title: C3

city: Toledo

first: Javier

last: Cabrera

address: Avda. Carlos III s/n

country: Spain

institute: UCLM

description: small RNAs

data_processing:
The very basic figure from sequencing was converted into sequence data by the base calling step in a fastq format. Clean sequences were obtained after discarding of low quality reads, reads with 5' primer contaminants, reads without 3' primer, reads without the insert tag, reads with poly A and reads shorter than 18nt.   Reads per million (RPM) value was obtained for each sequence in each library (No. of reads for a sequence/No. of total reads for all sequences in that library*1000000). Each sequence was tested for changes in expression by performing a two tailed t-test between their three RPM values in galls and their three RPM values in control roots. Expression differences between galls and roots were considered to be significant with P < 0.05. Fold Change was used as a measure of the change in the expression between galls and roots
Clean reads were mapped to Arabidopsis or M. incognita genome (http://www.arabidopsis.org/ or http://www6.inra.fr/meloidogyne_incognita) by SOAP to analyze their expression and distribution on the genome and subsequently categorized into different types of small RNAs as follows: rRNA, tRNA, snRNA, etc, (in which Genbank > Rfam), known miRNAs and their isomiRs (miRBase19), repeat, exon and intron. Unannotated sequeces were screened by using the prediction software Mireap (http://sourceforge.net/projects/mireap/) that predicts novel miRNA by exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the unannotated small RNA tags, using the following restrictions: minimal miRNA sequence length (18 nt), maximal miRNA sequence length (25 nt), minimal miRNA reference sequence length (20 nt), maximal miRNA reference sequence length (23 nt), maximal copy number of miRNAs on reference (20 nt), maximal free energy allowed for a miRNA precursor (-18 kcal/mol), maximal space between miRNA and miRNA* (300 nt), minimal base pairs of miRNA and miRNA* (16 nt), maximal bulge of miRNA and miRNA* (4 nt), maximal asymmetry of miRNA/miRNA* duplex (4 nt). Target prediction was performed on the Plant Small RNA Target Analysis Server (psRNATarget; http://plantgrn.noble.org/psRNATarget/; Dai and Zhao, 2011) by establishing the following restrictions: maximum expectation (3.0), length for complementarity scoring (20), allowed maximum energy to unpair the target site (UPE; 25); flanking length around target site for target accessibility analysis (17 bp in upstream /  13 bp in downstream), range of central mismatch leading to translational inhibition (9-11 nt).
Genome_build: TAIR10
Supplementary_files_format_and_content: "Counts_" files This file contain clean tags, 18-30 nt, tab delimited, length | number | sequence
Supplementary_files_format_and_content: "miRNAs_RPM.txt" Reads Per Million of each known miRNA in each smallRNA library generated

organism: Arabidopsis thaliana

source_name: Root Segments

growth_protocol: All Arabidopsis thaliana (L.) Heynh Columbia-0 (Col-0) seeds either wild type or transgenics were surface sterilized with 30% commercial bleach and sown in 0.3% Gamborg medium (Gamborg et al., 1968) supplemented with 1.5% sucrose. Plates were incubated at 4°C for 2 days and grown vertically at 25°C, 60% relative humidity,18h light-6h darkness.

extract_protocol:
Gall collection: To perform the RNA isolation from galls with a good efficiency, 250-300 hand dissected galls at 3 days post infection (3 dpi), should be collected. Collect galls and rapidly freeze them to a 1.5 ml Eppendorf® tube in liquid nitrogen. Store at -80 °C until further processing (step C) Homogenization: Clean mortar and pestles with acetone, let them dry on the bench and autoclaved to avoid RNase activity. CAUTION: Check that mortar, pestle and pipettes used during the extraction have not been in contact with RNases. Sometimes it is preferable to keep material exclusively for RNA extraction.  Add liquid nitrogen into the mortar with the pestle to cold them down.  Add the galls into the mortar and proceed into a fume hood. When liquid nitrogen is nearly evaporated, add TRI Reagent® (500-750 μl/200-300 galls at 3 dpi); the total volume should not exceed 10% of the volume of TRI Reagent used for homogenization, as suggested by the TRI Reagent® protocol. Grind galls with a mortar and pestle. TRI Reagent solution initially becomes frozen, but it will melt gradually as a result of the homogenization. Proceed until a liquid appearance is observed and no visible tissue pieces are identified within the Reagent solution.  Note: Do not leave traces of galls without homogenizing, since this step can be limiting for good efficiency. Transfer the gall homogenate with a pipette to a 1.5 ml Eppendorf® tube and place it on ice while you homogenize the rest of the samples.  Phase separation Centrifuge at 12,000 x g for 10 min at 4 °C and transfer the supernatant containing the RNA to a new 1.5 ml Eppendorf® tube.  Note: The resulting pellet contains membranes, polysaccharides and high molecular weight DNA while the supernatant contains RNA. All insoluble material should be removed from the homogenate. Add 100 μl of chloroform per 500 μl of TRl Reagent® in a fume hood. Cap sample tubes securely. Shake tubes vigorously by hand for 15 s and incubate them at room temperature (RT) for 5 to 10 min. Note: Do not use vortex. Centrifuge the samples at 12,000 x g for 15 min at 4 °C. Transfer the upper aqueous phase to a new tube.  RNA precipitation Add 125 μl of isopropanol and 125 μl of high salt buffer per 500 μl of TRl Reagent®. Mix the solution and store it for 5-10 min at RT. Note: The high salt precipitation solution removes contaminating compounds as proteoglycan and polysaccharide from the isolated RNA. Centrifuge at 12,000 x g for 8 min at 4 °C. Discard the supernatant.  RNA Wash Wash the RNA pellet with 1 ml of 75% ethanol and mix by inversion several times. Centrifuge at 7,500 x g for 5 min at 4 °C and discard the supernatant. Repeat steps E-1 and 2.  Spin 10 sec in a microfuge and discard carefully the remaining liquid. Air dry the pellet for 3-5 min. Do not let the RNA over-dry, as this will make it difficult to dissolve. The white RNA pellet will turn clear when it dries out. Add 100 μl DEPC-water or RNase-free water immediately after the pellet becomes clear. Dissolve RNA by incubating for 10 min at 37 °C followed by 5 min at 60 °C. Store RNA solution at -80 °C or continue with further RNA Cleanup by DNase digestion.  Combined in column DNase I Digestion and RNA Cleanup. This procedure is based on the combined use of two different commercial kits (RNase-Free DNase Set and RNeasy Mini Kit). Please, use handling instructions of all buffers and reagents following their recommendations. Note: Buffers as RPE, RTL, RW1, RDD are supplied by the companies within the kits. Before starting RNA cleanup, make sure the DNase I and Buffer RPE are ready to use. Preparation of DNase I stock solution: Inject 550 μl RNase-free water into the lyophilized DNase I vial using an RNase-free needle and syringe. Mix gently by inverting the vial and divide it in 10 μl single-use aliquots. Store at -20 °C for up 9 months. Preparation of Buffer RPE: Add 4 volumes of 96-100% ethanol (44 ml) as indicated in the bottle. Adjust the RNA sample volume to 100 μl with RNase-free water.  Add 350 μl of Buffer RLT and mix well by pipetting. Add 250 μl EtOH, mix well by pipetting. Transfer the sample to an RNeasy Mini spin column placed in a 2 ml collection tube. Close the lid gently and centrifuge at 8,000 x g for 15 sec. Discard the flow-through. Add 350 μl buffer RW1 to the RNeasy spin column. Close the lid gently and centrifuge at 8,000 x g for 15 sec. Discard the flow-through. Add 70 μl buffer RDD (supplied with the RNase-Free DNase Set) to 10 μl DNase I stock solution. Mix gently by inverting the tube. Note: Do not vortex. Add 80 μl of the DNase I incubation Mix to the RNeasy spin column, and place on the bench at RT for 15 min. Note: Add the Mix directly to the center of the RNeasy spin column membrane. Add 350 μl buffer RW1 to the RNeasy spin column. Close the lid gently and centrifuge at 8,000 x g for 15 sec. Discard the flow-through. Add 500 μl buffer RPE to the RNeasy spin column. Close the lid gently and centrifuge at 8,000 x g for 15 sec. Discard the flow-through. Add 500 μl buffer RPE to the RNeasy spin column. Close the lid gently and centrifuge at 8,000 x g for 2 min.  Note: The long centrifugation dries the spin column membrane, eliminating ethanol contamination. Quickly remove the RNeasy spin column from the collection tube so that the column does not contact the flow through. Place the RNeasy spin column in a new 2 ml collection tube. Close the lid gently and centrifuge at full speed for 1 min.  Note: It is important to eliminate any possible buffer RPE carryover. Place the RNeasy spin column in a new 1.5 ml collection tube. Add 30 μl RNase-free water or DEPC-water to the center of the spin column membrane. Incubate 1 min at RT. Close the lid gently and centrifuge at 8,000 x g for 1 min to elute the RNA. Add 20 μl RNase free water or DEPC-water to the center of spin column membrane to elute the maximum RNA. Incubate 1 min at RT. Close the lid gently and centrifuge at 8,000 x g for 1 min. Use Nanodrop and/or Bioanalyzer to test the RNA quantity and quality. You should get 5-10 μg total RNA from 250-300 collected galls at 3 dpi of a high quality. Store the RNA sample in -80 °C for future use.
Previously to sequencing, small RNAs were isolated by polyachrilamide gel electrophoresis and amplified by subsequently steps of RT-PCR and PCR with the help of 5’ and 3’ modified primers that specifically targeted microRNAs and other small RNAs that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Illumina Solexa Sequencing-By-Synthesis technology was used to generate three small RNA libraries from 3dpi galls and three small RNA libraries from control root segments at Beijing Genomics Institute (Shenzhen, China).

treatment_protocol: Five days post germination the plants were inoculated just over the root tip with 7-10 M. javanica J2 per main root 2-3 days after hatching. A thin temperate (30-37°C) film of 0.3% Gamborg medium was poured over the roots to facilitate nematode penetration. Plants were monitored every 12 hours under a Leica Mz125 stereomicroscope to establish an infection timeline, resulting in a maximum error of 12 h when assessing galls age.

tag: days post infection

value: Equivalent to 3 days post infection

tag: nematode

value: Uninfected


title: C2

status: Public on Nov 19 2015

type: SRA

description: small RNAs

library_source: transcriptomic

molecule: total RNA


title: C1

description: small RNAs


title: Eto2 WT Rep1

city: Oxford

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: The Weatherall Institute of Molecular Medicine

description: processed data file: Eto2_WT_Vs_KD.txt

data_processing:
For ChIP-seq, reads were mapped against NCBI build 37.1 of the mouse genome using Bowtie (Langmead et al. 2009). Uniquely mapped reads were extended to 200 bp in the 3' direction and were transformed into a genome-wide read density (coverage) using custom R scripts. MACS (Zhang et al. 2008), CCAT (Xu et al. 2010), and in-house peak calling software with default parameters were used to comprehensively identify binding sites. We combined binding sites identified by all three methods to define consensus-binding regions using GenomicRanges (Lawrence et al. 2013). Consensus-binding regions were given p-values based on a negative binomial distribution (Rozowsky et al. 2009) and assigned p-values were adjusted using the Benjamini-Hochberg (BH) method.
For RNA-seq, raw reads were mapped with Tophat2 (Daehwan Kim, et al., Genome Biology 2013) against the mouse genome (mm9) NCBI build 37.1 with default parameters using "no-coverage-search", and "segment-length 18" as the input options. We next quantified the expression per UCSC RefSeq (mm9) gene to obtain read count and RPKM values using the rpkmforgenes software (Ramsköld D, et al., PLos Comput Biol., 2009). The non-adjusted read counts for each gene were used for statistical calculation of global differential expression using DESeq2 (Michael I Love, et al., Genome Biology, 2014).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files, tab-delimited text files

organism: Mus musculus

source_name: MEL_Eto2 WT

growth_protocol: Mouse erythroleukemia (MEL) cells were maintained in DMEM containing 10% FCS and penicillin/streptomycin. ETO2-V5-Bio MEL cells expressing BirA were generated and maintained as previously described (Soler et al. 2010; Soler et al. 2011).

