_A04_S100


title: 1mpf_77


title: HO-0.5-21R

source_name: cell culture of strain HO-0.5-21R


title: HO-0.5-21W

source_name: cell culture of strain HO-0.5-21W


title: 1mpf_78


title: PT089_P9_A02_S98

source_name: breast


title: PT089_P9_A03_S99


title: PT089_P7_G12_S84


title: 1mpf_76

source_name: beta-cells


title: 1mpf_75


title: HO-0.5-1W

source_name: cell culture of strain HO-0.5-1W


title: PT089_P7_G10_S82


title: PT089_P7_G11_S83


title: HO-0.5-1R

source_name: cell culture of strain HO-0.5-1R


title: HO-0.5-12W

source_name: cell culture of strain HO-0.5-12W


title: PT089_P7_G08_S80


title: PT089_P7_G09_S81


title: 1mpf_74


title: PT089_P7_G07_S79


title: HO-0.5-12R

source_name: cell culture of strain HO-0.5-12R


title: PT089_P7_G06_S78


title: HO-0.5-11W

source_name: cell culture of strain HO-0.5-11W

source_name: cell culture of JSC24


title: 1mpf_72


title: 1mpf_71


title: PT089_P7_G03_S75


title: PT089_P9_A01_S97


title: PT089_P7_G04_S76


title: 1mpf_70


title: PT089_P7_G01_S73


title: PT089_P7_G02_S74


title: Pig 1

city: Utrecht

first: Martijn

last: van Herwijnen

address: Yalelaan 2

department: Biochemistry & Cell Biology

country: Netherlands

institute: Utrecht University

data_processing:
Data quality was checked with FastQC, low quality reads were removed with cutadapt v1.8
Sequences with minimal length of 15 bp (human) or 25 bp (pig) were retained after adapter trimming
Trimmed sequences were mapped using bowtie (v1.1.1 for human, v1.2.2. for pig) with default settings, miRNA sequences were retrieved from miRbase (v21)
Genome_build: miRbase v21
Supplementary_files_format_and_content: Count_table.xls contains all miRNA counts for the different samples (different tabs for pig and human)

organism: Sus scrofa

source_name: milk-derived EV

extract_protocol:
EV were isolated from milk samples as described in Zonneveld et al, J. Extracell Vesicles 2014, and van Herwijnen et al., Mol. Cell. Proteomics, 2016. RNA was isolated from the EV using the miRNeasy micro kit (Qiagen)
NebNext with following adaptations (for human): overnight 3' adapter ligation, amplification with 2x Kapa HiFi PCR mastermix (15 cycles). Illumina Truseq (for pig) with 17 PCR amplification cycles, followed by TBE gel cleanup

value: extracellular vesicles from milk


title: Pig 5


title: PT089_P7_F11_S71


title: PT089_P7_F09_S69


title: PT089_P7_F12_S72


title: HO-0.5-11R

source_name: cell culture of strain HO-0.5-11R


title: PT089_P7_F10_S70


title: 1mpf_68


title: PT089_P7_F07_S67


title: 1mpf_73


title: PT089_P7_G05_S77


title: 1mpf_67


title: HO-0.5-8W

source_name: cell culture of strain HO-0.5-8W


title: HO-0.5-10R

source_name: cell culture of strain HO-0.5-10R


title: HO-0.5-10W

source_name: cell culture of strain HO-0.5-10W


title: PT089_P7_F08_S68


title: PT089_P7_F06_S66


title: PT089_P7_F05_S65


title: 1mpf_66


title: PT089_P7_F04_S64


title: PT089_P7_F03_S63


title: 1mpf_65


title: tnbc_ffpe_wes_PT039_3442

library_source: genomic

data_processing:
pooled samples were demultiplexed using the Picard tools
read pairs were aligned to the hg19 reference sequence using the Burrows-Wheeler Aligner (Li and Durbin, 2009)
data were sorted and duplicate-marked using Picard tools
the alignments were further refined using the Genome Analysis Toolkit (GATK) (McKenna et al., 2010; DePristo et al., 2011) for localized realignment around indel sites (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_indels_IndelRealigner.php).
recalibration of quality scores was also performed using the GATK (http://gatkforums.broadinstitute.org/discussion/44/base-quality-score-recalibration-bqsr)
mutation analysis for single nucleotide variants (SNV) was performed using MuTect v1.1.4 and annotated by Variant Effect Predictor (VEP). We used the SomaticIndelDetector tool that is part of the GATK for indel calling. MuTect was run in paired mode using CEPH1408 as the project normal.
copy number variants were identified using RobustCNV, an algorithm in development at the Center for Cancer Genome Discovery at the Dana-Farber Cancer Institute. RobustCNV relies on localized changes in the mapping depth of sequenced reads in order to identify changes in copy number at the loci sampled during targeted capture. This strategy includes a normalization step in which systematic bias in mapping depth is reduced or removed using robust regression to fit the observed tumor mapping depth against a panel of normals (PON) sampled with the same capture bait set. Observed values are then normalized against predicted values and expressed as log2 ratios. A second normalization step is then done to remove GC bias using a loess fit. Finally, log2 ratios are centered on segments determined to be diploid based on the allele fraction of heterozygous SNPs in the targeted panel.
normalized coverage data was next segmented using Circular Binary Segmentation (Olshen et al., 2004) with the DNAcopy Bioconductor package. Finally, segments were assigned gain, loss, or normal-copy calls using a cutoff derived from the within-segment standard deviation of post-normalized mapping depths and a tuning parameter which is set based on comparisons to array-CGH calls in separate validation experiments.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files representing: copy number values for each gene in each sample (gene_level_calls.txt); copy number values for each chromosome arm in each sample (arm_level_calls.txt); copy numebr variants (indels_phased.txt)

extract_protocol:
total nucleic acid was extracted from formalin-fixed paraffin embedded tissues using a standard protocol.
libraries were prepared using standard Illumina protocols.


title: tnbc_ffpe_wes_PT084_3437


title: tnbc_ffpe_wes_PT089_3434


title: tnbc_ffpe_wes_PT081_3439


title: PT089_P7_F02_S62


title: wes_CEPH1408

source_name: cell line

tag: cell line

value: CEPH1408 lymphoblastoid cell line


title: PT089_P7_E11_S59


title: PT089_P7_E10_S58


title: 1mpf_63


title: C4-BRWD1-shRNA197

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description:
hs_rna_b_control-C4-BRWD1-shRNA197
processed data: rna_counts.txt (RNA-seq counts table)

data_processing:
Genome alignment: Raw reads were aligned to the reference genome using STAR v2.4.2a.
Gene expression quantification: Counts per gene were generated using featureCounts v1.5.0.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts per gene: tab-delimited text table

molecule: polyA RNA

source_name: B cells

extract_protocol: RNA was isolated from flow sorted B cell populations with the Qiagen RNeasy kit (Qiagen). Concentration and purity was analyzed on a Nanodrop 1000 Spectrophotometer. mRNA was isolated by oligo-dT beads and library was prepared using standard Illumina library protocol (Kit: RS-122-2101 TruSeq® Stranded mRNA LT-SetA). Libraries were sequenced on the Illumina Hiseq2500.