extract_protocol:
For endogenous co-immunoprecipitations, MEL nuclear extracts were diluted to reach 100mM KCl salt concentration using Heng 0 buffer (20mM HEPES KOH pH7.9, 20% glycerol, 0.25mM EDTA, 0.05% Np40). For co-IP experiments in MEL cells, 0.5 mg nuclear extract was used per IP. Extracts were treated with 1U Benzonase nuclease (Millipore). For RNA-seq, total RNA was extracted from MEL or E13.5 sorted fetal liver populations using the RNeasy mini kit (Qiagen).
Libraries were prepared according to Illumina's standard instructions

tag: cell type

value: Mouse erythroleukemia (MEL) cells

tag: genotype/variation

value: Eto2 WT


title: 928_input_neuroblastoma tumor

city: Ghent

first: Anneleen

last: Decock

address: De Pintelaan 185

country: Belgium

institute: Ghent University

library_source: genomic

data_processing:
Quality control by FastQC (version 0.9.2)
Paired-end read mapping to the human reference genome using Bowtie2 (version 2.0.0 beta7) and SAMtools (version 0.1.18)
Marking PCR duplicates by Picard (version 1.79)
Mapping quality control by SAMStat (version 1.08) and bamUtil (version 1.0.2)
Peak calling using MACS (version 1.4.0 beta)
Genome_build: hg19
Supplementary_files_format_and_content: .bam: .bam format was used as output file type for read mapping (Bowtie2; duplicates are removed); .bed: location and score of the identified peaks (MACS); .wig.gz: visualization (MACS); .tdf: visualization of the methyl-seq data in IGV.

molecule: genomic DNA

organism: Homo sapiens

source_name: primary tumor

extract_protocol:
DNA fragmentation by shearing, followed by MBD capture (MethylCap kit of Diagenode)
PrepX ILM DNA Library Kit (IntegenX) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)

tag: age of the patient at diagnosis (months)

tag: inss stage

tag: mycn amplification status

value: amplified

tag: overall survival time (days)

tag: overall survival status

value: died of disease

tag: event-free survival status

value: event


title: Gfi1b WT Rep2

description: processed data file: Gfi1b_WT_Vs_KD.txt

source_name: MEL_Gfi1b WT

value: Gfi1b WT


title: LSD1 IgG Control

source_name: MEL_LSD1 IgG Control

tag: chip antibody

value: normal rabbit IgG

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot


title: LSD1 ChIP

source_name: MEL_LSD1 ChIP

value: Anti-KDM1 / LSD1 antibody

value: Abcam


title: 610_input_neuroblastoma tumor


title: A2

description: small RNAs

source_name: Hand Dissected Galls

value: 3 days post infection

value: Meloidogyne javanica


title: 41_input_neuroblastoma tumor

value: non-amplified


title: IRF2BP2 IgG Control

source_name: MEL_IRF2BP2 IgG Control

value: normal rat IgG


title: 1646_MBD_neuroblastoma tumor

value: alive

tag: event-free survival time (days)

value: no event


title: IRF2BP2 ChIP

description: processed data file: Eto2_and_Irf2bp2.peaks.txt

source_name: MEL_IRF2BP2 ChIP

value: Irf2bp2 Absea antibody 10G3

tag: chip antibody info

value: custom-made


title: GFI1B IgG Control

source_name: MEL_GFI1B IgG Control

value: Mouse erythroleukemia (MEL) cells

value: normal goat IgG


title: GFI1B ChIP

source_name: MEL_GFI1B ChIP

value: Gfi-1B Antibody (D-19)


title: 1486_MBD_neuroblastoma tumor


title: 1699_MBD_neuroblastoma tumor

extract_protocol:
DNA fragmentation by shearing, followed by MBD capture (MethylCap kit of Diagenode)
NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)

value: event


title: 926_MBD_neuroblastoma tumor


title: 1650_MBD_neuroblastoma tumor


title: 1476_MBD_neuroblastoma tumor


title: 916_MBD_neuroblastoma tumor


title: 1484_MBD_neuroblastoma tumor


title: 1469_MBD_neuroblastoma tumor


title: 914_MBD_neuroblastoma tumor


title: 1039_MBD_neuroblastoma tumor


title: 1038_MBD_neuroblastoma tumor


title: 809_MBD_neuroblastoma tumor


title: A3

description: small RNAs


title: 747_MBD_neuroblastoma tumor


title: 1028_MBD_neuroblastoma tumor


title: 912_MBD_neuroblastoma tumor


title: 1509_MBD_neuroblastoma tumor


title: 823_MBD_neuroblastoma tumor


title: 566_MBD_neuroblastoma tumor


title: 744_MBD_neuroblastoma tumor


title: 822_MBD_neuroblastoma tumor


title: MERS_Vero_Gleevec_48hrs

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

country: USA

institute: University of Maryland School of Medicine

data_processing:
NOT PROVIDED
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: NOT PROVIDED

organism: Chlorocebus sabaeus

source_name: Vero E6 cells

growth_protocol: Vero E6 cells were grown in MEM with 10% Fetal Bovine Serum

extract_protocol:
RNA was extracted using Trizol from cells infected in culture.
Poly-A RNA was isolated and indexed libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RNA was isolated at 24 and 48 hours post infection at an MOI of 0.1 and 3 with each virus.

tag: cell line

value: Vero E6


title: 1488_MBD_neuroblastoma tumor


title: 1483_MBD_neuroblastoma tumor


title: 711_MBD_neuroblastoma tumor


title: 820_MBD_neuroblastoma tumor


title: MOCK_Vero_Gleevec_48hrs


title: 530_MBD_neuroblastoma tumor


title: A1

description: small RNAs

tag: days post infection


title: MERS_Vero_IFNbeta_48hrs


title: Eto2 KD-sh3 Rep2

description: processed data file: Eto2_WT_Vs_KD.txt

source_name: MEL_Eto2 KD-sh3

value: Eto2 KD-sh3


title: 397_MBD_neuroblastoma tumor


title: 1803_MBD_neuroblastoma tumor

value: amplified


title: 529_MBD_neuroblastoma tumor


title: 1863_MBD_neuroblastoma tumor


title: 1800_MBD_neuroblastoma tumor


title: 410_MBD_neuroblastoma tumor


title: 278_MBD_neuroblastoma tumor


title: MOCK_Vero_IFNbeta_48hrs


title: MOCK_Vero_Gleevec_24hrs


title: MERS_Vero_IFNbeta_24hrs


title: E700_MBD_neuroblastoma tumor


title: MERS_Vero_Gleevec_24hrs


title: 1793_MBD_neuroblastoma tumor


title: 1789_MBD_neuroblastoma tumor


title: E685_MBD_neuroblastoma tumor


title: SARS_VEROlowMOI_48hr_3


title: 1794_MBD_neuroblastoma tumor


title: 1649_MBD_neuroblastoma tumor


title: MOCK_Vero_IFNbeta_24hrs


title: E579_MBD_neuroblastoma tumor


title: SARS_VEROlowMOI_24hr_2


title: 1515_MBD_neuroblastoma tumor


title: 1647_MBD_neuroblastoma tumor


title: 2868_MBD_neuroblastoma tumor


title: 1501_MBD_neuroblastoma tumor


title: SARS_VEROlowMOI_24hr_1


title: Vero-3_20ulEMC_48hrs_RNA3


title: 2863_MBD_neuroblastoma tumor


title: 2857_MBD_neuroblastoma tumor


title: Vero-3_20ulEMC_48hrs_RNA2


title: 1384_MBD_neuroblastoma tumor


title: 1616_MBD_neuroblastoma tumor


title: SARS_VEROHighMOI_48hr_2


title: Vero-3_2ulEMC_48hrs_RNA3


title: 1524_MBD_neuroblastoma tumor


title: E598_MBD_neuroblastoma tumor


title: 1431_MBD_neuroblastoma tumor


title: 1030_MBD_neuroblastoma tumor


title: 1382_MBD_neuroblastoma tumor


title: 1381_MBD_neuroblastoma tumor


title: 1017_MBD_neuroblastoma tumor


title: 1521_MBD_neuroblastoma tumor


title: 11_MBD_neuroblastoma tumor


title: Vero-3_20ulEMC_48hrs_RNA1


title: Vero-3_2ulEMC_48hrs_RNA1


title: 526_MBD_neuroblastoma tumor


title: 1795_MBD_neuroblastoma tumor

value: died of disease


title: 1796_MBD_neuroblastoma tumor


title: Vero-3_2ulEMC_48hrs_RNA2


title: Vero-3_20ulEMC_24hrs_RNA3


title: Vero-3_20ulEMC_24hrs_RNA2


title: 1790_MBD_neuroblastoma tumor


title: E282_MBD_neuroblastoma tumor

value: dead of disease


title: 1791_MBD_neuroblastoma tumor


title: E069_MBD_neuroblastoma tumor


title: 1784_MBD_neuroblastoma tumor


title: first Mmi1-HTP CRAC sample

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

description:
cross-linked RNA
Mmi1_merged_homopolymer_filtered_intervals.gtf

data_processing:
CRAC data processing steps: All processing steps were performed using the pyCRAC package version 1.2.2.4. Demultiplexing was performed using pyBarcodeFilter.py (version 2.3.4). 3' adapter removal and 3' end quality trimming (min Phred = 30) was performed using FlexBar (version 2.5). Reads were collapsed using random nucleotides present in 5' barcodes using pyFastqDuplicateRemover.py (version 0.0.2). Reads were mapped to the S. pombe genome (ASM294v2.19; source ENSEMBL) using novoalign (version 2.0.4) and feature counts were generated using pyReadCounters (version 0.5.3).
RNA-seq data processing steps: Reads were quality trimmed (min Phred =30) using FlexBar (version 2.5). Reads were mapped to the S. pombe genome (ASM294v2.19; source ENSEMBL) using novoalign (version 2.0.4) and feature counts were generated using pyReadCounters (version 0.5.3).
The gtf files were used to generate begraph files for viewing the data in the Integrated Genome Browser (bioviz.org).
Genome_build: ASM294v2.19
Supplementary_files_format_and_content: The data format of the processed data is the gene transfer format (gtf). This contains the genomic positions of the mapped reads. For the CRAC data mutation information was also included. PyReadCounters version 0.5.3 from the pyCRAC package (Webb et al Genome Biology, version 1.2.2.4) was used.