tag: cell type

value: B cells

tag: shRNA treatment


title: PT089_P7_E09_S57


title: C3-BRWD1-shRNA197

description:
hs_rna_b_control-C3-BRWD1-shRNA197
processed data: rna_counts.txt (RNA-seq counts table)


title: 1mpf_62


title: C2-BRWD1-shRNA197

description:
hs_rna_b_control-C2-BRWD1-shRNA197
processed data: rna_counts.txt (RNA-seq counts table)


title: PT089_P7_E07_S55


title: PT089_P7_E08_S56


title: PT089_P7_E06_S54


title: PT089_P7_E04_S52


title: PT089_P7_E05_S53


title: 1mpf_61


title: C4-BRWD1-shRNA40

description:
hs_rna_b_control-C4-BRWD1-shRNA40
processed data: rna_counts.txt (RNA-seq counts table)


title: 1mpf_60


title: PT089_P7_E03_S51


title: PT089_P7_E02_S50


title: PT089_P7_E12_S60


title: 1mpf_59


title: C2-BRWD1-shRNA40

description:
hs_rna_b_control-C2-BRWD1-shRNA40
processed data: rna_counts.txt (RNA-seq counts table)


title: PT089_P7_D11_S47


title: PT089_P7_E01_S49


title: C3-BRWD1-shRNA40

description:
hs_rna_b_control-C3-BRWD1-shRNA40
processed data: rna_counts.txt (RNA-seq counts table)


title: 1mpf_64


title: C4-mock-shRNA

description:
hs_rna_b_control-C4-mock-shRNA
processed data: rna_counts.txt (RNA-seq counts table)

value: mock shRNA


title: PT089_P7_D10_S46


title: 1mpf_57


title: C3-mock-shRNA

description:
hs_rna_b_control-C3-mock-shRNA
processed data: rna_counts.txt (RNA-seq counts table)


title: PT089_P7_D09_S45


title: PT089_P7_D12_S48


title: PT089_P7_D07_S43


title: PT089_P7_D06_S42


title: 1mpf_55


title: C2-mock-shRNA

description:
hs_rna_b_control-C2-mock-shRNA
processed data: rna_counts.txt (RNA-seq counts table)


title: PT089_P7_D05_S41


title: PT089_P7_D03_S39


title: 1mpf_54


title: PT089_P7_D02_S38


title: PT089_P7_D01_S37


title: PT089_P7_C11_S35


title: PT089_P7_C12_S36


title: 1mpf_58


title: 1mpf_53


title: 1mpf_52


title: PT089_P7_C10_S34


title: PT089_P7_C09_S33


title: 1mpf_51


title: PT089_P7_C07_S31


title: PT089_P7_D08_S44


title: 1mpf_50


title: PT089_P7_C06_S30


title: PT089_P7_C08_S32


title: PT089_P7_C05_S29


title: 1mpf_56


title: PT089_P7_C03_S27


title: 1mpf_48


title: PT089_P7_C02_S26


title: 1mpf_49


title: PT089_P7_C01_S25


title: PT089_P7_B12_S24


title: PT089_P7_B11_S23


title: PT089_P7_B09_S21


title: PT089_P7_B10_S22


title: PT089_P7_B07_S19


title: 1mpf_46


title: 1mpf_44


title: PT089_P7_B08_S20


title: 1mpf_47


title: PT089_P7_B06_S18


title: 1mpf_45


title: PT089_P7_B05_S17


title: PT089_P7_B04_S16


title: PT089_P7_B03_S15


title: 1mpf_42


title: PT089_P7_C04_S28


title: PT089_P7_B02_S14


title: PT089_P7_A12_S12


title: 1mpf_43


title: PT089_P7_A11_S11


title: 1mpf_40


title: PT089_P7_A09_S9


title: PT089_P7_A08_S8


title: 1mpf_38


title: PT089_P7_A07_S7


title: 1mpf_39


title: PT089_P7_A05_S5


title: PT089_P7_B01_S13


title: PT089_P7_A10_S10


title: 1mpf_37


title: PT089_P7_A06_S6


title: PT089_P7_A02_S2


title: 1mpf_36


title: PT089_P7_A01_S1


title: 1mpf_35


title: PT089_P3_H12_S384


title: PT089_P3_H11_S383


title: PT089_P7_A03_S3


title: PT089_P3_H10_S382


title: 1mpf_34


title: 1mpf_33


title: 1mpf_41


title: 1mpf_32


title: PT089_P3_H04_S376


title: PT089_P3_H03_S375


title: PT089_P3_H05_S377


title: PT089_P3_H09_S381


title: PT089_P3_H02_S374


title: 1mpf_31


title: PT089_P3_G09_S369


title: PT089_P3_G12_S372


title: PT089_P7_A04_S4


title: PT089_P3_G10_S370


title: 1mpf_30


title: 1mpf_29


title: PT089_P3_G08_S368


title: PT089_P3_G06_S366


title: 1mpf_28


title: PT089_P3_G07_S367


title: PT089_P3_G04_S364


title: 1mpf_27


title: PT089_P3_G05_S365


title: PT089_P3_G03_S363


title: PT089_P3_F12_S360


title: PT089_P3_G02_S362


title: 1mpf_25


title: 1mpf_26


title: PT089_P3_F11_S359


title: 1mpf_24


title: PT089_P3_H01_S373


title: PT089_P3_F09_S357


title: PT089_P3_F07_S355


title: 1mpf_23


title: PT089_P3_F06_S354


title: 1mpf_22


title: PT089_P3_F03_S351


title: PT089_P3_F08_S356


title: PT089_P3_F05_S353


title: 1mpf_21


title: PT089_P3_F01_S349


title: PT089_P3_E10_S346


title: 1mpf_19


title: PT089_P3_E09_S345


title: PT089_P3_E08_S344


title: 1mpf_18


title: PT089_P3_E07_S343


title: PT089_P3_E05_S341


title: 1mpf_17


title: PT089_P3_E06_S342


title: 1mpf_16


title: 1mpf_69


title: PT089_P3_F10_S358


title: PT089_P3_E02_S338


title: 1mpf_15


title: PT089_P3_F02_S350


title: PT089_P3_D10_S334


title: PT089_P3_D12_S336


title: 1mpf_14


title: 1mpf_20


title: PT089_P3_E11_S347


title: PT089_P3_D08_S332


title: 1mpf_13


title: PT089_P3_D05_S329


title: PT089_P3_D04_S328


title: PT089_P3_D03_S327


title: 1mpf_12


title: PT089_P3_D02_S326


title: 1mpf_11


title: PT089_P3_D01_S325


title: 1mpf_10


title: PT089_P3_C10_S322


title: PT089_P3_C05_S317


title: 1mpf_8


title: PT089_P3_C02_S314


title: PT089_P3_E01_S337


title: PT089_P3_C03_S315


title: PT089_P3_B12_S312


title: PT089_P3_B10_S310


title: 1mpf_7


title: PT089_P3_D09_S333


title: PT089_P3_E04_S340


title: PT089_P3_B09_S309


title: PT089_P3_B06_S306


title: PT089_P3_B08_S308


title: 1mpf_6


title: PT089_P3_B05_S305


title: PT089_P3_B01_S301


title: 1mpf_5


title: PT089_P3_B02_S302


title: PT089_P3_A06_S294


title: PT089_P3_A05_S293


title: PT089_P3_A03_S291


title: 1mpf_2


title: PT089_P3_C04_S316


title: 1mpf_9


title: PT089_P1_D08


title: PT089_P1_D09


title: PT089_P1_D03


title: PT089_P1_C12


title: PT089_P1_D02


title: PT089_P1_D01


title: PT089_P1_C10


title: PT089_P1_D06


title: PT089_P1_C08


title: PT089_P1_C09


title: 1mpf_4


title: PT089_P1_C06


title: PT089_P1_C05


title: PT089_P1_C11


title: PT089_P1_D04


title: 1mpf_3


title: PT089_P3_A08_S296


title: PT089_P1_C03


title: PT089_P1_C02


title: PT089_P1_C07


title: PT089_P1_C04


title: PT089_P1_C01


title: PT089_P1_D07


title: PT089_P1_B11


title: PT089_P1_B09


title: 1mpf_1


title: PT089_P1_B07


title: PT089_P1_B05


title: PT089_P1_B06


title: PT089_P1_B08


title: PT089_P1_D05


title: PT089_P1_B04


title: PT089_P1_B02


title: PT089_P1_B01


title: PT089_P1_A11


title: PT089_P1_B03


title: PT089_P1_A12


title: PT089_P1_A08


title: PT089_P1_A10


title: PT089_P1_A03


title: Human


title: PT089_P1_A07


title: PT089_P1_A04


title: PT089_P1_B12


title: PT089_P1_A09


title: PT089_P1_A01


title: PT089_P1_A06


title: PT089_P1_A05


title: PT089_P1_A02


title: bone marrow_Gr-1+CD11b+ cells_LPS

type: RNA

city: suzhou

first: Yi

last: Yang

state: Jiangsu

address: 199 Renai Road

department: Institutes of Biology and Medical Sciences

institute: Soochow University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Then the slides were scanned using the Agilent Microarray Scanner (part number G2505C).

data_processing: GenePix pro V6.0 is used to read the raw intensity of the image. The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.Median Normalization was used. Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction. After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test. Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

organism: Mus musculus

source_name: bone marrow_LPS

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: Bone marrow cells were harvested by flushing the tibias and femurs with PBS, followed by lysis of red blood cells with ACK (ammonium-chloride-potassium) lysing buffer. For sorting, bone marrow cells were stained with anti-mouse mAbs against CD11b and Gr-1 diluted with PBS. Cells before and after sorting were maintianed in complete culture media.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: 6-8 weeks

tag: treatment

value: injected with LPS(ip)

value: bone marrow

tag: cell population

value: double positive for Gr-1 and CD11b


title: bone marrow_Gr-1+CD11b+ cells_PBS

source_name: bone marrow_PBS

value: injected with PBS(ip)


title: 165OE_5

city: Victoria

first: C. Peter

last: Constabel

state: British Columbia

address: 3800 Finnerty Rd

department: Biology

country: Canada

institute: University of Victoria

data_processing:
The alignment of sequence was performed using Tophat2 version 2.1.1.OSX_x86_64. A P. tremula genome sequence (version 1.0) was used as reference genome (Sjödin et al., 2009; http://popgenie.org/).
Cufflinks and Cuffmerge (version 2.2.1.OSX_x86_64) were used to generate a reference transcriptome and use a Populus tremula transcriptome as reference (http://popgenie.org/).
Htseq-count (version 0.6.1) was used to calculate the raw counts.
Genome_build: P. tremula genome sequence (version 1.0)
Supplementary_files_format_and_content: raw counts in csv files

organism: Populus tremula x Populus tremuloides

source_name: poplar leaves LPI7-10

growth_protocol: Hybrid poplar were transfer from tissue culture to mist chamber and grown for one month. They were then transfer to greenhouse for two months. For sunlight treatment, plants were moved outside greenhouse and exposed to sunlight for a week.

extract_protocol:
Leaves number 7-10 (LPI 7-10) were harvested. Total RNA was extracted from frozen poplar hairy roots or ground leaf powder using the modified cetyl trimethyl ammonium bromide method for polyphenol-rich plant tissue described by Muoki et al. (2012).
MagJET enrichment kit (ThermoScientific) was used to purify mRNA from crude RNA. The mRNA was fragmented by heating the samples at 94℃ for 5 minutes. To make cDNA libraries with adaptors NEBNext ultra RNA Library Prep Kit for Illumina (NEB) was used. GeneJET NGS Cleanup Kit (ThermoScientific) was used to clean the extra adaptors.  Primers for RNA-Seq were added to cDNA using NEBNext Multiplex Oligo kit (NEB). MagJET NGS Cleanup and Size Selection kit (ThermoScientific) was used to select DNA fragments around 350bp. Twelve libraries with same concentration (250ng/ul) each were pooled and sent to McGill University/GenomeQuébec

treatment_protocol: To generate MYB165-overexpressing poplars, the binary vectors pMDC32 with MYB165 were transformed into the Agrobacterium tumefaciens strain GV3101::pMP90 by electroporation. P. tremula x P. tremuloides  (clone INRA 353-38) leaves were excised and transformed

tag: growth condition

value: greenhouse

tag: genotype

value: leaves LPI 7-10


title: 165OE_3

tag: tissue


title: 165OE_2

value: sunlight-exposed


title: 165OE_1


title: NS1WO

city: Madison

first: Xiang

last: Li

state: Wisconsin

address: University of Wisconsin

institute: University of Wisconsin-Madison

data_processing:
The transcriptome reads were proceeded and mapped using the HISAT2>Cufflinks>CuffDiff
The gene expression level was calculated by using FPKM method.
Genome_build: hg38

source_name: Not-Transgenic induced astrocytes

growth_protocol: Primary astrocytes were purchased and cultured according to the manufacture's instructions. Induced astrocytes were generated by transgenic/not transgenic induction according to the methods presented in the paper.

extract_protocol:
RNA was extracted by the Qiagen RNeasy kit
RNA sequencing library construction and sequencing was performed as standard HiSeq HighOutput 1×100, by the Biotechnology Center, University of Wisconsin-Madison (https://www.biotech.wisc.edu/services/dnaseq)

value: Not-Transgenic induced astrocytes


title: NS2W

source_name: Transgenic induced astrocytes

value: Transgenic induced astrocytes


title: 165OE_4


title: NS2WO


title: WT_6

value: wild type


title: NS1W


title: treatment 3

city: Moscow

first: Kirill

middle: S.