organism: Schizosaccharomyces pombe

growth_protocol: Schizosaccharonyces pome were grown in YES medium to exponential phase at 30ºC

extract_protocol:
none provided by submitter
For the RNASeq experiments, total RNA was extracted from three separate cultures of wt and mmi1Δ grown to mid-log phase and DNase-treated. Ribodepletion and library preparation were performed by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics according to the TruSeq protocol. Note that with the TruSeq protocol the cDNA strand is sequenced. Thus all the strand information needs to be reversed after mapping the reads to the genome (i.e - to + and + to -). Paired-end CRAC libraries were generated essentailly as described by Granneman et al PNAS 2009. A paired-end compatible 3' adapter was used for making the CRAC library (5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’). The N in the sequence indicates a random nucleotide.
PCR oligonucleotides for making CRAC libraries
3' adapter:
App_PE 5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’
5' adapters:
L5Aa 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrUrArArGrCrN-OH-3'
L5Ab 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrArUrUrArGrCrN-OH-3'
L5Ad 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrCrGrCrUrUrArGrCrN-OH-3'
L5Bb 5'-invddT-ACACrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrNrNrCrArCrUrArGrCrN-OH-3'
P5_forward 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’
P3_reverse 5’-CAAGCAGAAGACGGCATACGAGAT(6nt barcode)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’

tag: genotype

value: h+ ura4delta18 leu1-32 ade6-M216 imr1R(NcoI)::ura4+ mmi1-his6-TEV-Prot A::kanMX


title: 1786_MBD_neuroblastoma tumor


title: 1648_MBD_neuroblastoma tumor


title: 1783_MBD_neuroblastoma tumor


title: 1527_MBD_neuroblastoma tumor


title: first untagged control CRAC sample

description:
cross-linked RNA
Control_merged_homopolymer_filtered_intervals.gtf

value: h+ ura4delta18 leu1-32 ade6-M216  imr1R(NcoI)::ura4+


title: 1782_MBD_neuroblastoma tumor


title: 1780_MBD_neuroblastoma tumor


title: 1522_MBD_neuroblastoma tumor


title: 1520_MBD_neuroblastoma tumor


title: second untagged control CRAC sample


title: E290_MBD_neuroblastoma tumor


title: 1473_MBD_neuroblastoma tumor


title: 1517_MBD_neuroblastoma tumor

value: non-amplified


title: 1507_MBD_neuroblastoma tumor


title: 1430_MBD_neuroblastoma tumor


title: 610_MBD_neuroblastoma tumor


title: 928_MBD_neuroblastoma tumor


title: 41_MBD_neuroblastoma tumor


title: E061_MBD_neuroblastoma tumor


title: second Mmi1-HTP CRAC sample


title: second RNAseq sample from parental strain

description: rRNA depleted total RNA


title: third RNAseq sample from parental strain

description: rRNA depleted total RNA


title: Small RNA-seq from individual #5

city: Durham

first: Jen-Tsan

middle: Ashley

last: Chi

state: North Carolina

address: 101 Science Drive

department: MGM

institute: Duke University

data_processing:
Illumina Casava 1.8.2 software was used for basecalling
Sequenced reads were trimmed, then filtered for size (17-28 nt).
Processed sequences were then clustered into unique reads, then mapped to the human (GRCh37/hg19) reference genome using the mapper.pl module from miRDeep2 with defaut parameters.
Novel miRNA and precursors were identified using miRDeep2 core module miRDeep2.pl using defaut parameters.  Novel miRNA datasets were created by adding to known miRNA of the species (miRBase v20) miRNA predicted with a miRDeep2 score> 0.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: miRDeep2 prediction output file contains known and novel microRNA sequence, sequence number, and scores based on miRDeep2 microRNA prediction criteria. Quantifier file contains sequence reads for known microRNAs based on initial mapping to genome with the quantifier.pl module.

source_name: Purified human mature erythrocytes

extract_protocol:
Blood samples were obtained from five healthy adults via venipuncture into EDTA tubes. Blood was washed three times with PBS, centrifuged, and plasma and buffy coat removed. Leukocytes were then depleted from the sample using a Purecell® Leukocyte Reduction Filtration System. Reticulocytes (immature red blood cells) were removed in the CD71 positive fraction using CD71 microbeads with the autoMACS® Separator (Miltenyi Biotec). The erythrocyte purification protocol reflects methods previously described (Sangokoya et. al, Methods in Molecular Biology, 2010). RNA was extracted using the miRVana miRNA Isolation kit (Life Technologies).
Small RNA-seq libraries were prepared with 100ng purified erythrocyte total RNA input using the TruSeq Small RNA Sample Prep Kit (Illumina). Samples were muliplexed, libraries pooled, and run on a single flowcell with the Illumina HiSeq 2000 sequencing system. Barcode IDs are as follows: Sample 1-ATCACG, Sample 2-CGATGT, Sample 3-TTAGGC, Sample 4-TGACCA, Sample 5-ACAGTG.

tag: cell type

value: mature erythrocyte


title: 1713_MBD_neuroblastoma tumor


title: first RNAseq sample from parental strain

description: rRNA depleted total RNA


title: Small RNA-seq from individual #3


title: 1477_MBD_neuroblastoma tumor


title: third RNAseq sample from Mmi1 deletion strain

description: rRNA depleted total RNA

value: h+ ura4delta18 leu1-32 ade6-M216 his3delta::1 mei4delta(828-1554nt)::GFP-hph mmi1delta::natMX


title: Small RNA-seq from individual #2


title: TAF15

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

data_processing:
ChIP-seq reads were aligned to the human genome hg19 assembly using BWA (0.6.1-r104) with default "aln" options.
Find peaks using MACS (version 14) with the following options: -g hs -w --call-subpeaks
Genome_build: hg19

source_name: HEK293 cells

growth_protocol: HEK-293 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) with 10% Fetal Bovine Serum, streptomycin (2.0 g/l), penicillin (1.2 g/l) and glutamine (0.3 g/l) (complete DMEM). HEK-293 cells were obtained from the American Type Culture Collection (CRL-1573). Cells were grown at 37 °C and 5% CO2.

extract_protocol:
For each ChIP experiment, material corresponding to 5x106 starting cells was used. Samples were diluted with an equal volume of D-Buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 1% Triton X-100). 5 µg of antibody (FUS sc-47711 Santa Cruz and EWS sc-48404 Santa Cruz) or 2 µg antibody for acetylated histone protein (ac-H3K9 ab4441-50 Abcam) were used for each ChIP. Samples were incubated in an ultrasonic water bath for 25 min, at 4°C, and afterwards centrifuged at 12,000 g for 10 min, at 4°C. 20 µl magnetic AG-beads (Invitrogen) were used for each ChIP. Beads were washed 3 times in 1 ml of supplemented IP-Buffer before use. After the final wash, beads were suspended in 40 µl of supplemented IP-Buffer and mixed with 90% of the chromatin supernatant described above. The mix was incubated in rotation overnight, at 4°C. Beads were washed twice with 200 µl of ice-cold supplemented IP-Buffer and three times with 200 µl ice-cold D-Buffer supplemented with protease inhibitors. Cross-linking was reversed by adding Reverse X-link Buffer and Protease K (Invitrogen) and incubating in water bath for 20 min, at 55°C. The remaining 10% of the reversed cross-linking chromatin supernatant was used as input. Supernatants were transferred to fresh tubes and incubated at 95°C to inactivate Protease K. DNA was purified using DNA Purification Buffer plus DNA purification magnetic beads, as recommended (Invitrogen). DNA was stored at -20°C.
DNA from FUS, EWS, and Ac-H3K9 ChIP experiments, as well as the corresponding input, was sequenced using the Illumina Hiseq 2000 platform at BGI in Shenzhen, China. Library preparation, cluster generation and sequencing by synthesis were performed according to manufacturer's protocol. All raw reads were aligned using Burrows-Wheeler Aligner (BWA version 0.5.8c (r1536) [48]) to the human reference genome (hg19). Aligned reads were processed by Model-based Analysis of ChIP-Seq (MACS) 1.4.0rc2 [49] for peak calling. Significant peaks were defined using the criteria of a threshold of minimally 9 reads and p-value less than 10-8 as suggested previously [50]. Input ChIP DNA was used as negative control.

treatment_protocol: The protocol used was merged from [75], [54] and Magnify chromatin immunoprecipitation system (Invitrogen). Briefly, HEK-293 cells (1x107per 10 cm petri dish) were cross-linked directly on plates by adding 37% formaldehyde to the media in a 1.4% final concentration for 15 min at room temperature. Cross-linking was stopped by adding glycine (final concentration 125 mM) followed by incubation for 5 min, at room temperature. Cells were scraped off in 500 µl of ice-cold 2x Phosphate Buffered Saline (PBS) and transferred to eppendorf-tubes and placed on ice. Cells were centrifuged at 2,000 g for 5 min, at 4°C, and washed twice with ice-cold PBS. Cells were lysed in 500 µl of ice-cold immunoprecipitation (IP)-Buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 1% Triton X-100, 0.5% NP40) supplemented with Complete Mini protease inhibitor cocktail (Roche), hereafter referred to as supplemented IP-Buffer. Samples were centrifuged at 12,000 g for 1 min, at 4°C, and washed once in ice-cold supplemented IP-Buffer. 500 µl of ice-cold supplemented IP-Buffer were added to the pelleted nuclei and sample re-suspended. Chromatin was fragmented by sonication using a Bioruptor (Diagnode) at high effect (80 cycles, 30s on plus 30s off) to generate fragments of 150-300 bp. Fragment lengths were examined by agarose gel electrophoresis. Samples were centrifuged at 12,000 g for 10 min, at 4°C. Supernatants were transferred to fresh ice-cold tubes and stored at -80°C.

tag: antibody


title: second RNAseq sample from Mmi1 deletion strain

description: rRNA depleted total RNA


title: H3K9

tag: antibody vendor/catalog

value: ab4441-50 Abcam


title: 1467_MBD_neuroblastoma tumor

tag: age of the patient at diagnosis (months)

tag: inss stage


title: 1429_MBD_neuroblastoma tumor

tag: mycn amplification status

tag: overall survival time (days)


title: Small RNA-seq from individual #1


title: first RNAseq sample from Mmi1 deletion strain

description: rRNA depleted total RNA


title: FUS

value: FUS

value: sc-47711 Santa Cruz


title: 811_MBD_neuroblastoma tumor

tag: overall survival status

tag: event-free survival status


title: Type-A-control-10dpi-Rep2

status: Public on Nov 18 2015

city: Chapel Hill

first: Carly

middle: Michelle

last: Shanks

state: NC

address: Genome Sciences Building, Room 4163

department: Biology

institute: UNC Chapel Hill

data_processing:
Quality control using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequences were aligned to the Arabidopsis Col-0 genome assembly (TAIR10) with TopHat version 2.0.11 (Langmead et al., 2009) and Bowtie version 1.1.0 (Langmead et al., 2009)
SAMtools version 0.1.18 (Li et al., 2009) was used to index BAM files for viewing the mapped reads using the Integrative Genomics Viewer (IGV) genome browser (Robinson et al., 2011).
The number of single-mapping reads that overlap each annotated gene was counted using featureCounts (Liao et al., 2014)
The counts files were supplied as inputs to EdgeR version 3.0 (Robinson et al., 2010) from the Bioconductor library for statistical analysis of differential gene expression between wild type and mutants.
The false discovery rate was controlled at 5% using the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995)
Genome_build: TAIR10
Supplementary_files_format_and_content: The edgeR output for differentially regulated genes with a fdr cut off of 0.05. The files include the gene annotation, a decription of the gene, the fdr and LogFC. We focused on three different sets of differentially regulated genes. First we examined at 4dpi and 10dpi wild-type controls compared to infected wild-type plants (4dpi-WT-infected.txt, 10dpi-WT-infected.txt). We also looked at genes differentially regulated between the control plants and the type-A mutant plants (4dpi-WT-vs-Type-A-control.txt, 10dpi-WT-vs-Type-A-control.txt). Then we looked at genes differentially regulated between infected wild-type and infected type-A mutant plants (4dpi-WT-vs-Type-A-infected.txt, 10dpi-WT-vs-Type-A-infected.txt).