last: Mironov

address: Botanicheskaya str., 35

department: Molecular Biosystems

country: Russia

institute: K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Science

description:
pooled 3 tech. reps.
alc.csv

data_processing:
Torrent Suite 5.10.0
BBDuk
bwa mem v0.7.17
samtools  v1.9
ReadXplorer v.2.2.2
DESeq2
Genome_build: ASM972v1
Supplementary_files_format_and_content: DESeq2 results for all genes

organism: Synechocystis sp. PCC 6803

source_name: Cyanobacterial axenic culture

growth_protocol: BG-11 medium with 20 mM HEPES-NaOH pH 7.5; 100 µE·m2·s; 1.6% CO2 in a sterile air-gas mixture

extract_protocol:
Mironov KS, Los DA. RNA isolation from Synechocystis, https://bio-protocol.org/e1428
Ion Total RNA-Seq Kit v2

tag: substrain

value: GT-L

tag: cultural vessel no.

tag: technical reps

value: aliphatic alcohol


title: WT_5


title: control 3

description:
pooled 3 tech. reps.
alc.csv


title: WT_4


title: PA

source_name: Primary astrocytes

value: Primary astrocytes


title: control 2

description:
pooled 3 tech. reps.
alc.csv


title: treatment 2

description:
pooled 3 tech. reps.
alc.csv


title: treatment 1

description:
pooled 3 tech. reps.
alc.csv


title: 165OE_6


title: WT_1


title: WT_3


title: control 1

description:
pooled 3 tech. reps.
alc.csv


title: WT_2


title: 10_ChMAP-28_1.25 µM

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

description: SAMPLE 3

hyb_protocol: Hybridization was performed according to 4x2k CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 1,0 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: Data was quantile normalized using R statistical programming language and 'preprocessCore' library

label: biotin

source_name: HL-60 cell line

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturers protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

growth_protocol: Cell cultivation was performed in a complete medium prepared on the basis of RPMI-1640 (Gibco) medium containing 10% FBS (Gibco), penicillin (100 μg / ml) and streptomycin (100 U / ml).  Cells were cultured in flasks (25 and 75 cm3) or in plates (24- and 6-well plates) in a CO2 incubator (37 ° C, CO2 content 5%) with subculturing every 72 hours maintaininig cell density between 2x10^5 and 1x10^6 cells/ml

extract_protocol: Cell pellets were dissolved in TRI Reagent (MRC), Direct-zol™ RNA MiniPrep (Zymo Research) was used for RNA extraction. RNA was quantified using Nanodrop (Thermo Fisher Scientific).

treatment_protocol: HL-60 cells (1 x10^6) were treated in culture medium containing ChMAP-28 (1.25, 2.5 or 5 µM) for 6 h in 24-well plates. After 6 h cells were centrigfued at 200 g and 4 C.

tag: agent

value: antimicrobial peptide ChMAP-28

tag: agent concentration


title: 9_ChMAP-28_2.5 µM

description: SAMPLE 2


title: 8_ChMAP-28_5 µM

description: SAMPLE 1


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS15

status: Public on Aug 10 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS15

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Fourteen healthy lean young men (Age: 22.4 ± 2.8 years; BMI: 22.3 ± 2.1 kg/m2; Mean ± SD) participated in the study. Participants were non-smokers, had no active diseases, used no medication and did not engage in exercise for more than 3 hours per week, verified by questionnaires. In addition, participants reported regular bedtimes (11 PM ± 2 hours), regular sleep duration of 7-9 hours, did not perform shift-work or traveled across more than one time zone in the last three months and were not definite morning larks or night owls, assessed with a morningness-eveningness questionnaire (MEQ-SA: 54 ± 7, Mean ± SD). The study was conducted in accordance with the principles of the declaration of Helsinki, approved by the Ethics Committee of the Maastricht University Medical Center and monitored by the Clinical Trial Center Maastricht. All participants provided written informed consent. The included measurements were performed between February 2016 and February 2017. The study was registered at clinicaltrials.gov with identifier NCT02580513.

extract_protocol: Total RNA was prepared from the muscle biopsies (50 mg) using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Pre-study conditions: Seven days prior to the study periods, participants were instructed to maintain a standardized normal lifestyle, including (trying to) sleep from 11 PM until 7 AM and consuming meals at regular times, consistent with the times during the study (breakfast, lunch, snack and dinner at 8 AM, 12:30 PM, 3 PM and 8 PM, respectively). In addition, participants were asked to abstain from consumption of caffeine and alcohol during those 7 days. Three days before the study periods, participants were instructed not to perform physical exercise. Two days before each in-laboratory study protocol, participants were provided with meals to ensure standardized distribution of calories and macronutrients (see below). Compliance to the prescribed lifestyle was monitored with food- and sleep diaries and by a light-detecting wrist accelerometer (Actiwatch Spectrum, Philips-Respironics, Murrysville PA, USA). Study conditions: In the study, each participant underwent one control protocol and one circadian misalignment protocol, in a randomized, crossover fashion, with a wash-out of 3 to 9 weeks. Prior to the first study period, the participants were not aware of the order of the study periods. During their stay, the participants resided in a private respiration chamber; a small room with a bed, toilet, sink, desk, chair, TV and computer. In the respiration chamber environmental conditions were tightly controlled, including dim-light (4 lux in the horizontal angle of gaze) during wake phases and darkness during sleep opportunities, no devices that can display time (e.g. watch, mobile phone, laptop, tablet), no internet and no live television or radio. The screen emittance of the TV and computer in the respiration chamber were adapted to not exceed the permitted light intensity of 4 lux and could be used to work, listen to music or watch movies. During their stay, participants were isolated from external time cues and could only be in contact with the researchers. For specific study procedures (placement of intravenous canula, indirect calorimetry, skeletal muscle biopsy and the hyperinsulinemic euglycemic clamp), participants were transported to an adjacent clinical room in a wheelchair, during which they wore a blindfold and earplugs to prevent excess light and possible audiovisual signals that might indicate whether it was day or night. The clinical room had similar dim-light conditions. During procedures for which light was required (placement of intravenous canula, muscle biopsy), participants wore welding goggles shade 5 (Uvex Ultravision 9301-245, Uvex, Fürth, Germany) to limit light exposure. During each study period, two skeletal muscle biopsies were obtained according to the Bergström method (PMID: 5584523) from the m. vastus lateralis under local anasthesia (1% lidocaine, without epinephrine) at 7 AM and 7 PM. Biopsies were taken moving from distal to proximal, alternating between the left or right leg. The leg of the first biopsy was randomized and subsequent biopsies were taken from the other leg. Muscle fiber type was similar between control and misalignment condition. Samples were snap-frozen in liquid nitrogen, and stored at -80 degrees centigrade until RNA isolation.

tag: gender

value: male

tag: subjectid

tag: age (yrs)

tag: height (m)

tag: weight (kg)

tag: bmi (kg/m2)

tag: time of sampling

tag: experimental condition

value: circadian misaligned

tag: fasting glucose (mmol/l)

tag: fasting insulin (uu/ml)

tag: fasting ffa (umol/l)

tag: fasting triglycerides (mmol/l)