source_name: roots

extract_protocol:
Total RNA extracted with the Quiagen Rneasy Plus Kit, Dnase treated with TURBO DNA-freeTM kit and cleaned with the Quiagen Rneasy Plus Kit
TruSeq Stranded mRNA preparation kit according to manufacturer’s instructions

tag: agent

value: none, control

value: Type-A mutant

tag: 4dpi or 10dpi

value: 10 days post infection


title: Col-infected-10dpi-Rep3

description:
10dpi-WT-infected.txt
10dpi-WT-vs-Type-A-infected.txt

value: Heterodera schachti nematodes

value: wild-type


title: Type-A-infected-10dpi-Rep2


title: Input DNA


title: Type-A-infected-10dpi-Rep3


title: Type-A-control-10dpi-Rep3


title: Col-control-10dpi-Rep2

description:
10dpi-WT-infected.txt
10dpi-WT-vs-Type-A-control.txt


title: Col-infected-10dpi-Rep2


title: Type-A-control-10dpi-Rep1


title: Type-A-infected-10dpi-Rep1


title: Col-control-10dpi-Rep3


title: Type-A-infected-4dpi-Rep3

value: 4 days post infection


title: Type-A-control-4dpi-Rep3


title: Small RNA-seq from individual #4


title: EWS

value: EWS

value: sc-48404 Santa Cruz


title: Col-control-10dpi-Rep1


title: Type-A-control-4dpi-Rep2


title: Col-infected-4dpi-Rep2

description:
4dpi-WT-infected.txt
4dpi-WT-vs-Type-A-infected.txt


title: Type-A-infected-4dpi-Rep1


title: Col-control-4dpi-Rep2

description:
4dpi-WT-infected.txt
4dpi-WT-vs-Type-A-control.txt


title: Type-A-control-4dpi-Rep1


title: Col-control-4dpi-Rep3


title: Col-infected-4dpi-Rep3


title: non-targeting siRNA in C4-2 cell rep 5

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description: RNA seq from C4-2 cells transfected with non-targeting siRNA

data_processing:
Single-end 40 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.05.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts

source_name: prostate cancer epithelium

growth_protocol: Cells were grown in RPMI media with 10% FBS at 37C

extract_protocol:
Total RNA (miRNeasy kit, Qiagen) from the flow sorted cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit

treatment_protocol: 50nM of siRNA pool was used using Lipofectamine RNAi MAX reagents transfected using Reverse transfection protocol.

tag: sample group

value: SiNTCONTROL


title: Col-infected-4dpi-Rep1


title: non-targeting siRNA in C4-2 cell rep 6


title: non-targeting siRNA in C4-2 cell rep 4


title: Col-infected-10dpi-Rep1


title: non-targeting siRNA in C4-2 cell rep 3


title: CHKA knockdown in C4-2 cell rep 4

description: RNA seq from C4-2 cells knocking down CHKA

value: SiCHKA

tag: antibodies

value: anti-CHKA (Sigma) cat no. HPA024153


title: CHKA knockdown in C4-2 cell rep 5


title: CHKA knockdown in C4-2 cell rep 6


title: Human_4924_BA46_7

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Single-end 100bp reads were aligned in a staged manner. First, reads were aligned with tophat2 using default options to a reference sequence comprised of mitochondrial DNA, mitochondrial cDNA, and ribosomal cDNA (GRCh37, Ensembl release 67). These reads were excluded from further analysis.
The reads that did not map in the first iterations were then mapped using tophat2 to GRCh37 using the GTF provided in Ensembl release 67.  RPKMs were then quantified using cufflinks, providing gene definitions (Ensembl release 67 GTF), and enabling several options (fragment bias correction, multi-read correction, upper quartile normalization, and compatible hits normalization).
Gene-level RPKM quantifications were used for all downstream processing.
Scaled by multiplying the appropriate factor to set each 80th percentile RPKM to be the geometric mean 80th percentile RPKM among samples.
Genome_build: GRCh37, Ensembl release 67
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.

source_name: Human brain

growth_protocol: Frozen tissue samples from human post-mortem brains were used.

extract_protocol:
All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent). Samples were randomized for RNA extractions and sequencing. 5ug of total RNA were treated with a Ribominus column according to the manufacturer’s instructions to remove ribosomal RNA.
Libraries were prepared using an Illumina TruSeq kit according to the manufacturer’s instructions.

treatment_protocol: Samples were dissected from frozen tissue pieces provided by the Maryland Brain and Tissue Bank.  Total RNA was extracted using Qiagen’s RNeasy or miRNeasy kits according to the manufacturer’s instructions.

tag: brain region

tag: identifier

tag: Sex

value: M

tag: age


title: Human_4924_BA9_6


title: CHKA knockdown in C4-2 cell rep 3

tag: cell line


title: CHKA knockdown in C4-2 cell rep 2


title: non-targeting siRNA in C4-2 cell rep 1


title: Type-A-infected-4dpi-Rep2

tag: genotype


title: Human_4924_BA40_3


title: Human_4924_BA44_6


title: Human_4924_BA6_9


title: Human_4924_BA6_8


title: Mg64

city: Storrs

first: Edan

last: Tulman

state: CT

address: 61 North Eagleville Rd

institute: University of Connecticut

description: rRNA depleted RNA

data_processing:
Illumina RTA v2 was used for base-calling
Fastq data were assembled and mapped, and RPKM values were calculated using Rockhopper (v 2.0.3). Bowtie2 parameters allowing 0 mismatches were used to map sequence reads to the Rlow genome
Genome_build: Mycoplasma gallisepticum Rlow (GeneBank accession no. AE015450)
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each gene. Each file representes a single sample from 1 bird at 1 timepoint or one in-vitro culture)

organism: Mycoplasmoides gallisepticum

source_name: TRIzol extraction of tracheal mucosa taken from chickens infected with M. gallisepticum at days 1-7 postinfection  (7 DPI)

extract_protocol:
Total RNA was collected in TRIzol, extracted using the zymo direct-zol mini prep, and enriched using Illumina RiboZero (epidemology) per product instructions
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA library prep kit HT)

tag: strain

value: Rlow

tag: enrichment treatment

value: PolyA removal


title: Human_4915_BA46_10


title: Mg63

description: rRNA depleted RNA


title: Human_4915_BA6_7


title: Human_4924_BA39_7


title: Mg62

description: rRNA depleted RNA


title: Human_4924_BA21_8


title: Human_4924_BA22_3


title: Human_4915_BA21_7


title: non-targeting siRNA in C4-2 cell rep 2


title: Human_4915_BA45_8


title: CHKA knockdown in C4-2 cell rep 1


title: Mg60

description: rRNA depleted RNA


title: Mg61

description: rRNA depleted RNA


title: Human_4924_BA47_7


title: Human_4915_BA9_1


title: Human_4915_BA39_8


title: Human_4915_BA22_9


title: Mg54

description: rRNA depleted RNA

source_name: TRIzol extraction of tracheal mucosa taken from chickens infected with M. gallisepticum at days 1-7 postinfection  (6 DPI)


title: Mg53

description: rRNA depleted RNA


title: Mg52

description: rRNA depleted RNA


title: Human_4915_BA47_2


title: Human_4915_BA44_12


title: Human_4915_BA40_7


title: Human_4924_BA45_4


title: Mg51

description: rRNA depleted RNA


title: Mg44

description: rRNA depleted RNA

source_name: TRIzol extraction of tracheal mucosa taken from chickens infected with M. gallisepticum at days 1-7 postinfection  (5 DPI)


title: Mg50

description: rRNA depleted RNA


title: Mg43

description: rRNA depleted RNA


title: Human_1905_BA47_1


title: Mg42

description: rRNA depleted RNA


title: Mg41

description: rRNA depleted RNA


title: Human_1905_BA46_8


title: Human_1905_BA6_10


title: Human_1905_BA9_4


title: Mg40

description: rRNA depleted RNA


title: Human_1905_BA45_5


title: Human_1905_BA44_4


title: Mg34

description: rRNA depleted RNA

source_name: TRIzol extraction of tracheal mucosa taken from chickens infected with M. gallisepticum at days 1-7 postinfection  (4 DPI)


title: Human_1905_BA22_12


title: Mg33

description: rRNA depleted RNA


title: Human_1905_BA21_3


title: Mg32

description: rRNA depleted RNA


title: Human_1905_BA40_4


title: Human_1905_BA39_11


title: Human_1581_BA47_11


title: Human_1581_BA21_6


title: Mg30

description: rRNA depleted RNA


title: Human_4593_BA45_2


title: Human_1581_BA44_5


title: Human_1581_BA46_7


title: Human_1581_BA45_12


title: Human_1581_BA22_11


title: Human_1581_BA39_9


title: Mg22

description: rRNA depleted RNA

source_name: TRIzol extraction of tracheal mucosa taken from chickens infected with M. gallisepticum at days 1-7 postinfection  (3 DPI)


title: Human_1581_BA6_10


title: Human_1029_BA39_10


title: Human_1581_BA9_1


title: Mg23

description: rRNA depleted RNA


title: Human_1029_BA45_10


title: Human_1581_BA40_12


title: Mg21

description: rRNA depleted RNA


title: Mg20

description: rRNA depleted RNA


title: Human_1029_BA46_10


title: Human_1029_BA44_6


title: Mg31

description: rRNA depleted RNA


title: Human_1029_BA40_9


title: Human_1029_BA9_6


title: Mg14

description: rRNA depleted RNA

source_name: TRIzol extraction of tracheal mucosa taken from chickens infected with M. gallisepticum at days 1-7 postinfection  (2 DPI)


title: Human_1029_BA47_11


title: Mg13

description: rRNA depleted RNA


title: Mg12

description: rRNA depleted RNA


title: Human_1029_BA21_1


title: Mg4

description: rRNA depleted RNA

source_name: TRIzol extraction of tracheal mucosa taken from chickens infected with M. gallisepticum at days 1-7 postinfection  (1 DPI)


title: Mg10

description: rRNA depleted RNA


title: Human_1029_BA22_2


title: Ifnb1_ko24

city: Fontenay aux Roses

first: Germain

last: Rousselet

address: 18 route du Panorama

department: Cellular and Molecular Radiobiology (IRCM)

country: France

institute: CEA

description: chromosome conformation capture protocol (3c)

data_processing:
Library strategy: 3C-Seq
Data were demultiplexed using the first 6 bases without mismatches, and trimmed for the primer bases on the 5' end, and then on the 3' end to reach 36bp
Trimmed sequences were aligned using Bowtie
Data were normalized as reads per million reads per EcoRI fragment
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph results as reads per million reads per EcoRI fragment

source_name: bone marrow derived macrophages (BMDM)

growth_protocol: Bone marrow was flushed from mice bones, and adherent cells were eliminated by adhesion on Petri dishes for 3 hours. Cells were differentiated in Petri dishes (typically 20 millions cells per 10 cm dish) for 7 days in the presence of 25 ng/ml M-CSF in IMDM supplemented with 10% fetal calf serum, 10 µM thioglycerol and antibiotics

extract_protocol:
Cells were fixed in 2% formaldehyde for 10 min at room temperature, quenched with 125 mM glycine, washed twice with PBS, and nuclei were prepared and frozen as a dry pellet in liquid nitrogen. Nuclei were digested with EcoRI overnight at 37°C, then diluted 10 times and ligated at least 4hrs at 16°C.
Extracted DNA was digested with DpnII and purified, and then ligated in 15 ml for at least 4hrs at 16°C. After precipitation, DNA was amplified by PCR using a forward primer containing the P5 Illumina adaptor sequence followed by a 4 base tag and an EcoRI site specific sequence, and a reverse primer composed of the P7 illumina adapter sequence followed by a DpnII site specific sequence. Products were verified on gel for linearity and reproducibility.

treatment_protocol: BMDM were left untreated or induced for 24 hrs with LPS (100 ng/ml) in IMDM supplemented with 2.5% fetal calf serum and antibiotics

tag: treatment

value: LPS 24hrs

tag: viewpoint


title: Mg24

description: rRNA depleted RNA


title: Mg5

description: rRNA depleted RNA


title: Ifnb1_wt0

value: WT

value: control


title: Mg1

description: rRNA depleted RNA


title: Ifnb1_ko0


title: tlr5a morphants: Flagellin-injected ; Biological replica 1

city: Leiden

first: shuxin

last: yang

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

description: tlr5a morphants: Flagellin-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 1

data_processing:
GeneTiles was used for quantification and visualization of the RNAseq data
Bowtie2 is used to align the reads in the fastq file to the genome (obtained from Ensemble). Bowtie2 generates SAM files that contain the reads together with the location on the genome.
Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome, resulting in a sorted BAM file.
The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome, i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file.
Using the available annotation from Ensemble we can search the BAM file for reads within a gene (using exon starting positions and lengths). This is done with a python script. The output of this script is a tab separated file (tsv) containing the read counts per gene.
We used DESeq, an R-script to perform statistical analysis. The DESeq script is used to normalise the reads per gene, based on (divided by) the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P-value, by calculating the dispersion per gene using DESeq. The size factors as well as the P-values are stored in ‘tsv’ files.
Using a script, all tsv files are combined into tsv files , e.g. per experiment, chromosome, per filtered results of most significant reads or highest ratio between measurement and control.
Genome_build: Zv9_toplevel

organism: Danio rerio

source_name: Danio rerio embryo 1 day post fertilization

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Zebrafish embryos were micro-injected into the caudal vein (27 hours post fertilization) with Pam3CSK4, flagellin or water as a control. At 1 hour post injection 10 to 15 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

tag: developmental stage

value: embryo 1 day post fertilization

value: Flagellin-injected 1 HPI

tag: genotype/variation

value: tlr5a morphants


title: Mg11

description: rRNA depleted RNA


title: tlr5a morphants: Flagellin-injected ; Biological replica 2

description: tlr5a morphants: Flagellin-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 2


title: tlr5a morphants: Flagellin-injected ; Biological replica 3

description: tlr5a morphants: Flagellin-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 3


title: ICE_ko0

value: ICE


title: Human_1029_BA6_5


title: Ifnb1_wt24


title: ICE_wt24


title: tlr5a morphants: water-injected control; Biological replica 1

description: tlr5a morphants: water-injected control; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 1

value: water-injected 1 HPI


title: ICE_ko24


title: tlr2 morphants: Pam3CSK4-injected ; Biological replica 3

description: tlr2 morphants: Pam3CSK4-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 3

value: Pam3CSK4-injected 1 HPI

value: tlr2 morphants


title: Mg3

description: rRNA depleted RNA


title: Mg2

description: rRNA depleted RNA


title: tlr5a morphants: water-injected control; Biological replica 2

description: tlr5a morphants: water-injected control; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 2


title: tlr2 morphants: Pam3CSK4-injected ; Biological replica 2

description: tlr2 morphants: Pam3CSK4-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 2


title: tlr5a morphants: water-injected control; Biological replica 3

description: tlr5a morphants: water-injected control; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 3


title: ICE_wt0


title: tlr2 morphants: water-injected control; Biological replica 1

description: tlr2 morphants: water-injected control; RNA isolated at 1 hour post injection (=1HPI timepoint). Biological replica 1


title: tlr2 morphants: Pam3CSK4-injected ; Biological replica 1

description: tlr2 morphants: Pam3CSK4-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 1


title: tlr2 morphants: water-injected control; Biological replica 2

description: tlr2 morphants: water-injected control; RNA isolated at 1 hour post injection (=1HPI timepoint). Biological replica 2


title: Wildtype: Flagellin-injected ; Biological replica 2

description: Wildtype: Flagellin-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 2

value: wild type


title: Wildtype: Flagellin-injected ; Biological replica 1

description: Wildtype: Flagellin-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 1


title: Wildtype: Pam3CSK4-injected ; Biological replica 2

description: Wildtype: Pam3CSK4-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 2


title: Wildtype: Pam3CSK4-injected ; Biological replica 3

description: Wildtype: Pam3CSK4-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 3


title: tlr2 morphants: water-injected control; Biological replica 3

description: tlr2 morphants: water-injected control; RNA isolated at 1 hour post injection (=1HPI timepoint). Biological replica 3


title: Wildtype: Flagellin-injected ; Biological replica 3

description: Wildtype: Flagellin-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 3


title: Slow cycling condition time point 23

data_processing:
Strand-specific single-end (50-bp) reads were sequenced (by Illumina HiSeq 2500 sequencer) at McDermott DNA Next Generation Sequencing Facility at UTSW.
The quality of the raw reads (in fastq file) were checked by FastQC (version 0.10.1). Based on the FastQC analyses, eleven bases on the left and four bases on the right of the reads were trimmed out before mapping the reads against the sacCer3 yeast reference genome.
The fasta sequences for sacCer3 genome and gtf annotations of 6784 genes for sacCer3 yeast reference genome were obtained via UCSC genome browser. ERCC Spike-In Mix 1 (from Ambion/Life Technologies) were utilized in this project and the ERCC controls' fasta sequences and gtf annotations were obtained from Life Technologies' web site (https://www.lifetechnologies.com/order/catalog/product/4456740?CID=search-4456740).
TopHat v2.0.10 program was used as the mapping program; the unmapped reads and the reads with mapping quality score less than 10 were filtered out after mapping.
Big Wig data (which tracks to be viewed under UCSC genome browser) were obtained via RSeQC package (http://rseqc.sourceforge.net/) from the mapped and filtered reads which were also used to calculate the RPKM values with HOMER program (http://homer.salk.edu/homer/index.html).
Genome_build: yeast CEN.PK sequencing reads mapped to UCSC/sacCer3 genome build
Supplementary_files_format_and_content: bigWig tracks for each sample to be viewed under UCSC genome browser; tab-delimited text file include RPKM values for each Sample.

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Briefly, fermentors were from New Brunswick Scientific (Model BioFlo 110). Each fermentor run was started by the addition of a 10-20 mL starter culture that had been grown overnight to saturation at 30°. The fermentors were operated at an agitation rate of 400 rpm, an aeration rate of 1 L/min, a temperature of 30°, a pH of 3.4, with a working volume of 1 L. Once the batch culture reached maximal density, the culture was starved for a minimum of 4 hours. Continuous culture was then initiated by the constant infusion of media containing 1% glucose at a dilution rate of ~0.045-0.05 per hour for slow cycling and 0.12-0.13 per hour for fast cycling. The growth media is a minimal media consisting of 5 g/L (NH4)2SO4, 2 g/L KH2PO4, 0.5 g/L MgSO4•7H2O, 0.1 g/L CaCl2•2H2O, 0.02 g/L FeSO4•7H2O, 0.01 g/L ZnSO4•7H2O, 0.005 g/L CuSO4•5H2O, 0.001 g/L MnCl2•4H2O, 1 g/L yeast extract, 10 g/L glucose, 0.5 mL/L 70% H2SO4, and 0.5 mL/L Antifoam 204 (Sigma).

extract_protocol:
Approximately 2.0 x 108 cells per time interval were rapidly harvested from the fermentor and frozen at -80°. The 44 samples were randomly assigned to four different groups for RNA harvest. The cells from each sample were lysed by adding 200 μLof 425-600 μm glass beads (Sigma-Aldrich) and 700 μLof RNA Stat-60 (amsbio) to the cell pellet and disrupting the mixture with a Mini-Beadbeater-24 (BioSpec Products) in five, 30 second intervals with 2 minutes on ice between each interval. 200 μLof chloroform was added to the disrupted cells, and the samples were centrifuged for 15 minutes (12,000 x g) at 4°C. Subsequently, 500 μLof the aqueous layer was collected, and 200 μL isopropanol was added to this. After incubating at room temperature for 10 minutes, the samples were centrifuged for 10 minutes (12,000 x g) at 4°C, and the supernatants were discarded. The pellets were washed once with 100% and again with 75% molecμLar biology grade ethanol. The pellets were air dried and resuspended in 200 μL water.
The quality of the total RNA was verified on a Bioanalyzer RNA 6000 Nano chip (Agilent). The total RNA was spiked in with 1 μL of ERCC RNA Spike-In Mix at 1:30 dilution (Ambion). Subsequently, mRNA pull-down was performed using  NEXTflex™ Poly(A) Beads as per manufacturer’s instructions (Bioo Scientific). The removal of ribosomal RNAs was confirmed on a Bioanalyzer RNA 6000 Pico chip using the mRNA assay (Agilent). Stranded mRNA libraries were prepared using in-house enzyme mixes and buffers. 20 ng of mRNA was fragmented by chemical fragmentation at 95°C for 10 minutes. Fragmented RNA was reverse transcribed using Enzscript™ (M-MLV Reverse Transcriptase Rnase H-) (Enzymatics), followed by directional second strand synthesis. Subsequently, adenylation was performed and then adapter ligation. The adapters were ordered from Bioo Scientific. Uracil DNA Glycosylase treatment was performed prior to amplification by PCR.  The quality of the libraries was checked on a Bioanalyzer High Sensitivity DNA chip (Agilent) and the libraries were quantified by qPCR using Kapa library quantification kit (Kapa Biosystems)

treatment_protocol: Continuous culture was then initiated by the constant infusion of media containing 1% glucose at a dilution rate of ~0.045-0.05 hour-1 for slow cycling and 0.12-0.13 hour-1 for fast cycling

tag: culture condition

value: 1% glucose added at a dilution rate of ~.045-.05 hr-1


title: Slow cycling condition time point 19


title: Wildtype: Pam3CSK4-injected ; Biological replica 1

description: Wildtype: Pam3CSK4-injected ; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 1


title: Slow cycling condition time point 21


title: Slow cycling condition time point 20


title: Wildtype: water-injected control; Biological replica 3

description: Wildtype: water-injected control; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 3


title: Slow cycling condition time point 18


title: Wildtype: water-injected control; Biological replica 1

description: Wildtype: water-injected control; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 1


title: Slow cycling condition time point 17


title: Slow cycling condition time point 16


title: Slow cycling condition time point 15


title: Wildtype: water-injected control; Biological replica 2

description: Wildtype: water-injected control; RNA isolated at 1hour post injection (=1HPI timepoint). Biological replica 2


title: Slow cycling condition time point 14


title: Slow cycling condition time point 8


title: Slow cycling condition time point 11


title: Slow cycling condition time point 9


title: Slow cycling condition time point 13


title: Slow cycling condition time point 10


title: Slow cycling condition time point 12


title: Slow cycling condition time point 6


title: Slow cycling condition time point 7


title: Slow cycling condition time point 4


title: Slow cycling condition time point 2


title: Slow cycling condition time point 3


title: Slow cycling condition time point 24


title: Slow cycling condition time point 22


title: Slow cycling condition time point 5


title: Fast cycling condition time point 17

value: 1% glucose added at a dilution rate of ~.12-.13 hr-1


title: Fast cycling condition time point 20


title: Slow cycling condition time point 1


title: Fast cycling condition time point 19


title: K279a_liquid_culture_at_32h_Replicate2

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Fastq to fasta conversion using FastX  FastX (version 0.0.13)
Size filtering: discarding reads shorter than 20 nt (READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (READemption version 0.3.5)
Coverage calculation and normalisation (READemption version 0.3.5)
Genome_build: NC_010943.1
Supplementary_files_format_and_content: Read coverages normalized by total number of aligned reads in wiggle format

organism: Stenotrophomonas maltophilia K279a

source_name: K279a cells

growth_protocol: Stenotrophonomas maltophilia was grown on LB agar plates (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl and agar) at 37°C with/without ampicillin (100 μg/mL) for 48 h.