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS15

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS15

value: circadian aligned


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS14

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS14


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS14

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS14


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS15

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS15


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS16

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS16


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS17

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS17


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS16

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS16


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS17


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS16

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS16


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS17

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS17


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS16

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS16


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS14

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS14


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS17

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS17


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS10

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS10


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS13

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS13


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS9

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS9


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS13

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS13


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS9

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS9


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS15

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS15


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS7

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS7


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS6

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS6


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS13

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS13


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS10

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS10


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS10

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS10


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS8

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS8


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS14

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS14


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS8

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS8


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS13

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS13


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS10

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS10


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS6

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS6


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS2

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS2


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS2

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS2


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS2

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS2


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS1

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS1


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS2

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS2


title: skeletal muscle, circadian misaligned intervention, morning sample, subject RAS8

source_name: m. vastus lateralis, circadian misaligned intervention, morning sample, from subject RAS8


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS7

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS7


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS8

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS8


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS6

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS6


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS7

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS7


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS9

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS9


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS6

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS6


title: HEK293_2

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: rRNA depleted RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM values for each Sample ...

source_name: Embryonic kidney cell line

growth_protocol: HEK293 cells were cultured in DMEM with Pen/Strep and heat inactivated FBS.

extract_protocol:
5 million cells were collected in duplicate and RNA was isolated by Qiagen RNeasy Plus Kit.
Ribosomal RNA was depleted using the RiboGone H/M/R kit from Illumina. Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired-end reads.

tag: cell line


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS7

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS7


title: skeletal muscle, circadian aligned intervention, morning sample, subject RAS1

source_name: m. vastus lateralis, circadian aligned intervention, morning sample, from subject RAS1


title: U937_2

description: rRNA depleted RNA

source_name: Leukemic cell line

growth_protocol: U937 and EaHy cells were cultured in RPMI media with Pen/Strep and heat inactivated FBS.


title: U937_1

description: rRNA depleted RNA


title: HEK293_1

description: rRNA depleted RNA


title: skeletal muscle, circadian misaligned intervention, evening (baseline) sample, subject RAS1

source_name: m. vastus lateralis, circadian misaligned intervention, evening (baseline) sample, from subject RAS1


title: skeletal muscle, circadian aligned intervention, evening (baseline) sample, subject RAS1

source_name: m. vastus lateralis, circadian aligned intervention, evening (baseline) sample, from subject RAS1


title: T4_repeat2

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
Sequencing reads from RNA-seq were aligned to the Chicken reference genome (Version galGal4 from Emsebl) using Tophat (2.1.0) with default parameters.
The expression values of each gene were quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) using cufflinks (v2.2.1)
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Gallus gallus

source_name: dermal papilla

extract_protocol:
Total RNAs were extracted by using Trizol reagent and standard protocols were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: feather follicle

tag: genotype/variation


title: ZJ53_Wk26

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Reads were aligned to an assembly of Indian Rhesus macaque (Macaca mulatta) (MacaM_Rhesus_Genome_v7.fasta) using STAR software (v2.5.2b)
Insert size was estimated with Picard Tools v1.74
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.3.3.
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: PBMC

growth_protocol: PBMC were isolated using ficoll

extract_protocol:
After thaw and wash, PBMC pellets were resuspended in RNAzolRT prior to RNA extraction. Purified RNA was used for transcriptome analysis. Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform.
Modified Illumina TruSeq. Illumina-ready libraries were sequenced by 2x75 paired-end reads on a HiSeq 4000.

treatment_protocol: Samples for RNA extraction were resuspended in 10% DMSO-FBS and store in liquid nitrogen until use

tag: donor id

tag: time point

tag: art-treatment

value: ART

tag: ifn-1ant treatment

value: Placebo


title: Wnt5a-over expression

value: Wnt5a-over expression


title: shlnc3500

value: lnc3500 knockdown


title: shlnc7831

value: lnc7831 knockdown


title: T4_repeat1


title: ZJ53_Wk22


title: ZJ53_Wk19


title: ZJ53_Wk17


title: A3: Huh7 untreated 24h rep2

city: Oxford

first: Joao

last: Arezes

state: Oxfordshire

address: Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: control replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were noemalized using the lumi package (Bioconductor) and compared using LIMMA (Bioconductor)

source_name: Huh7 cells, control replicate 2

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Huh7 and HepG2 were cultured in Dulbecco's Modified Eagle's Medium – High Glucose (Sigma), supplemented with 10% Fetal Bovine Serum (Sigma), 1% Penicillin-Streptomycin (Sigma) and 1% L-Glutamine (Sigma)

extract_protocol: Total RNA exctracted using the RNEasy mini kit (Qiagen)

treatment_protocol: Treatment with 10µg/ml of recombinant human or mouse ERFE for 24h. Untretaed cells used as control


title: B2: Huh7 humanERFE 24h rep3

description: human ERFE replicate 3

source_name: Huh7 cells, human ERFE replicate 3


title: B4: Huh7 mouseERFE 24h rep3

description: mouse replicate 3

source_name: Huh7 cells, mouse replicate 3


title: ZJ53_Wk14


title: A2: Huh7 humanERFE 24h rep2

description: human ERFE replicate 2

source_name: Huh7 cells, human ERFE replicate 2


title: C2: Huh7 mouseERFE 24h rep2

description: mouse replicate 2

source_name: Huh7 cells, mouse replicate 2


title: Peptide treated K562_3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Gene expression of K562 cell line after 9 hours peptide treatment

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Agilent's human GXP_8X60k Array (AMADID: 039494). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method .

source_name: K562 Peptide treated

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: For micro-array analysis K562 cells were grown upto  5 × 106/ml counts and were taken for peptide treatment.

extract_protocol: RNA extraction was performed by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: K562 cells were grown in RPMI-1640 media containing 10% FBS and Antibiotic Antimycotic Solution in a 5% CO2 incubator at 37°C and treated with peptide for 9 hours.