extract_protocol:
Total RNA was isolated using the hot phenol method followed by two chloroform-isoamyl alcohol treatments and precipitation with sodium acetate and ethanol.
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina

treatment_protocol: S. maltophilia was grown on LB agar plates with/without ampicillin. Then two samples from each colony morphotype (small big and colonies) and from uniform colonies were scrapped from agar plates after 48 h of growth, pooled and immediately frozen in liquid nitrogen. About 10 -15 mg of wet biomass were generally used for each biological replicate, 10 mg of cell material corresponded to an OD600 of 6.35.

tag: condition

value: liquid medium for 32 h


title: Fast cycling condition time point 18


title: K279a_liquid_culture_at_32h_Replicate1


title: Fast cycling condition time point 15


title: K279a_liquid_culture_at_27h_Replicate2

value: liquid medium for 27 h


title: Fast cycling condition time point 13


title: Fast cycling condition time point 12


title: Fast cycling condition time point 11


title: Fast cycling condition time point 9


title: Fast cycling condition time point 10


title: K279a_big_colonies_Replicate2

value: big colonies from LB agar plates grown on ampicillin for 48 h


title: K279a_big_colonies_Replicate1


title: K279a_small_colonies_Replicate_2

value: small colonies from LB agar plates grown on ampicillin for 48 h


title: Fast cycling condition time point 16


title: K279a_small_colonies_Replicate_1


title: Broth (Input) culture

description: rRNA depleted RNA

source_name: cultured bacteria

value: Rlow


title: Fast cycling condition time point 6


title: Fast cycling condition time point 5


title: Fast cycling condition time point 7


title: Chicken B, 10 pass

description: rRNA depleted RNA


title: K279a_without_ampicillin_Replicate2

value: colonies from LB agar plates grown without ampicillin for 48 h as a control


title: Col-control-4dpi-Rep1

description:
4dpi-WT-infected.txt
4dpi-WT-vs-Type-A-control.txt

tag: agent

value: none, control

value: wild-type

tag: 4dpi or 10dpi

value: 4 days post infection


title: Fast cycling condition time point 4


title: Fast cycling condition time point 14


title: K279a_liquid_culture_at_27h_Replicate1


title: Chicken A, 10 pass

description: rRNA depleted RNA


title: Chicken B, 5 pass

description: rRNA depleted RNA


title: Fast cycling condition time point 2


title: Fast cycling condition time point 3


title: Chicken A, 5 pass

description: rRNA depleted RNA


title: Fast cycling condition time point 8


title: Fast cycling condition time point 1


title: HuMPost30

status: Public on Nov 17 2015

city: Dublin

first: Rashmi

last: Gupta

state: CALIFORNIA

address: 5529 Esprit Way

institute: UCSF

data_processing:
Quality was assessed using FastQC (v0.11.1)
Sequencing reads were trimmed by removing adaptors and low-quality sequences using Trimmomatic (v0.3) with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
The trimmed reads were mapped using Tophat2 (v2.0.9) using default parameters.
FPKMS (Fragments Per Kilobase of transcript per Million mapped reads) were calculated using the Cufflinks package (v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Post-Treated Psoriasis

extract_protocol:
RNA extraction using RNeasy kit
ScriptSeq complete kits from Epicenter.

tag: subject status

value: psoriasis patient

tag: tissue type

value: lesional skin from psoriasis patient

tag: time point

value: after 1 month of adalimumab treatment


title: K279a_without_ampicillin_Replicate1


title: HuMPost26


title: HuMPost25


title: HuMPost22


title: HuMPost24


title: HuMPost20


title: HuMPost19


title: HuMPost18


title: HuMPost15


title: HuMPost17


title: HuMPost14


title: HuMPost9


title: HuMPost8


title: HuMPost1


title: HuMPost6


title: HuMPre25

source_name: Pre-Treated Psoriasis

value: before adalimumab treatment


title: HuMPre30


title: HuMPost2


title: HuMPre24


title: HuMPre22


title: HuMPre26


title: HuMPost4


title: HuMPre17


title: HuMPre20


title: HuMPre19


title: HuMPre18


title: HuMPre14


title: HuMPre6


title: HuMPre2


title: HuMPre15


title: HuMPre8


title: HuMPre1


title: HuMPre4


title: HuMPre5


title: V008

source_name: Normal Skin

value: healthy control

value: normal skin


title: M32ACtrl


title: HuMPost5


title: 107


title: C15


title: C12


title: C11


title: V003ACtrl


title: C13


title: BC

city: Beijing

first: Guangrui

last: Huang

address: 11 Beisanhuandong Road, Chaoyang District

country: China

institute: Beijing University of Chinese Medicine

description: SAPAS method

data_processing:
The SAPAS-generated raw reads were trimmed, filtered, and mapped to the zebrafish genome (Zv9)
After internal priming filtering, the resulting uniquely mapped reads (called effective reads) were clustered to define poly(A) sites. The total read counts from each sample were normalized to the libraries with fewer effective reads (e.g., the BC library), and poly(A) sites with two or more normalized reads were used for further analysis. A poly(A) site that overlapped with an annotated 3’ UTR from Ensembl was defined as a tandem poly(A) site.
We used a linear model to test APA switch events (26), and a gene with an absolute value of test-resulted tandem 3’ UTR switching index (TUSI) greater than 0.1 and a P value smaller than the threshold corresponding to a BH-sense false discovery rate (FDR) of 0.05 was defined as an APA gene.
A list of immune genes was collected according to KEGG pathways of zebrafish (http://www.genome.jp/kegg/)
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

growth_protocol: Wild type zebrafish were cultured in recirculating systems at 28 °C.

extract_protocol:
spleens from 20 bacterially challenged fish or 20 naive fish were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
SAPAS libraries were prepared using a protocol from Fu et al., Genome Research, 2011. Briefly, total RNA was extracted from samples using QIAGEN RNeasy Mini kits. Approximately 10 μg of total RNA was fragmented by heating, and the first strand cDNA was synthesized by reverse transcription with anchored oligo d(T) primers and a 5’ template switching adaptor. PCR was then performed to amplify the cDNA, and the number of cycles was optimized to ensure that the double-stranded cDNA remained in the exponential phase of amplification. After the PCR, fragments of 200-300 bp in size were excised from a PAGE gel and purified. The final pooled fragments were quantified and sequenced from the 3’ end with Solexa.

treatment_protocol: Adult zebrafish were anesthetized in 160 μg/ml tricaine and injected intraperitoneally with 4×10E6 clonal formation unit (CFU) S. aureus for fifteen hours later.

tag: tissue

value: spleen

value: 6 months

tag: gender

value: male


title: UC

description: SAPAS method

tag: age


title: C10


title: HuMPre9


title: C9


title: C8


title: C6


title: Old SAMP8 treated with J147 3

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
alignment with STAR 2.3.0e
gene-level read counts with featureCounts 1.4.6 (Subread package)
Genome_build: mm9
Supplementary_files_format_and_content: per-gene raw read count (CSV)

molecule: polyA RNA

source_name: Brain hippocampus

growth_protocol: All experiments were performed in accordance with the US Public Health Service Guide for Care and Use of Laboratory Animals and protocols approved by the IACUC at the Salk Institute.

extract_protocol:
RNA was isolated using the RNeasy Plus Universal mini kit (Qiagen)
Illumina TruSeq Stranded mRNA

treatment_protocol: Mice were fed control diet and diet containing J147

value: Brain

value: ten months old


title: Old SAMP8 treated with J147 2


title: Old SAMP8 treated with J147 1


title: Old SAMP8 3

value: control


title: Old SAMP8 2


title: Old SAMP8 1


title: Young SAMP8 control 3

value: three months old


title: Young SAMP8 control 4


title: GSLv3-7_35

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description:
Sample 6
Results_DEXseq.txt

data_processing:
Basecalls performed using CASAVA version 1.8.4
Calculating insert size and standard deviation performed using Picard v.1.126
Reads were mapped to hg19 using STAR guided by GTF version GRCh37.70
read counting performed using HT-seq v0.6.0
Normalization and Differential expression analysis performed using DESeq, DEXSeq for exon usage and MISO for event-based analysis
BAM to bedgraph performed using bedtools v2.17.0, Normalized by RPM
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.1.1
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (coverage for mapped reads)
Supplementary_files_format_and_content: [Results_DEXseq.txt] DEXSeq results for RNA-Seq (differential exon usage analysis); normalized count table
Supplementary_files_format_and_content: [Deseq-rip_significant_sites.txt] DESeq results for RIP-Seq (differential binding analysis); normalized count table
Supplementary_files_format_and_content: [*ExonCounts.txt] Exon Segment Count Table; read counts for genomic features

source_name: human cell line

growth_protocol: MEG-01 cells and RBM15 knockdown MEG-01 cells were cultured in RPMI-1640 medium with 10% fetal bovine serum.

extract_protocol:
see details in Zhang et. al.
For samples 1-4, we used sureselect single strand RNA selection kit. For sample 5-7, we used HundsonAlpha service for library construction, no strand information.

tag: lentiviral transgenes

value: yes

tag: passage number

tag: cell line

value: leukemia cell line MEG-01

tag: knockdown

value: RBM15 (via shRBM15#1)

tag: culture protocols

tag: harvest time

value: exponential phase


title: C3


title: C2


title: GSLv3-7_36

description:
Sample 7
Results_DEXseq.txt

value: RBM15 (via shRBM15#2)


title: GSLv3-7_34

description:
Sample 5
Results_DEXseq.txt


title: XZ6

description:
Sample 4
DEseq-rip_significant_sites.txt

tag: rip antibody

value: RBM15 antibody


title: C4


title: Young SAMP8 control 2

tag: strain

tag: treatment


title: XZ4

description:
Sample 2
DEseq-rip_significant_sites.txt

value: normal immunoglobulin antibody


title: Young SAMP8 control 1


title: XZ3

description:
Sample 1
DEseq-rip_significant_sites.txt


title: C5


title: ccRCC_FG2

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
Sequence tags were then mapped to the reference human genome (hg19) with TopHat software using default parameters (Kim et al 2013). Reads from samples with multiple sequencing lanes were merged and only the best score alignment was accepted for each read.
BigWig files were produced using BedTools (Quinlan and Hall, 2010) and bedGraphToBigWig (UCSC Tool).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: Clear cell renal cell carcinoma cell line, FG2

growth_protocol: ccRCC cells (Caki-1, Caki-2, MF, ER, AB and FG2, Cell Line Services Eppelheim, Germany) were grown as monolayers in Dulbecco’s modified Eagle medium (DMEM, Invitrogen), supplemented with 10% (v/v) FBS, 1% (v/v) nonessential amino acids, 1% (v/v) L-glutamine and 100U/ml penicillin-streptomycin, and maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted with trizol.
The samples were barcoded and prepared for sequencing  by the Centro Nacional de Análisis Genómico (CNAG, Barcelona) using Illumina standard protocols.

tag: genotype/variation

value: SETD2 mutated


title: ccRCC_AB

source_name: Clear cell renal cell carcinoma cell line, AB

value: AB


title: ccRCC_MF

source_name: Clear cell renal cell carcinoma cell line, MF

value: MF


title: O+10bp sgRNA replicate 3

city: El Paso

first: Ying

last: Dang

address: 5001 El Paso Dr

institute: TTUHSC

description:
second round replicate 3
second round replicate 3raw

data_processing:
Fastq quality filter by fastq_illumina_filter
Trimed the sequences missing 3' adaptor
Trimed the sequences missing 5' adaptor
Trimed the sequences that is shorter than 15bp
Trimed the sequences contains "N"
Merged reads
Removed the reads with <5 copies
Supplementary_files_format_and_content: tables contain the #reads and sequences (target) for each sample

source_name: TZM-bl cell

growth_protocol: TZM-bl cell was cultured in DMEM with 10% FBS and 1X PS.