value: Human chronic myelogenous leukemia


title: C1: Huh7 humanERFE 24h rep1

description: human ERFE replicate 1

source_name: Huh7 cells, human ERFE replicate 1


title: A1: Huh7 untreated 24h rep1

description: control replicate 1

source_name: Huh7 cells, control replicate 1


title: K562_1

description: Gene expression of untreated K562 cell line

source_name: K562 Untreated


title: B3: Huh7 untreated 24h rep3

description: control replicate 3

source_name: Huh7 cells, control replicate 3


title: C3: Huh7 humanERFE 24h rep4

description: human replicate 4

source_name: Huh7 cells, human replicate 4


title: K562_2


title: C4: Huh7 untreated 24h rep4

description: control replicate 4

source_name: Huh7 cells, control replicate 4


title: Peptide treated K562_1


title: ZJ53_Wk6


title: A4: Huh7 mouseERFE 24h rep3

description: mouse replicate 3


title: ZJ24_Wk22


title: ZJ24_Wk19


title: B1: Huh7 mouseERFE 24h rep1

description: mouseERFE replicate 1

source_name: Huh7 cells, mouseERFE replicate 1


title: ZJ53_Wk18


title: Peptide treated K562_2


title: ZJ24_Wk18


title: ZJ24_Baseline

value: Baseline


title: ZJ24_Wk17


title: ZJ24_Wk6


title: ZJ07_Wk19


title: ZJ07_Wk22


title: ZJ07_Wk26


title: ZJ07_Wk17


title: ZJ24_Wk26


title: ZJ24_Wk14


title: ZJ07_Wk6


title: ZJ07_Wk18


title: ZJ07_Baseline


title: ZJ06_Wk19


title: ZJ06_Wk26


title: ZJ06_Wk22


title: ZJ06_Wk17


title: ZJ06_Wk18


title: ZJ06_Wk14


title: ZJ06_Wk6


title: ZJ06_Baseline


title: ZH56_Wk26


title: ZH56_Wk19


title: ZH56_Wk18


title: ZH56_Wk17


title: ZH56_Wk14


title: ZH56_Wk6


title: ZH56_Baseline


title: ZH40_Wk26


title: ZH40_Wk19


title: ZJ07_Wk14


title: ZH40_Wk17


title: ZH40_Wk18


title: ZH40_Wk14


title: ZH40_Wk6


title: ZH40_Baseline


title: ZH40_Wk22


title: KiF_Wk22

value: KiF


title: ZJ53_Baseline


title: KiF_Wk26


title: KiF_Wk6


title: KiF_Wk19


title: KiF_Baseline


title: KiF_Wk14


title: KiF_Wk18


title: BA50_Wk19


title: BA50_Wk14


title: BA50_Wk22


title: BA50_Wk18


title: BA50_Wk6


title: BA50_Baseline


title: A11V152_Wk26


title: A11V152_Wk22


title: A11V152_Wk19


title: A11V152_Wk14


title: A11V152_Wk18


title: A11V152_Wk6


title: A11V111_Wk26


title: A11V152_Baseline


title: A11V111_Wk14


title: A11V111_Wk18


title: A11V038_Wk6


title: A11V038_Baseline


title: ZH56_Wk22


title: A11V111_Baseline


title: A11E103_Wk26


title: A11V002_Wk26


title: A11V002_Wk14


title: A11V002_Baseline


title: A11V002_Wk22


title: A11E103_Wk22


title: A11E103_Wk19


title: BA50_Wk26


title: A11E103_Wk17


title: A11E103_Wk14


title: A11V002_Wk6


title: A11E103_Baseline


title: A11E061_Wk19


title: A11V111_Wk22


title: A11E061_Wk26


title: A11E061_Wk17


title: A11E061_Wk18


title: A11E103_Wk6


title: A11E061_Wk14


title: A11V111_Wk6


title: A11E061_Wk6


title: A11E061_Baseline


title: A11E030_Wk26


title: A11E030_Wk22


title: A11E030_Wk18


title: A11E030_Wk19


title: A11E030_Wk17


title: A11E103_Wk18


title: A10V155_Wk26


title: A11E030_Wk14


title: A10V155_Wk22


title: A11E030_Baseline


title: A10V155_Wk18


title: EaHy_1

description: rRNA depleted RNA

source_name: Endothelial cell line

value: EaHy


title: A11E030_Wk6


title: A10V155_Wk14


title: A10V155_Wk19


title: A10V012_Wk26


title: A11E061_Wk22


title: A10V012_Wk22


title: A10V155_Wk6


title: A10V012_Wk18


title: A10V155_Baseline


title: A10V012_Wk17


title: A10V012_Wk6


title: A10V012_Baseline


title: A10E060_Wk26


title: A10E060_Wk19


title: A10V012_Wk14


title: A10V012_Wk19


title: A10E060_Wk17


title: A10E060_Wk6


title: A10E060_Wk14


title: A9P012_Wk26


title: A9P012_Wk19


title: A9P012_Wk22


title: A9P012_Wk18


title: A9P012_Wk17


title: A9P012_Wk14


title: A9P012_Wk6


title: A9P012_Baseline


title: 29512_Wk22


title: 29512_Wk19


title: 29512_Wk18


title: 29512_Wk17


title: 29512_Wk14


title: A10E060_Wk22


title: A10E060_Wk18


title: 29512_Wk6


title: 26711_Wk26


title: 29512_Baseline


title: 26711_Wk22


title: 26711_Wk19


title: A10E060_Baseline


title: 26711_Wk14


title: 26711_Wk6


title: 26711_Wk18


title: 29512_Wk26


title: 26711_Baseline


title: IP_Dhp1_WT_MM+thiamine_exp2

city: Sherbrooke

first: Pierre-Étienne

last: Jacques

state: Quebec

address: 2500 Boulevard de l'Université

department: Biologie

institute: Université de Sherbrooke

description: without spike-in

data_processing:
Briefly, the raw reads were trimmed using Trimmomatic version 0.32 (Bolger et al. 2014) with param ILLUMINACLIP:2:30:15 LEADING:30 TRAILING:30 MINLEN:23, and quality inspection was conducted using FastQC version 0.11.4 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Considering that most of the samples were generated from chromatin contain exogenous spiked-in from S. cerevisiae, the trimmed reads from all datasets were aligned using BWA version 0.7.12-r1039 (Li and Durbin 2010) with the algorithm mem or aln depending on the read length (above or below 70 nt) and default parameters, onto a concatenated reference genome containing both the sequences of the S. pombe ASM294v2 and S. cerevisiae sacCer3 assemblies, inpired by others (Orlando et al. 2014). Note that <0.28 % of reads coming from samples without spike-in were aligning to the S. cerevisiae genome. Note that no filtering on mapQ was performed in order to avoid discarding the signal at regions of the genome that are duplicated (BWA is randomly assigning the reads).
Signal density files in BedGraph format were then generated using BEDTools genomecov version 2.17 (Quinlan and Hall 2010) with default parameters, then converted in uniform 10 nt bins WIG files for further normalisation steps (inspired by the script bedgraph_to_wig.py [https://gist.github.com/svigneau/8846527]).
Each signal density file of the datasets without spike-in was scaled such that the total sum of the signal over the S. pombe genome is equivalent to 1M reads of 100 nt, then the signal of the input dataset was subtracted from its corresponding IP dataset to generate the “scl-Ctrl” files.
The normalization of the datasets with spike-in was inpired by the method of presented by Orlando et al. (Orlando et al. 2014). For each dataset, the sum of the signal coming from the reads aligned to the S. cerevisiae genome was first scaled to the equivalent of 1M mapped reads of 100 nt, and the same scaling factor was applied to the signal coming from the reads aligned to the S. pombe genome to generate the “normSI” files. For the datasets generated in a WT and mutant strains, the S. pombe signal was next scaled to a total signal equivalent to 1M mapped reads of 100 nt and the same scaling factor was applied to the corresponding mutant dataset to generate the “Spknorm” files. The signal of the input dataset was then subtracted from its corresponding IP to generate the final “Spknorm-Ctrl” files used in downstream analyses.
The normalized WIG files were then encoded in bigWig format using the Kent utilities (Kent et al. 2010). Visual inspection of the data was performed using an AssemblyHub on the UCSC Genome Browser (Casper et al. 2018) (https://genome.ucsc.edu/cgi-bin/hgHubConnect?hubUrl=https://datahub-i8kms5wt.udes.genap.ca/CTD_sno_pombe/hub.txt&hgHub_do_firstDb=on&hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on).
Genome_build: ASM294v2-SacCer3
Supplementary_files_format_and_content: IP: bigwig files of the normalized IP signal after substraction of the WCE signal; WCE: bigwig files of the normalized WCE signal

organism: Schizosaccharomyces pombe

growth_protocol: Cells were routinely grown at 30°C in Edinburgh minimal media (EMM) or in yeast extract medium (YES) supplemented with adenine, uracil, histidine and leucine.

extract_protocol:
ChIP-seq experiments of total RNAPII and phospho-CTD modifications in wild-type and dhp1-depleted cells were performed with a spike-in adjustment procedure that allows a quantitative comparison between independent strains or conditions (Orlando et al. 2014). Chromatin preparations of S. pombe FBY1995 (Rpb3-HA; WT) and FBY2016 (Rpb3-HA; Pnmt-dhp1) strains and S. cerevisiae FBY2064 strain (reference strain containing a copy of HA-tagged histone H2B) were done as a regular ChIP, except that chromatin extracts have been frozen in liquid nitrogen and stored at -80°C before affinity purifications. For Tyr1-P, Ser2-P, Ser5-P, Ser7-P, and 8WG16 IPs, a S. pombe/S. cerevisiae chromatin ratio of 0.9:0.1 was used, whereas a chromatin ratio of 0.995:0.005 was used for Rpb3/H2B-HA purifications. Following combination of S. pombe/S. cerevisiae chromatin extracts, ChIP assays were performed as described above using antibody-coated beads. ChIP-seq profiles of total RNAPII from WT and ysh1-AA strains were also performed with a spike-in adjustment (ratio S. pombe/S. cerevisiae of 0.9:0.1) using extracts from S. pombe that were previously grown in EMM leu- and treated for 4 hours with 2.5 μg/ml of rapamycin.
DNA librairies for ChIP-seq experiments were prepared as described previously (Lemay et al. 2016) using either the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina kit (New England BioLabs) or the SPARK DNA Sample Prep Kit Illumina Platform (Enzymatics) according to the manufacturer’s instructions.

treatment_protocol: Conditional strains, in which the genomic copy of the essential genes pcf11, dhp1 and seb1 are expressed from the thiamine-sensitive nmt promoter (Pnmt), were repressed by the addition of 60 μM of thiamine in the EMM media for 12-15 hours as previously described (Lemay et al. 2014; Lemay et al. 2016). Depletion of nuclear Ysh1 was done by an anchor-away strategy (Ding et al. 2014). Briefly, wild-type (WT) and Ysh1- FRB-GFP (ysh1-AA) strains were grown in EMM without leucine and rapamycin was added at a final concentration of 2.5 μg/ml for 4h. Cells were collected at OD 600nm of ∼0.5-0.8.

tag: pombe strain

tag: chip antibody

value: Pan Mouse IgG Dynabeads

tag: chip target

tag: genotype

value: h+ ade6-M216 leu1-32 ura4-D18 his3-D1 Dhp1-4XTAP::URA4

tag: growth media

value: EMM media (MM) + thiamine


title: WCE_Dhp1_WT_MM+thiamine_exp2

description: without spike-in

value: WCE


title: 26311_Wk26


title: 26311_Wk22


title: WCE_Pcf11_WT_MM+thiamine_exp2

description: without spike-in

value: h+ ade6-M216 leu1-32 ura4-D18 his3-D1 Pcf11-4XTAP::natMX6


title: IP_Ysh1_WT_MM+thiamine_exp2

description: without spike-in

value: h+ ade6-M216 leu1-32 ura4-D18 his3-D1 Ysh1-4XTAP::natMX6


title: IP_Pcf11_WT_MM+thiamine_exp2

description: without spike-in


title: 26311_Wk18


title: 26311_Wk14


title: IP_Rna14_WT_MM+thiamine_exp2

description: without spike-in

value: h+ ade6-M216 leu1-32 ura4-D18 his3-D1 Rna14-4XTAP::natMX6


title: 26311_Wk6


title: TGKO3: K14-TCL1 transgenic 3

city: Roma

first: Elisabetta

last: Caprini

state: Italy

address: Via dei Monti di Creta 104

country: Italy

institute: IDI-IRCCS

description: Gene expression data from 3-day post-depilation epidermis

hyb_protocol: Affymetrix GeneChip Mouse Genome 430 assay protocol

scan_protocol: Affymetrix GeneChip scanner 3000-7G

data_processing: R, Bioconductor. RMA was used for normalization.

label: Biotin

source_name: epidermal keratinocytes

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were depilated to induce hair regeneration and keratinocyte activation. Skin patches were harvested 3-day post-depilation

value: epidermal keratinocytes

value: K14-TCL1 transgenic


title: KO3: Tcl1 knockout 3

label_protocol: Affymetrix GeneChip Mouse Genome 430 assay protocol


title: TGKO1: K14-TCL1 transgenic 1


title: KO1: Tcl1 knockout 1


title: WT2: wild type 2

value: wild type


title: 26311_Baseline

value: ART


title: WCE_CTD_WT_MM+thiamine_exp2

description: without spike-in

value: h+ ade6-M216 leu1-32 ura4-D18 his3-D1 Rpb3-3HA::kanMX6


title: TGKO2: K14-TCL1 transgenic 2


title: WT1: wild type 1


title: 25011_Wk26


title: IP_Ser2P_WT_MM+thiamine_exp2

description: without spike-in

value: Abcam, ab5095


title: 25011_Wk22


title: WCE_Ysh1_WT_MM+thiamine_exp2

description: without spike-in


title: KO2: Tcl1 knockout 2


title: IP_Ser5P_WT_MM+thiamine_exp2

description: without spike-in

value: Abcam, ab5131


title: IP_Ser7P_WT_MM+thiamine_exp2

description: without spike-in

value: clone 4E12, EMD Millipore, 04-1570


title: 26311_Wk19


title: WCE_Rpb3_WT_MM+thiamine_exp2

description: without spike-in


title: 25011_Wk18


title: 25011_Wk14


title: WCE_Rna14_WT_MM+thiamine_exp2

description: without spike-in


title: 25011_Wk6


title: 25011_Baseline

value: Baseline


title: WCE_Rpb1_WT_MM+thiamine_exp2

description: without spike-in


title: IP_Tyr1P_WT_MM+thiamine_exp2

description: without spike-in

value: clone 3D12, Active Motif, 61383


title: IP_Rpb1_WT_MM+thiamine_exp2

description: without spike-in

value: clone 8WG16; Convance, MMS-126R


title: 23212_Wk26


title: 23212_Wk14


title: 23212_Wk22


title: 23212_Wk6


title: 23212_Baseline


title: 25011_Wk19


title: IP_Rpb3_WT_MM+thiamine_exp2

description: without spike-in


title: BG3_CG7372

city: Planegg-Martinsried

first: Sandro

last: Baldi

address: Großhaderner Strasse 9

department: BMC Molecular Biology

country: Germany

institute: LMU Munich

description:
primer pair 1: TAATACGACTCACTATAGGGTGGAA GAGGCTGAGGTGG/TAATACGACTCACTATAGGGTACCGCCGAT CGTTCTTGTG
primer pair 2: TAATACGACTCACTATAGGGGCACA CAGGTGAAAAACC/TAATACGACTCACTATAGGGTGTCATCGAG CTGGACAAAG