extract_protocol:
Genomic DNA was extracted from the sorted cells using QIAamp DNA blood mini kit (QIAGEN)
The library construction follows Illumina’s TruSeq method. Briefly, sgRNA sequences were amplified by 2 rounds PCR with the first pair of primers, ACACTCTTTCCCTACACGACGCTCTTCCGATCT TCTACCTGCTCAACCTGGCC (forward) and GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC AAGTCCCACTGGGCGGC (reverse), followed by amplification with the second pair of primers, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA (forward) and CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTG(reverse, where NNNNNNN indicates index sequences).
TruSeq

treatment_protocol: TZM-bl cells were transfected with Lipofectamine 2000 in 6-well plate according to the manufacturer’s instructions. Cells were collected 48 hours after transfection. GFP positive cells were sorted using FACSAria II cell sorter (BD Bioscience)

value: TZM-bl


title: O+10bp sgRNA replicate 1

description:
second round replicate 2
second round replicate 2raw


title: O+10bp sgRNA replicate 2


title: O+8bp sgRNA replicate 3


title: Lis1 rep2

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
mRNA aligned using Tophat 2.0.13
human mRNA reads counted using Ensembl 72 annotations; mouse mRNA reads counted using NCBIM37 annotations
Genome_build: hg19; mm9
Supplementary_files_format_and_content: read counts for mRNA  in tab deliminated format

source_name: embryonic stem cell

growth_protocol: Lis1 was cultured as previously described in Gafni et al, Nature, 2013. H1 4iLIF was cultured in the following conditions:DMEM/F12 media, 20% knock-out serum replacer (KSR), 1mM sodium pyruvate, 0.1mM nonessential amino acids (NEAA), 50U/ml (penicillin), 50µg/ml (streptomycin), 0.1mM β-mercaptoethanol, 1µM GSK3 inhibitor (CHIR99021), 1µM MEK inhibitor (PD0325901), 10µM JNK inhibitor (SB600125), 10µM p38 inhibitor (SB203580),10ng/ml human LIF, 5ng/ml IGF1 and 10ng/ml bFGF

extract_protocol:
Total RNA was extracted using trizol
Standard Illumina protocol

tag: cell type

value: Lis1 embryonic stem cell

tag: pluripotency state

value: naïve


title: O+8bp sgRNA replicate 2


title: RNA_Sample_1952

city: Berlin

first: Florian

last: Mertes

address: Ihnestraße 63-73

institute: Max Planck Institute for Molecular Genetics

data_processing:
RNA-seq data was mapped to the human genome by Tophat v1.3.3. Prebuild bowtie index files and annotations in GTF-format were downloaded from Illuminas iGenomes ftp-server (ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/). To compare Tophat mappings to Illumina BeadArray data, we considered only reads that mapped to annotated exons (UCSC genes) and reached a peak coverage of 5 or higher. Furthermore we restricted the analysis to Refseq genes.
Genomic DNA sequencing reads were mapped using bowtie with the same parameters that Tophat uses for its first mapping round (-v 2). Genomic coverage was visualized as Manhattan plot via the mhtplot function from the R package gap.
Genome_build: hg19

source_name: stem cells

growth_protocol: Human embryonic stem cells (line H1) were obtained from WiCell Research Institute. Cells were cultured in 6-well-plates (TPP) coated with Matrigel (Becton Dickinson) on Mitomycin C-inactivated mouse embryonic fibroblasts (MEFs) as described before (Bjorn replace Prigione with your biomatrial paper )[28]. After 1 week, undifferentiated colonies were mechanically fragmented using the StemProEZPassage Disposable Stem Cell Passaging Tool (Invitrogen, cat# 23181-010) according to the recommendations of the manufacturer, leading to squares of relatively uniform size (ca. 200 µm x 200 µm, see fig 1B). Fragments from the middle of undifferentiated colonies were detached using a non-rotatable cell spatula (TPP, cat#99010) under microscopic control (Stereo microscope Leica MZ9.5 with cold light source KL 1500 LCD; Leica Microsystems)and sterile conditions inside a HERAguard® HPH 9 Laminar flow clean bench (Heraeus). Detached single squares were individually isolated by very gentle aspiration using a sterile 20 µl filter pipette tip (Biozym Scientific) and used for further downstream processing.

extract_protocol:
Preparation and amplification of nucleic acids were performed with a customized version of the μMACSSuperAmpKit (MiltenyiBiotec); if not mentioned explicitly, procedures were according to the manufacturer protocol. The protocol is based on magnetic coupling of mRNA and retaining the nucleic acid in low volume flow-through columns for greatly simplified handling. For selective mRNA isolation, magnetic micro beads coupled to oligo-dT primers were applied. To retain the genomic DNA the eluates from the first two washing steps after loading the cell lysate onto the column were collected into a 1.5 mL reaction tube for later DNA precipitation and whole genome amplification. On column cDNA synthesis was performed at 42°C for 60 min according to the following protocol by applying the total reaction master mix onto the column: 20 µL contained 2 µL 10x Reverse Transcriptase Buffer (Ambion), 0.5 mM dNTPs, 1µg T4 Gene 32 Protein (NEB), 400 U M-MLV Reverse Transcriptase (Enzymatics), 20 U RNase Inhibitor (Ambion). After collection of magnetic beads containing synthesized cDNA by centrifugation and 3’-tailing according to the manufacturer, PCR amplification was performed. To the 3’-tailing reaction, in total 30 µL, the following PCR master mix was added: 76.5 µL PCR master mix  contained 14 µL 5x PhusionHF buffer (Finnzymes), 0.5 mMdNTPs, 60 µL resuspended μMACSSuperAmp PCR mix, 2 U PhusionTaq (Finnzymes); the following cycling conditions were applied on a PTC-200 (MJ Research) thermal cycler: 78°C for 30 sec, 95°C for 1 min, [98°C for 3 sec, 64°C for 30 sec, 72°C for 2 min]x 40 cycles, 72°C for 5 min.
Amplification of genomic DNA was performed with the REPLI-g Midi Kit (Qiagen) for 16 hours at 30° C according to the manufacturer’s recommendations. Before whole genome amplification, DNA was ethanol precipitated by adding 0.1 volumes of 3M sodium acetate solution and 5 µg glycogen (Ambion) to 1 volume of DNA sample. After precipitation the pellet was resuspended in 10 µL of Elution Buffer (Qiagen).


title: genomic DNA


title: O+5bp sgRNA replicate 3


title: ccRCC_ER

source_name: Clear cell renal cell carcinoma cell line, ER

value: ER


title: O+5bp sgRNA replicate 2


title: O+8bp sgRNA replicate 1


title: O+5bp sgRNA replicate 1


title: XZ5

description:
Sample 3
DEseq-rip_significant_sites.txt


title: Lis1 rep1


title: ccRCC_Caki1

source_name: Clear cell renal cell carcinoma cell line, Caki1

value: SETD2 wild-type


title: RNA_Sample_1953


title: O+3bp sgRNA replicate 3


title: O+1bp sgRNA replicate 3


title: input for ELF H3K27me3 ChIP-seq

data_processing:
smRNA counts generated using the miRExpress pipeline
mRNA aligned using gsnap
mRNA reads counted using Ensembl 72 annotations
H3K27me3 ChIP-seq read depth counted using samtools mpileup
Genome_build: hg19
Supplementary_files_format_and_content: read counts for mRNA and smRNA in tab deliminated format
Supplementary_files_format_and_content: wiggle file with a ChIP-seq read count every 10bp window and with a minimum depth of 3

growth_protocol: Primed human ESCs [H1 (WA-01) and H7 (WA-07)] and naïve hESCs [Elf-1(NIHhESC-12- 0156)] were cultured as previously described. Briefly, the cells were cultured on a feeder layer of irradiated primary mouse embryonic fibroblasts (MEF) in hESC media: high glucose (3.151g/L) DMEM/F-12 media supplemented with 20% serum replacer, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 50 U/ml penicillin, 50 μg/ml streptomycin (all from Invitrogen, Carlsbad, CA) and 0.1 mM β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO). hESC media was supplemented with 4 ng/ml basic fibroblast growth factor (bFGF) for primed hESCs and 1μM GSK3 inhibitor (CHIR99021, Selleckchem), 1μM of MEK inhibitor (PD0325901, Selleckchem), 10ng/mL human LIF (Chemicon), 5ng/mL IFG1 (Peprotech), 10ng/mL bFGF for naïve hESCs, Elf1 (2iLIF). One passage prior to the experiments, the cells were transferred to growth factor reduced Matrigel (Becton Dickinson, Moutainview, CA) in MEF conditioned media (CM). Dispase and Trypsin/EDTA (Invitrogen) were used to passage primed and naïve hESCs, respectively.

extract_protocol:
Naïve hESCs Elf1 2iLIF grown on matrigel were treated with 100μM of STAT3 inhibitor (Selleckchem) for 6h or 24h and analyzed for methylation marks by Western blot and ChIP Seq. For ChIP-seq analysis, cells were crosslinked and chromatin processed as previously described with minor modifications. Briefly, cells were harvested with accutase and crosslinked in suspension with 1% formaldehyde solution for 10min at room temperature. Reaction was quenched with glycine and crosslinked cells were rinsed with ice-cold PBS. Nuclei were isolated and chromatin sonicated using a Covaris E210 to approximately 200-500bp size range. ChIP-seq was conducted as previously described with minor modifications. Briefly, magnetic Dynabeads were incubated overnight rotating at 4C with antibody against H3K27me3 (Active Motif, cat # 39155, Lot# 26611010). Sonicated chromatin from approximately 200 thousand cells was added to the bead-bound-antibodies and allowed to incubate at 4C rotating overnight. Beads were washed to remove unbound chromatin. Bound chromatin was eluted from beads and reverse crosslinked overnight.
Purified DNA was prepared for next-generation sequencing via end repair, A-tailing, ligation of custom Y-adapters and PCR amplification to generate final DNA library following gel size selection.