data_processing:
mapping of Illumina reads: bowtie 1.1.1, default settings
In R with libraries "ShortRead", "rtracklayer": Nucleosoome dyad coverage vectors were obtained by size-selecting fragments of length >=120 and <=200 bp and resizing their length to 50 bp fixed at the fragment center. Genome coverage of nucleosome dyads was exported to .bedgraph file.
Genome_build: dm3
Supplementary_files_format_and_content: .bedgraph files containing nucleosome dyad coverages

organism: Drosophila melanogaster

source_name: larval L3, central nervous system

growth_protocol: BG3-c2 cells were cultured at 26°C in Schneider’s Drosophila Medium (Gibco) including 10% fetal calf serum (FCS), Penicillin-Streptomycin and 10 µg/ml human insulin.

extract_protocol:
9 x 106 cells per condition were washed in 10 ml cold PBS and resuspended in 1 ml TM2 buffer (10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 1 mM PMSF). The cells were incubated 1 min on ice and NP-40 added to 1.5 %, gently vortexed, and again incubated on ice for 10 min for lysis and release of the nuclei. After a 10 min centrifugation at 93 x g and 4°C the nuclei were resuspended in 600 ml of TM2 buffer with 2 mM CaCl2 and distributed into three 200 ml aliquots. Those were treated with 2.3/5.9/11.7 x 10-3 units of MNase for 20 min at 37°C. The reaction was then quenched by adding 5 ml 0.5 M EDTA and 100 mg RNase A, followed by a 20 min incubation at 37°C. Proteins were digested away at 50°C for 2 h after the addition of 12 ml 10% SDS and 200 mg Proteinase K. The DNA was then purified by Phenol/Chloroform extraction, precipitated in 2.5 V EtOH, 1/10 V NaOAC 3M and 20 mg glycogen and run on a 1.2% agarose gel in 0.5x TAE buffer. The samples with the best digestion degree (predominantly nucleosomes, achieved with 11.7 x 10-3 U of MNase) were chosen and the mononucleosomal bands cut out and purified (NucleoSpin Gel and PCR Clean-up, Macherey-Nagel). The purified DNA was then used for Next-Generation-Sequencing library preparation.
Libraries were prepared on 10 ng of DNA with the iDeal library preparation kit (Diagenode). PCR amplification was monitored by quantifying amplified libraries.

treatment_protocol: For knockdown of su(Hw) and CG7372 two different dsRNAs per gene were simultaneously used. For each knockdown condition, 1.5 x 107 cells were resuspended in 4 ml medium (containing antibiotics and insulin but no FCS), seeded in T-75 flask, and incubated with 100 mg (GST, su(Hw), CG7372) of in vitro transcribed dsRNA (MEGAscript T7 Transcription Kit). After gentle shaking for 45 min at room temperature, 16 ml of medium (+FCS/+antibiotics/+insulin) was added to the cells. After 5 days cells were treated again with dsRNA in the same manner, but this time two T-75 flasks per condition were seeded. After 5 more days, the cells were harvested.

value: BG3-c2 cells

value: RNAi:CG7372 dsRNA

tag: molecule

value: mononucleosomal DNA


title: PC3M_2

city: Boston

description: rRNA depleted RNA

source_name: Prostate cancer cell line

growth_protocol: PC3M-LN4 cells were cultured in RPMI media with Pen/Strep, heat inactivated FBS, and L-glutamine.


title: gDNA_acf_rescue

source_name: in vitro assembled chromatin on genomic DNA

growth_protocol: Drosophila embryo extract was prepared from preblastoderm embryos 0-90 min AEL according to (Becker and Wu, Mol Cell Biol, 1992) with the following modifications: After collection, the embryos were dechorionated in 200 ml embryo wash buffer (0.7% NaCl, 0.04% Triton X-100) and 60 ml 13% sodium hypochlorite (VWR) for 3 min at room temperature while stirring. Embryos were rinsed for 5 min with cold water and transferred into a glass cylinder with embryo wash buffer. After settling of the embryos, the buffer was decanted and the embryos were washed first in 0.7% NaCl and then in extract buffer (10 mM HEPES, pH7.6, 10 mM KCI, 1.5 mM MgCl2, 0.5mM EGTA, 10% glycerol, 10 mM 3-glycerophosphate; 1 mM DTT, protease inhibitors added freshly before use: 0.2 mM PMSF, 1 mM Aprotinin, 1 mM Leupeptin, 1 mM Pepstatin). After the last wash, embryo wash buffer was decanted and embryos were homogenized with one stroke at 3000 rpm and 10 strokes at 1500 rpm using a homgenplus homogenizer  (Schuett-Biotec). The homogenate was adjusted to a final MgCl2 concentration of 5 mM and centrifuged for 15 min at 27000 g at 4°C. The white lipid layer was discarded and the supernatant was centrifuged for 2 h at 245420 g at 4°C. The clear supernatant was aspirated with a needle, leaving the lipid layer and pelleted nuclei in the tube. Genomic DNA was purified from Drosophila BG3-c2 cells with the Blood & Cell Culture Midi Kit (Qiagen). 1 μg of genomic or plasmid DNA were added to 60 μl Drosophila embryo extract supplied with 10 mM 3-glycerophosphate and an ATP-regenerating buffer (3 mM ATP, 30 mM creatine phosphate, 10 μg/ml creatine kinase, 3 mM MgCl2, 1 mM DTT) and filled up to a total volume of 120 μl with EX50 buffer (10 mM HEPES, pH 7.6, 50 mM KCI, 1.5 mM MgCl2, 0.5 mM EGTA, 10% glycerol, 10 mM 3-glycerophosphate; 1 mM DTT, 0.2 mM PMSF, 1 mM Aprotinin, 1 mM Leupeptin, 1 mM Pepstatin). Chromatin was assembled at 26°C for 6 h. ACF was purified from insect cells as described in (Fyodorov and Kadonaga, Methods Enzymology, 2003) and 2.4 pmol added to the chromatin assembly reaction

extract_protocol:
1.5 mM f.c. CaCl2 and 1.4 x 10-3 U MNase were added to digest the chromatin at 30°C for 15 min. After quenching the reaction with 10 mM f.c. EDTA, samples were treated with 20 RNase mg A for 30 min. Proteins were digested overnight after adding 16 ml 2% SDS and 100 mg Proteinase K and incubating at 37°C. The DNA was purified with the GenElute PCR clean-up kit (Sigma-Aldrich).
Libraries were prepared using the MicroPlex Library Preparation kit (Diagenode). PCR amplification was monitored by quantifying amplified libraries.

value: chromatin assembled with Drosophila preblastoderm extract

value: Acf1C 0-2 h embryos