value: ELF embryonic stem cell

tag: chip antibody


title: O+1bp sgRNA replicate 2


title: ELF H3K27me3 ChIP-seq

value: anti-H3K27me3 (Active Motif, catalog# 39155, lot# 26611010)


title: input for STAT3i 6hr H3K27me3, rep 1

value: STAT3 inhibitor 6h


title: STAT3i 6hr H3K27me3 ChIP-seq, rep 1


title: Original sgRNA replicate 3


title: ELF smRNA rep 2

description:
uE2_2
small RNA
processed data file: smrna-counts.tsv


title: ccRCC_Caki2

source_name: Clear cell renal cell carcinoma cell line, Caki2


title: ELF smRNA rep 1

description:
uE1_1
small RNA
processed data file: smrna-counts.tsv


title: Original sgRNA replicate 2


title: ELF mRNA rep 2

description:
E2_1
processed data file: mrna-counts.tsv


title: Mock sgRNA replicate 2

description:
first round replicate 2
first round replicate 2raw


title: mouse preimplantation inner cell mass rep3

value: preimplantation inner cell mass


title: O+3bp sgRNA replicate 1


title: O+3bp sgRNA replicate 2


title: mouse preimplantation inner cell mass rep2


title: mouse preimplantation inner cell mass rep1


title: P(N)-testing9

status: Public on Nov 16 2015

first: xiaomeng

last: liu

state: Beijing

address: Yiheyuan Road No.5

institute: Biodynamics Optical Imaging Center (BIOPIC), Peking University

description:
cell-free DNA
MCTA-Seq

data_processing:
Adapters, first 6bp, last 12bp were trimed.
Low quality reads were discarded(N bases more than 10%, phred33<5 more than 50% and phred score of first 5bp <20 after trimming) .
For plasma sample, reads with more than 3 CpH were discarded.
clean reads were mapped to hg19 by Bismark and Bowtie
Reads were retained for subsequent analysis if there were more than 2 CG in the human genome around mapping site (-3~+3).
PCR duplicates were removed if reads had the same barcode and leftmost mapping position
Reads located in the CpG islands were normalized by total unique mapping reads
Genome_build: hg19
Supplementary_files_format_and_content: 5bp.cgcgmat.rmd.CGI.bed include reads number mapped  to each CpG Islands

source_name: plasma of healthy individuals

extract_protocol: Genomic DNA of tissue samples, WBC or cancer cell lines including the human liver hepatocellular carcinoma cell line (HePG2) and the human cervical cancer cell line (HeLa) were extracted using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s protocol.The fully methylated human genomic DNA is purchased (Chemicon/Millipore, CpGenome Universal Methylated DNA, S7821).The plasma cell-free DNAs were extracted using the QIAamp DNA Blood Midi Kit (Qiagen) according to the manufacturer’s protocol.  1) bisulfite treatment of the DNA, 2) a single-tube three-step amplification of methylated CpG islands, 3) gel-purification of the PCR product that serves as the final sequencing library, and 4) high-throughput sequencing using a next-generation sequencer.

treatment_protocol: Bisulfite conversion was performed using the MethyCode bisulfite conversion kit (Invitrogen) according to the manufacturer’s protocol. Briefly, the reaction containing the genomic or cell-free DNAs and the conversion reagent were incubated at 98°C for 10 min and then at 65°C for 2.5 h. After this, the converted DNAs along with 100 ng carrier tRNA (Roche) were purified using the Zymo-Spin columns (Zymo) with a step of on-column desulfonation, being finally eluted in 10 uL elution buffer.

tag: patient id


title: P(N)-testing10

description:
cell-free DNA
MCTA-Seq


title: P(N)-testing6

description:
cell-free DNA
MCTA-Seq


title: P(N)-testing8

description:
cell-free DNA
MCTA-Seq


title: P(N)-testing5

description:
cell-free DNA
MCTA-Seq


title: P(N)-testing7

description:
cell-free DNA
MCTA-Seq


title: P(N)-testing4

description:
cell-free DNA
MCTA-Seq


title: P(N)-testing3

description:
cell-free DNA
MCTA-Seq


title: P(N)-testing1

description:
cell-free DNA
MCTA-Seq


title: O+1bp sgRNA replicate 1


title: P(N)-testing2

description:
cell-free DNA
MCTA-Seq


title: Original sgRNA replicate 1

description:
second round replicate 1
second round replicate 1raw


title: P(HCC)-testing9

description:
cell-free DNA
MCTA-Seq

source_name: plasma of HCC patient


title: Mock sgRNA replicate 3

description:
first round replicate 3
first round replicate 3raw


title: Mock sgRNA replicate 1

description:
first round replicate 1
first round replicate 1raw


title: P(HCC)-testing4

description:
cell-free DNA
MCTA-Seq


title: P(HCC)-testing7

description:
cell-free DNA
MCTA-Seq


title: mouse postimplantation epiblast rep1

value: postimplantation epiblast

value: primed


title: P(HCC)-testing6

description:
cell-free DNA
MCTA-Seq


title: P(HCC)-testing5

description:
cell-free DNA
MCTA-Seq


title: P(HCC)-testing3

description:
cell-free DNA
MCTA-Seq


title: mouse postimplantation epiblast rep2


title: P(HCC)-testing2

description:
cell-free DNA
MCTA-Seq


title: RRBS_NL_rep2

data_processing:
Adapters, first 6bp, last 12bp were trimmed.
Low quality reads were discarded (N bases more than 10%, phred33<5 more than 50% and phred score of first 5bp <20 after trimming) .
For plasma samples, reads with more than 3 CpH were discarded.
Clean reads were mapped to hg19 by Bismark and Bowtie
Reads were retained for subsequent analysis if there were more than 2 CG in the human genome around mapping site (-3~+3).
PCR duplicates were removed if reads had the same barcode and leftmost mapping position
Reads located in the CpG islands were normalized by total unique mapping reads
Genome_build: hg19
Supplementary_files_format_and_content: 5bp.cgcgmat.rmd.CGI.bed include reads number mapped  to each CpG Islands; CG.bed include 5mC level in each CpG site

source_name: normal liver tissue_Reduced Representation Bisulfite Sequencing

growth_protocol: Standard condition for culture of HePG2 and Hela cells

extract_protocol:
Genomic DNA of tissue samples, WBC or cancer cell lines including the human liver hepatocellular carcinoma cell line (HePG2) and the human cervical cancer cell line (HeLa) were extracted using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s protocol.The fully methylated human genomic DNA is purchased (Chemicon/Millipore, CpGenome Universal Methylated DNA, S7821).The plasma cell-free DNAs were extracted using the QIAamp DNA Blood Midi Kit (Qiagen) according to the manufacturer’s protocol.
1) bisulfite treatment of the DNA, 2) a single-tube three-step amplification of methylated CpG islands, 3) gel-purification of the PCR product that serves as the final sequencing library, and 4) high-throughput sequencing using a next-generation sequencer.

tag: tissue

value: normal liver tissue


title: RRBS_NL_rep1


title: P(HCC)-testing1

description:
cell-free DNA
MCTA-Seq


title: RRBS_WBC_rep1

source_name: white blood cells_Reduced Representation Bisulfite Sequencing

value: white blood cells


title: Dilution_7.5_rep2-1

description: protocol: MCTA-Seq

source_name: CpGenome Universal Methylated DNA (diluted) and white blood cells

tag: validation sample source

value: 7.5 pg FMG diluted into 0.75 ng WBC replicate 2-1


title: Dilution_7.5_rep2-2

description: protocol: MCTA-Seq

value: 7.5 pg FMG diluted into 0.75 ng WBC replicate 2-2


title: Dilution_15_rep2

description: protocol: MCTA-Seq

value: 15 pg FMG diluted into 1.5 ng WBC replicate 2


title: Dilution_15_rep1

description: protocol: MCTA-Seq

value: 15 pg FMG diluted into 1.5 ng WBC replicate 1


title: Dilution_30_rep2

description: protocol: MCTA-Seq

value: 30 pg FMG diluted into 3 ng WBC replicate 2


title: Dilution_30_rep1

description: protocol: MCTA-Seq

value: 30 pg FMG diluted into 3 ng WBC replicate 1


title: Dilution_60_rep1

description: protocol: MCTA-Seq

value: 60 pg FMG diluted into 6 ng WBC replicate 1


title: Dilution_60_rep2

description: protocol: MCTA-Seq

value: 60 pg FMG diluted into 6 ng WBC replicate 2


title: Dilution_0.25%_rep2

description: protocol: MCTA-Seq

value: 0.25% dilution of FMG in WBC replicate 2


title: P(HCC)-testing8

description:
cell-free DNA
MCTA-Seq


title: Dilution_150_rep2

description: protocol: MCTA-Seq

value: 150 pg FMG diluted into 15 ng WBC replicate 2


title: ELF mRNA rep 1

description:
E1_1
processed data file: mrna-counts.tsv

value: ELF embryonic stem cell

value: naïve


title: Dilution_0.25%_rep1

description: protocol: MCTA-Seq

value: 0.25% dilution of FMG in WBC replicate 1


title: Dilution_0.5%_rep2

description: protocol: MCTA-Seq

value: 0.5% dilution of FMG in WBC replicate 2


title: Dilution_1%_rep1

description: protocol: MCTA-Seq

value: 1% dilution of FMG in WBC replicate 1


title: RRBS_WBC_rep2


title: Dilution_0.5%_rep1

description: protocol: MCTA-Seq

value: 0.5% dilution of FMG in WBC replicate 1


title: Dilution_2%_rep1

description: protocol: MCTA-Seq

value: 2.5% dilution of FMG in WBC replicate 1


title: Dilution_2%_rep2

description: protocol: MCTA-Seq

value: 2.5% dilution of FMG in WBC replicate 2


title: Dilution_1%_rep2

description: protocol: MCTA-Seq

value: 1% dilution of FMG in WBC replicate 2


title: Dilution_10%_rep2

description: protocol: MCTA-Seq

value: 10% dilution of FMG in WBC replicate 2


title: Dilution_5%_rep2

description: protocol: MCTA-Seq

value: 5% dilution of FMG in WBC replicate 2


title: Dilution_5%_rep1

description: protocol: MCTA-Seq

value: 5% dilution of FMG in WBC replicate 1


title: Dilution_7.5_rep1

description: protocol: MCTA-Seq

value: 7.5 pg FMG diluted into 0.75 ng WBC replicate 1


title: HELA_rep1

description: protocol: MCTA-Seq

source_name: Hela  cell line

value: HELA genomic DNA replicate 1


title: Dilution_10%_rep1

description: protocol: MCTA-Seq

value: 10% dilution of FMG in WBC replicate 1


title: HEPG2_rep1

description: protocol: MCTA-Seq

source_name: HePG2  cell line

value: HEPG2 genomic DNA replicate 1


title: WBC_rep2

description: protocol: MCTA-Seq

source_name: human white blood cells

value: white blood cell genomic DNA replicate 2


title: HELA_rep2

description: protocol: MCTA-Seq

value: HELA genomic DNA replicate 2


title: FMG_rep2

description: protocol: MCTA-Seq

source_name: CpGenome Universal Methylated DNA (Chemicon/Millipore, S7821)

value: fully methylated genomic DNA replicate 2


title: P(N)-N28

description:
protocol: MCTA-Seq
cell-free DNA

value: plasma of healthy individuals


title: Dilution_150_rep1

description: protocol: MCTA-Seq

value: 150 pg FMG diluted into 15 ng WBC replicate 1


title: HEPG2_rep2

description: protocol: MCTA-Seq

value: HEPG2 genomic DNA replicate 2


title: WBC_rep1

description: protocol: MCTA-Seq

value: white blood cell genomic DNA replicate 1


title: P(N)-N29

description:
protocol: MCTA-Seq
cell-free DNA


title: FMG_rep1

description: protocol: MCTA-Seq

value: fully methylated genomic DNA(FMG) replicate 1


title: P(N)-N27

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N26

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N23

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N24

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N25

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N21

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N20

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N18

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N19

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N12

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N17

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N10

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N14

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N16

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N13

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N15

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N11

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N9

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N6

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N5

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N3

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N2

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N4

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N7

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N8

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P112

description:
protocol: MCTA-Seq
cell-free DNA

source_name: plasma of cirrhosis patient

value: plasma of cirrhosis patient


title: P(N)-N22

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P96

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P84

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P71

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P94

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P73

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P70

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P83

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P69

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P68

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P65

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P66

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P67

description:
protocol: MCTA-Seq
cell-free DNA


title: P(Ci)-P55

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P115

description:
protocol: MCTA-Seq
cell-free DNA

value: plasma of HCC patient


title: P(Ci)-P61

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P114

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P119

description:
protocol: MCTA-Seq
cell-free DNA


title: P(N)-N1

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P101

description:
protocol: MCTA-Seq
cell-free DNA


title: P(HCC)-P85

description:
protocol: MCTA-Seq
cell-free DNA